Promoter directionality is controlled by U1 snRNP and polyadenylation signals

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

An upstream promoter element blocks the reverse transcription of the mouse insulin-degrading enzyme gene

(2012) Lang Zhang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

U1 snRNP Determines mRNA Length and Regulates Isoform Expression

(2012) Michael G. Berg et al.   CELL

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

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

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

Hominoid-Specific De Novo Protein-Coding Genes Originating from Long Non-Coding RNAs

(2012) Chen Xie et al.   PLoS Genetics

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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

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

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

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

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome

(2010) Yong E. Zhang et al.   PLOS BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME 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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY