High-resolution mapping of chromatin packaging in mouse embryonic stem cells and sperm

Benjamin R. Carone, Jui Hung Hung, Sarah J. Hainer, Min Te Chou, Dawn M. Carone, Zhiping Weng, Thomas G. Fazzio, Oliver J. Rando

Research output: Contribution to journalArticlepeer-review

185 Scopus citations


Mammalian embryonic stem cells (ESCs) and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ESCs and sperm. In ESCs, we recover well-characterized features of chromatin such as promoter nucleosome depletion and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ESCs and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome.

Original languageEnglish (US)
Pages (from-to)11-22
Number of pages12
JournalDevelopmental Cell
Issue number1
StatePublished - Jul 14 2014
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • General Biochemistry, Genetics and Molecular Biology
  • Developmental Biology
  • Cell Biology


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