Different distribution of histone modifications in genes with unidirectional and bidirectional transcription and a role of CTCF and cohesin in directing transcription

CTCF: an architectural protein bridging genome topology and function

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Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

Divergent Transcription: A Driving Force for New Gene Origination?

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JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

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Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

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RNA Polymerase II Elongation Control

(2012) Qiang Zhou et al.   Annual Review of Biochemistry

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

(2012) Guoliang Li et al.   CELL

H2A.Z Facilitates Access of Active and Repressive Complexes to Chromatin in Embryonic Stem Cell Self-Renewal and Differentiation

(2012) Gangqing Hu et al.   Cell Stem Cell

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

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FIMO: scanning for occurrences of a given motif

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Divergent transcription: A new feature of active promoters

(2011) Amy C. Seila et al.   CELL CYCLE

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

(2011) Sanjeev Shukla et al.   NATURE

RAD21 Cooperates with Pluripotency Transcription Factors in the Maintenance of Embryonic Stem Cell Identity

(2011) Anja Nitzsche et al.   PLoS One

Histone modification: cause or cog?

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seqMINER: an integrated ChIP-seq data interpretation platform

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SICTIN: Rapid footprinting of massively parallel sequencing data

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Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

(2009) M. Y. Tolstorukov et al.   GENOME RESEARCH

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

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

Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

(2009) Mehdi Motallebipour et al.   GENOME BIOLOGY

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

(2008) A. Rada-Iglesias et al.   GENOME RESEARCH

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains

(2008) S. Cuddapah et al.   GENOME RESEARCH

Nucleosome organization in the Drosophila genome

(2008) Travis N. Mavrich et al.   NATURE

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

(2008) Daniel Zilberman et al.   NATURE

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

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

(2008) Leighton J. Core et al.   SCIENCE