The non-coding snRNA 7SK controls transcriptional termination, poising, and bidirectionality in embryonic stem cells

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Long Noncoding RNAs: Cellular Address Codes in Development and Disease

(2013) Pedro J. Batista et al.   CELL

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

(2013) Xiong Ji et al.   CELL

Widespread and extensive lengthening of 3' UTRs in the mammalian brain

(2013) P. Miura et al.   GENOME RESEARCH

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation

(2013) Ilana Livyatan et al.   NUCLEIC ACIDS RESEARCH

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

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

Disengaging polymerase: Terminating RNA polymerase II transcription in budding yeast

(2012) Hannah E. Mischo et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Microprocessor, Setx, Xrn2, and Rrp6 Co-operate to Induce Premature Termination of Transcription by RNAPII

(2012) Alexandre Wagschal et al.   CELL

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

Polycomb Associates Genome-wide with a Specific RNA Polymerase II Variant, and Regulates Metabolic Genes in ESCs

(2012) Emily Brookes et al.   Cell Stem Cell

Bromodomain and Extra-terminal (BET) Bromodomain Inhibition Activate Transcription via Transient Release of Positive Transcription Elongation Factor b (P-TEFb) from 7SK Small Nuclear Ribonucleoprotein

(2012) Koen Bartholomeeusen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease

(2012) Irfan A. Qureshi et al.   NATURE REVIEWS NEUROSCIENCE

Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation

(2012) Konstantinia Skreka et al.   NUCLEIC ACIDS RESEARCH

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Divergent transcription: A new feature of active promoters

(2011) Amy C. Seila et al.   CELL CYCLE

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

(2011) I. M. Min et al.   GENES & DEVELOPMENT

Dynamic transcriptional events in embryonic stem cells mediated by the super elongation complex (SEC)

(2011) C. Lin et al.   GENES & DEVELOPMENT

Two-pronged Binding with Bromodomain-containing Protein 4 Liberates Positive Transcription Elongation Factor b from Inactive Ribonucleoprotein Complexes

(2011) Sebastian Schröder et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia

(2011) Mark A. Dawson et al.   NATURE

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

(2011) Matthew D. Young et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HMGA1-dependent and independent 7SK RNA gene regulatory activity

(2011) Sebastian Eilebrecht et al.   RNA Biology

7SK snRNA-mediated, gene-specific cooperativity of HMGA1 and P-TEFb

(2011) Sebastian Eilebrecht et al.   RNA Biology

7SK snRNA: a noncoding RNA that plays a major role in regulating eukaryotic transcription

(2011) B. Matija Peterlin et al.   Wiley Interdisciplinary Reviews-RNA

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Polycomb Group Proteins Set the Stage for Early Lineage Commitment

(2010) Lauren E. Surface et al.   Cell Stem Cell

Characterization of the RNA content of chromatin

(2010) T. Mondal et al.   GENOME RESEARCH

Nuclear Organization and Dynamics of 7SK RNA in Regulating Gene Expression

(2010) Kannanganattu V. Prasanth et al.   MOLECULAR BIOLOGY OF THE CELL

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation

(2010) Iván D'Orso et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

7SK small nuclear RNA directly affects HMGA1 function in transcription regulation

(2010) S. Eilebrecht et al.   NUCLEIC ACIDS RESEARCH

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Gene loops function to maintain transcriptional memory through interaction with the nuclear pore complex

(2009) Sue Mei Tan-Wong et al.   GENES & DEVELOPMENT

Evolution of 7SK RNA and Its Protein Partners in Metazoa

(2009) M. Marz et al.   MOLECULAR BIOLOGY AND EVOLUTION

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Post-transcriptional processing generates a diversity of 5′-modified long and short RNAs

(2009)   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development

(2009) M. Barboric et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

Global Transcription in Pluripotent Embryonic Stem Cells

(2008) Sol Efroni et al.   Cell Stem Cell

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Antisense transcripts are targets for activating small RNAs

(2008) Jacob C Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

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