Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Three-dimensional proximity mapping of the DRGFP DNA double-strand break site in U2OS cells

ABSTRACT: We mapped the DNA sequences located in physical proximity to an I-SceI endonuclease-dependent DNA double-strand break (DSB) site to be able to study the impact of DSBs on the break-associated chromatin micro-environment. The I-SceI DSB site is part of a DRGFP transgene that serves as a reporter for homology-directed DSB repair and was stably integrated into U2OS human osteosarcoma cells (Pierce et al., Genes Dev, 1999). DRGFP-U2OS cells were modified to carry a stable Doxycycline (Dox)-inducible I-SceI transgene (TRE-I-SceI) as well as the Tet-ON vector from Contech. Circular chromosome conformation capture (4C) was used to identify DSB-proximal DNA. 4C amplified DNA was subjected to Illumina Hi-Seq 200 100 bp paired end sequencing and reads were mapped to the human genome. The resulting genome-wide map of I-SceI/DRGFP-proximal DNA allows for the investigation of changes in DSB-surrounding chromatin features following I-SceI-mediated DSB induction. 4C library of I-SceI (DRGFP)-proximal DNA contacts in DRGFP-U2OS cells was generated using Illumina Hi-Seq 2000 sequencing, data sets are from two independent experiments.

ORGANISM(S): Homo sapiens

SUBMITTER: Philipp Oberdoerffer 

PROVIDER: E-GEOD-58563 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

A macrohistone variant links dynamic chromatin compaction to BRCA1-dependent genome maintenance.

Khurana Simran S   Kruhlak Michael J MJ   Kim Jeongkyu J   Tran Andy D AD   Liu Jinping J   Nyswaner Katherine K   Shi Lei L   Jailwala Parthav P   Sung Myong-Hee MH   Hakim Ofir O   Oberdoerffer Philipp P  

Cell reports 20140814 4

Appropriate DNA double-strand break (DSB) repair factor choice is essential for ensuring accurate repair outcome and genomic integrity. The factors that regulate this process remain poorly understood. Here, we identify two repressive chromatin components, the macrohistone variant macroH2A1 and the H3K9 methyltransferase and tumor suppressor PRDM2, which together direct the choice between the antagonistic DSB repair mediators BRCA1 and 53BP1. The macroH2A1/PRDM2 module mediates an unexpected shif  ...[more]

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