Conserved DNA sequence features underlie pervasive RNA polymerase pausing

Comparative analysis of ChIP-exo peak-callers: impact of data quality, read duplication and binding subtypes

(2020) Vasudha Sharma et al.   BMC BIOINFORMATICS

A Two-Layered Targeting Mechanism Underlies Nuclear RNA Sorting by the Human Exosome

(2020) Guifen Wu et al.   Cell Reports

XACT-Seq Comprehensively Defines the Promoter-Position and Promoter-Sequence Determinants for Initial-Transcription Pausing

(2020) Jared T. Winkelman et al.   MOLECULAR CELL

Identification of the human DPR core promoter element using machine learning

(2020) Long Vo ngoc et al.   NATURE

Causes and consequences of RNA polymerase II stalling during transcript elongation

(2020) Melvin Noe Gonzalez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The elemental mechanism of transcriptional pausing

(2019) Jason Saba et al.   eLife

Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation

(2019) Leighton Core et al.   GENES & DEVELOPMENT

Reporter-ChIP-nexus reveals strong contribution of the Drosophila initiator sequence to RNA polymerase pausing

(2019) Wanqing Shao et al.   eLife

Mechanisms of Transcriptional Pausing in Bacteria

(2019) Jin Young Kang et al.   JOURNAL OF MOLECULAR BIOLOGY

Organization and regulation of gene transcription

(2019) Patrick Cramer   NATURE

NET-CAGE characterizes the dynamics and topology of human transcribed cis-regulatory elements

(2019) Shigeki Hirabayashi et al.   NATURE GENETICS

Nascent RNA and the Coordination of Splicing with Transcription

(2019) Karla M. Neugebauer   Cold Spring Harbor Perspectives in Biology

cis Elements that Mediate RNA Polymerase II Pausing Regulate Human Gene Expression

(2019) Jason A. Watts et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The pause-initiation limit restricts transcription activation in human cells

(2019) Saskia Gressel et al.   Nature Communications

Native elongation transcript sequencing reveals temperature dependent dynamics of nascent RNAPII transcription in Arabidopsis

(2019) Peter Kindgren et al.   NUCLEIC ACIDS RESEARCH

Widespread transcriptional pausing and elongation control at enhancers

(2018) Telmo Henriques et al.   GENES & DEVELOPMENT

Distinguishing RNA modifications from noise in epitranscriptome maps

(2018) Anya V Grozhik et al.   Nature Chemical Biology

Born to run: control of transcription elongation by RNA polymerase II

(2018) Fei Xavier Chen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Eukaryotic core promoters and the functional basis of transcription initiation

(2018) Vanja Haberle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA template sequence control of bacterial RNA polymerase escape from the promoter

(2018) Ewa Heyduk et al.   NUCLEIC ACIDS RESEARCH

Identification and removal of sequencing artifacts produced by mispriming during reverse transcription in multiple RNA-seq technologies

(2018) Haridha Shivram et al.   RNA

Structure of paused transcription complex Pol II–DSIF–NELF

(2018) Seychelle M. Vos et al.   NATURE

A new sequence logo plot to highlight enrichment and depletion

(2018) Kushal K. Dey et al.   BMC BIOINFORMATICS

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

BET Bromodomain Proteins Function as Master Transcription Elongation Factors Independent of CDK9 Recruitment

(2017) Georg E. Winter et al.   MOLECULAR CELL

Transcription elongation factors represent in vivo cancer dependencies in glioblastoma

(2017) Tyler E. Miller et al.   NATURE

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections

(2017) Jaime Abraham Castro-Mondragon et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Structure of a transcribing RNA polymerase II–DSIF complex reveals a multidentate DNA–RNA clamp

(2017) Carrie Bernecky et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

CDK9-dependent RNA polymerase II pausing controls transcription initiation

(2017) Saskia Gressel et al.   eLife

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data

(2016) Giovanna Ambrosini et al.   BMC GENOMICS

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts

(2016) Austin E. Gillen et al.   BMC GENOMICS

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

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

Genome-wide profiling of RNA polymerase transcription at nucleotide resolution in human cells with native elongating transcript sequencing

(2016) Andreas Mayer et al.   Nature Protocols

TT-seq maps the human transient transcriptome

(2016) Björn Schwalb et al.   SCIENCE

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

Comprehensive RNA Polymerase II Interactomes Reveal Distinct and Varied Roles for Each Phospho-CTD Residue

(2016) Kevin M. Harlen et al.   Cell Reports

The core promoter: At the heart of gene expression

(2015) Yehuda M. Danino et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Starcode: sequence clustering based on all-pairs search

(2015) Eduard Zorita et al.   BIOINFORMATICS

DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding

(2015) Tsu-Pei Chiu et al.   BIOINFORMATICS

Detrimental effects of duplicate reads and low complexity regions on RNA- and ChIP-seq data

(2015) Mikhail G Dozmorov et al.   BMC BIOINFORMATICS

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

GC skew defines distinct RNA polymerase pause sites in CpG island promoters

(2015) Wendy A. Kellner et al.   GENOME RESEARCH

Effects of Transcription Elongation Rate and Xrn2 Exonuclease Activity on RNA Polymerase II Termination Suggest Widespread Kinetic Competition

(2015) Nova Fong et al.   MOLECULAR CELL

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

RNA polymerase II pausing during development

(2014) B. Gaertner et al.   DEVELOPMENT

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A pause sequence enriched at translation start sites drives transcription dynamics in vivo

(2014) M. H. Larson et al.   SCIENCE

Interactions between RNA polymerase and the "core recognition element" counteract pausing

(2014) I. O. Vvedenskaya et al.   SCIENCE

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

(2014) Iris Jonkers et al.   eLife

CrossMap: a versatile tool for coordinate conversion between genome assemblies

(2013) Hao Zhao et al.   BIOINFORMATICS

BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure

(2013) Priti Anand et al.   CELL

Enhancer transcripts mark active estrogen receptor binding sites

(2013) N. Hah et al.   GENOME RESEARCH

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Gene regulation by antisense transcription

(2013) Vicent Pelechano et al.   NATURE REVIEWS GENETICS

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

(2013) H. Kwak et al.   SCIENCE

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A Movie of RNA Polymerase II Transcription

(2012) Alan C.M. Cheung et al.   CELL

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Non-B DB v2.0: a database of predicted non-B DNA-forming motifs and its associated tools

(2012) Regina Z. Cer et al.   NUCLEIC ACIDS RESEARCH

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Factor-independent transcription pausing caused by recognition of the RNA-DNA hybrid sequence

(2011) Aleksandra Bochkareva et al.   EMBO JOURNAL

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Unravelling the means to an end: RNA polymerase II transcription termination

(2011) Jason N. Kuehner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Signals for pre-mRNA cleavage and polyadenylation

(2011) Bin Tian et al.   Wiley Interdisciplinary Reviews-RNA

Translocation by multi-subunit RNA polymerases

(2010) Maria Kireeva et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

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

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen et al.   BIOINFORMATICS

ConsensusPathDB—a database for integrating human functional interaction networks

(2008) Atanas Kamburov et al.   NUCLEIC ACIDS RESEARCH

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

Promoter elements associated with RNA Pol II stalling in the Drosophila embryo

(2008) D. A. Hendrix et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA