4sUDRB-seq: measuring genomewide transcriptional elongation rates and initiation frequencies within cells

Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNFα signaling revealed by integrated genomic analyses

(2014) Xin Luo et al.   BMC GENOMICS

Mechanistic Interpretation of Promoter-Proximal Peaks and RNAPII Density Maps

(2013) Andreas H. Ehrensberger et al.   CELL

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

(2013) A. Saunders et al.   GENES & DEVELOPMENT

Signaling Pathways Differentially Affect RNA Polymerase II Initiation, Pausing, and Elongation Rate in Cells

(2013) Charles G. Danko et al.   MOLECULAR CELL

HDAC inhibitors induce transcriptional repression of high copy number genes in breast cancer through elongation blockade

(2013) Y J Kim et al.   ONCOGENE

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

Transcriptional Amplification in Tumor Cells with Elevated c-Myc

(2012) Charles Y. Lin et al.   CELL

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

(2012) L. Windhager et al.   GENOME RESEARCH

Expression Noise and Acetylation Profiles Distinguish HDAC Functions

(2012) Leehee Weinberger et al.   MOLECULAR CELL

RNF20 and USP44 Regulate Stem Cell Differentiation by Modulating H2B Monoubiquitylation

(2012) Gilad Fuchs et al.   MOLECULAR CELL

Suppression of the antiviral response by an influenza histone mimic

(2012) Ivan Marazzi et al.   NATURE

RNA polymerase II kinetics inpolopolyadenylation signal selection

(2011) Pedro A B Pinto et al.   EMBO JOURNAL

New Insights into the Control of HIV-1 Transcription: When Tat Meets the 7SK snRNP and Super Elongation Complex (SEC)

(2011) Nanhai He et al.   Journal of Neuroimmune Pharmacology

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner

(2011) H.-L. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster

(2011) Hang Yin et al.   PLoS Genetics

Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation

(2010) J. Y. Ip et al.   GENOME RESEARCH

HIV-1 Tat and Host AFF4 Recruit Two Transcription Elongation Factors into a Bifunctional Complex for Coordinated Activation of HIV-1 Transcription

(2010) Nanhai He et al.   MOLECULAR CELL

AFF4, a Component of the ELL/P-TEFb Elongation Complex and a Shared Subunit of MLL Chimeras, Can Link Transcription Elongation to Leukemia

(2010) Chengqi Lin et al.   MOLECULAR CELL

HIV-1 Tat Assembles a Multifunctional Transcription Elongation Complex and Stably Associates with the 7SK snRNP

(2010) Bijan Sobhian et al.   MOLECULAR CELL

ENCODE whole-genome data in the UCSC genome browser (2011 update)

(2010) Brian J. Raney et al.   NUCLEIC ACIDS RESEARCH

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Rates of in situ transcription and splicing in large human genes

(2009) Jarnail Singh et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Tracking rates of transcription and splicing in vivo

(2009) M Behfar Ardehali et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing

(2009) I. E. Schor 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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

(2008) L. Dolken et al.   RNA

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE