Discovery of active enhancers through bidirectional expression of short transcripts

Paused RNA Polymerase II as a Developmental Checkpoint

(2011) Michael Levine   CELL

Promoter proximal pausing and the control of gene expression

(2011) Jian Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA

(2011) Dong Wang et al.   NATURE

Detection and Removal of Biases in the Analysis of Next-Generation Sequencing Reads

(2011) Schraga Schwartz et al.   PLoS One

Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Global Epigenomic Analysis of Primary Human Pancreatic Islets Provides Insights into Type 2 Diabetes Susceptibility Loci

(2010) Michael L. Stitzel et al.   Cell Metabolism

The Meaning of Pausing

(2010) Joaquín M. Espinosa   MOLECULAR CELL

Splicing-Dependent RNA Polymerase Pausing in Yeast

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

Global Analysis of Nascent RNA Reveals Transcriptional Pausing in Terminal Exons

(2010) Fernando Carrillo Oesterreich et al.   MOLECULAR CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers

(2010) Francesca De Santa et al.   PLOS BIOLOGY

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

(2010) Alexandra C. Nica et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

Does CTCF mediate between nuclear organization and gene expression?

(2009) Rolf Ohlsson et al.   BIOESSAYS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

(2009) M. P. Schnetz et al.   GENOME RESEARCH

A wave of nascent transcription on activated human genes

(2009) Y. Wada et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global Analysis of Short RNAs Reveals Widespread Promoter-Proximal Stalling and Arrest of Pol II in Drosophila

(2009) S. Nechaev et al.   SCIENCE

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

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

Coupling and coordination in gene expression processes: a systems biology view

(2007) Suzanne Komili et al.   NATURE REVIEWS GENETICS