RNA Pol II transcription model and interpretation of GRO-seq data

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq

(2017) Joseph G. Azofeifa et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Pausing of RNA Polymerase II Regulates Mammalian Developmental Potential through Control of Signaling Networks

(2015) Lucy H. Williams et al.   MOLECULAR CELL

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

(2014) Iris Jonkers et al.   eLife

Vespucci: a system for building annotated databases of nascent transcripts

(2013) Karmel A. Allison et al.   NUCLEIC ACIDS RESEARCH

Promoter-proximal CCCTC-factor binding is associated with an increase in the transcriptional pausing index

(2012) Sur Herrera Paredes et al.   BIOINFORMATICS

mRNA Decapping Factors and the Exonuclease Xrn2 Function in Widespread Premature Termination of RNA Polymerase II Transcription

(2012) Kris Brannan et al.   MOLECULAR CELL

Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans

(2012) Karen Adelman et al.   NATURE REVIEWS GENETICS

A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells

(2011) Nasun Hah et al.   CELL

Regulating RNA polymerase pausing and transcription elongation in embryonic stem cells

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

X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila

(2011) Erica Larschan et al.   NATURE

Discovery of active enhancers through bidirectional expression of short transcripts

(2011) Michael F Melgar et al.   GENOME BIOLOGY

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

NELF-mediated stalling of Pol II can enhance gene expression by blocking promoter-proximal nucleosome assembly

(2008) D. A. Gilchrist et al.   GENES & DEVELOPMENT

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE