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Transcription of tandemly repetitive DNA: functional roles

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Abstract

A considerable fraction of the eukaryotic genome is made up of satellite DNA constituted of tandemly repeated sequences. These elements are mainly located at centromeres, pericentromeres, and telomeres and are major components of constitutive heterochromatin. Although originally satellite DNA was thought silent and inert, an increasing number of studies are providing evidence on its transcriptional activity supporting, on the contrary, an unexpected dynamicity. This review summarizes the multiple structural roles of satellite noncoding RNAs at chromosome level. Indeed, satellite noncoding RNAs play a role in the establishment of a heterochromatic state at centromere and telomere. These highly condensed structures are indispensable to preserve chromosome integrity and genome stability, preventing recombination events, and ensuring the correct chromosome pairing and segregation. Moreover, these RNA molecules seem to be involved also in maintaining centromere identity and in elongation, capping, and replication of telomere. Finally, the abnormal variation of centromeric and pericentromeric DNA transcription across major eukaryotic lineages in stress condition and disease has evidenced the critical role that these transcripts may play and the potentially dire consequences for the organism.

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Abbreviations

ATRX:

Alpha thalassemia/mental retardation syndrome X-linked protein

BRG1:

Brahma-related gene 1

CENP:

Centromeric protein

Chp1:

Chromodomain protein 1

DKC1:

Dyskerin

CLRC:

Clr4-Rik1-Cul4 complex

CPC:

Chromosomal passenger complex

CTCF:

Chromatin organizing factor

dsRNA:

Double-stranded RNA

Exo 1:

Exonuclease 1

HAC:

Human artificial chromosome

hnRPA1:

Heterogeneous nuclear ribonucleoprotein A1

HOR:

High-order repeat

HP1:

Heterochromatin protein-1

HSF1:

Heat shock factor 1

H3:

Histone H3

ICF:

Immunodeficiency, centromere instability, and human facial anomalies syndrome

INCENP:

Inner centromere protein

lncRNA:

Long noncoding RNA

LncRNA-TAREs:

Long telomere-associated noncoding RNAs

ncRNA:

Noncoding RNA

NS:

Nucleostemin

nSB:

Nuclear stress body

ORC:

Origin recognition complex

Paf1C:

Polymerase-associated factor1 complex

RDRC:

RNA-directed RNA polymerase complex

RdRP:

RNA-directed RNA polymearse

RISC:

RNA-induced silencing complex

RITS:

RNA-induced initiation of transcriptional gene silencing

RNAi:

RNA interference

RNAPol II:

RNA polymerase II

RPA:

Replication protein A

satDNA:

Satellite DNA

siRNA:

Small interfering RNA

Tas3:

Targeting complex subunit 3

TCAB1:

Telomerase Cajal body protein 1

TER:

Telomerase template RNA

TERRA:

Telomeric repeat-containing RNA

TERT:

Telomerase reverse transcriptase

TPE:

Telomere position effect

T-Recs:

Telomerase recruitment clusters

WDHD1:

WD repeat and HMG-box DNA binding protein 1

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Acknowledgments

We apologize to colleagues whose work could not be cited because of space limitations.

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All authors have made contributions to conception and write the manuscript. They have given final approval of the version to be published.

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  1. Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131, Ancona, Italy

    Maria Assunta Biscotti, Adriana Canapa, Mariko Forconi, Ettore Olmo & Marco Barucca

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  1. Maria Assunta Biscotti
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  2. Adriana Canapa
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  3. Mariko Forconi
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  4. Ettore Olmo
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Correspondence to Maria Assunta Biscotti.

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Biscotti, M.A., Canapa, A., Forconi, M. et al. Transcription of tandemly repetitive DNA: functional roles. Chromosome Res 23, 463–477 (2015). https://doi.org/10.1007/s10577-015-9494-4

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