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Chromosome Research

, Volume 26, Issue 3, pp 115–138 | Cite as

Alpha satellite DNA biology: finding function in the recesses of the genome

  • Shannon M. McNulty
  • Beth A. SullivanEmail author
Waldeyer-Flemming Special Collection

Abstract

Repetitive DNA, formerly referred to by the misnomer “junk DNA,” comprises a majority of the human genome. One class of this DNA, alpha satellite, comprises up to 10% of the genome. Alpha satellite is enriched at all human centromere regions and is competent for de novo centromere assembly. Because of the highly repetitive nature of alpha satellite, it has been difficult to achieve genome assemblies at centromeres using traditional next-generation sequencing approaches, and thus, centromeres represent gaps in the current human genome assembly. Moreover, alpha satellite DNA is transcribed into repetitive noncoding RNA and contributes to a large portion of the transcriptome. Recent efforts to characterize these transcripts and their function have uncovered pivotal roles for satellite RNA in genome stability, including silencing “selfish” DNA elements and recruiting centromere and kinetochore proteins. This review will describe the genomic and epigenetic features of alpha satellite DNA, discuss recent findings of noncoding transcripts produced from distinct alpha satellite arrays, and address current progress in the functional understanding of this oft-neglected repetitive sequence. We will discuss unique challenges of studying human satellite DNAs and RNAs and point toward new technologies that will continue to advance our understanding of this largely untapped portion of the genome.

Keywords

satellite centromere kinetochore variation transcription noncoding RNA repetitive DNA epiallele 

Abbreviations

ASO

Antisense oligonucleotide

bp

Base pair

Cas9

CRISPR-associated protein 9

CENP

Centromere protein

ChIP

Chromatin immunoprecipitation

dCas9

Nuclease-deficient Cas9

DNA

Deoxyribonucleic acid

dsRNA

Double-stranded RNA

GFP

Green fluorescent protein

HAC

Human artificial chromosome

HJURP

Holliday Junction Recognition Protein

HOR

Higher-order repeat

HP1

Heterochromatin protein 1

HSA

Homo sapiens

kb

Kilobase

kDa

Kilodalton

KRAB

Krüppel-associated box

Mb

Megabase

RNA

Ribonucleic acid

RNAP

RNA polymerase

shRNA

Short hairpin RNA

tRNA

Transfer RNA

VP16

Virus protein 16

Notes

Acknowledgements

We thank Megan Aldrup-Macdonald for data contributing to Fig. 3 and Karen Miga (University of California, Santa Cruz) for helpful discussions and sharing data prior to publication.

Author contribution

SMM and BAS conceived and jointly wrote the manuscript.

Funding information

Our research is supported by the National Science Foundation Graduate Research Fellowship DGE-1644868 (S.M.M.) and the National Institutes of Health grant R01 GM124041 (B.A.S.).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

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© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Molecular Genetics and MicrobiologyDuke University Medical CenterDurhamUSA
  2. 2.Division of Human GeneticsDuke University Medical CenterDurhamUSA

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