Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

An efficient method for genome-wide polyadenylation site mapping and RNA quantification

(2013) Stefan Wilkening 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

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Promoter-proximal polyadenylation sites reduce transcription activity

(2012) P. K. Andersen et al.   GENES & DEVELOPMENT

A quantitative atlas of polyadenylation in five mammals

(2012) Adnan Derti et al.   GENOME RESEARCH

RNA Polymerase II Pausing Downstream of Core Histone Genes Is Different from Genes Producing Polyadenylated Transcripts

(2012) Krishanpal Anamika et al.   PLoS One

Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation

(2012) C. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

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

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

Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes

(2011) Eivind Valen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters

(2011) Pascal Preker 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

Pol II waiting in the starting gates: Regulating the transition from transcription initiation into productive elongation

(2010) Sergei Nechaev et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

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

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Transcription termination by nuclear RNA polymerases

(2009) P. Richard et al.   GENES & DEVELOPMENT

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

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

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Phosphorylation of the RNA polymerase II C-terminal domain dictates transcription termination choice

(2008) Rajani Kanth Gudipati et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Asap: A Framework for Over-Representation Statistics for Transcription Factor Binding Sites

(2008) Troels T. Marstrand et al.   PLoS One

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