Yong Zhang

TL;DR: This work presents Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer, and uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions.

TL;DR: This protocol provides a detailed demonstration of how to install MACS and how to use it to analyze three common types of ChIP-seq data sets with different characteristics: the sequence-specific transcription factor FoxA1, the histone modification mark H3K4me3 with sharp enrichment and theH3K36me3 mark with broad enrichment.

TL;DR: It is demonstrated that genome-wide positional analyses suggest that methylation of histone H3 lysine 4 is part of the epigenetic signature that defines lineage-specific FoxA1 recruitment sites in chromatin.

TL;DR: The role of AR in androgen-independent cancer cells is not to direct the androgen -dependent gene expression program without androgen, but rather to execute a distinct program resulting in androgens-independent growth.

TL;DR: Peroxisome proliferator-activated receptor gamma (PPARgamma), a nuclear receptor and the target of anti-diabetic thiazolinedione drugs, and C/EBPbeta also plays a role at many of these genes, such that both C/EBPalpha and beta are required along with PPARGamma for robust adipocyte-specific gene expression.