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Epigenome characterization at single base-pair resolution.

Publication ,  Journal Article
Henikoff, JG; Belsky, JA; Krassovsky, K; MacAlpine, DM; Henikoff, S
Published in: Proc Natl Acad Sci U S A
November 8, 2011

We have combined standard micrococcal nuclease (MNase) digestion of nuclei with a modified protocol for constructing paired-end DNA sequencing libraries to map both nucleosomes and subnucleosome-sized particles at single base-pair resolution throughout the budding yeast genome. We found that partially unwrapped nucleosomes and subnucleosome-sized particles can occupy the same position within a cell population, suggesting dynamic behavior. By varying the time of MNase digestion, we have been able to observe changes that reflect differential sensitivity of particles, including the eviction of nucleosomes. To characterize DNA-binding features of transcription factors, we plotted the length of each fragment versus its position in the genome, which defined the minimal protected region of each factor. This process led to the precise mapping of protected and exposed regions at and around binding sites, and also determination of the degree to which they are flanked by phased nucleosomes and subnucleosome-sized particles. Our protocol and mapping method provide a general strategy for epigenome characterization, including nucleosome phasing and dynamics, ATP-dependent nucleosome remodelers, and transcription factors, from a single-sequenced sample.

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Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

November 8, 2011

Volume

108

Issue

45

Start / End Page

18318 / 18323

Location

United States

Related Subject Headings

  • Transcription Factors
  • Genome
  • Epigenomics
  • Chromatin
  • Binding Sites
  • Base Pairing
 

Citation

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ICMJE
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Henikoff, J. G., Belsky, J. A., Krassovsky, K., MacAlpine, D. M., & Henikoff, S. (2011). Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A, 108(45), 18318–18323. https://doi.org/10.1073/pnas.1110731108
Henikoff, Jorja G., Jason A. Belsky, Kristina Krassovsky, David M. MacAlpine, and Steven Henikoff. “Epigenome characterization at single base-pair resolution.Proc Natl Acad Sci U S A 108, no. 45 (November 8, 2011): 18318–23. https://doi.org/10.1073/pnas.1110731108.
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318–23.
Henikoff, Jorja G., et al. “Epigenome characterization at single base-pair resolution.Proc Natl Acad Sci U S A, vol. 108, no. 45, Nov. 2011, pp. 18318–23. Pubmed, doi:10.1073/pnas.1110731108.
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):18318–18323.
Journal cover image

Published In

Proc Natl Acad Sci U S A

DOI

EISSN

1091-6490

Publication Date

November 8, 2011

Volume

108

Issue

45

Start / End Page

18318 / 18323

Location

United States

Related Subject Headings

  • Transcription Factors
  • Genome
  • Epigenomics
  • Chromatin
  • Binding Sites
  • Base Pairing