4.7 Article

Transcriptomic Reprogramming, Alternative Splicing and RNA Methylation in Potato (Solanum tuberosum L.) Plants in Response to Potato Virus Y Infection

Related references

Note: Only part of the references are listed.
Review Cell Biology

Gene regulation by long non-coding RNAs and its biological functions

Luisa Statello et al.

Summary: Recent studies have shed new light on the biogenesis and functions of long non-coding RNAs (lncRNAs), showcasing their diverse roles in gene regulation and signaling pathways, particularly in the contexts of neuronal disorders, immune responses, and cancer. The discovery of unique biogenesis pathways and subcellular localizations of lncRNAs has opened up potential therapeutic avenues for targeting lncRNAs in various biological and pathophysiological conditions.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Rfam 14: expanded coverage of metagenomic, viral and microRNA families

Ioanna Kalvari et al.

Summary: Rfam is a database of RNA families with 3444 families, each represented by a multiple sequence alignment of known RNA sequences and a covariance model for searching additional members. Recent developments focused on improving data quality and coverage, adding new families like microRNAs, viral and bacterial RNAs through expert collaborations. The database saw significant growth with 759 new families added in Rfam 14, along with new features such as the Rfam Cloud family curation system.

NUCLEIC ACIDS RESEARCH (2021)

Review Biotechnology & Applied Microbiology

A systematic review of computational methods for predicting long noncoding RNAs

Xinran Xu et al.

Summary: This review introduces the development of computational methods for lncRNA prediction and presents a new Python package, ezLncPred, which provides a convenient way to utilize nine state-of-the-art lncRNA prediction methods. The challenges and future directions of lncRNA prediction are also discussed in the paper.

BRIEFINGS IN FUNCTIONAL GENOMICS (2021)

Article Genetics & Heredity

Combined drought and heat stresses trigger different sets of miRNAs in contrasting potato cultivars

Zahide Neslihan Ozturk Gokce et al.

Summary: MicroRNAs play a crucial role in regulating gene expression during plant growth and development, with their profiles varying in different potato cultivars under abiotic stress. Unica cultivar showed more changes in miRNA expression and higher tolerance to combined drought and heat stress compared to Russet Burbank. Key miRNAs identified in this study target genes involved in response to drought and heat stress, indicating their important roles in post-transcriptional regulation and plant development. Further research is needed to explore the potential of miRNA overexpression in enhancing plant tolerance against abiotic stresses, especially in the context of combined stress conditions.

FUNCTIONAL & INTEGRATIVE GENOMICS (2021)

Article Biochemistry & Molecular Biology

Rapid and accurate alignment of nucleotide conversion sequencing reads with HISAT-3N

Yun Zhang et al.

Summary: The paper presents HISAT-3N, a method for efficiently and accurately aligning converted sequences, showing that it outperforms other modern systems in speed, accuracy, scalability, and memory requirements.

GENOME RESEARCH (2021)

Article Biotechnology & Applied Microbiology

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

Ploy N. Pratanwanich et al.

Summary: The computational method xPore is developed to identify differential RNA modifications from nanopore direct RNA sequencing data, enabling analysis of RNA modifications and expression from a single high-throughput experiment. The study demonstrates that m(6)A RNA modifications can be accurately quantified in cancer patient samples and cell lines using nanopore sequencing.

NATURE BIOTECHNOLOGY (2021)

Article Virology

The Resistance Responses of Potato Plants to Potato Virus Y Are Associated with an Increased Cellular Methionine Content and an Altered SAM:SAH Methylation Index

Nadezhda Spechenkova et al.

Summary: Plant-virus interactions can be influenced by elevated temperature, affecting susceptibility to viruses. The Gala potato cultivar shows temperature-independent resistance to PVY by upregulating major enzymes associated with the methionine cycle, while the Chicago cultivar's susceptibility to PVY is linked to reduced levels of S-adenosyl methionine at high temperatures.

VIRUSES-BASEL (2021)

Article Plant Sciences

Blocking miR530 Improves Rice Resistance, Yield, and Maturity

Yan Li et al.

Summary: miR530 acts as a crucial regulator in rice, balancing blast disease resistance, yield, and maturity. Overexpression of miR530 compromises resistance, reduces yield, and delays maturity, while blocking miR530 enhances resistance, increases yield, and promotes early maturity.

FRONTIERS IN PLANT SCIENCE (2021)

Article Plant Sciences

Role of the methionine cycle in the temperature-sensitive responses of potato plants to potato virus Y

Igor Fesenko et al.

Summary: The interaction between plants and viruses is greatly affected by environmental factors such as temperature, with higher temperatures increasing plant susceptibility to virus infections. One of the key mechanisms involved in this regulation is the down-regulation of enzymes in the methionine cycle at elevated temperatures. Treatment with methionine can restore metabolite levels and reduce susceptibility to viruses at higher temperatures.

MOLECULAR PLANT PATHOLOGY (2021)

Article Agronomy

Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja

Lesley Torrance et al.

THEORETICAL AND APPLIED GENETICS (2020)

Review Biochemistry & Molecular Biology

Diverse Functions of Polyamines in Virus Infection

Mason R. Firpo et al.

BIOMOLECULES (2020)

Article Biotechnology & Applied Microbiology

ICTV Virus Taxonomy Profile: Alphaflexiviridae

Jan F. Kreuze et al.

JOURNAL OF GENERAL VIROLOGY (2020)

Review Plant Sciences

Roles of Aquaporins in Plant-Pathogen Interaction

Guangjin Li et al.

PLANTS-BASEL (2020)

Article Biochemical Research Methods

MinIONQC: fast and simple quality control for MinION sequencing data

R. Lanfear et al.

BIOINFORMATICS (2019)

Review Plant Sciences

Perception of double-stranded RNA in plant antiviral immunity

Annette Niehl et al.

MOLECULAR PLANT PATHOLOGY (2019)

Article Biochemistry & Molecular Biology

g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)

Uku Raudvere et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Plant Sciences

The significance of methionine cycle enzymes in plant virus infections

Kristiina Makinen et al.

CURRENT OPINION IN PLANT BIOLOGY (2019)

Article Biochemistry & Molecular Biology

The miR396-GRF Regulatory Module Controls the Embryogenic Response in Arabidopsis via an Auxin-Related Pathway

Aleksandra Szczygiel-Sommer et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biotechnology & Applied Microbiology

Transcriptome assembly from long-read RNA-seq alignments with StringTie2

Sam Kovaka et al.

GENOME BIOLOGY (2019)

Review Immunology

Small RNA-based antimicrobial immunity

Zhongxin Guo et al.

NATURE REVIEWS IMMUNOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Immunology

Long non-coding RNAs as molecular players in plant defense against pathogens

Madiha Zaynab et al.

MICROBIAL PATHOGENESIS (2018)

Review Cell Biology

RNA methylation in nuclear pre-mRNA processing

Helena Covelo-Molares et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2018)

Article Virology

Dissection of RNAi-based antiviral immunity in plants

Zhirui Yang et al.

CURRENT OPINION IN VIROLOGY (2018)

Review Biochemistry & Molecular Biology

Cajal bodies and their role in plant stress and disease responses

Andrew J. Love et al.

RNA BIOLOGY (2017)

Review Biotechnology & Applied Microbiology

m 6 A RNA methylation, a new hallmark in virus-host interactions

Michele Brocard et al.

JOURNAL OF GENERAL VIROLOGY (2017)

Article Biochemistry & Molecular Biology

The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants

Rui Xia et al.

PLANT CELL (2017)

Article Multidisciplinary Sciences

Arabidopsis m6A demethylase activity modulates viral infection of a plant virus and the m6A abundance in its genomic RNAs

Mireya Martinez-Perez et al.

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

Article Multidisciplinary Sciences

Genome-wide identification of the potato WRKY transcription factor family

Chao Zhang et al.

PLOS ONE (2017)

Article Biochemistry & Molecular Biology

Unveiling the functional diversity of the alpha/beta hydrolase superfamily in the plant kingdom

Jeffrey T. Mindrebo et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2016)

Review Biochemistry & Molecular Biology

Plant PARPs, PARGs and PARP-like Proteins

Julia P. Vainonen et al.

CURRENT PROTEIN & PEPTIDE SCIENCE (2016)

Article Biotechnology & Applied Microbiology

Near-optimal probabilistic RNA-seq quantification

Nicolas L. Bray et al.

NATURE BIOTECHNOLOGY (2016)

Article Plant Sciences

Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants

Annette Niehl et al.

NEW PHYTOLOGIST (2016)

Review Genetics & Heredity

Roles, Functions, and Mechanisms of Long Non-coding RNAs in Cancer

Yiwen Fang et al.

GENOMICS PROTEOMICS & BIOINFORMATICS (2016)

Review Virology

Insect vector-mediated transmission of plant viruses

Anna E. Whitfield et al.

VIROLOGY (2015)

Review Cell Biology

The RNAissance family: SR proteins as multifaceted regulators of gene expression

Jonathan M. Howard et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2015)

Article Biochemical Research Methods

InterProScan 5: genome-scale protein function classification

Philip Jones et al.

BIOINFORMATICS (2014)

Article Biochemical Research Methods

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme

Aimin Li et al.

BMC BIOINFORMATICS (2014)

Article Computer Science, Software Engineering

UpSet: Visualization of Intersecting Sets

Alexander Lex et al.

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Review Biochemistry & Molecular Biology

Post-Transcriptional Regulation by Poly(ADP-ribosyl)ation of the RNA-Binding Proteins

Yingbiao Ji et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2013)

Article Biochemistry & Molecular Biology

The Immunity Regulator BAK1 Contributes to Resistance Against Diverse RNA Viruses

Camilla Julie Korner et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2013)

Letter Biotechnology & Applied Microbiology

Integrative genomics viewer

James T. Robinson et al.

NATURE BIOTECHNOLOGY (2011)

Review Plant Sciences

Poly(ADP-ribosyl)ation in plants

Amy G. Briggs et al.

TRENDS IN PLANT SCIENCE (2011)

Article Biochemical Research Methods

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics

Eric Bonnet et al.

BIOINFORMATICS (2010)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

Disruption of Two Defensive Signaling Pathways by a Viral RNA Silencing Suppressor

Mathew G. Lewsey et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2010)

Review Immunology

RNA-based antiviral immunity

Shou-Wei Ding

NATURE REVIEWS IMMUNOLOGY (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Review Cell Biology

Plant responses against invasive nucleic acids: RNA silencing and its suppression by plant viral pathogens

Veria Alvarado et al.

SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2009)

Article Genetics & Heredity

Poly (ADP-Ribose) Polymerase 1 Is Required for Protein Localization to Cajal Body

Elena Kotova et al.

PLOS GENETICS (2009)

Article Biotechnology & Applied Microbiology

Association of the transcriptional response of soybean plants with soybean mosaic virus systemic infection

Mohan Babu et al.

JOURNAL OF GENERAL VIROLOGY (2008)

Article Multidisciplinary Sciences

DICER-LIKE2 Plays a Primary Role in Transitive Silencing of Transgenes in Arabidopsis

Sizolwenkosi Mlotshwa et al.

PLOS ONE (2008)

Review Biochemistry & Molecular Biology

Global impact: Elucidating plant responses to viral infection

Steven A. Whitham et al.

MOLECULAR PLANT-MICROBE INTERACTIONS (2006)

Article Plant Sciences

Potato virus Y induced changes in the gene expression of potato (Solanum tuberosum L.)

Marusa Pompe-Novak et al.

PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY (2005)

Article Plant Sciences

Effect of temperature on geminivirus-induced RNA silencing in plants

P Chellappan et al.

PLANT PHYSIOLOGY (2005)

Article Biochemistry & Molecular Biology

Low temperature inhibits RNA silencing-mediated defence by the control of siRNA generation

G Szittya et al.

EMBO JOURNAL (2003)