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Biochemistry (Moscow)

, Volume 83, Issue 4, pp 450–466 | Cite as

Who Needs This Junk, or Genomic Dark Matter

  • O. I. Podgornaya
  • D. I. Ostromyshenskii
  • N. I. Enukashvily
Review

Abstract

Centromeres (CEN), pericentromeric regions (periCEN), and subtelomeric regions (subTel) comprise the areas of constitutive heterochromatin (HChr). Tandem repeats (TRs or satellite DNA) are the main components of HChr forming no less than 10% of the mouse and human genome. HChr is assembled within distinct structures in the interphase nuclei of many species–chromocenters. In this review, the main classes of HChr repeat sequences are considered in the order of their number increase in the sequencing reads of the mouse chromocenters (ChrmC). TRs comprise ~70% of ChrmC occupying the first place. Non-LTR (-long terminal repeat) retroposons (mainly LINE, long interspersed nuclear element) are the next (~11%), and endogenous retroviruses (ERV; LTR-containing) are in the third position (~9%). HChr is not enriched with ERV in comparison with the whole genome, but there are differences in distribution of certain elements: while MaLR-like elements (ERV3) are dominant in the whole genome, intracisternal A-particles and corresponding LTR (ERV2) are prevalent in HChr. Most of LINE in ChrmC is represented by the 2-kb fragment at the end of the 2nd open reading frame and its flanking regions. Almost all tandem repeats classified as CEN or periCEN are contained in ChrmC. Our previous classification revealed 60 new mouse TR families with 29 of them being absent in ChrmC, which indicates their location on chromosome arms. TR transcription is necessary for maintenance of heterochromatic status of the HChr genome part. A burst of TR transcription is especially important in embryogenesis and other cases of radical changes in the cell program, including carcinogenesis. The recently discovered mechanism of epigenetic regulation with noncoding sequences transcripts, long noncoding RNA, and its role in embryogenesis and pluripotency maintenance is discussed.

Keywords

heterochromatin sequencing tandem repeats dispersed repeats transposable elements retrotransposons long noncoding RNA in situ hybridization 

Abbreviations

CEN

centromeres

CENP-B box

CEN-binding site of CENP-B protein

ChrmC

dataset of sequence reads from mouse chromocenters

eDNA

extracellular DNA

ERV

endogenous retrovirus

FISH

fluorescent in situ hybridization

GPG

golden path gap (unfilled gap in assembled genomes with size of 3 Mb reserved for CEN)

HAC

human artificial chromosome

HChr

heterochromatin

HOR

high order repeat

HP1

heterochromatic protein 1

HS1-3

human satellites 1–3

HSF-1

heat shock factor-1 (transcription factor)

IAPs

intracisternal A-particles

LINE

long interspersed nuclear element

lncRNA

long non-coding RNA

LTR

long terminal repeats in ERV

MaSat

mouse major satellite (periCEN)

MiSat

mouse minor satellite (CEN)

periCEN

pericentromeric regions

satDNA

satellite DNA

SINE

short interspersed nuclear element

subTel

subtelomeric region

TE

transposable elements

TR

tandem repeats

WGS

Whole Genome Shotgun (dataset of reads assembled to genome contigs).

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Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • O. I. Podgornaya
    • 1
    • 2
    • 3
  • D. I. Ostromyshenskii
    • 1
    • 3
  • N. I. Enukashvily
    • 1
  1. 1.Institute of CytologyRussian Academy of SciencesSt. PetersburgRussia
  2. 2.St. Petersburg State UniversitySt. PetersburgRussia
  3. 3.Far Eastern Federal UniversityVladivostokRussia

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