Regulatory feedback from nascent RNA to chromatin and transcription

Co-transcriptional splicing and the CTD code

(2016) Noélia Custódio et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Diverse regulatory interactions of long noncoding RNAs

(2016) Tae-Kyung Kim et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

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

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

RBFox2 Binds Nascent RNA to Globally Regulate Polycomb Complex 2 Targeting in Mammalian Genomes

(2016) Chaoliang Wei et al.   MOLECULAR CELL

Prevalent, Dynamic, and Conserved R-Loop Structures Associate with Specific Epigenomic Signatures in Mammals

(2016) Lionel A. Sanz et al.   MOLECULAR CELL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

RNA modifications: what have we learned and where are we headed?

(2016) Michaela Frye et al.   NATURE REVIEWS GENETICS

Enhancers as non-coding RNA transcription units: recent insights and future perspectives

(2016) Wenbo Li et al.   NATURE REVIEWS GENETICS

Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

(2016) N. J. Proudfoot   SCIENCE

Extra-coding RNAs regulate neuronal DNA methylation dynamics

(2016) Katherine E. Savell et al.   Nature Communications

Regulation of Alternative Splicing Through Coupling with Transcription and Chromatin Structure

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

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

Toward a Consensus on the Binding Specificity and Promiscuity of PRC2 for RNA

(2015) Chen Davidovich et al.   MOLECULAR CELL

Locus-Specific Targeting to the X Chromosome Revealed by the RNA Interactome of CTCF

(2015) Johnny T. Kung et al.   MOLECULAR CELL

BRCA1 Recruitment to Transcriptional Pause Sites Is Required for R-Loop-Driven DNA Damage Repair

(2015) Elodie Hatchi et al.   MOLECULAR CELL

SMN and symmetric arginine dimethylation of RNA polymerase II C-terminal domain control termination

(2015) Dorothy Yanling Zhao et al.   NATURE

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

R loops: new modulators of genome dynamics and function

(2015) José M. Santos-Pereira et al.   NATURE REVIEWS GENETICS

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Head-to-head antisense transcription and R-loop formation promotes transcriptional activation

(2015) Raquel Boque-Sastre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

R loops regulate promoter-proximal chromatin architecture and cellular differentiation

(2015) Poshen B Chen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long non-coding RNA ROR decoys gene-specific histone methylation to promote tumorigenesis

(2015) Jiayan Fan et al.   GENOME BIOLOGY

Stable C0T-1 Repeat RNA Is Abundant and Is Associated with Euchromatic Interphase Chromosomes

(2014) Lisa L. Hall et al.   CELL

CTCF regulates the human p53 gene through direct interaction with its natural antisense transcript, Wrap53

(2014) R. Saldana-Meyer et al.   GENES & DEVELOPMENT

Nascent RNA interaction keeps PRC2 activity poised and in check

(2014) Syuzo Kaneko et al.   GENES & DEVELOPMENT

Rate of elongation by RNA polymerase II is associated with specific gene features and epigenetic modifications

(2014) A. Veloso et al.   GENOME RESEARCH

Regulatory Interactions between RNA and Polycomb Repressive Complex 2

(2014) Catherine Cifuentes-Rojas et al.   MOLECULAR CELL

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

A Splicing-Dependent Transcriptional Checkpoint Associated with Prespliceosome Formation

(2014) Keerthi T. Chathoth et al.   MOLECULAR CELL

R-loops induce repressive chromatin marks over mammalian gene terminators

(2014) Konstantina Skourti-Stathaki et al.   NATURE

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

A strand-specific switch in noncoding transcription switches the function of a Polycomb/Trithorax response element

(2014) Veronika A Herzog et al.   NATURE GENETICS

Sudemycin E influences alternative splicing and changes chromatin modifications

(2014) Paolo Convertini et al.   NUCLEIC ACIDS RESEARCH

Short sequences can efficiently recruit histone H3 lysine 27 trimethylation in the absence of enhancer activity and DNA methylation

(2014) P. Jermann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional regulatory functions of nuclear long noncoding RNAs

(2014) Keith W. Vance et al.   TRENDS IN GENETICS

Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions

(2014) John M. Pagano et al.   PLoS Genetics

Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons

(2014) Iris Jonkers et al.   eLife

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

SR Proteins Collaborate with 7SK and Promoter-Associated Nascent RNA to Release Paused Polymerase

(2013) Xiong Ji et al.   CELL

GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination

(2013) P. A. Ginno et al.   GENOME RESEARCH

R Loops Are Linked to Histone H3 S10 Phosphorylation and Chromatin Condensation

(2013) Maikel Castellano-Pozo et al.   MOLECULAR CELL

Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation

(2013) Wenbo Li et al.   NATURE

lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs

(2013) Liuqing Yang et al.   NATURE

DNMT1-interacting RNAs block gene-specific DNA methylation

(2013) Annalisa Di Ruscio et al.   NATURE

Activating RNAs associate with Mediator to enhance chromatin architecture and transcription

(2013) Fan Lai et al.   NATURE

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

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Genome Regulation by Long Noncoding RNAs

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

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

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

RNA modulation of the human DNA methyltransferase 3A

(2012) Celeste Holz-Schietinger et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Regulation by Long Noncoding RNAs

(2012) J. T. Lee   SCIENCE

YY1 Tethers Xist RNA to the Inactive X Nucleation Center

(2011) Yesu Jeon et al.   CELL

Human Senataxin Resolves RNA/DNA Hybrids Formed at Transcriptional Pause Sites to Promote Xrn2-Dependent Termination

(2011) Konstantina Skourti-Stathaki et al.   MOLECULAR CELL

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

(2011) Kevin C. Wang et al.   NATURE

Nucleation of nuclear bodies by RNA

(2011) Sergey P. Shevtsov et al.   NATURE CELL BIOLOGY

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pre-mRNA splicing is a determinant of histone H3K36 methylation

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

When one is better than two: RNA with dual functions

(2010) Damien Ulveling et al.   BIOCHIMIE

Splicing-Dependent RNA Polymerase Pausing in Yeast

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

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

(2010) Jing Zhao et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Interactions between DSIF (DRB sensitivity inducing factor), NELF (negative elongation factor), and the Drosophila RNA polymerase II transcription elongation complex

(2010) A. Missra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Heterogeneous Nuclear Ribonucleoprotein L Is a Subunit of Human KMT3a/Set2 Complex Required for H3 Lys-36 Trimethylation Activityin Vivo

(2009) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2008) Radha Raman Pandey et al.   MOLECULAR CELL

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

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

(2008) J. Zhao et al.   SCIENCE