Satellite DNA and related diseases

Rich, Jeremy; Ogryzko, Vasily; Pirozhkova, Iryna

doi:10.7124/bc.00089e

Cited by 13 publications

(22 citation statements)

References 104 publications

(115 reference statements)

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“…The changes in the copy number of repetitive sequences in genomic DNA are important causes of hereditary disorders (J. Rich et al, 2014;Mirkin, 2006Mirkin, , 2007. The insertion of 18 beta satellite units in the gene coding a transmembraine serine protease causes congenital and childhood onset autosomal recessive deafness (Scott et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

“…The global DNA hypomethylation frequently observed in cancers is mostly taken place at satDNAs (J. Rich et al, 2014). The loss of the BRCA1 tumor suppressor gene provokes satDNA derepression in breast and ovarian tumors in both mice and humans (Zhu et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

“…Facioscapulohumeral muscular dystrophy (FSHD), a autosomal dominant hereditary disease, is associated with the macrosatellite (D4Z4) and beta-satellite (4qA allele) DNA sequences (J. Rich et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Parasites Acquired Beta Satellite DNAs from Hominid Hosts via Horizontal Gene Transfer

Yang

Zhou

et al. 2019

Preprint

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Highlights1. The ever largest scale analysis on beta satDNAs.2. The origin of beta satDNAs was traced back to ~80 MYA. 3.Mass existence of beta satDNAs in non-primate species was contributed by multiple HGT events. AbstractBeta satellite DNA (satDNA) sequences are repeated DNA elements located in primate centromeres and telomeres, and might play roles in genome stability and chromosome segregation. Beta satDNAs mainly exist in great apes. Previous studies suggested that beta satDNAs may originate in old world monkeys. In this study, we searched both GenBank and SRA database, and identified beta satDNA sequences from the genomic sequences of 22 species. The beta satDNA sequences found in Prosimian, Dermoptera and Scandentia indicated that the origin of beta satDNAs might be as early as 80 MYA. Strikingly, beta satDNA sequences were also found in a number of some species evolutionarily far from primates, including several endoparasites of human and other great apes, which could be the results of multiple horizontal gene transfer (HGT) events. The similar phylogenic profiles between beta satDNAs in the parasite genomes and the human genome indicates that the parasite beta satDNAs have undergone similar concerted evolution and play similar roles as the beta satDNAs in primates.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Parasites Acquired Beta Satellite DNAs from Hominid Hosts via Horizontal Gene Transfer

Yang

Zhou

et al. 2019

Preprint

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“…Although some methods 36,37 try to model ambiguous mapping and repeat structure, only particular situations are addressed and, as a consequence, low-mappability regions are just scarcely covered in the most recent CNV catalogs 33 . This is unfortunate given that CNVs in such regions have already been associated with various diseases 12,38,39,40,41 and that these regions are also more likely variable. Indeed, different types of genomic repeats are likely to contribute to CNV formation.…”

Section: Introductionmentioning

confidence: 99%

Human copy number variants are enriched in regions of low mappability

Monlong

Meloche

Rouleau

et al. 2015

Preprint

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Germline copy number variants (CNVs) are known to affect a large portion of the human genome and have been implicated in many diseases. Although whole-genome sequencing can help identify CNVs, existing analytical methods suffer from limited sensitivity and specificity. Here we show that this is in large part due to the non-uniformity of read coverage, even after intra-sample normalization, and that this is exacerbated in regions of low-mappability. To improve on this, we propose PopSV, an analytical method that uses multiple samples to control for technical variation and enables the robust detection of CNVs. We show that PopSV is able to detect up to 2.7 times more variants compared to previous methods, with an accuracy of about 90%. Applying PopSV to 640 normal and cancer whole-genome datasets, we demonstrate that CNVs affect on average 7.4 million DNA bases in each individual, a 23% increase over previous estimates. Notably, we find that regions of low-mappability are approximately 8 times more likely to harbor CNVs than the rest of the genome, which contrasts with somatic CNVs that are nearly uniformly distributed. In addition to the known enrichment in segmental duplication, we also observe that CNVs are enriched near centromeres and telomeres, in specific types of satellite and short tandem repeats, and in some of the most recent families of transposable elements. Although CNVs are found to be depleted in protein-coding genes, we identify 7206 genes with at least one exonic CNV, 682 of which harbored CNVs in low-mappability regions that would have been missed by other methods. Our results provide the most exhaustive map of CNVs across the human genome to date and demonstrate the broad functional impact of this type of genetic variation including in regions of low-mappability.

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“…beta satDNA unit in the gene coding a transmembraine serine protease causes congenital and childhood onset autosomal recessive deafness [9]. The global DNA hypomethylation frequently observed in cancers is mostly taken place at satDNAs [8]. The loss of the BRCA1 tumor suppressor gene provokes satDNA derepression in breast and ovarian tumors in both mice and humans [10].…”

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confidence: 99%

The Wide Distribution and Horizontal Transfers of Beta Satellite DNA in Eukaryotes

Guo¹,

Yang²,

Bin³

et al. 2019

Preprint

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Beta satellite DNA (satDNA) sequences, also known as Sau3A sequences, are repeated DNA elements reported in human and primate genomes. Beta satDNAs may play roles in genome stability and chromosome segregation during mitosis. It is previously thought that beta satDNAs originated in old world monkeys and bursted in great apes. However, global and high-throughput studies on beta satDNAs are still absent.Results: In this study, we searched 7,821 genome assemblies of 3,767 eukaryotic species and found that beta satDNAs actually are widely distributed across eukaryotes. The four major branches of eukaryotes, animals, fungi, plants and Harosa/SAR, all have multiple clades containing beta satDNAs. These results were also confirmed by searching whole genome sequencing data (SRA) and PCR assay. Beta satDNA might have originated during the early evolution of eukaryotes. The widely patchy distribution of beta satDNAs across eukaryotes presents a typical scenario of multiple horizontal transfers (HT). In contrast, beta satDNA sequences were found in all the primate clades, Primatomorpha and Euarchonta, indicating an origin in the common ancestor and vertical transfers thereafter. Besides in eukaryotes, beta satDNAs were even found in some archaea and bacteria, which should have been acquired from eukaryotes via HTs.Conclusion:Beta satDNAs widely exist in eukaryotes. The current distribution landscape of beta satDNA is the result of countless HTs. Our study shows for the first time that satellite DNAs can also undergo HT, and will provide new ideas for the future investigations in HT/HGT field.Keywords: Beta satellite DNA, Sau3A sequences, Eukaryotes, Horizontal gene transfer, Primates

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Satellite DNA and related diseases

Cited by 13 publications

References 104 publications

Parasites Acquired Beta Satellite DNAs from Hominid Hosts via Horizontal Gene Transfer

Parasites Acquired Beta Satellite DNAs from Hominid Hosts via Horizontal Gene Transfer

Human copy number variants are enriched in regions of low mappability

The Wide Distribution and Horizontal Transfers of Beta Satellite DNA in Eukaryotes

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