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PMID: 21796450 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Chromatin affinity-precipitation using a small metabolic molecule: its application to analysis of O-acetyl-ADP-ribose.

Cellular and molecular life sciences : CMLS ·Vol. 69 ·No. 4 ·2012-02-00 ·Pages 641-50

Tung SY, Hong JY, Walz T, Moazed D, Liou GG

Abstract

In the cell, many small endogenous metabolic molecules are involved in distinct cellular functions such as modulation of chromatin structure and regulation of gene expression. O-acetyl-ADP-ribose (AAR) is a small metabolic molecule that is generated during NAD-dependent deacetylation by Sir2. Sir2 regulates gene expression, DNA repair, and genome stability. Here, we developed a novel chromatin affinity-precipitation (ChAP) method to detect the chromatin fragments at which small molecules interact with binding partners. We used this method to demonstrate that AAR associated with heterochromatin. Moreover, we applied the ChAP method to whole genome tiling array chips to compare the association of AAR and Sir2. We found that AAR and Sir2 displayed similar genomic binding patterns. Furthermore, we identified 312 potential association cluster regions of AAR. The ChAP assay may therefore be a generally useful strategy to study the small molecule association with chromosomal regions. Our results further suggest that the small metabolic molecule AAR associates with silent chromatin regions in a Sir2-dependent manner and provide additional support for the role of AAR in assembly of silent chromatin.

MeSH Terms
Chromatin Immunoprecipitation Chromosomes/metabolism DNA Repair Genomic Instability Heterochromatin/metabolism O-Acetyl-ADP-Ribose/metabolism Protein Binding Saccharomyces cerevisiae/metabolism Sirtuin 2/metabolism
Chemicals
Heterochromatin O-Acetyl-ADP-Ribose Sirtuin 2
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Tung Shu-Yun
Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan, ROC.
Hong Jia-Yang
Walz Thomas
Moazed Danesh
Liou Gunn-Guang
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Article Info
Journal
Cellular and molecular life sciences : CMLS
Abbr.
Cell Mol Life Sci
ISSN
1420-9071
DOI
10.1007/s00018-011-0771-x
Published
2012-02-00
Epub
2011-00-28
Pages
641-50
Language
English
Region
Switzerland
NLM ID
9705402
PMCID
PMC3266462
Subset
IM
Grants
Howard Hughes Medical Institute · United States
NIGMS NIH HHS · R01 GM061641 · United States
NIGMS NIH HHS · R01 GM061641-10 · United States
NIGMS NIH HHS · GM61641 · United States
External Links
PubMed source DOI: 10.1007/s00018-011-0771-x PMC Full Text View journal details
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