Alternative Splicing and Protein Diversity: Plants Versus Animals

Light Regulates Plant Alternative Splicing through the Control of Transcriptional Elongation

(2019) Micaela A. Godoy Herz et al.   MOLECULAR CELL

A gene expression map of shoot domains reveals regulatory mechanisms

(2019) Caihuan Tian et al.   Nature Communications

Perspective on Alternative Splicing and Proteome Complexity in Plants

(2019) Saurabh Chaudhary et al.   TRENDS IN PLANT SCIENCE

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

(2019) Ibtissam Jabre et al.   NUCLEIC ACIDS RESEARCH

Exploring the relationship between intron retention and chromatin accessibility in plants

(2018) Fahad Ullah et al.   BMC GENOMICS

Thermopriming triggers splicing memory in Arabidopsis

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

Heat-stress priming and alternative splicing-linked memory

(2018) Ravi P Sanyal et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Splicing regulation by long noncoding RNAs

(2018) Natali Romero-Barrios et al.   NUCLEIC ACIDS RESEARCH

Chromatin-based mechanisms of temperature memory in plants

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

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

(2018) Mohammed Albaqami et al.   Plant Methods

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

(2018) Lisa Hartmann et al.   PLANT PHYSIOLOGY

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

New human gene tally reignites debate

(2018) Cassandra Willyard   NATURE

RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing

(2018) Takayuki Nojima et al.   MOLECULAR CELL

Alternative splicing: the pledge, the turn, and the prestige

(2017) L. M. Gallego-Paez et al.   HUMAN GENETICS

Intron retention as a component of regulated gene expression programs

(2017) Aishwarya G. Jacob et al.   HUMAN GENETICS

Detection of Proteome Diversity Resulted from Alternative Splicing is Limited by Trypsin Cleavage Specificity

(2017) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

The code and beyond: transcription regulation by the RNA polymerase II carboxy-terminal domain

(2017) Kevin M. Harlen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2017) Runxuan Zhang et al.   NUCLEIC ACIDS RESEARCH

The Relationship between Alternative Splicing and Proteomic Complexity

(2017) Benjamin J. Blencowe   TRENDS IN BIOCHEMICAL SCIENCES

Most Alternative Isoforms Are Not Functionally Important

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

Alternative Splicing May Not Be the Key to Proteome Complexity

(2017) Michael L. Tress et al.   TRENDS IN BIOCHEMICAL SCIENCES

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

(2017) Igor Fesenko et al.   Scientific Reports

Impact of Alternative Splicing on the Human Proteome

(2017) Yansheng Liu et al.   Cell Reports

A dynamic intron retention program in the mammalian megakaryocyte and erythrocyte lineages

(2016) C. R. Edwards et al.   BLOOD

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Abiotic Stress Signaling and Responses in Plants

(2016) Jian-Kang Zhu   CELL

Alternative splicing and cell survival: from tissue homeostasis to disease

(2016) Maria Paola Paronetto et al.   CELL DEATH AND DIFFERENTIATION

Transcriptional regulation by complex interplay between post-translational modifications

(2016) Michael J Skelly et al.   CURRENT OPINION IN PLANT BIOLOGY

Selection on Position of Nonsense Codons in Introns

(2016) M. G. Behringer et al.   GENETICS

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

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2016) Xutong Wang et al.   Molecular Plant

Transcriptome Survey of the Contribution of Alternative Splicing to Proteome Diversity in Arabidopsis thaliana

(2016) Haopeng Yu et al.   Molecular Plant

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Examining plant physiological responses to climate change through an evolutionary lens

(2016) Katie M. Becklin et al.   PLANT PHYSIOLOGY

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

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Plant Abiotic Stress Challenges from the Changing Environment

(2016) Andy Pereira   Frontiers in Plant Science

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

(2015) Shiran Naftelberg et al.   Annual Review of Biochemistry

Priming for Enhanced Defense

(2015) Uwe Conrath et al.   Annual Review of Phytopathology

Intron retention in mRNA: No longer nonsense

(2015) Justin J.-L. Wong et al.   BIOESSAYS

Priming and memory of stress responses in organisms lacking a nervous system

(2015) Monika Hilker et al.   BIOLOGICAL REVIEWS

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

(2015) Takayuki Nojima et al.   CELL

Spliceosomes

(2015) Weijun Chen et al.   CURRENT BIOLOGY

Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress

(2015) Sergei Filichkin et al.   CURRENT OPINION IN PLANT BIOLOGY

Detained introns are a novel, widespread class of post-transcriptionally spliced introns

(2015) Paul L. Boutz et al.   GENES & DEVELOPMENT

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

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

(2015) Yamile Marquez et al.   GENOME RESEARCH

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Reproducible quantitative proteotype data matrices for systems biology

(2015) Hannes L. Röst et al.   MOLECULAR BIOLOGY OF THE CELL

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

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

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

(2015) A Sveen et al.   ONCOGENE

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

(2015) Kranthi K. Mandadi et al.   PLANT CELL

Genome-Wide Prediction and Validation of Intergenic Enhancers in Arabidopsis Using Open Chromatin Signatures

(2015) Bo Zhu et al.   PLANT CELL

The enduring mystery of intron-mediated enhancement

(2015) Jenna E. Gallegos et al.   PLANT SCIENCE

Unique Aspects of Plant Nonsense-Mediated mRNA Decay

(2015) Orit Shaul   TRENDS IN PLANT SCIENCE

Alternatively Spliced Homologous Exons Have Ancient Origins and Are Highly Expressed at the Protein Level

(2015) Federico Abascal et al.   PLoS Computational Biology

Post-transcriptional and post-translational regulations of drought and heat response in plants: a spider’s web of mechanisms

(2015) Davide Guerra et al.   Frontiers in Plant Science

Nascent Transcription Affected by RNA Polymerase IV in Zea mays

(2015) Karl F. Erhard et al.   GENETICS

Enter exitrons

(2015) Dorothee Staiger et al.   GENOME BIOLOGY

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

(2014) Young-Ju Kwon et al.   BMC PLANT BIOLOGY

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

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

(2014) Lu Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A day in the life of the spliceosome

(2014) A. Gregory Matera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Imaging of Endogenous Messenger RNA Splice Variants in Living Cells Reveals Nuclear Retention of Transcripts Inaccessible to Nonsense-Mediated Decay in Arabidopsis

(2014) J. Gohring et al.   PLANT CELL

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

(2014) S. R. Thatcher et al.   PLANT CELL

Global Dissection of Alternative Splicing in Paleopolyploid Soybean

(2014) Yanting Shen et al.   PLANT CELL

A Chloroplast Retrograde Signal Regulates Nuclear Alternative Splicing

(2014) E. Petrillo et al.   SCIENCE

Origin of Spliceosomal Introns and Alternative Splicing

(2014) M. Irimia et al.   Cold Spring Harbor Perspectives in Biology

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation

(2013) Justin J.-L. Wong et al.   CELL

RNA Polymerase II Transcription Elongation Control

(2013) Jiannan Guo et al.   CHEMICAL REVIEWS

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

(2013) Thomas C. Boothby et al.   DEVELOPMENTAL CELL

Temporal and spatial characterization of nonsense-mediated mRNA decay

(2013) T. Trcek et al.   GENES & DEVELOPMENT

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

The Arabidopsis thaliana MHX gene includes an intronic element that boosts translation when localized in a 5′ UTR intron

(2013) Tsofit Akua et al.   JOURNAL OF EXPERIMENTAL BOTANY

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

Alternative splicing: a pivotal step between eukaryotic transcription and translation

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

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nonsense-Mediated Decay of Alternative Precursor mRNA Splicing Variants Is a Major Determinant of the Arabidopsis Steady State Transcriptome

(2013) G. Drechsel et al.   PLANT CELL

Complexity of the Alternative Splicing Landscape in Plants

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

Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis

(2013) P. Juntawong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass Spectrometry–Based Proteomics and Network Biology

(2012) Ariel Bensimon et al.   Annual Review of Biochemistry

Co-transcriptional regulation of alternative pre-mRNA splicing

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

Introns in UTRs: Why we should stop ignoring them

(2012) Alicia A. Bicknell et al.   BIOESSAYS

Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes

(2012) Sergei A Filichkin et al.   Biology Direct

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

Transcriptome survey reveals increased complexity of the alternative splicing landscape inArabidopsis

(2012) Yamile Marquez et al.   GENOME RESEARCH

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

(2012) I. Ezkurdia et al.   MOLECULAR BIOLOGY AND EVOLUTION

Linear motifs confer functional diversity onto splice variants

(2012) Robert J. Weatheritt et al.   NUCLEIC ACIDS RESEARCH

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

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

A Role for Nonsense-Mediated mRNA Decay in Plants: Pathogen Responses Are Induced in Arabidopsis thaliana NMD Mutants

(2012) Samantha Rayson et al.   PLoS One

Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case

(2012) Gloria Lopez-Casado et al.   PROTEOMICS

Evolutionary Dynamics of Gene and Isoform Regulation in Mammalian Tissues

(2012) J. Merkin et al.   SCIENCE

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

(2012) N. L. Barbosa-Morais et al.   SCIENCE

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

The Spliceosome-Activating Complex: Molecular Mechanisms Underlying the Function of a Pleiotropic Regulator

(2012) Csaba Koncz et al.   Frontiers in Plant Science

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

The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment

(2011) Kang Ning et al.   BMC BIOINFORMATICS

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

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

(2011) G. Parra et al.   NUCLEIC ACIDS RESEARCH

Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

(2011) Maria Kalyna et al.   NUCLEIC ACIDS RESEARCH

Intron retention regulates the expression of pectin methyl esterase inhibitor (Pmei) genes during wheat growth and development

(2011) V. Rocchi et al.   PLANT BIOLOGY

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Alternative splicing and evolution: diversification, exon definition and function

(2010) Hadas Keren et al.   NATURE REVIEWS GENETICS

Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis

(2010) Pil Joon Seo et al.   PLANT JOURNAL

Transgenerational Adaptation of Arabidopsis to Stress Requires DNA Methylation and the Function of Dicer-Like Proteins

(2010) Alex Boyko et al.   PLoS One

Developments in RNA Splicing and Disease

(2010) M. G. Poulos et al.   Cold Spring Harbor Perspectives in Biology

Spliceosome Structure and Function

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

Comparative analysis indicates that alternative splicing in plants has a limited role in functional expansion of the proteome

(2009) Edouard I Severing et al.   BMC GENOMICS

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

(2009) S. A. Filichkin et al.   GENOME RESEARCH

Stochastic noise in splicing machinery

(2009) Eugene Melamud et al.   NUCLEIC ACIDS RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

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

(2008) Qun Pan et al.   NATURE GENETICS

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE

A General Definition and Nomenclature for Alternative Splicing Events

(2008) Michael Sammeth et al.   PLoS Computational Biology

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

(2008) Michael L Tress et al.   GENOME BIOLOGY