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

Harnessing CRISPR/Cas systems for programmable transcriptional and post-transcriptional regulation

(2018) Ahmed Mahas et al.   BIOTECHNOLOGY ADVANCES

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

(2018) Gang Wei et al.   BMC BIOLOGY

Exploring the relationship between intron retention and chromatin accessibility in plants

(2018) Fahad Ullah et al.   BMC GENOMICS

Regulation of alternative mRNA splicing: old players and new perspectives

(2018) Heidi Dvinge   FEBS LETTERS

Thermopriming triggers splicing memory in Arabidopsis

(2018) Yu Ling et al.   JOURNAL OF EXPERIMENTAL BOTANY

New insights into the plant epitranscriptome

(2018) Lee E Vandivier et al.   JOURNAL OF EXPERIMENTAL BOTANY

Photoperiodic control of the Arabidopsis proteome reveals a translational coincidence mechanism

(2018) Daniel D Seaton et al.   Molecular Systems Biology

Chromatin-based mechanisms of temperature memory in plants

(2018) Thomas Friedrich et al.   PLANT CELL AND ENVIRONMENT

Subcellular Compartmentation of Alternatively Spliced Transcripts DefinesSERINE/ARGININE-RICH PROTEIN30Expression

(2018) Lisa Hartmann et al.   PLANT PHYSIOLOGY

Targeted DNA demethylation of theArabidopsisgenome using the human TET1 catalytic domain

(2018) Javier Gallego-Bartolomé et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Importance of DNA Methylation of Exons on Alternative Splicing

(2018) Ronna Shayevitch et al.   RNA

Alternative Splicing Control of Abiotic Stress Responses

(2018) Tom Laloum et al.   TRENDS IN PLANT SCIENCE

Transient N-6-Methyladenosine Transcriptome Sequencing Reveals a Regulatory Role of m6A in Splicing Efficiency

(2018) Annita Louloupi et al.   Cell Reports

RNA methylation in nuclear pre-mRNA processing

(2018) Helena Covelo-Molares et al.   Wiley Interdisciplinary Reviews-RNA

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

(2018) Sergei A. Filichkin et al.   Frontiers in Plant Science

Contribution of major FLM isoforms to temperature-dependent flowering in Arabidopsis thaliana

(2017) Giovanna Capovilla et al.   JOURNAL OF EXPERIMENTAL BOTANY

Cell Cycle Control by Nuclear Sequestration of CDC20 and CDH1 mRNA in Plant Stem Cells

(2017) Weibing Yang et al.   MOLECULAR CELL

5-Methylcytosine RNA Methylation in Arabidopsis Thaliana

(2017) Xuean Cui et al.   Molecular Plant

RNA targeting with CRISPR–Cas13

(2017) Omar O. Abudayyeh et al.   NATURE

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

(2017) Maojun Wang et al.   NEW PHYTOLOGIST

Towards CRISPR/Cas crops - bringing together genomics and genome editing

(2017) Armin Scheben et al.   NEW PHYTOLOGIST

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

(2017) Md Shakhawat Hossain et al.   NEW PHYTOLOGIST

A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

Integrating Omics and Alternative Splicing Reveals Insights into Grape Response to High Temperature

(2017) Jianfu Jiang et al.   PLANT PHYSIOLOGY

CRISPR-Cpf1: A New Tool for Plant Genome Editing

(2017) Syed Shan-e-Ali Zaidi et al.   TRENDS IN PLANT SCIENCE

Stable transgenerational epigenetic inheritance requires a DNA methylation-sensing circuit

(2017) Ben P. Williams et al.   Nature Communications

Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain

(2017) Qiwen Hu et al.   PLoS Computational Biology

Regulation of mRNA splicing by MeCP2 via epigenetic modifications in the brain

(2017) Tian-Lin Cheng et al.   Scientific Reports

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgareL.)

(2016) Karolina Chwialkowska et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2016) Xutong Wang et al.   Molecular Plant

RNAi in Plants: An Argonaute-Centered View

(2016) Xiaofeng Fang et al.   PLANT CELL

Alternative Splicing Substantially Diversifies the Transcriptome during Early Photomorphogenesis and Correlates with the Energy Availability in Arabidopsis

(2016) Lisa Hartmann et al.   PLANT CELL

Nascent RNA sequencing reveals distinct features in plant transcription

(2016) Jonathan Hetzel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Messenger RNA modifications: Form, distribution, and function

(2016) W. V. Gilbert et al.   SCIENCE

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

(2016) Omar O. Abudayyeh et al.   SCIENCE

Nuclear m 6 A Reader YTHDC1 Regulates mRNA Splicing

(2016) Ian A. Roundtree et al.   TRENDS IN GENETICS

BRR2a Affects Flowering Time via FLC Splicing

(2016) Walid Mahrez et al.   PLoS Genetics

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

(2015) Takayuki Nojima et al.   CELL

NTR1 is required for transcription elongation checkpoints at alternative exons in Arabidopsis

(2015) J. Dolata et al.   EMBO JOURNAL

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity

(2015) Yamile Marquez et al.   GENOME RESEARCH

Core clock,SUB1, andABARgenes mediate flooding and drought responses via alternative splicing in soybean

(2015) Naeem H. Syed et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2015) Sergei A. Filichkin et al.   Molecular Plant

The Circadian Clock Modulates Global Daily Cycles of mRNA Ribosome Loading

(2015) Anamika Missra et al.   PLANT CELL

Chemical Modifications Mark Alternatively Spliced and Uncapped Messenger RNAs in Arabidopsis

(2015) Lee E. Vandivier et al.   PLANT CELL

Defective histone supply causes changes in RNA polymerase II elongation rate and cotranscriptional pre-mRNA splicing

(2015) Silvia Jimeno-González et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative regulation ofFLCvia coordinated transcriptional initiation and elongation

(2015) Zhe Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements

(2015) David Secco et al.   eLife

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

(2015) Manu J Dubin et al.   eLife

Enter exitrons

(2015) Dorothee Staiger et al.   GENOME BIOLOGY

Let there be light: Regulation of gene expression in plants

(2015) Ezequiel Petrillo et al.   RNA Biology

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop

(2014) Federico Ariel et al.   MOLECULAR CELL

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

The dynamic epitranscriptome: N6-methyladenosine and gene expression control

(2014) Kate D. Meyer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

(2014) E. Petrillo et al.   SCIENCE

Unique features of the m6A methylome in Arabidopsis thaliana

(2014) Guan-Zheng Luo et al.   Nature Communications

Regulation of Arabidopsis Flowering by the Histone Mark Readers MRG1/2 via Interaction with CONSTANS to Modulate FT Expression

(2014) Zhongyuan Bu et al.   PLoS Genetics

DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure

(2013) S. Gelfman et al.   GENOME RESEARCH

Temperature-dependent regulation of flowering by antagonistic FLM variants

(2013) David Posé et al.   NATURE

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

(2013) Yiliang Ding et al.   NATURE

Alternative splicing: a pivotal step between eukaryotic transcription and translation

(2013) Alberto R. Kornblihtt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Integrative analysis of tissue-specific methylation and alternative splicing identifies conserved transcription factor binding motifs

(2013) J. Wan et al.   NUCLEIC ACIDS RESEARCH

Complexity of the Alternative Splicing Landscape in Plants

(2013) A. S. N. Reddy et al.   PLANT CELL

An Autoregulatory Loop Controlling Arabidopsis HsfA2 Expression: Role of Heat Shock-Induced Alternative Splicing

(2013) J. Liu et al.   PLANT PHYSIOLOGY

RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee

(2013) H. Li-Byarlay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Emerging roles for RNA polymerase II CTD in Arabidopsis

(2013) Mohsen Hajheidari et al.   TRENDS IN PLANT SCIENCE

Alterations of Alternative Splicing Patterns of Ser/Arg-Rich (SR) Genes in Response to Hormones and Stresses Treatments in Different Ecotypes of Rice (Oryza sativa)

(2013) Peng ZHANG et al.   Journal of Integrative Agriculture

Co-transcriptional regulation of alternative pre-mRNA splicing

(2012) Sanjeev Shukla et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2012) H. Tilgner et al.   GENOME RESEARCH

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

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

(2012) A. B. James et al.   PLANT CELL

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

(2012) Irene S. Day et al.   PLANT JOURNAL

Genome-wide profiling of histone H3K4-tri-methylation and gene expression in rice under drought stress

(2012) Wei Zong et al.   PLANT MOLECULAR BIOLOGY

Ordered changes in histone modifications at the core of the Arabidopsis circadian clock

(2012) J. Malapeira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cotranscriptional splicing efficiency differs dramatically between Drosophila and mouse

(2012) Y. L. Khodor et al.   RNA

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

Multiple exposures to drought 'train' transcriptional responses in Arabidopsis

(2012) Yong Ding et al.   Nature Communications

Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

(2012) Anireddy S. N. Reddy et al.   Frontiers in Plant Science

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila

(2011) Y. L. Khodor et al.   GENES & DEVELOPMENT

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

ArabidopsisFloral Initiator SKB1 Confers High Salt Tolerance by Regulating Transcription and Pre-mRNA Splicing through Altering Histone H4R3 and Small Nuclear Ribonucleoprotein LSM4 Methylation

(2011) Zhaoliang Zhang et al.   PLANT CELL

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

(2011) Anna M. Mastrangelo et al.   PLANT SCIENCE

The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing

(2011) Yehuda Brody et al.   PLOS BIOLOGY

Genomic Screening with RNAi: Results and Challenges

(2010) Stephanie Mohr et al.   Annual Review of Biochemistry

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

(2010) Satu Nahkuri et al.   CELL CYCLE

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Splicing-Dependent RNA Polymerase Pausing in Yeast

(2010) Ross D. Alexander et al.   MOLECULAR CELL

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

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

(2010) Sabrina E. Sanchez et al.   NATURE

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

The organization of nucleosomes around splice sites

(2010) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing

(2010) X. Deng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

P-TEFb stimulates transcription elongation and pre-mRNA splicing through multilateral mechanisms

(2010) Tina Lenasi et al.   RNA Biology

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2009) Saiprasad G. Palusa et al.   NEW PHYTOLOGIST

A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy

(2009) Steven Penfield et al.   PLANT MOLECULAR BIOLOGY

Plant upstream ORFs can trigger nonsense-mediated mRNA decay in a size-dependent manner

(2009) Tünde Nyikó et al.   PLANT MOLECULAR BIOLOGY

Plant SMU-1 and SMU-2 Homologues Regulate Pre-mRNA Splicing and Multiple Aspects of Development

(2009) T. Chung et al.   PLANT PHYSIOLOGY

Assessing the Impact of Transgenerational Epigenetic Variation on Complex Traits

(2009) Frank Johannes et al.   PLoS Genetics

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay

(2008) Zoltán Kerényi et al.   EMBO JOURNAL

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

MTA Is an Arabidopsis Messenger RNA Adenosine Methylase and Interacts with a Homolog of a Sex-Specific Splicing Factor

(2008) S. Zhong et al.   PLANT CELL