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

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Pre-mRNA splicing: where and when in the nucleus

(2011) Joonhee Han et al.   TRENDS IN CELL BIOLOGY

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin

(2010) Rolf Ohlsson et al.   CHROMOSOMA

Aberrant Epigenetic Landscape in Cancer: How Cellular Identity Goes Awry

(2010) María Berdasco et al.   DEVELOPMENTAL CELL

Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged

(2010) C. J. David et al.   GENES & DEVELOPMENT

Context-Dependent Regulatory Mechanism of the Splicing Factor hnRNP L

(2010) Laura B. Motta-Mena et al.   MOLECULAR CELL

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Reciprocal intronic and exonic histone modification regions in humans

(2010) Jason T Huff et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers

(2010) Frank Lyko et al.   PLOS BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Nucleosomes are well positioned in exons and carry characteristic histone modifications

(2009) R. Andersson et al.   GENOME RESEARCH

Progression through the RNA Polymerase II CTD Cycle

(2009) Stephen Buratowski   MOLECULAR CELL

Biased Chromatin Signatures around Polyadenylation Sites and Exons

(2009) Noah Spies et al.   MOLECULAR CELL

Differential chromatin marking of introns and expressed exons by H3K36me3

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

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Alternative splicing and disease

(2008) Jamal Tazi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

Transient Reversal of RNA Polymerase II Active Site Closing Controls Fidelity of Transcription Elongation

(2008) Maria L. Kireeva et al.   MOLECULAR CELL

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

A cell-based screen for splicing regulators identifies hnRNP LL as a distinct signal-induced repressor of CD45 variable exon 4

(2008) J. D. Topp et al.   RNA

Regulation of CD45 Alternative Splicing by Heterogeneous Ribonucleoprotein, hnRNPLL

(2008) S. Oberdoerffer et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY