Small RNAs: essential regulators of gene expression and defenses against environmental stresses in plants

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

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

VIGS, HIGS and FIGS: small RNA silencing in the interactions of viruses or filamentous organisms with their plant hosts

(2015) David C Baulcombe   CURRENT OPINION IN PLANT BIOLOGY

Long non-coding RNAs and their functions in plants

(2015) Julia A Chekanova   CURRENT OPINION IN PLANT BIOLOGY

A First Line of Stress Defense: Small Heat Shock Proteins and Their Function in Protein Homeostasis

(2015) Martin Haslbeck et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

Towards a molecular understanding of microRNA-mediated gene silencing

(2015) Stefanie Jonas et al.   NATURE REVIEWS GENETICS

The alternative role of DNA methylation in splicing regulation

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

HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing

(2015) Ahuvi Yearim et al.   Cell Reports

Hypomethylation of the paternally inheritedLRRTM1promoter linked to schizophrenia

(2014) Nicolas Brucato et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

Ago2 facilitates Rad51 recruitment and DNA double-strand break repair by homologous recombination

(2014) Min Gao et al.   CELL RESEARCH

Long Noncoding RNA Modulates Alternative Splicing Regulators in Arabidopsis

(2014) Florian Bardou et al.   DEVELOPMENTAL CELL

Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

(2014) H. Wang et al.   GENOME RESEARCH

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis

(2014) Kate M. Creasey et al.   NATURE

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitivetrans-silencer locus inArabidopsis thaliana

(2014) Taku Sasaki et al.   PLANT JOURNAL

Argonaute-1 binds transcriptional enhancers and controls constitutive and alternative splicing in human cells

(2014) M. Allo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of genes preventing transgenerational transmission of stress-induced epigenetic states

(2014) M. Iwasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stress-induced endogenous siRNAs targeting regulatory intron sequences inBrachypodium

(2014) Hsiao-Lin V. Wang et al.   RNA

A global non-coding RNA system modulates fission yeast protein levels in response to stress

(2014) Hui Sun Leong et al.   Nature Communications

Widespread Inhibition of Posttranscriptional Splicing Shapes the Cellular Transcriptome following Heat Shock

(2014) Reut Shalgi et al.   Cell Reports

The SET Domain Proteins SUVH2 and SUVH9 Are Required for Pol V Occupancy at RNA-Directed DNA Methylation Loci

(2014) Zhang-Wei Liu et al.   PLoS Genetics

The influence of Argonaute proteins on alternative RNA splicing

(2014) Eric Batsché et al.   Wiley Interdisciplinary Reviews-RNA

tasiRNA-ARF Pathway Moderates Floral Architecture inArabidopsisPlants Subjected to Drought Stress

(2014) Akihiro Matsui et al.   Biomed Research International

Organizing Principles of Mammalian Nonsense-Mediated mRNA Decay

(2013) Maximilian Wei-Lin Popp et al.   Annual Review of Genetics

Classification and Comparison of Small RNAs from Plants

(2013) Michael J. Axtell   Annual Review of Plant Biology

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

(2013) Ignacio E Schor et al.   EMBO JOURNAL

Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression

(2013) J. M. Taliaferro et al.   GENES & DEVELOPMENT

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

(2013) Olga V. Popova et al.   Molecular Plant

Mechanisms of Small RNA Generation from Cis-NATs in Response to Environmental and Developmental Cues

(2013) Xiaoming Zhang et al.   Molecular Plant

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

Reconstructing de novo silencing of an active plant retrotransposon

(2013) Arturo Marí-Ordóñez et al.   NATURE GENETICS

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

(2013) D. Staiger et al.   PLANT CELL

Biogenesis, Turnover, and Mode of Action of Plant MicroRNAs

(2013) K. Rogers et al.   PLANT CELL

Complexity of the Alternative Splicing Landscape in Plants

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

MIR846 and MIR842 comprise a cistronic MIRNA pair that is regulated by abscisic acid by alternative splicing in roots of Arabidopsis

(2013) Fan Jia et al.   PLANT MOLECULAR BIOLOGY

Interplay among RNA polymerases II, IV and V in RNA-directed DNA methylation at a low copy transgene locus in Arabidopsis thaliana

(2013) Wanhui You et al.   PLANT MOLECULAR BIOLOGY

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs

(2013) S. Nuthikattu et al.   PLANT PHYSIOLOGY

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

(2013) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A direct role for small non-coding RNAs in DNA damage response

(2013) Fabrizio d’Adda di Fagagna   TRENDS IN CELL BIOLOGY

XRN4 and LARP1 Are Required for a Heat-Triggered mRNA Decay Pathway Involved in Plant Acclimation and Survival during Thermal Stress

(2013) Rémy Merret et al.   Cell Reports

DNA Methylation Mediated Control of Gene Expression Is Critical for Development of Crown Gall Tumors

(2013) Jochen Gohlke et al.   PLoS Genetics

Ago1 Interacts with RNA Polymerase II and Binds to the Promoters of Actively Transcribed Genes in Human Cancer Cells

(2013) Vera Huang et al.   PLoS Genetics

A Role for Small RNAs in DNA Double-Strand Break Repair

(2012) Wei Wei et al.   CELL

Different means, same end—heterochromatin formation by RNAi and RNAi-independent RNA processing factors in fission yeast

(2012) Francisca E Reyes-Turcu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

(2012) Tzuu-fen Lee et al.   Epigenetics

RNAi keeps Atf1-bound stress response genes in check at nuclear pores

(2012) K. J. Woolcock et al.   GENES & DEVELOPMENT

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

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

(2012) Kang Yan et al.   MOLECULAR CELL

Long Noncoding RNAs with snoRNA Ends

(2012) Qing-Fei Yin et al.   MOLECULAR CELL

A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

(2012) Yongyou Zhu et al.   MOLECULAR CELL

Site-specific DICER and DROSHA RNA products control the DNA-damage response

(2012) Sofia Francia et al.   NATURE

RNA therapeutics: beyond RNA interference and antisense oligonucleotides

(2012) Ryszard Kole et al.   NATURE REVIEWS DRUG DISCOVERY

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons

(2012) Xuehua Zhong et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Roles of DICER-LIKE and ARGONAUTE Proteins in TAS-Derived Small Interfering RNA-Triggered DNA Methylation

(2012) L. Wu et al.   PLANT PHYSIOLOGY

Transcriptional Regulation of Arabidopsis MIR168a and ARGONAUTE1 Homeostasis in Abscisic Acid and Abiotic Stress Responses

(2012) W. Li et al.   PLANT PHYSIOLOGY

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

MicroRNA regulation of plant innate immune receptors

(2012) F. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

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

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

Genome-wide analysis of plant nat-siRNAs reveals insights into their distribution, biogenesis and function

(2012) Xiaoming Zhang et al.   GENOME BIOLOGY

Arabidopsis HDA6 is required for freezing tolerance

(2011) Taiko Kim To et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Single-Molecule Imaging of Transcriptionally Coupled and Uncoupled Splicing

(2011) Diana Y. Vargas et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Cell-to-cell and long-distance siRNA movement in plants: mechanisms and biological implications

(2011) Christopher Andrew Brosnan et al.   CURRENT OPINION IN PLANT BIOLOGY

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs

(2011) J. Zhai et al.   GENES & DEVELOPMENT

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

Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila

(2011) Filippo M. Cernilogar et al.   NATURE

An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress

(2011) Hidetaka Ito et al.   NATURE

Molecular chaperones in protein folding and proteostasis

(2011) F. Ulrich Hartl et al.   NATURE

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons

(2011) Violaine Saint-André et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Ordered and Dynamic Assembly of Single Spliceosomes

(2011) A. A. Hoskins et al.   SCIENCE

Understanding splicing regulation through RNA splicing maps

(2011) Joshua T. Witten et al.   TRENDS IN GENETICS

Gene Silencing: Small RNAs Control RNA Polymerase II Elongation

(2010) Mariano Alló et al.   CURRENT BIOLOGY

Proper regulation of a sperm-specific cis-nat-siRNA is essential for double fertilization in Arabidopsis

(2010) M. Ron et al.   GENES & DEVELOPMENT

Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model

(2010) Y. Hua et al.   GENES & DEVELOPMENT

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

The snoRNA MBII-52 (SNORD 115) is processed into smaller RNAs and regulates alternative splicing

(2010) Shivendra Kishore et al.   HUMAN MOLECULAR GENETICS

Involvement of Arabidopsis histone deacetylase HDA6 in ABA and salt stress response

(2010) Li-Ting Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

An integrated genomic analysis of gene-function correlation on schizophrenia susceptibility genes

(2010) Tearina T Chu et al.   JOURNAL OF HUMAN GENETICS

MicroRNA Functions in Stress Responses

(2010) Anthony K.L. Leung et al.   MOLECULAR CELL

DNA Methylation Mediated by a MicroRNA Pathway

(2010) Liang Wu et al.   MOLECULAR CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

The DNA Damage Response: Making It Safe to Play with Knives

(2010) Alberto Ciccia et al.   MOLECULAR CELL

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Comparative analysis of non-autonomous effects of tasiRNAs and miRNAs in Arabidopsis thaliana

(2010) Felipe Fenselau de Felippes et al.   NUCLEIC ACIDS RESEARCH

siRNAs from miRNA sites mediate DNA methylation of target genes

(2010) Padmanabhan Chellappan et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training

(2010) N. R. Smalheiser et al.   RNA

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Nuclear Stress Bodies

(2010) G. Biamonti 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

Stress-Induced Activation of Heterochromatic Transcription

(2010) Mireille Tittel-Elmer et al.   PLoS Genetics

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Epigenetic Reprogramming and Small RNA Silencing of Transposable Elements in Pollen

(2009) R. Keith Slotkin et al.   CELL

The Spliceosome: Design Principles of a Dynamic RNP Machine

(2009) Markus C. Wahl et al.   CELL

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

Intergenic transcription by RNA Polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis

(2009) B. Zheng et al.   GENES & DEVELOPMENT

Pattern formation via small RNA mobility

(2009) D. H. Chitwood et al.   GENES & DEVELOPMENT

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Genome-wide mapping of alternative splicing in Arabidopsis thaliana

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

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

(2009) Dov Moldovan et al.   JOURNAL OF EXPERIMENTAL BOTANY

Eukaryotic Stress Granules: The Ins and Outs of Translation

(2009) J. Ross Buchan et al.   MOLECULAR CELL

qiRNA is a new type of small interfering RNA induced by DNA damage

(2009) Heng-Chi Lee et al.   NATURE

Nonsense-mediated mRNA decay (NMD) mechanisms

(2009) Saverio Brogna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Control of alternative splicing through siRNA-mediated transcriptional gene silencing

(2009) Mariano Alló et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues

(2009) Mark Carlile et al.   NUCLEIC ACIDS RESEARCH

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

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

Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide

(2008) Shijun Mi et al.   CELL

Noncoding Transcription by RNA Polymerase Pol IVb/Pol V Mediates Transcriptional Silencing of Overlapping and Adjacent Genes

(2008) Andrzej T. Wierzbicki et al.   CELL

A Link between RNA Metabolism and Silencing Affecting Arabidopsis Development

(2008) Brian D. Gregory et al.   DEVELOPMENTAL CELL

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

(2008) Qun Pan et al.   NATURE GENETICS

Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

(2008) Katsutomo Okamura et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Natural antisense transcripts are co-expressed with sense mRNAs in synaptoneurosomes of adult mouse forebrain

(2008) Neil R. Smalheiser et al.   NEUROSCIENCE RESEARCH

Evolution of Arabidopsis MIR genes generates novel microRNA classes

(2008) Franck Vazquez et al.   NUCLEIC ACIDS RESEARCH

Involvement of Arabidopsis HOS15 in histone deacetylation and cold tolerance

(2008) J. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA