Biochemistry (Moscow)

, Volume 83, Issue 4, pp 437–449 | Cite as

Link Between Double-Strand DNA Break Hotspots and Transcription Regulation: Forum Domains — 50–250 kb Chromosome Regions Containing Coordinately Expressed Genes

  • N. A. Tchurikov
  • Y. V. Kravatsky
  • O. V. Kretova
Review
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Abstract

The data on forum domains formed by DNA double-strand break (DSB) hotspots are reviewed including forum domain identification by pulsed-field gel electrophoresis, whole genome mapping of these domains using deep sequencing strategies, analysis of gene expression in forum domains, and binding of nuclear proteins to their boundaries. Earlier unpublished data by the authors are presented. The “piano playing” hypothesis is suggested based on coordinated active transcription in some of the forum domains and coordinated silencing in the majority of them. The data on the DSB hotspots in human ribosomal DNA gene clusters and their possible association with chromosomal translocations are presented. These clusters are the most actively transcribed DNA regions in cells, as well as the most fragile sites in human chromosomes. The need to revise the available data on DNase I-hypersensitive sites in various genomes, including endogenous DNA breaks of different nature, is discussed.

Keywords

endogenous DNA double-strand breaks (DSB) hotspots forum domains epigenetics coordinated expression PARP1 HNRNPA2B1 chromosomal silencing 4C inter-chromosomal contacts rDNA genes translocations DNase I-hypersensitive sites H3K4me3 H3K27ac CTCF 

Abbreviations

4C (method)

circular chromatin conformation capture

DSB

DNA double strand break

FT

forum termini

IGS

intergenic spacer

LAD

lamina-associated domain

LOCKs

large organized chromatin K9-modifications

Pc domains

Polycomb domains

RAFT

rapid amplification of forum domains termini

rDNA

ribosomal DNA

TAD

topologically associating domain

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Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • N. A. Tchurikov
    • 1
  • Y. V. Kravatsky
    • 1
  • O. V. Kretova
    • 1
  1. 1.Engelhardt Institute of Molecular BiologyRussian Academy of SciencesMoscowRussia

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