Steve Henikoff’s Lab
Zentner, GE and Henikoff, S (2014) High-resolution Digital Profiling of the Epigenome, Nature Reviews Genetics, in press.2014
The widespread adoption of short-read DNA sequencing as a digital epigenomic read-out platform has motivated the development of genome-wide tools that achieve base-pair resolution. New methods for footprinting and affinity purification of nucleosomes, RNA polymerases, chromatin remodelers, and transcription factors have increased the resolution of epigenomic profiling by two orders of magnitude, leading to new insights into how the chromatin landscape impacts gene regulation. These digital epigenomic tools have also been applied to directly profile both turnover kinetics and transcription in situ. Here, we describe how these new genome-wide tools allow interrogation of diverse aspects of the epigenome.
Doxorubicin, DNA Torsion, and Chromatin Dynamics. Biochim Biophys Acta. January 2014.
Doxorubicin, DNA torsion, and chromatin dynamics.
ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies. PLoS Genet. 2013.
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.
Regulation of Nucleosome Dynamics by Histone Modifications. Nat. Struct. Mol. Biol. March 2013
Regulation of nucleosome dynamics by histone modifications.
Heat Shock Reduces Stalled RNA Polymerase II and Nucleosome Turnover Genome-wide. Genes Dev. November 2011.
Heat shock reduces stalled RNA polymerase II and nucleosome turnover genome-wide.
Aberrant DNA Methylation Occurs in Colon Neoplasms Arising in the Azoxymethane Colon Cancer Model. Mol Carcinog. January 2010.
Aberrant DNA methylation occurs in colon neoplasms arising in the azoxymethane colon cancer model.
Tissue-specific variation in DNA Methylation Levels Along Human Chromosome 1. Epigenetics Chromatin. June 2009.
Tissue-specific variation in DNA methylation levels along human chromosome 1.