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

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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.

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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

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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.

Funding

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.).

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Authors and Affiliations

  1. Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, 27710, USA

    Shannon M. McNulty & Beth A. Sullivan

  2. Division of Human Genetics, Duke University Medical Center, Durham, NC, 27710, USA

    Beth A. Sullivan

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  1. Shannon M. McNulty
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SMM and BAS conceived and jointly wrote the manuscript.

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Correspondence to Beth A. Sullivan.

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Responsible Editor: Rachel J. O’Neill

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McNulty, S.M., Sullivan, B.A. Alpha satellite DNA biology: finding function in the recesses of the genome. Chromosome Res 26, 115–138 (2018). https://doi.org/10.1007/s10577-018-9582-3

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