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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation [DSBs]

ABSTRACT: Eukaryotic chromosomes are subjected to spontaneous fragmentation even under quick isolation of DNA in a solid phase by strong treatment with 0.1 M EDTA, 1% SDS and proteinase K (1 mg/ml). The long DNA fragments of excised chromosomal DNA were denoted as forum domains. Mostly forum domains are of 50-200 kb in length, although larger domains, up to 500 - 700 kb, are also observed. The domains are delimited by hot spots of double-strand breaks (DSBs). We performed a genome-wide mapping of DSBs in human HEK293T cells cultured cells using Illumina deep sequencing of the termini of forum domains. We found that in rDNA units the hot spots of DSBs are distributed non-randomly. Mostly they are located in IGS. Genome-wide mapping of DNA DSBs in HEK293T cells

ORGANISM(S): Homo sapiens

SUBMITTER: Nickolai Tchurikov

PROVIDER: E-GEOD-49302 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation.

Tchurikov Nickolai A NA Fedoseeva Daria M DM Sosin Dmitri V DV Snezhkina Anastasia V AV Melnikova Nataliya V NV Kudryavtseva Anna V AV Kravatsky Yuri V YV Kretova Olga V OV

Journal of molecular cell biology 20141003 4

DNA double-strand breaks (DSBs) are involved in many cellular mechanisms, including replication, transcription, and genome rearrangements. The recent observation that hot spots of DSBs in human chromosomes delimit DNA domains that possess coordinately expressed genes suggests a strong relationship between the organization of transcription patterns and hot spots of DSBs. In this study, we performed mapping of hot spots of DSBs in a human 43-kb ribosomal DNA (rDNA) repeated unit. We observed that ...[more]

PMID: 25280477

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High-throughput pyrosequencing of forum domains termini (FT) isolated and amplified from human HEK293T cells

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