H3K4 demethylase KDM5B regulates global dynamics of transcription elongation and alternative splicing in embryonic stem cells

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

(2015) Takayuki Nojima et al.   CELL

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

JARID1B Is a Luminal Lineage-Driving Oncogene in Breast Cancer

(2014) Shoji Yamamoto et al.   CANCER CELL

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency

(2014) Bérénice A. Benayoun et al.   CELL

Pre-mRNA splicing is facilitated by an optimal RNA polymerase II elongation rate

(2014) Nova Fong et al.   GENES & DEVELOPMENT

How Slow RNA Polymerase II Elongation Favors Alternative Exon Skipping

(2014) Gwendal Dujardin et al.   MOLECULAR CELL

KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation

(2014) Benjamin L Kidder et al.   GENOME BIOLOGY

PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data

(2014) Collin Tokheim et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2013) Alika K Maunakea et al.   CELL RESEARCH

The RNA Polymerase II Carboxy-Terminal Domain (CTD) Code

(2013) Dirk Eick et al.   CHEMICAL REVIEWS

Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation

(2013) Ignacio E Schor et al.   EMBO JOURNAL

Extended Self-Renewal and Accelerated Reprogramming in the Absence of Kdm5b

(2013) B. L. Kidder et al.   MOLECULAR AND CELLULAR BIOLOGY

The Histone Demethylase Jarid1b Ensures Faithful Mouse Development by Protecting Developmental Genes from Aberrant H3K4me3

(2013) Mareike Albert et al.   PLoS Genetics

Co-transcriptional regulation of alternative pre-mRNA splicing

(2012) Sanjeev Shukla et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Epigenetic features are significantly associated with alternative splicing

(2012) Yuanpeng Zhou et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

First Exon Length Controls Active Chromatin Signatures and Transcription

(2012) Nicole I. Bieberstein et al.   Cell Reports

Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data

(2011) Yun Chen et al.   BMC GENOMICS

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Jarid1b targets genes regulating development and is involved in neural differentiation

(2011) Sandra U Schmitz et al.   EMBO JOURNAL

KDM5B regulates embryonic stem cell self-renewal and represses cryptic intragenic transcription

(2011) Liangqi Xie et al.   EMBO JOURNAL

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

ChIP-Seq: technical considerations for obtaining high-quality data

(2011) Benjamin L Kidder et al.   NATURE IMMUNOLOGY

Histone Deacetylase Activity Modulates Alternative Splicing

(2011) Jarmila Hnilicová et al.   PLoS One

H3 Lysine 4 Is Acetylated at Active Gene Promoters and Is Regulated by H3 Lysine 4 Methylation

(2011) Benoit Guillemette et al.   PLoS Genetics

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

(2011) Chao Cheng et al.   GENOME BIOLOGY

Reversal of Histone Methylation: Biochemical and Molecular Mechanisms of Histone Demethylases

(2010) Nima Mosammaparast et al.   Annual Review of Biochemistry

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

A clustering approach for identification of enriched domains from histone modification ChIP-Seq data

(2009) Chongzhi Zang et al.   BIOINFORMATICS

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

Differential chromatin marking of introns and expressed exons by H3K36me3

(2009) Paulina Kolasinska-Zwierz et al.   NATURE GENETICS

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

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS