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PMID: 20211137 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Distinct factors control histone variant H3.3 localization at specific genomic regions.

Cell ·Vol. 140 ·No. 5 ·2010-03-05 ·Pages 678-91

Goldberg AD, Banaszynski LA, Noh KM, Lewis PW, Elsaesser SJ, Stadler S, Dewell S, Law M, Guo X, Li X, Wen D, Chapgier A, DeKelver RC, Miller JC, Lee YL, Boydston EA, Holmes MC, Gregory PD, Greally JM, Rafii S, Yang C, Scambler PJ, Garrick D, Gibbons RJ, Higgs DR, Cristea IM, Urnov FD, Zheng D, Allis CD

Abstract

The incorporation of histone H3 variants has been implicated in the epigenetic memory of cellular state. Using genome editing with zinc-finger nucleases to tag endogenous H3.3, we report genome-wide profiles of H3 variants in mammalian embryonic stem cells and neuronal precursor cells. Genome-wide patterns of H3.3 are dependent on amino acid sequence and change with cellular differentiation at developmentally regulated loci. The H3.3 chaperone Hira is required for H3.3 enrichment at active and repressed genes. Strikingly, Hira is not essential for localization of H3.3 at telomeres and many transcription factor binding sites. Immunoaffinity purification and mass spectrometry reveal that the proteins Atrx and Daxx associate with H3.3 in a Hira-independent manner. Atrx is required for Hira-independent localization of H3.3 at telomeres and for the repression of telomeric RNA. Our data demonstrate that multiple and distinct factors are responsible for H3.3 localization at specific genomic locations in mammalian cells.

MeSH Terms
Animals Binding Sites Cell Cycle Proteins/genetics,metabolism Embryonic Stem Cells/metabolism Genome Histone Chaperones/genetics,metabolism Histones/analysis,genetics,metabolism Mice Mice, Inbred C57BL Telomere/chemistry,metabolism Transcription Factors/genetics,metabolism Transcription Initiation Site
Chemicals
Cell Cycle Proteins Hira protein, mouse Histone Chaperones Histones Transcription Factors
Authors & Affiliations
29 authors, click to expand affiliations / ORCID
Goldberg Aaron D
Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
Banaszynski Laura A
Noh Kyung-Min
Lewis Peter W
Elsaesser Simon J
Stadler Sonja
Dewell Scott
Law Martin
Guo Xingyi
Li Xuan
Wen Duancheng
Chapgier Ariane
DeKelver Russell C
Miller Jeffrey C
Lee Ya-Li
Boydston Elizabeth A
Holmes Michael C
Gregory Philip D
Greally John M
Rafii Shahin
Yang Chingwen
Scambler Peter J
Garrick David
Gibbons Richard J
Higgs Douglas R
Cristea Ileana M
Urnov Fyodor D
Zheng Deyou
Allis C David
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Article Info
Journal
Cell
Abbr.
Cell
ISSN
1097-4172
DOI
10.1016/j.cell.2010.01.003
Published
2010-03-05
Pages
678-91
Language
English
Region
United States
NLM ID
0413066
PMCID
PMC2885838
Subset
IM
Grants
NIDA NIH HHS · DP1 DA026192 · United States
NIDA NIH HHS · DP1 DA026192-01 · United States
British Heart Foundation · United Kingdom
NIDA NIH HHS · DP1DA026192 · United States
NIGMS NIH HHS · GM07739 · United States
NIGMS NIH HHS · R37 GM053512-30 · United States
Biotechnology and Biological Sciences Research Council · BB/E009603/1 · United Kingdom
Medical Research Council · MC_U137961147 · United Kingdom
NCRR NIH HHS · RR022220 · United States
NCRR NIH HHS · P41 RR000862 · United States
NCRR NIH HHS · U54 RR022220 · United States
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · R37 GM053512 · United States
NIGMS NIH HHS · GM53512 · United States
NCRR NIH HHS · RR00862 · United States
NIGMS NIH HHS · GM53122 · United States
NIGMS NIH HHS · T32 GM007739 · United States
Databases
GEO
GSE16893, GSE19542
External Links
PubMed source DOI: 10.1016/j.cell.2010.01.003 PMC Full Text View journal details
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