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Who Needs This Junk, or Genomic Dark Matter

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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.

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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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Authors and Affiliations

  1. Institute of Cytology, Russian Academy of Sciences, 194064, St. Petersburg, Russia

    O. I. Podgornaya, D. I. Ostromyshenskii & N. I. Enukashvily

  2. St. Petersburg State University, 199034, St. Petersburg, Russia

    O. I. Podgornaya

  3. Far Eastern Federal University, 690922, Vladivostok, Russia

    O. I. Podgornaya & D. I. Ostromyshenskii

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  1. O. I. Podgornaya
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Original Russian Text © O. I. Podgornaya, D. I. Ostromyshenskii, N. I. Enukashvily1, 2018, published in Biokhimiya, 2018, Vol. 83, No. 4, pp. 607–624.

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Podgornaya, O.I., Ostromyshenskii, D.I. & Enukashvily, N.I. Who Needs This Junk, or Genomic Dark Matter. Biochemistry Moscow 83, 450–466 (2018). https://doi.org/10.1134/S0006297918040156

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