Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions

Abstract

The interaction of architectural proteins such as the linker histone H1 and high-mobility-group (HMG) proteins with nucleosomes leads to changes in chromatin structure and histone modifications and alters the cellular transcription profile. The interaction of HMG proteins with chromatin is dynamic. However, it is not clear whether the proteins are constantly and randomly redistributed among all the nucleosomes or whether they preferentially associate with, and turn over at, specific regions in chromatin. To address this question, we examined the genomewide distribution of the nucleosome binding protein HMGN1 and compared it to that of regulatory chromatin marks. We find that HMGN1 is not randomly distributed throughout the genome. Instead, the protein preferentially localizes to DNase I hypersensitive (HS) sites, promoters, functional enhancers, and transcription factor binding sites. Our results suggest that HMGN1 is part of the cellular machinery that modulates transcriptional fidelity by generating, maintaining, or preferentially interacting with specific sites in chromatin.

The Chromatin-binding Protein HMGN1 Regulates the Expression of Methyl CpG-binding Protein 2 (MECP2) and Affects the Behavior of Mice

“…Genomic profiling of human CD4ϩ T cells revealed that HMGN1 preferentially localizes to chromatin regulatory sites and to promoters of transcriptionally active genes (22), a finding that is in full agreement with its widespread effects on the cellular transcription profile (14). Among the regulatory sites bound by HMGN1 is the promoter of the gene coding for methyl CpG-binding protein 2 (MeCP2), a nuclear protein that is expressed postnatally during mammalian brain development and is highly abundant in neurons (23).…”

“…Anti-␤-actin mouse monoclonal, catalog #A5316 clone AC-74, anti-human HMGN1 (62,63), and anti-mouse HMGN1 (peptide 6) (12, 64) were from Sigma. ChIP sequence analysis of CD4ϩ human T cells was performed as described (22). All antibodies were used for chromatin immunoprecipitation except for anti-MeCP2 and anti-␤-actin, which were used for Western blot.…”

“…Likewise, given the widespread effects of HMGN1 on gene expression and its association with regulatory sites throughout chromatin (22), it is difficult to unequivocally identify all the genes downstream from HMGN1 that are directly responsible for the various phenotypes observed in the mice with altered HMGN1 expression. Nevertheless by focusing on a single gene it is possible to gain insights into the possible mechanisms whereby HMGN1 affects the global phenotype.…”

“…Promoter-Targeted analysis of the ChIP sequence data of human CD4ϩ T cells (22) revealed that the enrichment levels of HMGN1 are elevated in the regulatory regions overlapping the first exon of human MeCP2 (Fig. 1A).…”

“…Assays-ChIP sequence analysis of human CD4ϩ cells was described previously (22). For all other ChIP experiments, brain tissues were homogenized on 70-m Nylon Cell strainer (BD Biosciences) and washed twice in cold PBS.…”