Repetitive Fragile Sites: Centromere Satellite DNA As a Source of Genome Instability in Human Diseases

Maintenance of an intact genome is essential for cellular and organismal homeostasis. The centromere is a specialized chromosomal locus required for faithful genome inheritance at each round of cell division. Human centromeres are composed of large tandem arrays of repetitive alpha-satellite DNA, which are often sites of aberrant rearrangements that may lead to chromosome fusions and genetic abnormalities. While the centromere has an essential role in chromosome segregation during mitosis, the long and repetitive nature of the highly identical repeats has greatly hindered in-depth genetic studies, and complete annotation of all human centromeres is still lacking. Here, we review our current understanding of human centromere genetics and epigenetics as well as recent investigations into the role of centromere DNA in disease, with a special focus on cancer, aging, and human immunodeficiency–centromeric instability–facial anomalies (ICF) syndrome. We also highlight the causes and consequences of genomic instability at these large repetitive arrays and describe the possible sources of centromere fragility. The novel connection between alpha-satellite DNA instability and human pathological conditions emphasizes the importance of obtaining a truly complete human genome assembly and accelerating our understanding of centromere repeats’ role in physiology and beyond.

Download Full-text

Identification of a subdomain of CENP-B that is necessary and sufficient for localization to the human centromere.

The Journal of Cell Biology ◽

10.1083/jcb.116.5.1081 ◽

1992 ◽

Vol 116 (5) ◽

pp. 1081-1093 ◽

Cited By ~ 73

Author(s):

A F Pluta ◽

N Saitoh ◽

I Goldberg ◽

W C Earnshaw

Keyword(s):

Satellite Dna ◽

Centromeric Heterochromatin ◽

Amino Terminus ◽

Major Protein ◽

Alpha Satellite ◽

Alpha Satellite Dna ◽

Human Centromere ◽

Bacterial Enzyme

We have combined in vivo and in vitro approaches to investigate the function of CENP-B, a major protein of human centromeric heterochromatin. Expression of epitope-tagged deletion derivatives of CENP-B in HeLa cells revealed that a single domain less than 158 residues from the amino terminus of the protein is sufficient to localize CENP-B to centromeres. Centromere localization was abolished if as few as 28 amino acids were removed from the amino terminus of CENP-B. The centromere localization signal of CENP-B can function in an autonomous fashion, relocating a fused bacterial enzyme to centromeres. The centromere localization domain of CENP-B specifically binds in vitro to a subset of alpha-satellite DNA monomers. These results suggest that the primary mechanism for localization of CENP-B to centromeres involves the recognition of a DNA sequence found at centromeres. Analysis of the distribution of this sequence in alpha-satellite DNA suggests that CENP-B binding may have profound effects on chromatin structure at centromeres.

Download Full-text

Alpha satellite insertions and the evolutionary landscape of centromeres

10.1101/2021.03.10.434819 ◽

2021 ◽

Author(s):

Giuliana Giannuzzi ◽

Glennis A. Logsdon ◽

Nicolas Chatron ◽

Danny E. Miller ◽

Julie Reversat ◽

...

Keyword(s):

Satellite Dna ◽

Adaptive Sampling ◽

De Novo ◽

Regulatory Element ◽

Higher Order ◽

Alpha Satellite ◽

Chromosome 18 ◽

Alpha Satellite Dna ◽

Repeat Structure ◽

Human Genome Assembly

AbstractHuman centromeres are composed of alpha satellite DNA hierarchically organized as higher-order repeats and epigenetically specified by CENP-A binding. Current evolutionary models assert that new centromeres are first epigenetically established and subsequently acquire an alphoid array. We identified during routine prenatal aneuploidy diagnosis by FISH a de novo insertion of alpha satellite DNA array (~50-300 kbp) from the centromere of chromosome 18 (D18Z1) into chromosome 15q26 euchromatin. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by lack of constriction and absence of CENP-A binding. We characterized the rearrangement by FISH and sequencing using Illumina, PacBio, and Nanopore adaptive sampling which revealed that the insertion was associated with a 2.8 kbp deletion and likely occurred in the paternal germline. Notably, the site was located ~10 Mbp distal from the location where a centromere was ancestrally seeded and then became inactive sometime between 20 and 25 million years ago (Mya), in the common ancestor of humans and apes. Long reads spanning either junction showed that the organization of the alphoid insertion followed the 12-mer higher-order repeat structure of the D18Z1 array. Mapping to the CHM13 human genome assembly revealed that the satellite segment transposed from a specific location of chromosome 18 centromere. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the epigenetic status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name ‘alpha satellite insertion’. It also expands our knowledge about the evolutionary life cycle of centromeres, conveying the possibility that alphoid arrays can relocate near vestigial centromeric sites.

Download Full-text

Abstract 3471: Replication of megabase-size alpha-satellite DNA arrays in human centromere

10.1158/1538-7445.am2017-3471 ◽

2017 ◽

Author(s):

Indri Erliandri

Keyword(s):

Satellite Dna ◽

Dna Arrays ◽

Alpha Satellite ◽

Alpha Satellite Dna ◽

Human Centromere

Download Full-text

A functional neo-centromere formed through activation of a latent human centromere and consisting of non-alpha-satellite DNA

Nature Genetics ◽

10.1038/ng0697-144 ◽

1997 ◽

Vol 16 (2) ◽

pp. 144-153 ◽

Cited By ~ 195

Author(s):

Desirée du Sart ◽

Michael R. Cancilla ◽

Elizabeth Earle ◽

Jen-i Mao ◽

Richard Saffery ◽

...

Keyword(s):

Satellite Dna ◽

Alpha Satellite ◽

Alpha Satellite Dna ◽

Human Centromere

Download Full-text

CENP-C binds the alpha-satellite DNA in vivo at specific centromere domains

Journal of Cell Science ◽

10.1242/jcs.115.11.2317 ◽

2002 ◽

Vol 115 (11) ◽

pp. 2317-2327 ◽

Cited By ~ 1

Author(s):

Valeria Politi ◽

Giovanni Perini ◽

Stefania Trazzi ◽

Artem Pliss ◽

Ivan Raska ◽

...

Keyword(s):

Dna Sequences ◽

Satellite Dna ◽

Alpha Satellite ◽

Alpha Satellite Dna ◽

Human Centromere ◽

Ultrastructural Characterization ◽

First Time

CENP-C is a fundamental component of the centromere, highly conserved among species and necessary for the proper assembly of the kinetochore structure and for the metaphase-anaphase transition. Although CENP-C can bind DNA in vitro,the identification of the DNA sequences associated with it in vivo and the significance of such an interaction have been, until now, elusive. To address this problem we took advantage of a chromatin-immunoprecipitation procedure and applied this technique to human HeLa cells. Through this approach we could establish that: (1) CENP-C binds the alpha-satellite DNA selectively; (2) the CENP-C region between amino acids 410 and 537, previously supposed to contain a DNA-binding domain, is indeed required to perform such a function in vivo;and (3) the profile of the alpha-satellite DNA associated with CENP-C is essentially identical to that recognized by CENP-B. However, further biochemical and ultrastructural characterization of CENP-B/DNA and CENP-C/DNA complexes, relative to their DNA components and specific spatial distribution in interphase nuclei, surprisingly reveals that CENP-C and CENP-B associate with the same types of alpha-satellite arrays but in distinct non-overlapping centromere domains. Our results, besides extending previous observations on the role of CENP-C in the formation of active centromeres, show, for the first time, that CENP-C can associate with the centromeric DNA sequences in vivo and, together with CENP-B, defines a highly structured organization of the alpha-satellite DNA within the human centromere.

Download Full-text