We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated
by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the
shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding …

The estrogen receptor is the master transcriptional regulator of breast cancer phenotype and
the archetype of a molecular therapeutic target. We mapped all estrogen receptor and RNA
polymerase II binding sites on a genome-wide scale, identifying the authentic cis binding …

Estrogen plays an essential physiologic role in reproduction and a pathologic one in breast
cancer. The completion of the human genome has allowed the identification of the
expressed regions of protein-coding genes; however, little is known concerning the …

Complex organisms require tissue-specific transcriptional programs, yet little is known about
how these are established. The transcription factor FoxA1 is thought to contribute to gene
regulation through its ability to act as a pioneer factor binding to nucleosomal DNA. Through …

The transcription factor GATA-3 is required for normal mammary gland development, and its
expression is highly correlated with estrogen receptor α (ERα) in human breast tumors.
However, the functional role of GATA-3 in ERα-positive breast cancers is yet to be …

Estrogen stimulates the proliferation of the most common type of human breast cancer that
expresses estrogen receptor α (ERα) through the activation of the cyclin D1 (CCND1)
oncogene. However, our knowledge of ERα transcriptional mechanisms remains limited …

Transcription factors (TFs) bind specifically to discrete regions of mammalian genomes
called cis-regulatory elements. Among those are enhancers, which play key roles in
regulation of gene expression during development and differentiation. Despite the …

Genome-wide association studies (GWAS) have identified thousands of SNPs that are
associated with human traits and diseases. But, because the vast majority of these SNPs are
located in non-coding regions of the genome, the mechanisms by which they promote …

The nuclear receptor Rev-erb-α modulates hepatic lipid and glucose metabolism,
adipogenesis and the inflammatory response in macrophages. We show here that Rev-erb-
α is highly expressed in oxidative skeletal muscle and that its deficiency in muscle leads to …

Enhancers are developmentally controlled transcriptional regulatory regions whose
activities are modulated through histone modifications or histone variant deposition. In this
study, we show by genome-wide mapping that the newly discovered deoxyribonucleic acid …