Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes

(2012) Varodom Charoensawan et al.   MOLECULAR CELL

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Genome-wide occupancy links Hoxa2 to Wnt–β-catenin signaling in mouse embryonic development

(2012) Ian J. Donaldson et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Cooperative Transcription Factor Complexes in Control

(2012) G. J. Martinez et al.   SCIENCE

Overlapping ETS and CRE Motifs ( G / C CGGAAGTGACGTCA) Preferentially Bound by GABPα and CREB Proteins

(2012) Raghunath Chatterjee et al.   G3-Genes Genomes Genetics

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

Multiple Sequence-Specific Factors Generate the Nucleosome-Depleted Region on CLN2 Promoter

(2011) Lu Bai et al.   MOLECULAR CELL

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

p53 binds preferentially to genomic regions with high DNA-encoded nucleosome occupancy

(2010) E. Lidor Nili et al.   GENOME RESEARCH

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of histone sequence preferences to nucleosome organization: proposed definitions and methodology

(2010) Noam Kaplan et al.   GENOME BIOLOGY

p53 Binding to Nucleosomal DNA Depends on the Rotational Positioning of DNA Response Element

(2009) Geetaram Sahu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

(2009) S. H. Meijsing et al.   SCIENCE

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

(2008) Julian M Rozenberg et al.   BMC GENOMICS

Two strategies for gene regulation by promoter nucleosomes

(2008) I. Tirosh et al.   GENOME RESEARCH

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology