Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

Genomic Organization of Human Transcription Initiation Complexes

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Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

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Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing

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Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin

(2015) Benjamin S. Scruggs et al.   MOLECULAR CELL

Human Gene Promoters Are Intrinsically Bidirectional

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Human Promoters Are Intrinsically Directional

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An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

Genome-wide identification of transcript start and end sites by transcript isoform sequencing

(2014) Vicent Pelechano et al.   Nature Protocols

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

Dealing with Pervasive Transcription

(2013) Torben Heick Jensen et al.   MOLECULAR CELL

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Extensive transcriptional heterogeneity revealed by isoform profiling

(2013) Vicent Pelechano et al.   NATURE

The human cap-binding complex is functionally connected to the nuclear RNA exosome

(2013) Peter Refsing Andersen et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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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

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Genome-wide structure and organization of eukaryotic pre-initiation complexes

(2012) Ho Sung Rhee et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Interaction Profiling Identifies the Human Nuclear Exosome Targeting Complex

(2011) Michal Lubas et al.   MOLECULAR CELL

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

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

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

Perspectives on the RNA polymerase II core promoter

(2011) James T. Kadonaga   Wiley Interdisciplinary Reviews-Developmental Biology

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

U1 snRNP protects pre-mRNAs from premature cleavage and polyadenylation

(2010) Daisuke Kaida et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Tiny RNAs associated with transcription start sites in animals

(2009) Ryan J Taft et al.   NATURE GENETICS

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2009) Ben Langmead et al.   GENOME 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