☆ 4.7 Review

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

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Article Biochemistry & Molecular Biology

Alternative Splicing of TaHsfA2-7 Is Involved in the Improvement of Thermotolerance in Wheat

Zhenyu Ma et al.

Summary: High temperature reduces crop production, especially wheat. A novel splice variant, TaHsfA2-7-AS, was induced by heat and positively regulated thermotolerance in wheat. TaHsfA2-7-AS encodes a truncated isoform and its expression is up-regulated during heat shock.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2023)

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Article Genetics & Heredity

SpliceVault predicts the precise nature of variant-associated mis-splicing

Ruebena Dawes et al.

Summary: Even for splice-site variants that are likely to alter mRNA splicing, accurately predicting the resulting mis-splicing events is challenging. However, analyzing unannotated splicing events in large reference RNA-sequencing samples can predict the nature of variant-associated mis-splicing with high sensitivity. This method outperforms other predictive methods and is valuable for clinical interpretation and classification of splice-site variants.

NATURE GENETICS (2023)

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Review Biochemistry & Molecular Biology

Do not panic: An intron-centric guide to alternative splicing

Ezequiel Petrillo

Summary: This review aims to establish concepts of splicing and alternative splicing, with a focus on introns. It serves as a guide for those interested in understanding the impacts and underlying mechanisms of alternative splicing. The review critically evaluates some of the most relevant work in the field and highlights key unanswered questions, such as the physiological relevance and functional outcomes of alternative splicing, as well as the contribution of different splicing types to the proteome. The review also emphasizes the significance of intron retention as a common type of alternative splicing and proposes new sequencing technologies as a means to further investigate the role of introns in gene expression regulation.

PLANT CELL (2023)

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Article Biochemistry & Molecular Biology

The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

Zhen Zeng et al.

Summary: This study used multiple sequencing approaches to analyze the RNAome landscape in tomatoes during arbuscular mycorrhizal symbiosis (AMS). They discovered a variety of regulatory RNAs involved in AMS. The study found that 3,174 protein-coding genes were upregulated during AMS, with 42% of them being alternatively spliced. Comparative-transcriptome analysis revealed the induction of certain genes by AMS in different angiosperms. Additionally, they identified other RNA molecules, such as lncRNAs, miRNAs, and circRNAs, that respond to AMS and built a database to further study the AMS regulatory network.

PLANT COMMUNICATIONS (2023)

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Article Biochemistry & Molecular Biology

PlantExp: a platform for exploration of gene expression and alternative splicing based on public plant RNA-seq samples

Jinding Liu et al.

Summary: PlantExp is a platform for plant gene expression and alternative splicing analysis based on public RNA-seq datasets. It provides online analysis tools and visualization tools to allow users to reanalyze public datasets and gain new research insights.

NUCLEIC ACIDS RESEARCH (2023)

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Review Biochemistry & Molecular Biology

Cotranscriptional RNA processing and modification in plants

Sebastian Marquardt et al.

Summary: The activities of RNA polymerases have profound consequences for the epigenetic landscape of genomes. Recent studies have shown that there is coordination between transcription and RNA maturation in plants.

PLANT CELL (2023)

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Review Cell Biology

Alternative splicing: An efficient regulatory approach towards plant developmental plasticity

Sajid Muhammad et al.

Summary: Alternative splicing is a gene regulatory mechanism in plants that modulates gene expression through generating alternative isoforms. This review discusses the modulation of alternative splicing, from its interaction with noncoding RNAs to the roles of splicing factors in response to different stimuli. It emphasizes the importance of considering the dynamic changes in alternative splicing in plant research.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2023)

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Review Biochemistry & Molecular Biology

Rock, scissors, paper: How RNA structure informs function

Sarah M. Assmann et al.

Summary: RNA can adopt a wide range of structures through self-folding, ranging from simple hairpins to complex 3D structures, and can interact with metabolites and macromolecules for regulatory purposes. Recent years have seen the elucidation of various RNA structures, including tRNAs, ribozymes, riboswitches, ribosomes, splicesomes, and the complete RNA structuromes. These advances have deepened our understanding of fundamental biological processes and their structure-dependent responses to environmental signals.

PLANT CELL (2023)

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Article Biochemical Research Methods

FungiExp: a user-friendly database and analysis platform for exploring fungal gene expression and alternative splicing

Jinding Liu et al.

Summary: FungiExp is an online database that encompasses 35,821 curated RNA-seq samples from 220 fungal species, providing gene expression and alternative splicing profiles. It allows users to query and visualize gene expression and alternative splicing in the collected RNA-seq samples, and also offers online analysis tools for differential/specific, co-expression network, and cross-species gene expression conservation analysis, enabling users to gain new insights by re-analyzing public RNA-seq data or co-analyzing with personal data.

BIOINFORMATICS (2023)

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Article Biotechnology & Applied Microbiology

A role for heritable transcriptomic variation in maize adaptation to temperate environments

Guangchao Sun et al.

Summary: This study examined how changes in transcriptional regulation allow maize to adapt to temperate environments. Through RNA-seq analysis of maize genotypes, they identified genes with different heritability of expression and alternative splicing. They also discovered loci regulating co-expression modules involved in various biological processes. Additionally, a GWAS identified candidate genes related to adaptation to temperate environments.

GENOME BIOLOGY (2023)

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Article Biotechnology & Applied Microbiology

Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention

Fahad Ullah et al.

Summary: In this study, evidence is provided for the hypothesis that transcription factors are involved in the regulation of intron retention. By studying regions of open chromatin, deep learning models were used to distinguish between open chromatin regions in retained and non-retained introns. Motifs enriched in intron retention events with hits to known human transcription factors, particularly from the zinc finger family, were identified.

GENOME BIOLOGY (2023)

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Editorial Material Biochemistry & Molecular Biology

The importance of alternative splicing in adaptive evolution

Pooja Singh et al.

Summary: Alternative splicing is a widely present co-transcriptional gene regulatory mechanism in plants, animals and fungi, contributing to transcriptomic and proteomic diversity. Recent research suggests that alternative splicing plays a crucial role in ecological adaptations, highlighting its importance in adaptive evolution and speciation.

MOLECULAR ECOLOGY (2022)

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Article Biochemistry & Molecular Biology

MetazExp: a database for gene expression and alternative splicing profiles and their analyses based on 53 615 public RNA-seq samples in 72 metazoan species

Jinding Liu et al.

Summary: MetazExp is a database for gene expression and alternative splicing profiles based on 53,615 uniformly processed publicly available RNA-seq samples from 72 metazoan species. Users can conveniently query gene expression and alternative splicing profiles by gene IDs, symbols, functional terms, and sequence similarity, and flexibly customize experimental groups for differential and specific analyses. With data visualization tools and comprehensive links with external databases, users can efficiently explore results and gain insights.

NUCLEIC ACIDS RESEARCH (2022)

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Article Biochemistry & Molecular Biology

Genome-wide differences in gene expression and alternative splicing in developing embryo and endosperm, and between F1 hybrids and their parental pure lines in sorghum

Meishan Zhang et al.

Summary: The developing embryo and endosperm of sorghum exhibit significant differences in gene expression and alternative splicing, potentially contributing to heterosis. Through deep RNA-sequencing, researchers discovered dramatic disparities in genome-wide gene expression and AS between the two tissues, as well as between F1 hybrids and their pure-line parents. These findings offer valuable transcriptome resources and insights for studying seed yield heterosis in sorghum and related crops.

PLANT MOLECULAR BIOLOGY (2022)

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Article Agronomy

Fine-Tuning of the Grain Size by Alternative Splicing of GS3 in Rice

Lei Liu et al.

Summary: This study reveals the molecular mechanism underlying grain size regulation in rice. GS3 produces two isoforms, GS3.1 and GS3.2, through alternative splicing, with GS3.1 encoding a full-length protein and GS3.2 generating a truncated protein due to intronic sequence retention. Overexpression of GS3.1 reduces grain size, while GS3.2 has no significant effect on grain size. Furthermore, GS3.2 disrupts the signaling of GS3.1 by competitively occupying RGB1. This mechanism is conserved in cereals.

RICE (2022)

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Article Plant Sciences

Alternative splicing of OsGS1;1 affects nitrogen-use efficiency, grain development, and amylose content in rice

Xiaolan Liu et al.

Summary: This study identified an NUE-associated gene, OsGS1;1, through genome-wide association analysis and functional analysis. OsGS1;1 affects grain development and amylose content by regulating sugar metabolism, providing a potential avenue for breeding high-yield and high-quality rice.

PLANT JOURNAL (2022)

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Article Biochemistry & Molecular Biology

Alternative splicing diversifies the transcriptome and proteome of the rice blast fungus during host infection

Jongbum Jeon et al.

Summary: The study reveals that alternative splicing (AS) increases in the rice blast fungus Magnaporthe oryzae during infection process, and identifies dominant isoforms that potentially encode regulatory proteins, suggesting the potential role of AS in regulating rice infection.

RNA BIOLOGY (2022)

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Article Multidisciplinary Sciences

Empirical prediction of variant-activated cryptic splice donors using population-based RNA-Seq data

Ruebena Dawes et al.

Summary: This study demonstrates a method for predicting cryptic donor activation caused by genetic splicing variants, with an empirical method defined by analyzing a large amount of RNA-Seq data, revealing the important determinants of cryptic donor activation.

NATURE COMMUNICATIONS (2022)

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Article Cell Biology

The Rice Serine/Arginine Splicing Factor RS33 Regulates Pre-mRNA Splicing during Abiotic Stress Responses

Haroon Butt et al.

Summary: Abiotic stresses have significant impacts on plant growth, development, and crop productivity. The plant-specific splicing factor RS33 plays an important role in regulating pre-mRNA splicing and abiotic stress responses in rice.

CELLS (2022)

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Article Multidisciplinary Sciences

Expression complementation of gene presence/absence polymorphisms in hybrids contributes importantly to heterosis in sunflower

Joon Seon Lee et al.

Summary: This study elucidates the genetic and molecular mechanisms underlying heterosis in sunflower and demonstrates the contribution of expression complementation of PAVs in hybrids to heterosis and yield stability. The findings provide important insights into understanding hybrid vigor in crops and the stability of yield.

JOURNAL OF ADVANCED RESEARCH (2022)

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Article Biology

The value of genotype-specific reference for transcriptome analyses in barley

Wenbin Guo et al.

Summary: Different genotypes within a species have variable numbers of specific genes and different structures of core genes. The use of a common reference genome can lead to the loss of genotype-specific information and generate erroneous or incomplete results in transcriptomics analysis. In this study, genotype-specific and common reference-based Reference Transcript Datasets (RTDs) were assembled using RNA-seq data from cultivated barley. The results showed that the genotype-specific RTD had a higher diversity of transcripts and alternative splicing events, while the common reference-based RTD missed a significant proportion of transcripts and had less accurate transcript assemblies.

LIFE SCIENCE ALLIANCE (2022)

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Article Agriculture, Multidisciplinary

Global Landscape of Alternative Splicing in Maize Response to Low Temperature

Jiayue Zhang et al.

Summary: In this study, a genome-wide analysis of alternative splicing (AS) in response to low temperature stress in maize was conducted. The findings revealed AS genes associated with low-temperature resistance and their enrichment in hormone and oxidoreductase activity. Functional validation of an AS gene showed its significant impact on maize growth and development. These results contribute to a better understanding of the regulatory mechanism of maize in response to low-temperature stress.

JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY (2022)

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Article Biochemistry & Molecular Biology

Moderate Soil Drying-Induced Alternative Splicing Provides a Potential Novel Approach for the Regulation of Grain Filling in Rice Inferior Spikelets

Zhenning Teng et al.

Summary: This study reveals the function of alternative splicing (AS) in the grain filling process of inferior spikelets and provides potential applications in increasing rice yields through genetic approaches.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Biochemistry & Molecular Biology

Full-Length Transcriptome Sequencing Reveals Alternative Splicing and lncRNA Regulation during Nodule Development in Glycine max

Jing Liu et al.

Summary: Alternative splicing plays a vital role in regulating nodule development in soybean during the interaction with Rhizobium, and our study provides comprehensive transcriptomic data on isoforms and long non-coding RNAs, contributing to future research in multiple directions.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Review Biochemistry & Molecular Biology

Alternative Splicing and Its Roles in Plant Metabolism

Pui Ying Lam et al.

Summary: Plant metabolism plays a crucial role in plant survival, growth, development, and interaction with the environment. It is tightly regulated at transcriptional, post-transcriptional, translational, and post-translational levels in response to different growth stages and changing environment. Alternative splicing, a post-transcriptional regulatory mechanism, generates multiple protein isoforms from a single gene and regulates plant metabolism by altering biochemical activities, protein interactions, and subcellular localization.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2022)

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Article Plant Sciences

Transcriptomic and splicing changes underlying tomato responses to combined water and nutrient stress

Alessandra Ruggiero et al.

Summary: Tomato is a valuable horticultural crop that can be affected by suboptimal environmental conditions. A study on different tomato genotypes exposed to water deficit and low nitrate stress revealed variation in stress responses. The genotype T250 showed tolerance to the stresses applied, while T270 was severely affected. Transcriptome and alternative splicing analysis demonstrated that T250 had a more specific and efficient stress response compared to the susceptible genotype T270.

FRONTIERS IN PLANT SCIENCE (2022)

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Article Plant Sciences

Two alternative splicing variants of a wheat gene TaNAK1, TaNAK1.1 and TaNAK1.2, differentially regulate flowering time and plant architecture leading to differences in seed yield of transgenic Arabidopsis

Baowei Wu et al.

Summary: In wheat, a gene called TaNAK1 undergoes alternative splicing, producing three protein isoforms. These isoforms exhibit different expression patterns, subcellular localizations, and functions. Ectopic expression of two isoforms, TaNAK1.1 and TaNAK1.2, in Arabidopsis showed opposite roles in regulating flowering time and plant architecture, resulting in different seed yields.

FRONTIERS IN PLANT SCIENCE (2022)

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Article Biotechnology & Applied Microbiology

High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects

Huawei Tong et al.

Summary: Several engineered Cas13 variants have been found to have efficient targeted degradation activity with reduced collateral effects in mammalian cells. These variants show no off-target effects and cell growth arrest, making them suitable for targeted RNA degradation in basic research and therapeutic applications.

NATURE BIOTECHNOLOGY (2022)

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Article Biochemical Research Methods

Direct identification of A-to-I editing sites with nanopore native RNA sequencing

Tram Anh Nguyen et al.

Summary: This work combines nanopore native RNA sequencing with machine learning models to accurately identify inosine-containing sites in transcriptomes. By training convolutional neural network models, different nucleotides can be distinguished and the modification rate at each editing site can be estimated. This method expands the toolkit for studying RNA editing and can be applied to investigate other RNA modifications.

NATURE METHODS (2022)

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Article Plant Sciences

BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification

Max Coulter et al.

Summary: In this study, a comprehensive and highly resolved barley reference transcript dataset BaRTv2.18 was constructed using novel computational methods and multiple sequencing technologies. The accuracy of transcript level quantification, SJs, and transcript start and end sites in BaRTv2.18 was validated extensively. BaRTv2.18 represents the most comprehensive and resolved reference transcriptome in barley to date, providing a valuable resource for transcriptomic research.

PLANT JOURNAL (2022)

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Article Plant Sciences

Aberrant RNA splicing of the phytic acid synthesis gene inositol-1,3,4 trisphosphate 5/6-kinase in a low phytic acid soybean line

Dong Qin et al.

Summary: This study revealed the aberrant RNA splicing of the GmITPK3 gene in the low-phytic acid (LP) soybean line, and investigated the expression levels of phytic acid biosynthesis-related genes and inositol phosphate isomer concentrations. The results showed that the relative abundance of intron retention transcripts was higher in the LP line, leading to a lower production of phytic acid. Additionally, a potential involvement of splicing errors in the trait of low phytic acid production was suggested.

SOIL SCIENCE AND PLANT NUTRITION (2022)

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Article Agronomy

Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of Glycine max and Glycine soja

Neha Samir Roy et al.

Summary: This study characterized the transcriptomes of dwarf and normal soybean lines and found that the dwarf soybean had a greater number of isoforms, particularly in genes related to growth hormones and defense responses.

AGRONOMY-BASEL (2022)

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Article Biotechnology & Applied Microbiology

A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals

Jinding Liu et al.

Summary: LivestockExp is a web-based database server for exploring gene expression and alternative splicing, containing a large number of livestock animals and RNA-seq samples. It provides diverse analysis modules and visualization tools, serving as a valuable data resource and analysis platform.

BMC GENOMICS (2022)

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Article Plant Sciences

Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing

Shanlan Chen et al.

Summary: SR proteins from sweet potato have similar functional domains and gene structures as those from Arabidopsis and rice. However, their expression patterns and alternative splicing regulations have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes.

PLANTA (2022)

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Article Multidisciplinary Sciences

SWAP1-SFPS-RRC1 splicing factor complex modulates pre-mRNA splicing to promote photomorphogenesis in Arabidopsis

Praveen Kumar Kathare et al.

Summary: Light signals have significant effects on the physiology, growth, and development of plants. SWAP1, an RNA-binding splicing factor, regulates light-regulated alternative splicing by interacting with other splicing factors and photoactivated phyB.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Plant Sciences

Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses

Lingli Yang et al.

Summary: Alternative splicing is an important process in regulating plant development and stress responses. This study investigated the AS landscape in response to abiotic stresses in B. napus. The results showed that AS events increased under all stresses except dehydration for 1 hour, with intron retention being the most common mode. Differential alternative splicing genes were identified under different abiotic stresses, and co-expression modules associated with these stresses were identified using a weighted gene co-expression network analysis. Hub genes involved in responses to single or multiple stresses were identified, providing valuable resources for improving tolerance against multiple abiotic stresses in B. napus.

FRONTIERS IN PLANT SCIENCE (2022)

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Article Biochemistry & Molecular Biology

FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species

Suxu Tan et al.

Summary: FishExp is a web-based data platform that covers gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fish species. It allows users to query and analyze the data in various ways, including differential/specific expression and alternative splicing analysis, co-expression, and cross-species analysis. Users can also submit their own data and perform analyses with existing data.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2022)

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Article Biotechnology & Applied Microbiology

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Runxuan Zhang et al.

Summary: This study introduces a new comprehensive Arabidopsis transcriptome dataset, AtRTD3, which contains over 169,000 transcripts and provides accurate splice junctions and transcription start/end sites. Additionally, novel methods for identifying accurate splice junctions and transcription start/end sites have been developed, and the effectiveness of AtRTD3 has been validated through analysis of a cold response RNA-seq time-series.

GENOME BIOLOGY (2022)

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Review Food Science & Technology

Developing Germplasm and Promoting Consumption of Anthocyanin-Rich Grains for Health Benefits

Sangam L. Dwivedi et al.

Summary: This review focuses on the development of anthocyanin-rich grain crops through breeding and biotechnology, as well as the factors affecting the content and composition of anthocyanins. Significant progress has been made in characterizing genes associated with anthocyanin biosynthesis, and anthocyanin-rich crop cultivars have been developed. Despite the positive perception of anthocyanin-rich food, consumption is still limited by factors such as availability and price.

FRONTIERS IN SUSTAINABLE FOOD SYSTEMS (2022)

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Article Biotechnology & Applied Microbiology

Predicting RNA splicing from DNA sequence using Pangolin

Tony Zeng et al.

Summary: Pangolin is a deep learning model that outperforms existing methods in predicting splice site strength in multiple tissues, improving prediction of the impact of genetic variants on RNA splicing, and can accurately and recall loss-of-function mutations.

GENOME BIOLOGY (2022)

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Article Biochemistry & Molecular Biology

Error, noise and bias in de novo transcriptome assemblies

Adam H. Freedman et al.

Summary: De novo transcriptome assembly is a powerful tool for evolutionary inferences, but it often faces bias and noise issues in data analysis, leading to underestimation of diversity and gene expression estimates. Researchers should look for ways to minimize the impact of bias in transcriptome assemblies.

MOLECULAR ECOLOGY RESOURCES (2021)

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Letter Biotechnology & Applied Microbiology

PlantSPEAD: a web resource towards comparatively analysing stress-responsive expression of splicing-related proteins in plant

Mo-Xian Chen et al.

PLANT BIOTECHNOLOGY JOURNAL (2021)

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Editorial Material Biochemistry & Molecular Biology

Gene expression links genotype and phenotype during rapid adaptation

Emily B. Josephs

Summary: Natural environments can change rapidly, causing organisms to respond by migrating, going extinct, or adapting quickly. Understanding the genetic and phenotypic changes during rapid adaptation is crucial for predicting population responses to sudden environmental changes.

MOLECULAR ECOLOGY (2021)

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Review Biochemistry & Molecular Biology

CRISPR-Mediated Engineering across the Central Dogma in Plant Biology for Basic Research and Crop Improvement

Dibyajyoti Pramanik et al.

Summary: The central dogma of molecular biology involves transferring genetic information from DNA to RNA to proteins, which is crucial for gene regulation in plants. Precisely manipulating these processes can accelerate crop improvement to meet the growing global population's demands.

MOLECULAR PLANT (2021)

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Review Genetics & Heredity

Molecular and evolutionary processes generating variation in gene expression

Mark S. Hill et al.

Summary: Heritable variation in gene expression arises from mutations filtered by natural selection. High-throughput methods reveal regulatory variation generation mechanisms and compare mutational effects with wild variation to understand neutral and non-neutral evolutionary processes. Integrating molecular and evolutionary biology helps predict the evolution of gene expression variations.

NATURE REVIEWS GENETICS (2021)

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Article Plant Sciences

Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice

Huihui Yu et al.

Summary: Pre-mRNA splicing is crucial for gene expression regulation. Researchers developed a software tool called VaSP to quantify and visualize splicing variants in plants, and identified genotype-specific splicing events associated with shoot Na+ accumulation under salt stress conditions. VaSP proves to be a versatile and powerful tool for alternative splicing analysis and prioritizing candidate causal pre-mRNA splicing in GWAS.

NEW PHYTOLOGIST (2021)

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Article Biochemistry & Molecular Biology

3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists

Wenbin Guo et al.

Summary: 3D RNA-seq is a powerful tool for comprehensive analysis of RNA-seq data, with user-friendly features, rapid and accurate analysis of differential gene expression and alternative splicing.

RNA BIOLOGY (2021)

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Article Biochemistry & Molecular Biology

Alternative Splicing of TaGS3 Differentially Regulates Grain Weight and Size in Bread Wheat

Xiaoli Ren et al.

Summary: The study identified five splicing variants of the G(gamma) subunit gene TaGS3 in wheat, showing different functions in regulating grain weight and size during wheat polyploidization. TaGS3.1 overexpression reduces grain weight and length, while TaGS3.5 overexpression increases them significantly. Biochemical assays revealed the interaction of TaGS3 isoforms with different proteins, suggesting a differential regulation of grain size via alternative splicing.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Ecology

Gene expression dynamics during rapid organismal diversification in African cichlid fishes

Athimed El Taher et al.

Summary: The study focused on the evolution of gene expression in cichlid fishes from Lake Tanganyika, revealing variations in the rate of gene expression evolution among different organs, transcriptome parts, and subclades of the radiation. The study also found that noncoding parts of the transcriptome evolved more rapidly than coding parts, and that gonadal transcriptomes evolved faster than somatic ones. The rate of gene expression change was not constant and accelerated in the later phase of the radiation, with per-gene level evolution patterns dominated by stabilizing selection.

NATURE ECOLOGY & EVOLUTION (2021)

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Article Biochemical Research Methods

ASpli: integrative analysis of splicing landscapes through RNA-Seq assays

Estefania Mancini et al.

Summary: Genome-wide analysis of alternative splicing has been a popular research area since the early days of next generation sequencing, with various methods having strengths and weaknesses. ASpli, implemented in R, can identify changes in annotated and novel alternative splicing events and handle different experimental designs successfully.

BIOINFORMATICS (2021)

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Article Biochemical Research Methods

Effective gene expression prediction from sequence by integrating long-range interactions

Ziga Avsec et al.

Summary: Enformer leverages a new deep learning architecture to improve gene expression prediction accuracy based on DNA sequences, integrating information from long-range interactions in the genome and accurately predicting the impact of genetic variants on gene expression. Additionally, Enformer has learned to predict enhancer-promoter interactions directly from DNA sequences.

NATURE METHODS (2021)

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Review Biochemistry & Molecular Biology

The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status

Vesper Burjoski et al.

Summary: RNAs transmit information from DNA to encode proteins and regulate gene expression. Recent studies have uncovered a hidden landscape of RNA-protein interactions in plants. Application of modern techniques has led to the discovery of close to 2000 putative RNA-binding proteins in plants.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Article Biochemistry & Molecular Biology

Alternative splicing and gene expression play contrasting roles in the parallel phenotypic evolution of a salmonid fish

Arne Jacobs et al.

Summary: Research on the replicated postglacial divergence of Arctic charr into sympatric benthic and pelagic ecotypes reveals the significance of alternative splicing and differential gene expression, primarily controlled by independent cis-regulatory quantitative trait loci. While differentially spliced genes are enriched in muscle development, functioning, and highly central in regulatory networks, differentially expressed genes are associated with metabolism, immunity, and growth, indicating complementary molecular processes in rapid parallel adaptive evolution.

MOLECULAR ECOLOGY (2021)

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Article Biotechnology & Applied Microbiology

Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species

Peng Gao et al.

Summary: Research indicates that there is diversity in the regulation of alternative splicing in polyploid wheat and grass species, not only showing differences in different tissues but also between subgenomes. Analysis of homoeologous triads in polyploid wheat reveals evolutionary divergence in the regulation of embryogenesis between gene-level and transcript-level.

PLANT BIOTECHNOLOGY JOURNAL (2021)

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Article Plant Sciences

Identification of cassava alternative splicing-related genes and functional characterization of MeSCL30 involvement in drought stress

Xun Weng et al.

Summary: Alternative splicing is an important post-transcriptional regulation strategy in eukaryotes, which plays a crucial role in increasing proteome diversity and regulating mRNA levels. In plants, alternative splicing can enhance adaptation to external stress conditions. The study identified 365 genes encoding AS-related proteins in cassava, with 13 genes undergoing alternative splicing under diverse environmental stress conditions.

PLANT PHYSIOLOGY AND BIOCHEMISTRY (2021)

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Review Plant Sciences

The Roles of Temperature-Related Post-Transcriptional Regulation in Cereal Floral Development

Dominique Hirsz et al.

Summary: Temperature is a critical environmental signal in regulating plant growth and development, leading to the evolution of multiple temperature responsive regulatory mechanisms at the molecular level in plants. Recent studies have identified and understood these molecular mechanisms in temperate cereals, and developed methods to increase the robustness of crop yield.

PLANTS-BASEL (2021)

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Article Genetics & Heredity

Genome-wide analysis of the soybean root transcriptome reveals the impact of nitrate on alternative splicing

Binhui Guo et al.

Summary: In this study, we investigated the genome-wide alternative splicing events in soybean roots in response to different levels of nitrate supply using high-quality high-throughput RNA-sequencing data. Our results identified 355 nitrate-responsive AS events between optimal and high nitrate levels, 335 nitrate-responsive AS events between optimal and low nitrate levels, and 588 nitrate-responsive AS events between low and high nitrate levels. The most common AS types were RI and A355, which accounted for 67% of all AS events under all conditions.

G3-GENES GENOMES GENETICS (2021)

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Review Biology

Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance

Showkat Ahmad Ganie et al.

Summary: When facing environmental stresses, alternative splicing (AS) plays a crucial role in rice by rapidly regulating gene expression to help the plant adapt to various pressures. Studies have shown that AS is important for rice growth and development, especially under stress conditions. Understanding the impact of AS on rice and its pathogens can provide valuable insights for developing stress-resistant rice varieties in the future.

BIOLOGY-BASEL (2021)

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Article Ecology

Aberrant RNA splicing due to genetic incompatibilities in sunflower hybrids

Chris C. R. Smith et al.

Summary: Genome-scale studies have revealed divergent mRNA splicing patterns between closely related species or populations, which may be due to genetic variation at the genomic level. The research in wild x domesticated sunflower hybrids discovered a large number of novel splice forms, with aberrant transcripts being regulated by multiple genetic loci. Splice variation in these genes was found to be correlated with the cumulative expression of transcripts and had a significant impact on growth rate.

EVOLUTION (2021)

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Article Agronomy

Global Survey of Alternative Splicing in Rice by Direct RNA Sequencing During Reproductive Development: Landscape and Genetic Regulation

Haoxuan Li et al.

Summary: The study investigated alternative splicing during reproductive development in rice and identified a large number of novel splicing events, with intron retention being the most common splicing subtype. Differential expression and splicing of splicing factors could lead to global alternative splicing regulation.

RICE (2021)

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Article Genetics & Heredity

Investigation of Thermomorphogenesis-Related Genes for a Multi-Silique Trait in Brassica napus by Comparative Transcriptome Analysis

Liang Chai et al.

Summary: In this study, analysis of DEGs in rapeseed buds identified environment-specific genes and potential thermomorphogenesis-related genes, shedding light on flower/fruit development in Brassica plants.

FRONTIERS IN GENETICS (2021)

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Letter Cell Biology

Proximity editing to identify RNAs in phase-separated RNA binding protein condensates

Guilong Zhou et al.

CELL DISCOVERY (2021)

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Article Agronomy

Genome-wide alternative splicing variation and its potential contribution to maize immature-ear heterosis

Xiaojiao Hu et al.

Summary: The study reveals a large number of significant differential alternative splicing events in the maize hybrid ZD808 compared to its parents, with NG5-dominant events playing a prevalent role and mainly involved in regulating genes associated with carbon/nitrogen metabolism and cell division processes.

CROP JOURNAL (2021)

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Article Biotechnology & Applied Microbiology

Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Guiomar Martin et al.

Summary: The study provides a comprehensive analysis of alternative splicing (AS) in Arabidopsis thaliana, revealing a high level of AS involvement in stress responses compared to animals. It also identifies core sets of genes regulated specifically by AS or transcription upon stresses or among tissues, showing a regulatory specialization unique to plants.

GENOME BIOLOGY (2021)

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Article Horticulture

Genome-wide analysis of alternative splicing events during response to drought stress in tomato (Solanum lycopersicum L.)

Hee Ju Lee et al.

JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY (2020)

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Article Plant Sciences

Phytochrome Coordinates with a hnRNP to Regulate Alternative Splicing via an Exonic Splicing Silencer

Bou-Yun Lin et al.

PLANT PHYSIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Global Co-transcriptional Splicing in Arabidopsis and the Correlation with Splicing Regulation in Mature RNAs

Shaofang Li et al.

MOLECULAR PLANT (2020)

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Article Biochemistry & Molecular Biology

The Features and Regulation of Co-transcriptional Splicing in Arabidopsis

Danling Zhu et al.

MOLECULAR PLANT (2020)

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Article Plant Sciences

Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR3

Jie Dong et al.

PLANT PHYSIOLOGY (2020)

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Review Biochemical Research Methods

Systematic evaluation of differential splicing tools for RNA-seq studies

Arfa Mehmood et al.

BRIEFINGS IN BIOINFORMATICS (2020)

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Article Biochemistry & Molecular Biology

Organismal benefits of transcription speed control at gene boundaries

Xueyuan Leng et al.

EMBO REPORTS (2020)

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Article Biochemistry & Molecular Biology

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

Salah E. Abdel-Ghany et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Biochemistry & Molecular Biology

Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

Peter Kindgren et al.

NUCLEIC ACIDS RESEARCH (2020)

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Article Biochemistry & Molecular Biology

Mediator Subunit MED25 Couples Alternative Splicing of JAZ Genes with Fine-Tuning of Jasmonate Signaling

Fangming Wu et al.

PLANT CELL (2020)

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Review Cell Biology

Transcription and splicing: A two-way street

Michael Tellier et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2020)

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Article Biology

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

Matthew T. Parker et al.

ELIFE (2020)

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Article Genetics & Heredity

Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes

Muthusamy Muthusamy et al.

GENES (2020)

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Editorial Material Plant Sciences

Plant signaling in biotic and abiotic stress

Scott Peck et al.

JOURNAL OF EXPERIMENTAL BOTANY (2020)

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Article Multidisciplinary Sciences

Ribosome profiling at isoform level reveals evolutionary conserved impacts of differential splicing on the proteome

Marina Reixachs-Sole et al.

NATURE COMMUNICATIONS (2020)

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Article Biochemistry & Molecular Biology

Large-Scale Discovery of Non-conventional Peptides in Maize and Arabidopsis through an Integrated Peptidogenomic Pipeline

Shunxi Wang et al.

MOLECULAR PLANT (2020)

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Article Plant Sciences

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Ai Lin et al.

PLANTS-BASEL (2020)

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Article Biochemistry & Molecular Biology

Profiling of circular RNA N6-methyladenosine in moso bamboo (Phyllostachys edulis) using nanopore-based direct RNA sequencing

Yongsheng Wang et al.

JOURNAL OF INTEGRATIVE PLANT BIOLOGY (2020)

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Article Biochemistry & Molecular Biology

Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity

Jie Huang et al.

MOLECULAR PLANT (2020)

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Article Biochemistry & Molecular Biology

New insights into Arabidopsis transcriptome complexity revealed by direct sequencing of native RNAs

Shoudong Zhang et al.

NUCLEIC ACIDS RESEARCH (2020)

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Article Biochemistry & Molecular Biology

Nonsense-mediated RNA Decay Factor UPF1 is Critical for Post-transcriptional and Post-translational Gene Regulation in Arabidopsis

Vivek Kumar Raxwal et al.

PLANT CELL (2020)

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Article Plant Sciences

Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity

Daniel Niyikiza et al.

PLANT JOURNAL (2020)

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Article Multidisciplinary Sciences

Analysis of the genes controlling three quantitative traits in three diverse plant species reveals the molecular basis of quantitative traits

Meiping Zhang et al.

SCIENTIFIC REPORTS (2020)

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Review Plant Sciences

Alternative Splicing for Improving Abiotic Stress Tolerance and Agronomic Traits in Crop Plants

Seojung Kim et al.

JOURNAL OF PLANT BIOLOGY (2020)

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Article Plant Sciences

Changes in Alternative Splicing in Response to Domestication and Polyploidization in Wheat

Kuohai Yu et al.

PLANT PHYSIOLOGY (2020)

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Article Plant Sciences

Alternatively SplicedBnaPAP2.A7Isoforms Play Opposing Roles in Anthocyanin Biosynthesis ofBrassica napusL.

Daozong Chen et al.

FRONTIERS IN PLANT SCIENCE (2020)

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Article Multidisciplinary Sciences

Investigation for a multi-silique trait in Brassica napus by alternative splicing analysis

Liang Chai et al.

PEERJ (2020)

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Review Biochemistry & Molecular Biology

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies

Anireddy S. N. Reddy et al.

BIOCHEMICAL SOCIETY TRANSACTIONS (2020)

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Article Genetics & Heredity

Analysis of Whole Transcriptome RNA-seq Data Reveals Many Alternative Splicing Events in Soybean Roots under Drought Stress Conditions

Li Song et al.

GENES (2020)

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Article Plant Sciences

Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) Roots

Evgeny A. Zorin et al.

PLANTS-BASEL (2020)

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Article Biochemistry & Molecular Biology

Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L.

Stephanie Schaarschmidt et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

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Article Biotechnology & Applied Microbiology

Illuminating the dark side of the human transcriptome with long read transcript sequencing

Richard I. Kuo et al.

BMC GENOMICS (2020)

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Article Plant Sciences

Post-transcriptional splicing of nascent RNA contributes to widespread intron retention in plants

Jinbu Jia et al.

NATURE PLANTS (2020)

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Article Biology

Patterns of alternative splicing in response to cold acclimation in fish

Timothy M. Healy et al.

JOURNAL OF EXPERIMENTAL BIOLOGY (2019)

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Article Biochemical Research Methods

Deep-learning augmented RNA-seq analysis of transcript splicing

Zijun Zhang et al.

NATURE METHODS (2019)

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Article Biochemistry & Molecular Biology

Does co-transcriptional regulation of alternative splicing mediate plant stress responses?

Ibtissam Jabre et al.

NUCLEIC ACIDS RESEARCH (2019)

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Article Biochemistry & Molecular Biology

The PROTEIN PHOSPHATASE4 Complex Promotes Transcription and Processing of Primary microRNAs in Arabidopsis

Suikang Wang et al.

PLANT CELL (2019)

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Review Plant Sciences

Perspective on Alternative Splicing and Proteome Complexity in Plants

Saurabh Chaudhary et al.

TRENDS IN PLANT SCIENCE (2019)

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Review Genetics & Heredity

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

Liangzhen Zhao et al.

FRONTIERS IN GENETICS (2019)

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Article Biotechnology & Applied Microbiology

Identification of genomic regions associated with multi-silique trait in Brassica napus

Liang Chai et al.

BMC GENOMICS (2019)

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Review Plant Sciences

Alternative Splicing in the Regulation of Plant-Microbe Interactions

Richard Rigo et al.

PLANT AND CELL PHYSIOLOGY (2019)

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Article Biochemistry & Molecular Biology

The Arabidopsis splicing regulator SR45 confers salt tolerance in a splice isoform-dependent manner

Mohammed Albaqami et al.

PLANT MOLECULAR BIOLOGY (2019)

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Article Plant Sciences

Genome-wide analysis of alternative splicing divergences between Brassica hexaploid and its parents

Ruihua Wang et al.

PLANTA (2019)

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Article Agronomy

A single-base change at a splice site in Wx-A1 caused incorrect RNA splicing and gene inactivation in a wheat EMS mutant line

Mi Luo et al.

THEORETICAL AND APPLIED GENETICS (2019)

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Article Plant Sciences

Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato

Sarah Clark et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Article Genetics & Heredity

Insights into transcriptional characteristics and homoeolog expression bias of embryo and de-embryonated kernels in developing grain through RNA-Seq and Iso-Seq

Jun Wei et al.

FUNCTIONAL & INTEGRATIVE GENOMICS (2019)

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Article Biochemistry & Molecular Biology

Coordinated Regulation of Pre-mRNA Splicing by the SFPS-RRC1 Complex to Promote Photomorphogenesis

Ruijiao Kin et al.

PLANT CELL (2019)

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Article Biochemistry & Molecular Biology

Identified trans-splicing of YELLOW-FRUITED TOMATO 2 encoding the PHYTOENE SYNTHASE 1 protein alters fruit color by map-based cloning, functional complementation and RACE

Lulu Chen et al.

PLANT MOLECULAR BIOLOGY (2019)

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Review Biochemistry & Molecular Biology

Serine/Arginine-rich protein family of splicing regulators: New approaches to study splice isoform functions

Mitchell Morton et al.

PLANT SCIENCE (2019)

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Article Multidisciplinary Sciences

Programmable mutually exclusive alternative splicing for generating RNA and protein diversity

Melina Mathur et al.

NATURE COMMUNICATIONS (2019)

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Article Multidisciplinary Sciences

Effect of de novo transcriptome assembly on transcript quantification

Ping-Han Hsieh et al.

SCIENTIFIC REPORTS (2019)

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Article Plant Sciences

Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe

Shouli Feng et al.

BMC PLANT BIOLOGY (2019)

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Editorial Material Biochemistry & Molecular Biology

Slow Down to Catch Up

Sujatha Jagannathan et al.

CELL (2019)

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Review Plant Sciences

Alternative Splicing and Protein Diversity: Plants Versus Animals

Saurabh Chaudhary et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Article Plant Sciences

New Era in Plant Alternative Splicing Analysis Enabled by Advances in High-Throughput Sequencing (HTS) Technologies

Renesh Bedre et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Review Plant Sciences

Role of Arbuscular Mycorrhizal Fungi in Plant Growth Regulation: Implications in Abiotic Stress Tolerance

Naheeda Begum et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Article Multidisciplinary Sciences

Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites

Geeng Loo Chong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Plant Sciences

Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes of Arabidopsis thaliana

Waqas Khokhar et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Article Biochemistry & Molecular Biology

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

Micaela A. Godoy Herz et al.

MOLECULAR CELL (2019)

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Article Biochemistry & Molecular Biology

The APETALA2-Like Transcription Factor SUPERNUMERARY BRACT Controls Rice Seed Shattering and Seed Size

Liyun Jiang et al.

PLANT CELL (2019)

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Article Plant Sciences

The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress

Xiaoming Yu et al.

PLANT CELL REPORTS (2019)

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Article Genetics & Heredity

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

Andrea Minio et al.

G3-GENES GENOMES GENETICS (2019)

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Article Plant Sciences

Alternative Splicing of Circadian Clock Genes Correlates With Temperature in Field-Grown Sugarcane

Luiza L. B. Dantas et al.

FRONTIERS IN PLANT SCIENCE (2019)

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Article Biotechnology & Applied Microbiology

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

Jun Cheng et al.

GENOME BIOLOGY (2019)

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Article Plant Sciences

A global survey of alternative splicing in allopolyploid cotton: landscape, complexity and regulation

Maojun Wang et al.

NEW PHYTOLOGIST (2018)

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Article Biotechnology & Applied Microbiology

Global profiling of alternative splicing landscape responsive to drought, heat and their combination in wheat (Triticum aestivum L.)

Zhenshan Liu et al.

PLANT BIOTECHNOLOGY JOURNAL (2018)

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Article Biology

Position-specific intron retention is mediated by the histone methyltransferase SDG725

Gang Wei et al.

BMC BIOLOGY (2018)

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Article Biotechnology & Applied Microbiology

RNA-seq analysis reveals alternative splicing under salt stress in cotton, Gossypium davidsonii

Guozhong Zhu et al.

BMC GENOMICS (2018)

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Article Biotechnology & Applied Microbiology

Exploring the relationship between intron retention and chromatin accessibility in plants

Fahad Ullah et al.

BMC GENOMICS (2018)

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Article Biology

RNA thermosensors: how might animals exploit their regulatory potential?

George N. Somero

JOURNAL OF EXPERIMENTAL BIOLOGY (2018)

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Article Biochemistry & Molecular Biology

Extensive Differential Splicing Underlies Phenotypically Plastic Aphid Morphs

Mary E. Grantham et al.

MOLECULAR BIOLOGY AND EVOLUTION (2018)

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Article Biochemical Research Methods

Identification of RNA-binding protein targets with HyperTRIBE

Reazur Rahman et al.

NATURE PROTOCOLS (2018)

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Review Genetics & Heredity

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

Fritz J. Sedlazeck et al.

NATURE REVIEWS GENETICS (2018)

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Article Biotechnology & Applied Microbiology

Alternative splicing of OsLG3b controls grain length and yield in japonica rice

Jianping Yu et al.

PLANT BIOTECHNOLOGY JOURNAL (2018)

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Article Biochemistry & Molecular Biology

Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome

Cristiane P. G. Calixto et al.

PLANT CELL (2018)

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Article Biochemistry & Molecular Biology

Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize

Qiuyue Chen et al.

PLANT CELL (2018)

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Article Biochemical Research Methods

Development of an in vitro pre-mRNA splicing assay using plant nuclear extract

Mohammed Albaqami et al.

PLANT METHODS (2018)

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Article Multidisciplinary Sciences

Genetics of alternative splicing evolution during sunflower domestication

Chris C. R. Smith et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

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Review Plant Sciences

Alternative Splicing Control of Abiotic Stress Responses

Tom Laloum et al.

TRENDS IN PLANT SCIENCE (2018)

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Article Plant Sciences

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

Sergei A. Filichkin et al.

FRONTIERS IN PLANT SCIENCE (2018)

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Article Biochemistry & Molecular Biology

Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

Chunlan Dong et al.

PLANT CELL (2018)

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Article Plant Sciences

Functional Analysis of PsAvr3c Effector Family From Phytophthora Provides Probes to Dissect SKRP Mediated Plant Susceptibility

Ying Zhang et al.

FRONTIERS IN PLANT SCIENCE (2018)

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Article Plant Sciences

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses

Jeremie Bazin et al.

FRONTIERS IN PLANT SCIENCE (2018)

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Article Multidisciplinary Sciences

Mutations in the DNA demethylase OsROS1 result in a thickened aleurone and improved nutritional value in rice grains

Jinxin Liu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)

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Review Plant Sciences

Plant Growth-Promoting Rhizobacteria: Context, Mechanisms of Action, and Roadmap to Commercialization of Biostimulants for Sustainable Agriculture

Rachel Backer et al.

FRONTIERS IN PLANT SCIENCE (2018)

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Article Biochemistry & Molecular Biology

ISOdb: A Comprehensive Database of Full-Length Isoforms Generated by Iso-Seq

Shang-Qian Xie et al.

INTERNATIONAL JOURNAL OF GENOMICS (2018)

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Article Biotechnology & Applied Microbiology

SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions

Juan L. Trincado et al.

GENOME BIOLOGY (2018)

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Article Evolutionary Biology

The Role of Alternative Splicing and Differential Gene Expression in Cichlid Adaptive Radiation

Pooja Singh et al.

GENOME BIOLOGY AND EVOLUTION (2017)

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Review Biochemistry & Molecular Biology

Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants

Xudong Shang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2017)

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Article Multidisciplinary Sciences

SPF45-related splicing factor for phytochrome signaling promotes photomorphogenesis by regulating pre-mRNA splicing in Arabidopsis

Ruijiao Xin et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

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Article Agronomy

The alternative splicing of EAM8 contributes to early flowering and short-season adaptation in a landrace barley from the Qinghai-Tibetan Plateau

Tengfei Xia et al.

THEORETICAL AND APPLIED GENETICS (2017)

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Letter Biochemistry & Molecular Biology

The Relationship between Alternative Splicing and Proteomic Complexity

Benjamin J. Blencowe

TRENDS IN BIOCHEMICAL SCIENCES (2017)

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Review Biochemistry & Molecular Biology

Alternative Splicing May Not Be the Key to Proteome Complexity

Michael L. Tress et al.

TRENDS IN BIOCHEMICAL SCIENCES (2017)

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Review Plant Sciences

RNA-Binding Proteins Revisited - The Emerging Arabidopsis mRNA Interactome

Tino Koester et al.

TRENDS IN PLANT SCIENCE (2017)

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Article Multidisciplinary Sciences

An oomycete plant pathogen reprograms host pre-mRNA splicing to subvert immunity

Jie Huang et al.

NATURE COMMUNICATIONS (2017)

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Article Genetics & Heredity

Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes

Qingqing Yan et al.

PLOS GENETICS (2017)

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Article Multidisciplinary Sciences

Domestication reduces alternative splicing expression variations in sorghum

Vincent Ranwez et al.

PLOS ONE (2017)

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Article Multidisciplinary Sciences

Identified of a novel cis-element regulating the alternative splicing of LcDREB2

Zhujiang Liu et al.

SCIENTIFIC REPORTS (2017)

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Article Biotechnology & Applied Microbiology

Transcriptome analyses reveal SR45 to be a neutral splicing regulator and a suppressor of innate immunity in Arabidopsis thaliana

Xiao-Ning Zhang et al.

BMC GENOMICS (2017)

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Article Biochemical Research Methods

Integrative deep models for alternative splicing

Anupama Jha et al.

BIOINFORMATICS (2017)

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Article Biotechnology & Applied Microbiology

Histone H3 lysine 36 methylation affects temperature-induced alternative splicing and flowering in plants

A. Pajoro et al.

GENOME BIOLOGY (2017)

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Review Plant Sciences

Genetic assimilation: a review of its potential proximate causes and evolutionary consequences

Ian M. Ehrenreich et al.

ANNALS OF BOTANY (2016)

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Article Plant Sciences

Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize

Shawn R. Thatcher et al.

PLANT PHYSIOLOGY (2016)

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Article Biochemistry & Molecular Biology

TRIBE: Hijacking an RNA-Editing Enzyme to Identify Cell-Specific Targets of RNA-Binding Proteins

Aoife C. McMahon et al.

CELL (2016)

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Review Biochemistry & Molecular Biology

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

Tassa Saldi et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

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Letter Biochemistry & Molecular Biology

DNA Methylation Affects Gene Alternative Splicing in Plants: An Example from Rice

Xutong Wang et al.

MOLECULAR PLANT (2016)

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Article Multidisciplinary Sciences

A survey of the sorghum transcriptome using single-molecule long reads

Salah E. Abdel-Ghany et al.

NATURE COMMUNICATIONS (2016)

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Article Biology

A new view of transcriptome complexity and regulation through the lens of local splicing variations

Jorge Vaquero-Garcia et al.

ELIFE (2016)

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Article Multidisciplinary Sciences

Alternative Splicing of Barley Clock Genes in Response to Low Temperature

Cristiane P. G. Calixto et al.

PLOS ONE (2016)

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Review Biochemistry & Molecular Biology

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

Shiran Naftelberg et al.

ANNUAL REVIEW OF BIOCHEMISTRY, VOL 84 (2015)

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Article Biotechnology & Applied Microbiology

Identification of alternative splicing events by RNA sequencing in early growth tomato fruits

Yuan Sun et al.

BMC GENOMICS (2015)

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Article Biochemistry & Molecular Biology

Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis

Sergei A. Filichkin et al.

MOLECULAR PLANT (2015)

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Article Genetics & Heredity

Intron retention is a widespread mechanism of tumor-suppressor inactivation

Hyunchul Jung- et al.

NATURE GENETICS (2015)

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Article Plant Sciences

Differential Recruitment of Splice Variants from SR Pre-mRNAs to Polysomes During Development and in Response to Stresses

Saiprasad Goud Palusa et al.

PLANT AND CELL PHYSIOLOGY (2015)

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Article Biochemistry & Molecular Biology

Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing

Denghui Xing et al.

PLANT CELL (2015)

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Article Biochemistry & Molecular Biology

Genome-Wide Analysis of Alternative Splicing Landscapes Modulated during Plant-Virus Interactions in Brachypodium distachyon

Kranthi K. Mandadi et al.

PLANT CELL (2015)

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Article Multidisciplinary Sciences

The spliceosome assembly factor GEMIN2 attenuates the effects of temperature on alternative splicing and circadian rhythms

Ruben Gustavo Schlaen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

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Article Multidisciplinary Sciences

An alternative splicing event amplifies evolutionary differences between vertebrates

Serge Gueroussov et al.

SCIENCE (2015)

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Article Plant Sciences

Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

Young-Ju Kwon et al.

BMC PLANT BIOLOGY (2014)

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Article Biochemistry & Molecular Biology

Widespread intron retention in mammals functionally tunes transcriptomes

Ulrich Braunschweig et al.

GENOME RESEARCH (2014)

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Article Biochemistry & Molecular Biology

Discovery and Expression Analysis of Alternative Splicing Events Conserved among Plant SR Proteins

Hypaitia B. Rauch et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

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Article Biochemistry & Molecular Biology

Correcting for Differential Transcript Coverage Reveals a Strong Relationship between Alternative Splicing and Organism Complexity

Lu Chen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2014)

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Article Multidisciplinary Sciences

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Yiliang Ding et al.

NATURE (2014)

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Editorial Material Biotechnology & Applied Microbiology

The devil in the details of RNA-seq

Anton Kratz et al.

NATURE BIOTECHNOLOGY (2014)

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Article Biochemistry & Molecular Biology

Genome-Wide Analysis of Alternative Splicing in Zea mays: Landscape and Genetic Regulation

Shawn R. Thatcher et al.

PLANT CELL (2014)

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Article Biochemistry & Molecular Biology

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

Yanting Shen et al.

PLANT CELL (2014)

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Article Multidisciplinary Sciences

Role for LSM genes in the regulation of circadian rhythms

Soledad Perez-Santangelo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

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Article Multidisciplinary Sciences

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Shihao Shen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

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Article Plant Sciences

Genome-wide survey of Alternative Splicing in Sorghum Bicolor

Bahman Panahi et al.

PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS (2014)

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Article Cell Biology

Removal of Retained Introns Regulates Translation in the Rapidly Developing Gametophyte of Marsilea vestita

Thomas C. Boothby et al.

DEVELOPMENTAL CELL (2013)

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Article Biochemical Research Methods

Assessment of transcript reconstruction methods for RNA-seq

Tamara Steijger et al.

NATURE METHODS (2013)

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Review Biochemistry & Molecular Biology

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

Dorothee Staiger et al.

PLANT CELL (2013)

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Review Biochemistry & Molecular Biology

Complexity of the Alternative Splicing Landscape in Plants

Anireddy S. N. Reddy et al.

PLANT CELL (2013)

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Article Multidisciplinary Sciences

Drift and conservation of differential exon usage across tissues in primate species

Alejandro Reyes et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

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Article Cell Biology

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

Karen Yap et al.

GENES & DEVELOPMENT (2012)

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Article Biochemistry & Molecular Biology

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for IncRNAs

Hagen Tilgner et al.

GENOME RESEARCH (2012)

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Article Biochemistry & Molecular Biology

Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis

Yamile Marquez et al.

GENOME RESEARCH (2012)

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Article Plant Sciences

Contribution of the different omega-3 fatty acid desaturase genes to the cold response in soybean

Angela Roman et al.

JOURNAL OF EXPERIMENTAL BOTANY (2012)

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Article Biochemistry & Molecular Biology

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data

Shihao Shen et al.

NUCLEIC ACIDS RESEARCH (2012)

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Article Biochemistry & Molecular Biology

Mutation of Arabidopsis SPLICEOSOMAL TIMEKEEPER LOCUS1 Causes Circadian Clock Defects

Matthew A. Jones et al.

PLANT CELL (2012)

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Article Biochemistry & Molecular Biology

Alternative Splicing Mediates Responses of the Arabidopsis Circadian Clock to Temperature Changes

Allan B. James et al.

PLANT CELL (2012)

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Article Biochemistry & Molecular Biology

SKIP Is a Component of the Spliceosome Linking Alternative Splicing and the Circadian Clock in Arabidopsis

Xiaoxue Wang et al.

PLANT CELL (2012)

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Article Biochemistry & Molecular Biology

A Self-Regulatory Circuit of CIRCADIAN CLOCK-ASSOCIATED1 Underlies the Circadian Clock Regulation of Temperature Responses in Arabidopsis

Pil Joon Seo et al.

PLANT CELL (2012)

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Article Plant Sciences

Interactions of SR45, an SR-like protein, with spliceosomal proteins and an intronic sequence: insights into regulated splicing

Irene S. Day et al.

PLANT JOURNAL (2012)

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Article Plant Sciences

Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing of SCL33 pre-mRNA

Julie Thomas et al.

PLANT JOURNAL (2012)

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Editorial Material Plant Sciences

Localization and Dynamics of Nuclear Speckles in Plants

Anireddy S. N. Reddy et al.

PLANT PHYSIOLOGY (2012)

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Review Biochemistry & Molecular Biology

Alternative splicing: Enhancing ability to cope with stress via transcriptome plasticity

Anna M. Mastrangelo et al.

PLANT SCIENCE (2012)

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Article Agronomy

Identification and characterization of the soybean IPK1 ortholog of a low phytic acid mutant reveals an exon-excluding splice-site mutation

Feng-Jie Yuan et al.

THEORETICAL AND APPLIED GENETICS (2012)

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Article Biotechnology & Applied Microbiology

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

Mark F. Rogers et al.

GENOME BIOLOGY (2012)

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Article Multidisciplinary Sciences

The evolution of gene expression levels in mammalian organs

David Brawand et al.

NATURE (2011)

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Review Biochemistry & Molecular Biology

Coping with Stresses: Roles of Calcium- and Calcium/Calmodulin-Regulated Gene Expression

Anireddy S. N. Reddy et al.

PLANT CELL (2011)

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Article Agronomy

Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.)

Zhenqi Su et al.

THEORETICAL AND APPLIED GENETICS (2011)

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Review Cell Biology

Plant serine/arginine-rich proteins: roles in precursor messenger RNA splicing, plant development, and stress responses

Anireddy S. N. Reddy et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2011)

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Review Biochemistry & Molecular Biology

A role for SR proteins in plant stress responses

Paula Duque

PLANT SIGNALING & BEHAVIOR (2011)

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Article Biochemistry & Molecular Biology

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

Sergei A. Filichkin et al.

GENOME RESEARCH (2010)

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Article Multidisciplinary Sciences

A methyl transferase links the circadian clock to the regulation of alternative splicing

Sabrina E. Sanchez et al.

NATURE (2010)

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Article Biochemical Research Methods

Analysis and design of RNA sequencing experiments for identifying isoform regulation

Yarden Katz et al.

NATURE METHODS (2010)

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Article Plant Sciences

Extensive coupling of alternative splicing of pre-mRNAs of serine/arginine (SR) genes with nonsense-mediated decay

Saiprasad G. Palusa et al.

NEW PHYTOLOGIST (2010)

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Article Multidisciplinary Sciences

Type II protein arginine methyltransferase 5 (PRMT5) is required for circadian period determination in Arabidopsis thaliana

Sunghyun Hong et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

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Review Biochemistry & Molecular Biology

The SR protein family of splicing factors: master regulators of gene expression

Jennifer C. Long et al.

BIOCHEMICAL JOURNAL (2009)

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Review Cell Biology

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Mo Chen et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2009)

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Article Plant Sciences

CIRCADIAN CLOCK ASSOCIATED1 and LATE ELONGATED HYPOCOTYL Function Synergistically in the Circadian Clock of Arabidopsis

Sheen X. Lu et al.

PLANT PHYSIOLOGY (2009)

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Article Oncology

Co-localisation studies of Arabidopsis SR splicing factors reveal different types of speckles in plant cell nuclei

Zdravko J. Lorkovic et al.

EXPERIMENTAL CELL RESEARCH (2008)

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Review Biochemistry & Molecular Biology

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

W. Brad Barbazuk et al.

GENOME RESEARCH (2008)

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Article Multidisciplinary Sciences

Analyses of In Vivo Interaction and Mobility of Two Spliceosomal Proteins Using FRAP and BiFC

Gul Shad Ali et al.

PLOS ONE (2008)

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Article Multidisciplinary Sciences

Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements

Liana F. Lareau et al.

NATURE (2007)

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Article Plant Sciences

Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses

Saiprasad Goud Palusa et al.

PLANT JOURNAL (2007)

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Review Genetics & Heredity

The evolutionary significance of cis-regulatory mutations

Gregory A. Wray

NATURE REVIEWS GENETICS (2007)

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Article Biochemistry & Molecular Biology

Insights into nuclear organization in plants as revealed by the dynamic distribution of Arabidopsis SR splicing factors

Vinciane Tillemans et al.

PLANT CELL (2006)

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Article Biochemistry & Molecular Biology

Evolutionary conservation and regulation of particular alternative splicing events in plant SR proteins

Maria Kalyna et al.

NUCLEIC ACIDS RESEARCH (2006)

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Article Multidisciplinary Sciences

Genomewide comparative analysis of alternative splicing in plants

BB Wang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

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Article Cell Biology

ATP, phosphorylation and transcription regulate the mobility of plant splicing factors

Gul Shad Ali et al.

JOURNAL OF CELL SCIENCE (2006)

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Article Biochemistry & Molecular Biology

Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences

K Iida et al.

NUCLEIC ACIDS RESEARCH (2004)

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Article Cell Biology

Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis

YD Fang et al.

MOLECULAR BIOLOGY OF THE CELL (2004)

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Article Plant Sciences

Nuclear localization and in vivo dynamics of a plant-specific serine/arginine-rich protein

GS Ali et al.

PLANT JOURNAL (2003)

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Article Cell Biology

Ectopic expression of atRSZ33 reveals its function in splicing and causes pleiotropic changes in development

M Kalyna et al.

MOLECULAR BIOLOGY OF THE CELL (2003)

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