RNA-mediated epigenetic regulation of gene expression

Regulation of Transcription by Long Noncoding RNAs

(2014) Roberto Bonasio et al.   Annual Review of Genetics

Molecular Mechanism of Action of Plant DRM De Novo DNA Methyltransferases

(2014) Xuehua Zhong et al.   CELL

Starvation-Induced Transgenerational Inheritance of Small RNAs in C. elegans

(2014) Oded Rechavi et al.   CELL

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

Small but sturdy: small RNAs in cellular memory and epigenetics

(2014) E. Stuwe et al.   GENES & DEVELOPMENT

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing

(2014) Adrien Le Thomas et al.   GENES & DEVELOPMENT

lncRNA recruits RNAi and the exosome to dynamically regulate pho1 expression in response to phosphate levels in fission yeast

(2014) S. Shah et al.   GENES & DEVELOPMENT

A Two-Step Process for Epigenetic Inheritance in Arabidopsis

(2014) Todd Blevins et al.   MOLECULAR CELL

Jarid2 Is Implicated in the Initial Xist-Induced Targeting of PRC2 to the Inactive X Chromosome

(2014) Simão Teixeira da Rocha et al.   MOLECULAR CELL

Interactions between JARID2 and Noncoding RNAs Regulate PRC2 Recruitment to Chromatin

(2014) Syuzo Kaneko et al.   MOLECULAR CELL

Determinants of Heterochromatic siRNA Biogenesis and Function

(2014) Ruby Yu et al.   MOLECULAR CELL

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice

(2014) Katharina Gapp et al.   NATURE NEUROSCIENCE

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

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

Transcriptional control of a whole chromosome: emerging models for dosage compensation

(2014) Francesco Ferrari et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex

(2014) E. D. Egan et al.   RNA

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 Proper Splicing of RNAi Factors Is Critical for Pericentric Heterochromatin Assembly in Fission Yeast

(2014) Scott P. Kallgren et al.   PLoS Genetics

Mtr4-like Protein Coordinates Nuclear RNA Processing for Heterochromatin Assembly and for Telomere Maintenance

(2013) Nathan N. Lee et al.   CELL

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Long Noncoding RNAs Usher In a New Era in the Biology of Enhancers

(2013) Ulf Andersson Ørom et al.   CELL

Argonautes Promote Male Fertility and Provide a Paternal Memory of Germline Gene Expression in C. elegans

(2013) Colin C. Conine et al.   CELL

Role and control of X chromosome dosage in mammalian development

(2013) Edda G Schulz et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The C. elegans CSR-1 Argonaute Pathway Counteracts Epigenetic Silencing to Promote Germline Gene Expression

(2013) Meetu Seth et al.   DEVELOPMENTAL CELL

Protection of Germline Gene Expression by the C. elegans Argonaute CSR-1

(2013) Christopher J. Wedeles et al.   DEVELOPMENTAL CELL

A Major Epigenetic Programming Mechanism Guided by piRNAs

(2013) Xiao A. Huang et al.   DEVELOPMENTAL CELL

Multiple roles for Piwi in silencing Drosophila transposons

(2013) N. V. Rozhkov et al.   GENES & DEVELOPMENT

Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state

(2013) A. Le Thomas et al.   GENES & DEVELOPMENT

Transcription-induced chromatin association of RNA surveillance factors mediates facultative heterochromatin formation in fission yeast

(2013) Sanki Tashiro et al.   GENES TO CELLS

Argonaute and Triman Generate Dicer-Independent priRNAs and Mature siRNAs to Initiate Heterochromatin Formation

(2013) Mirela Marasovic et al.   MOLECULAR CELL

Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

(2013) Michael T. Y. Lam et al.   NATURE

Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1

(2013) Julie A. Law et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

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

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

Promiscuous RNA binding by Polycomb repressive complex 2

(2013) Chen Davidovich et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells

(2013) Syuzo Kaneko et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV

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

Noncoding RNA and Polycomb recruitment

(2013) N. Brockdorff   RNA

Long noncoding RNAs: fresh perspectives into the RNA world

(2013) Lin Yang et al.   TRENDS IN BIOCHEMICAL SCIENCES

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

(2013) Yunkun Dang et al.   PLoS Genetics

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

C. elegans piRNAs Mediate the Genome-wide Surveillance of Germline Transcripts

(2012) Heng-Chi Lee et al.   CELL

Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression

(2012) Grzegorz Sienski et al.   CELL

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans

(2012) Alyson Ashe et al.   CELL

piRNAs Initiate an Epigenetic Memory of Nonself RNA in the C. elegans Germline

(2012) Masaki Shirayama et al.   CELL

A novel RNAi protein, Dsh1, assembles RNAi machinery on chromatin to amplify heterochromatic siRNA

(2012) K. Kawakami et al.   GENES & DEVELOPMENT

In Vitro Transcription Activities of Pol IV, Pol V, and RDR2 Reveal Coupling of Pol IV and RDR2 for dsRNA Synthesis in Plant RNA Silencing

(2012) Jeremy R. Haag et al.   MOLECULAR CELL

Cytoplasmic Assembly and Selective Nuclear Import of Arabidopsis ARGONAUTE4/siRNA Complexes

(2012) Ruiqiang Ye et al.   MOLECULAR CELL

A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality

(2012) Bethany A. Buckley et al.   NATURE

Paramutation in Drosophila linked to emergence of a piRNA-producing locus

(2012) Augustin de Vanssay et al.   NATURE

Amplification of siRNA in Caenorhabditis elegans generates a transgenerational sequence-targeted histone H3 lysine 9 methylation footprint

(2012) Sam Guoping Gu et al.   NATURE GENETICS

Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly

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

Ers1 links HP1 to RNAi

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

Function, Targets, and Evolution of Caenorhabditis elegans piRNAs

(2012) M. P. Bagijn et al.   SCIENCE

Hexanucleotide motifs mediate recruitment of the RNA elimination machinery to silent meiotic genes

(2012) A. Yamashita et al.   Open Biology

Mechanisms for the Inheritance of Chromatin States

(2011) Danesh Moazed   CELL

Gatekeepers for Piwi–piRNA complexes to enter the nucleus

(2011) Hirotsugu Ishizu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Red1 promotes the elimination of meiosis-specific mRNAs in vegetatively growing fission yeast

(2011) Tomoyasu Sugiyama et al.   EMBO JOURNAL

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II

(2011) Mikel Zaratiegui et al.   NATURE

Coordination of DNA replication and histone modification by the Rik1–Dos2 complex

(2011) Fei Li et al.   NATURE

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line

(2011) S. H. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans

(2011) N. O. Burton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus

(2011) T. Watanabe et al.   SCIENCE

RNA Elimination Machinery Targeting Meiotic mRNAs Promotes Facultative Heterochromatin Formation

(2011) M. Zofall et al.   SCIENCE

A Pre-mRNA–Associating Factor Links Endogenous siRNAs to Chromatin Regulation

(2011) Kirk B. Burkhart et al.   PLoS Genetics

Stc1: A Critical Link between RNAi and Chromatin Modification Required for Heterochromatin Integrity

(2010) Elizabeth H. Bayne et al.   CELL

Dicer-Independent Primal RNAs Trigger RNAi and Heterochromatin Formation

(2010) Mario Halic et al.   CELL

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Importance of polyadenylation in the selective elimination of meiotic mRNAs in growing S. pombe cells

(2010) Soichiro Yamanaka et al.   EMBO JOURNAL

piRNAs, transposon silencing, andDrosophilagermline development

(2010) Jaspreet S. Khurana et al.   JOURNAL OF CELL BIOLOGY

Short RNAs Are Transcribed from Repressed Polycomb Target Genes and Interact with Polycomb Repressive Complex-2

(2010) Aditi Kanhere et al.   MOLECULAR CELL

The Methyltransferase Activity of Clr4Suv39h Triggers RNAi Independently of Histone H3K9 Methylation

(2010) Erica L. Gerace et al.   MOLECULAR CELL

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao et al.   MOLECULAR CELL

Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription

(2010) Shouhong Guang et al.   NATURE

An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation

(2010) Zhihuan Gao et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Paramutation’s Properties and Puzzles

(2010) Vicki L. Chandler   SCIENCE

The piRNA pathway: a fly's perspective on the guardian of the genome

(2010) Kirsten-André Senti et al.   TRENDS IN GENETICS

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

(2010) Sylvain Maenner et al.   PLOS BIOLOGY

The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase

(2010) Heng-Chi Lee et al.   PLOS BIOLOGY

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

The Argonaute CSR-1 and Its 22G-RNA Cofactors Are Required for Holocentric Chromosome Segregation

(2009) Julie M. Claycomb et al.   CELL

Small RNAs as Guardians of the Genome

(2009) Colin D. Malone et al.   CELL

NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation

(2009) X.-J. He et al.   GENES & DEVELOPMENT

Involvement of the Spliceosomal U4 Small Nuclear RNA in Heterochromatic Gene Silencing at Fission Yeast Centromeres

(2009) Madoka Chinen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes

(2009) Yanli Wang et al.   NATURE

Small RNAs in transcriptional gene silencing and genome defence

(2009) Danesh Moazed   NATURE

RNA polymerase V transcription guides ARGONAUTE4 to chromatin

(2009) Andrzej T Wierzbicki et al.   NATURE GENETICS

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

(2008) Andrzej T. Wierzbicki et al.   CELL

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Direct Interaction between DNA Methyltransferase DIM-2 and HP1 Is Required for DNA Methylation in Neurospora crassa

(2008) S. Honda et al.   MOLECULAR AND CELLULAR BIOLOGY

HP1 Proteins Form Distinct Complexes and Mediate Heterochromatic Gene Silencing by Nonoverlapping Mechanisms

(2008) Mohammad R. Motamedi et al.   MOLECULAR CELL

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Piwi and piRNAs Act Upstream of an Endogenous siRNA Pathway to Suppress Tc3 Transposon Mobility in the Caenorhabditis elegans Germline

(2008) Partha P. Das et al.   MOLECULAR CELL

PRG-1 and 21U-RNAs Interact to Form the piRNA Complex Required for Fertility in C. elegans

(2008) Pedro J. Batista et al.   MOLECULAR CELL

Kcnq1ot1 Antisense Noncoding RNA Mediates Lineage-Specific Transcriptional Silencing through Chromatin-Level Regulation

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Subunit Compositions of the RNA-Silencing Enzymes Pol IV and Pol V Reveal Their Origins as Specialized Forms of RNA Polymerase II

(2008) Thomas S. Ream et al.   MOLECULAR CELL

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE

Splicing Factors Facilitate RNAi-Directed Silencing in Fission Yeast

(2008) E. H. Bayne et al.   SCIENCE

Polycomb Proteins Targeted by a Short Repeat RNA to the Mouse X Chromosome

(2008) J. Zhao et al.   SCIENCE

An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus

(2008) S. Guang et al.   SCIENCE

SRA-Domain Proteins Required for DRM2-Mediated De Novo DNA Methylation

(2008) Lianna M. Johnson et al.   PLoS Genetics