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A CHD ATP-dependent Chromatin Remodeler Regulates Nucleosome Repeat-Length Phasing in the Mid-coding Sequence of a Limited Gene Set.

Thursday, October 11, 2012 — Poster Session III

10:00 a.m. – Noon

Natcher Conference Center, Building 45




  • J.L. Platt
  • A.J. Harwood
  • A.R. Kimmel


CHD (Chromodomain-Helicase-DNA binding) proteins utilize energy from ATP hydrolysis to alter nucleosome position and access of DNA to transcription factors/polymerases. CHDs are linked to both activation and repression of gene expression and are involved in various developmental disorders. Using homologous recombination, I knocked out a CHD gene member. Compared to wild-type (WT), cells deficient for CHD grow poorly with defects in developmental cell fate specificity. These defects correlate with changes in transcriptome profiling, as assayed by RNAseq. We then collaboratively developed a method to map nucleosome positioning on a genome-wide scale. Chromatin from WT and mutant cells was digested with micrococcal nuclease (MNase) to generate nucleosomal protected DNA; purified nucleosomal DNA was analyzed by high-throughput paired-end sequencing. Sequence reads were globally aligned to the reference genome to call nucleosome centers. Most genes in the CHD mutant were organized identically to WT. However, I identified chromatin differences in ~1700 genes. In this subset, nucleosomes were more distantly spaced (~185bp) than in WT. Significantly, the ~1700 chromatin-remodeled genes show a correlation with the gene expression changes identified by RNAseq. I suggest that distinct CHDs may regulate nucleosome spacing in specific genes classes, which ultimately alters transcription activity.

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