4.0 Review

Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Review Biotechnology & Applied Microbiology

Genome editing interventions to combat rice blast disease

Vaishali Khanale et al.

Summary: Rice, as a major food crop, faces threats from various biotic and abiotic stresses. Traditional methods of resistance are becoming less effective, but genome editing offers a promising alternative. Mutation breeding and transgenic approaches also have potential to increase rice yield and protect against diseases. However, these approaches have limitations, and combining different breeding resources can help establish disease resistance.

PLANT BIOTECHNOLOGY REPORTS (2023)

Article Biochemistry & Molecular Biology

Sites of transcription initiation drive mRNA isoform selection

Carlos Alfonso-Gonzalez et al.

Summary: The generation of distinct messenger RNA isoforms through alternative RNA processing modulates the expression and function of genes, often in a cell-type-specific manner. Transcription initiation and 3' end site selection have regulatory relationships with alternative splicing. Dominant promoters, identified by specific epigenetic signatures, impose a transcriptional constraint to define splice and polyadenylation variants. Our study demonstrates the crucial impact of transcription start site choice on the regulation of transcript diversity and tissue identity.
Review Plant Sciences

Coupling epigenetics and RNA polyadenylation: missing links

Juncheng Lin et al.

Summary: Precise regulation of gene expression is essential for plant survival. Pre-mRNA polyadenylation, as a cotranscriptional regulatory mechanism, plays a crucial role in fine-tuning gene expression. Epigenetic modification, including DNA methylation, histone modifications, and epitranscriptomic modification, has been found to be involved in regulating polyadenylation in plants. This article summarizes the links between epigenetics and polyadenylation and discusses their novel biological efficacy for plant development and environmental responses.

TRENDS IN PLANT SCIENCE (2023)

Article Genetics & Heredity

Transcriptome sequencing suggests that pre-mRNA splicing counteracts widespread intronic cleavage and polyadenylation

Maria Vlasenok et al.

Summary: Alternative splicing and alternative polyadenylation are crucial steps in the regulation of gene expression. Analysis of RNA-seq data reveals that intronic polyadenylation is more abundant than exonic polyadenylation. Some intronic polyadenylation events lack splicing support, suggesting they are products of spliced polyadenylated introns.

NAR GENOMICS AND BIOINFORMATICS (2023)

Review Cell Biology

Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression

Lori A. Passmore et al.

Summary: Recent studies have shown that poly(A) tails play a complex role in the cytoplasm, including promoting translation and controlling mRNA stability through deadenylation. The length of poly(A) tails is correlated with translation rate and mRNA lifespan, indicating a significant role in gene regulation.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2022)

Editorial Material Cell Biology

Human pre-mRNA 3′ end processing: reconstituting is believing

Yoseop Yoon et al.

Summary: In this article, two independent studies successfully reconstituted the processing of human pre-mRNA 3' ends using defined components in vitro. These studies are of great importance for understanding the nature and essential components of this biological process.

GENES & DEVELOPMENT (2022)

Article Plant Sciences

Divergence in the Regulation of the Salt Tolerant Response Between Arabidopsis thaliana and Its Halophytic Relative Eutrema salsugineum by mRNA Alternative Polyadenylation

Hui Ma et al.

Summary: Salt tolerance is an important mechanism for plants to adapt to a saline environment. Through global analyses of mRNA alternative polyadenylation (APA), researchers found that Arabidopsis thaliana and its halophytic relative Eutrema salsugineum have different responses to salt stress. Arabidopsis is more sensitive to salt stress, while Eutrema exhibits an innate response to such conditions. The number of APA genes and the enriched pathways in response to salt stress also differ between the two species.

FRONTIERS IN PLANT SCIENCE (2022)

Review Cell Biology

Context-specific regulation and function of mRNA alternative polyadenylation

Sibylle Mitschka et al.

Summary: Alternative cleavage and polyadenylation (APA) is a widespread mechanism for generating mRNA isoforms with different 3' untranslated regions (UTRs). APA is dynamically regulated by multiple mechanisms, including cis-regulatory elements and factors that control transcription and post-transcriptional processes. Dysregulation of APA can impact cellular responses to environmental changes. APA also plays a role in regulating protein abundance, mRNA localization, and protein synthesis organization. Recent advances in single-cell RNA sequencing and CRISPR-Cas technologies have enabled the study of APA in various biological contexts. APA-based RNA therapeutics show promise in the treatment of cancer and degenerative diseases.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2022)

Article Genetics & Heredity

A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq

Wenbin Ye et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2022)

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)

Article Biochemistry & Molecular Biology

Arabidopsis N6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies

Peizhe Song et al.

Summary: This study reveals that CPSF30-L acts as an m(6)A reader in plants, with its m(6)A-binding function playing a crucial role in the floral transition and ABA response; The m(6)A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies and prolongs the untranslated regions of specific transcripts, leading to late flowering and ABA hypersensitivity.

MOLECULAR PLANT (2021)

Article Biochemistry & Molecular Biology

CPSF30-L-mediated recognition of mRNA m6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis

Yifeng Hou et al.

Summary: The study demonstrates that m(6)A modification regulates APA in plants, with CPSF30-L YTH domain binding to m(6)A and affecting nitrate signaling by controlling APA.

MOLECULAR PLANT (2021)

Article Biochemical Research Methods

QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering

Congting Ye et al.

Summary: Alternative polyadenylation, the dynamic choice of different polyadenylation sites in a gene, plays important roles in various biological processes. The QuantifyPoly(A) method accurately quantifies genome-wide polyadenylation choices and reshapes polyadenylation profiles into novel clusters, revealing dynamic usage across biological samples and species specificity.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biochemical Research Methods

FLEP-seq: simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site and poly(A) tail length at genome-wide scale by single-molecule nascent RNA sequencing

Yanping Long et al.

Summary: The FLEP-seq method allows simultaneous detection of RNA polymerase II position, splicing status, polyadenylation site, and poly(A) tail length in plants. It enables calculation of cotranscriptional splicing kinetics and identification of polyadenylated transcripts with unspliced introns at specific positions posttranscriptionally.

NATURE PROTOCOLS (2021)

Article Plant Sciences

Intragenic heterochromatin-mediated alternative polyadenylation modulates miRNA and pollen development in rice

Li-Yuan You et al.

Summary: The ASI1 protein complex in rice plays a crucial role in regulating global poly(A) site usage and development, particularly in pollen development. It interacts with intronic heterochromatin to promote miRNA processing and ultimately impacts rice development. This study sheds light on the epigenetic mechanisms involved in miRNA abundance and crop development.

NEW PHYTOLOGIST (2021)

Article Biochemistry & Molecular Biology

Alternative polyadenylated mRNAs behave as asynchronous rhythmic transcription in Arabidopsis

Juncheng Lin et al.

Summary: The study reveals that alternative polyadenylation can affect the 3' end profile of transcripts in Arabidopsis, indicating significant differences in expression and translation activity between rhythmic and arrhythmic transcripts. Additionally, rhythmic transcripts contain a higher proportion of AAUAAA and UGUA signals.

RNA BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

Landscape of transcription termination in Arabidopsis revealed by single-molecule nascent RNA sequencing

Weipeng Mo et al.

Summary: Using single-molecule nascent RNA sequencing, we characterized transient RNAs during transcription termination in Arabidopsis, revealing a wide range of termination windows among genes. We observed new transcription phenomena in mutants, providing new insights into the termination mechanism.

GENOME BIOLOGY (2021)

Article Biochemical Research Methods

scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data

Xiaohui Wu et al.

Summary: APA plays a crucial role in transcriptome diversity and gene expression regulation. The newly developed tool scAPAtrap can accurately identify poly(A) sites at the whole genome level in individual cells, even for sites with low read coverage, without relying on priori genome annotation. Compared to existing methods, scAPAtrap shows higher accuracy and sensitivity in identifying poly(A) sites, making it a valuable tool for exploring APA dynamics and heterogeneous APA isoform expression at the single-cell level.

BRIEFINGS IN BIOINFORMATICS (2021)

Article Biotechnology & Applied Microbiology

FlsnRNA-seq: protoplasting-free full-length single-nucleus RNA profiling in plants

Yanping Long et al.

Summary: The study introduces a protoplasting-free approach for large-scale full-length RNA profiling at a single-nucleus level in plants, demonstrating its robustness in Arabidopsis root cells and developing endosperm. The method allows for uncovering alternative splicing and polyadenylation-related RNA isoform information at the single-cell level, facilitating the characterization of cell identities.

GENOME BIOLOGY (2021)

Article Biotechnology & Applied Microbiology

In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants

Zhenshan Liu et al.

Summary: This study identified specific RNA structures in nuclear mRNAs that are associated with splicing and polyadenylation events, revealing a new regulatory mechanism for mRNA processing.

GENOME BIOLOGY (2021)

Article Biochemistry & Molecular Biology

The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation

Yuchen Yang et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2020)

Review Plant Sciences

Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression

Willian Souza Bernardes et al.

FRONTIERS IN PLANT SCIENCE (2020)

Article Plant Sciences

Heat Shock Responsive Gene Expression Modulated by mRNA Poly(A) Tail Length

Xuan Wu et al.

FRONTIERS IN PLANT SCIENCE (2020)

Review Biochemistry & Molecular Biology

Discovery of alternative polyadenylation dynamics from single cell types

Congting Ye et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Biochemistry & Molecular Biology

Genome-Wide Comparative Analyses of Polyadenylation Signals in Eukaryotes Suggest a Possible Origin of the AAUAAA Signal

Zhixin Zhao et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biochemistry & Molecular Biology

Role of alternative polyadenylation dynamics in acute myeloid leukaemia at single-cell resolution

Congting Ye et al.

RNA BIOLOGY (2019)

Review Genetics & Heredity

Alternative cleavage and polyadenylation in health and disease

Andreas J. Gruber et al.

NATURE REVIEWS GENETICS (2019)

Article Biochemistry & Molecular Biology

Sequence determinants of polyadenylation-mediated regulation

Ilya Vainberg Slutskin et al.

GENOME RESEARCH (2019)

Article Biochemistry & Molecular Biology

Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation

Zhibo Yu et al.

PLANT CELL (2019)

Article Environmental Sciences

Genome-wide alternative polyadenylation dynamics in response to biotic and abiotic stresses in rice

Congting Ye et al.

ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY (2019)

Article Biochemical Research Methods

APAtrap: identification and quantification of alternative polyadenylation sites from RNA-seq data

Congting Ye et al.

BIOINFORMATICS (2018)

Article Biochemistry & Molecular Biology

3 ' UTR lengthening as a novel mechanism in regulating cellular senescence

Meng Chen et al.

GENOME RESEARCH (2018)

Article Multidisciplinary Sciences

Cellular stress alters 3 ' UTR landscape through alternative polyadenylation and isoform-specific degradation

Dinghai Zheng et al.

NATURE COMMUNICATIONS (2018)

Article Multidisciplinary Sciences

Widespread intronic polyadenylation inactivates tumour suppressor genes in leukaemia

Shih-Han Lee et al.

NATURE (2018)

Review Cell Biology

Alternative polyadenylation of mRNA precursors

Bin Tian et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Short poly(A) tails are a conserved feature of highly expressed genes

Sarah Azoubel Lima et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Biochemistry & Molecular Biology

Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia

Laura de Lorenzo et al.

PLANT CELL (2017)

Article Biochemistry & Molecular Biology

Short poly(A) tails are a conserved feature of highly expressed genes

Sarah Azoubel Lima et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2017)

Article Biotechnology & Applied Microbiology

The role of alternative Polyadenylation in regulation of rhythmic gene expression

Natalia Ptitsyna et al.

BMC GENOMICS (2017)

Article Plant Sciences

Seed Dormancy in Arabidopsis Is Controlled by Alternative Polyadenylation of DOG1

Malgorzata Cyrek et al.

PLANT PHYSIOLOGY (2016)

Article Biochemistry & Molecular Biology

Genome-wide dynamics of alternative polyadenylation in rice

Haihui Fu et al.

GENOME RESEARCH (2016)

Article Multidisciplinary Sciences

A Genome-wide Study of Non-3UTR Polyadenylation Sites in Arabidopsis thaliana

Cheng Guo et al.

SCIENTIFIC REPORTS (2016)

Article Cell Biology

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

Serena L. Chan et al.

GENES & DEVELOPMENT (2014)

Article Biochemical Research Methods

High throughput characterizations of poly(A) site choice in plants

Liuyin Ma et al.

METHODS (2014)

Editorial Material Multidisciplinary Sciences

Role of alternative polyadenylation in epigenetic silencing and antisilencing

Liuyin Ma et al.

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

Article Multidisciplinary Sciences

Arabidopsis EDM2 promotes IBM1 distal polyadenylation and regulates genome DNA methylation patterns

Mingguang Lei et al.

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

Review Cell Biology

Determinants and implications of mRNA poly(A) tail size - Does this protein make my tail look big?

Aimee L. Jalkanen et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2014)

Review Plant Sciences

Plant salt-tolerance mechanisms

Ulrich Deinlein et al.

TRENDS IN PLANT SCIENCE (2014)

Article Multidisciplinary Sciences

An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

Tokuji Tsuchiya et al.

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

Review Biochemistry & Molecular Biology

Unraveling the circadian clock in Arabidopsis

Xiaoxue Wang et al.

PLANT SIGNALING & BEHAVIOR (2013)

Article Biochemistry & Molecular Biology

In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii

Xiaohui Wu et al.

MOLECULAR GENETICS AND GENOMICS (2012)

Article Biochemistry & Molecular Biology

Genome-Wide Control of Polyadenylation Site Choice by CPSF30 in Arabidopsis

Patrick E. Thomas et al.

PLANT CELL (2012)

Article Multidisciplinary Sciences

Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation

Xiaohui Wu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)

Review Cell Biology

Alternative polyadenylation and gene expression regulation in plants

Denghui Xing et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2011)

Review Marine & Freshwater Biology

Mangrove forests: Resilience, protection from tsunamis, and responses to global climate change

Daniel M. Alongi

ESTUARINE COASTAL AND SHELF SCIENCE (2008)

Review Agriculture, Multidisciplinary

The epidemiology and management of bacterial blight (Pseudomonas syringae pv. pisi) of field pea (Pisum sativum) in Australia: a review

G. J. Hollaway et al.

AUSTRALIAN JOURNAL OF AGRICULTURAL RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Pricing medicines: Theory and practice, challenges and opportunities

N Gregson et al.

NATURE REVIEWS DRUG DISCOVERY (2005)