Identification of holocarboxylase synthetase chromatin binding sites in human mammary cell lines using the DamID technology

Authors

Dipika Singh, University of Nebraska-Lincoln
Angela K. Pannier, University of Nebraska-LincolnFollow
Janos Zempleni, University of Nebraska-LincolnFollow

Date of this Version

2011

Citation

Anal Biochem. 2011 June 1; 413(1): 55–59.

Comments

Copyright 2011 Singh et al. Used by permission.

Abstract

Holocarboxylase synthetase (HCS) is a chromatin protein that is essential for mediating the covalent binding of biotin to histones. Biotinylation of histones plays crucial roles in the repression of genes and repeats in the human genome. We tested the feasibility of DNA adenine methyltransferase identification (DamID) technology to map HCS binding sites in human mammary cell lines. Full-length HCS was fused to Dam for subsequent transfection into breast cancer (MCF-7) and normal breast (MCF-10A) cells. HCS docking sites in chromatin were identified by using the unique adenine methylation sites established by Dam in the fusion construct; docking sites were unambiguously identified using methylation sensitive digestion, cloning, and sequencing. Fifteen novel HCS binding sites were identified in the two cell lines and the following four out of the 15 overlapped between MCF-7 and MCF-10A cells: inositol polyphosphate-5-phosphatase A, corticotropin hormone precursor, ribosome biogenesis regulatory protein, and leptin precursor. We conclude that DamID is a useful technology to map HCS binding sites in human chromatin and propose that the entire set of HCS binding sites could be mapped by combining DamID with microarray technology.