First Come, First Served: Sui Generis Features of the First Intron

Organismal benefits of transcription speed control at gene boundaries

(2020) Xueyuan Leng et al.   EMBO REPORTS

The Histone Marks Signature in Exonic and Intronic Regions Is Relevant in Early Response of Tomato Genes to Botrytis cinerea and in miRNA Regulation

(2020) Óscar Crespo-Salvador et al.   Plants-Basel

Transcriptional regulation of genes bearing intronic heterochromatin in the rice genome

(2020) Nino A. Espinas et al.   PLoS Genetics

Introns are mediators of cell response to starvation

(2019) Julie Parenteau et al.   NATURE

Excised linear introns regulate growth in yeast

(2019) Jeffrey T. Morgan et al.   NATURE

Introns as Gene Regulators: A Brick on the Accelerator

(2019) Alan B. Rose   Frontiers in Genetics

Alternative Splicing and Transcription Elongation in Plants

(2019) Micaela A. Godoy Herz et al.   Frontiers in Plant Science

Antagonistic actions of FPA and IBM2 regulate transcript processing from genes containing heterochromatin

(2019) Aurélie Deremetz et al.   PLANT PHYSIOLOGY

Arabidopsis SME1 Regulates Plant Development and Response to Abiotic Stress by Determining Spliceosome Activity Specificity

(2019) Raul Huertas et al.   PLANT CELL

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

(2019) Ibtissam Jabre et al.   NUCLEIC ACIDS RESEARCH

Analysis of the Functional Relevance of Epigenetic Chromatin Marks in the First Intron Associated with Specific Gene Expression Patterns

(2019) Shin-Sang Jo et al.   Genome Biology and Evolution

Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses

(2019) Jinna Hou et al.   PLANTA

Coordinated regulation of pre-mRNA splicing by the SFPS-RRC1 complex to promote photomorphogenesis

(2019) Ruijiao Xin et al.   PLANT CELL

LEFKOTHEA Regulates Nuclear and Chloroplast mRNA Splicing in Plants

(2019) Gerasimos Daras et al.   DEVELOPMENTAL CELL

Alternative Splicing and Protein Diversity: Plants Versus Animals

(2019) Saurabh Chaudhary et al.   Frontiers in Plant Science

uORF and Phosphate-Regulated Expression of Rice OsNLA1 Controls Phosphate Transport and Reproduction

(2019) Shu-Yi Yang et al.   PLANT PHYSIOLOGY

Phytochrome B induces intron retention and translational inhibition of PHYTOCHROME-INTERACTING FACTOR 3

(2019) Jie Dong et al.   PLANT PHYSIOLOGY

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

(2019) Geeng Loo Chong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An intron-derived motif strongly increases gene expression from transcribed sequences through a splicing independent mechanism in Arabidopsis thaliana

(2019) Jenna E. Gallegos et al.   Scientific Reports

Introns: Good Day Junk Is Bad Day Treasure

(2019) Julie Parenteau et al.   TRENDS IN GENETICS

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

The exon–intron gene structure upstream of the initiation codon predicts translation efficiency

(2018) Chun Shen Lim et al.   NUCLEIC ACIDS RESEARCH

The cyclin-dependent kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A

(2018) Nicola Cavallari et al.   PLANT JOURNAL

UTR-Dependent Control of Gene Expression in Plants

(2018) Ashish Kumar Srivastava et al.   TRENDS IN PLANT SCIENCE

Alternative Splicing as a Regulator of Early Plant Development

(2018) Dóra Szakonyi et al.   Frontiers in Plant Science

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

(2017) Xudong Shang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA Pol II Dynamics Modulate Co-transcriptional Chromatin Modification, CTD Phosphorylation, and Transcriptional Direction

(2017) Nova Fong et al.   MOLECULAR CELL

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

Intron DNA Sequences Can Be More Important Than the Proximal Promoter in Determining the Site of Transcript Initiation

(2017) Jenna E. Gallegos et al.   PLANT CELL

Extremely fast and incredibly close: cotranscriptional splicing in budding yeast

(2017) Edward W.J. Wallace et al.   RNA

Intron retention is regulated by altered MeCP2-mediated splicing factor recruitment

(2017) Justin J. -L. Wong et al.   Nature Communications

Alternative splicing shapes transcriptome but not proteome diversity in Physcomitrella patens

(2017) Igor Fesenko et al.   Scientific Reports

Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis

(2017) Daniel Antony Pass et al.   PLoS Genetics

Identification of introns harboring functional sequence elements through positional conservation

(2017) Michal Chorev et al.   Scientific Reports

Upstream ORFs are prevalent translational repressors in vertebrates

(2016) Timothy G Johnstone et al.   EMBO JOURNAL

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

Intron sequences that stimulate gene expression in Arabidopsis

(2016) Alan B. Rose et al.   PLANT MOLECULAR BIOLOGY

The 5′UTR Intron of Arabidopsis GGT1 Aminotransferase Enhances Promoter Activity by Recruiting RNA Polymerase II

(2016) Miriam Laxa et al.   PLANT PHYSIOLOGY

Carotenogenesis Is Regulated by 5′UTR-Mediated Translation of Phytoene Synthase Splice Variants

(2016) Daniel Álvarez 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

Super-resolution ribosome profiling reveals unannotated translation events inArabidopsis

(2016) Polly Yingshan Hsu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Arabidopsis transcriptional repressor VAL1 triggers Polycomb silencing at FLC during vernalization

(2016) Julia I. Qüesta et al.   SCIENCE

Translational control by 5'-untranslated regions of eukaryotic mRNAs

(2016) A. G. Hinnebusch et al.   SCIENCE

Enhancement of Transcription by a Splicing-Competent Intron Is Dependent on Promoter Directionality

(2016) Neha Agarwal et al.   PLoS Genetics

Intron Lariat RNA Inhibits MicroRNA Biogenesis by Sequestering the Dicing Complex in Arabidopsis

(2016) Ziwei Li et al.   PLoS Genetics

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Takayuki Nojima et al.   CELL

Evidence That Base-pairing Interaction between Intron and mRNA Leader Sequences Inhibits Initiation ofHAC1mRNA Translation in Yeast

(2015) Leena Sathe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SKIP Confers Osmotic Tolerance during Salt Stress by Controlling Alternative Gene Splicing in Arabidopsis

(2015) Jinlin Feng et al.   Molecular Plant

High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis

(2015) Joo-Young Kim et al.   NEW PHYTOLOGIST

Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner

(2015) Isao Ebina et al.   NUCLEIC ACIDS RESEARCH

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

An upstream open reading frame represses expression of a tomato homologue of Arabidopsis ANAC096, a NAC domain transcription factor gene, in a peptide sequence-dependent manner

(2015) Abdul Latif Noh et al.   Plant Biotechnology

The enduring mystery of intron-mediated enhancement

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

The alternative role of DNA methylation in splicing regulation

(2015) Galit Lev Maor et al.   TRENDS IN GENETICS

Conservation in first introns is positively associated with the number of exons within genes and the presence of regulatory epigenetic signals

(2014) Seung Park et al.   BMC GENOMICS

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

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

(2014) Nova Fong et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

CLUMSY VEIN, the Arabidopsis DEAH-box Prp16 ortholog, is required for auxin-mediated development

(2014) Ryuji Tsugeki et al.   PLANT JOURNAL

Arabidopsis noncoding RNA mediates control of photomorphogenesis by red light

(2014) Y. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Intron Retention in the 5′UTR of the Novel ZIF2 Transporter Enhances Translation to Promote Zinc Tolerance in Arabidopsis

(2014) Estelle Remy et al.   PLoS Genetics

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

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

(2013) S. Gelfman 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

Competition between Pre-mRNAs for the Splicing Machinery Drives Global Regulation of Splicing

(2013) Elizabeth M. Munding et al.   MOLECULAR CELL

Circular Intronic Long Noncoding RNAs

(2013) Yang Zhang et al.   MOLECULAR CELL

The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana

(2013) K. D. Raczynska et al.   NUCLEIC ACIDS RESEARCH

The effects of a stimulating intron on the expression of heterologous genes inArabidopsis thaliana

(2013) Shahram Emami et al.   PLANT BIOTECHNOLOGY JOURNAL

Complexity of the Alternative Splicing Landscape in Plants

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

Regulation of plant translation by upstream open reading frames

(2013) Albrecht G. von Arnim et al.   PLANT SCIENCE

Genome-Wide Survey of Cold Stress Regulated Alternative Splicing in Arabidopsis thaliana with Tiling Microarray

(2013) Noam Leviatan et al.   PLoS One

Origin and evolution of spliceosomal introns

(2012) Igor B Rogozin et al.   Biology Direct

Stress-Induced Alternative Splicing Provides a Mechanism for the Regulation of MicroRNA Processing in Arabidopsis thaliana

(2012) Kang Yan et al.   MOLECULAR CELL

Differences in intron-mediated enhancement of gene expression by the first intron of cytosolic superoxide dismutase gene from rice in monocot and dicot plants

(2012) Shigeto Morita et al.   Plant Biotechnology

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

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

Arabidopsis ribosomal proteins control developmental programs through translational regulation of auxin response factors

(2012) A. Rosado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role for gene looping in intron-mediated enhancement of transcription

(2012) A. M. Moabbi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Whence genes in pieces: reconstruction of the exon-intron gene structures of the last eukaryotic common ancestor and other ancestral eukaryotes

(2012) Eugene V. Koonin et al.   Wiley Interdisciplinary Reviews-RNA

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

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

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

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

(2011) Miklos Csuros et al.   PLoS Computational Biology

Evidence for a DNA-Based Mechanism of Intron-Mediated Enhancement

(2011) Alan B. Rose et al.   Frontiers in Plant Science

Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana

(2010) Jeremy Grojean et al.   Biology Direct

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

Chromatin organization marks exon-intron structure

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

Stochastic noise in splicing machinery

(2009) Eugene Melamud et al.   NUCLEIC ACIDS RESEARCH

Involvement of the nuclear cap-binding protein complex in alternative splicing in Arabidopsis thaliana

(2009) Katarzyna Dorota Raczynska et al.   NUCLEIC ACIDS RESEARCH

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

(2009) S. E. Calvo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana

(2009) Xiaoyu Zhang et al.   GENOME BIOLOGY

Riboswitch RNAs: using RNA to sense cellular metabolism

(2008) T. M. Henkin   GENES & DEVELOPMENT

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

(2008) W. B. Barbazuk et al.   GENOME RESEARCH

Promoter-Proximal Introns in Arabidopsis thaliana Are Enriched in Dispersed Signals that Elevate Gene Expression

(2008) A. B. Rose et al.   PLANT CELL

Longer First Introns Are a General Property of Eukaryotic Gene Structure

(2008) Keith R. Bradnam et al.   PLoS One

Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana

(2008) S. Laubinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2008) Leighton J. Core et al.   SCIENCE

Intronic noncoding RNAs and splicing

(2008) John W.S. Brown et al.   TRENDS IN PLANT SCIENCE

Where Do Introns Come From?

(2008) Francesco Catania et al.   PLOS BIOLOGY