Genome-scale techniques highlight the epigenome and redefine fundamental principles of gene regulation

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites

(2010) Stephen A. Ramsey et al.   BIOINFORMATICS

Histone acetylation: Where to go and how to get there

(2010) Vicki E. MacDonald et al.   Epigenetics

A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution

(2010) S. V. Ramagopalan et al.   GENOME RESEARCH

Epigenetics and gene expression

(2010) E R Gibney et al.   HEREDITY

A Downstream Intergenic Cluster of Regulatory Enhancers Contributes to the Induction ofCYP24A1Expression by 1α,25-Dihydroxyvitamin D3

(2010) Mark B. Meyer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide analysis of the VDR/RXR cistrome in osteoblast cells provides new mechanistic insight into the actions of the vitamin D hormone

(2010) Mark B. Meyer et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC

(2010) N. Ahmadiyeh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

The Long Arm of Long Noncoding RNAs: Roles as Sensors Regulating Gene Transcriptional Programs

(2010) X. Wang et al.   Cold Spring Harbor Perspectives in Biology

Cistromics of hormone-dependent cancer

(2009) Mathieu Lupien et al.   ENDOCRINE-RELATED CANCER

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

A Novel Distal Enhancer Mediates Cytokine Induction of MouseRanklGene Expression

(2009) Kathleen A. Bishop et al.   MOLECULAR ENDOCRINOLOGY

Multifunctional Enhancers Regulate Mouse and Human Vitamin D Receptor Gene Transcription

(2009) Lee A. Zella et al.   MOLECULAR ENDOCRINOLOGY

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs

(2009) Alain Jacquier   NATURE REVIEWS GENETICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Cracking the coregulator codes

(2008) Bert W O’Malley et al.   CURRENT OPINION IN CELL BIOLOGY

Genome-wide profiling of PPAR :RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis

(2008) R. Nielsen et al.   GENES & DEVELOPMENT

Interaction of the Glucocorticoid Receptor with the Chromatin Landscape

(2008) Sam John et al.   MOLECULAR CELL

Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription

(2008) Xiangting Wang et al.   NATURE

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

(2008) Anton Valouev et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Targeted Deletion of a Distant Transcriptional Enhancer of the Receptor Activator of Nuclear Factor-κB Ligand Gene Reduces Bone Remodeling and Increases Bone Mass

(2007) Carlo Galli et al.   ENDOCRINOLOGY