Mouse centromeric tandem repeats in silico and in situ

Komissarov, Aleksei S.; Kuznetsova, Irina M.; Podgornaya, O. I.

doi:10.1134/s1022795410090176

Cited by 5 publications

(9 citation statements)

References 16 publications

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“…Despite sharing ~70% sequence identity in their genes, mice and humans carry completely different satellite repeats. Mus musculus centromeres consist of tandem arrays of 120-bp minor satellite (MiSat), which contains the CENP-B box and comprise 1–2% of the genome [ 33 , 34 ]. MiSats are more homogeneous within a Mus species as compared to α-satellites of primate species [ 24 , 33 , 34 , 70 ].…”

Section: Satellite Dna Sequencesmentioning

confidence: 99%

“…Mus musculus centromeres consist of tandem arrays of 120-bp minor satellite (MiSat), which contains the CENP-B box and comprise 1–2% of the genome [ 33 , 34 ]. MiSats are more homogeneous within a Mus species as compared to α-satellites of primate species [ 24 , 33 , 34 , 70 ]. Additional centromeric satellites are the ~150-bp MS3 and the ~300-bp MS4, both of which cytologically co-localize with MiSats at M. musculus centromeres [ 35 , 71 ].…”

Section: Satellite Dna Sequencesmentioning

confidence: 99%

“…Similarly, mouse telocentric ends that span pericentric regions are hotspots for Rb translocations in wild populations of M. musculus located in Western Europe and North Africa [ 109 , 115 ]. Mouse pericentric regions are occupied by major satellites (MaSats,), the TRPC-21A family repeats and TLC (TeLoCentric) repeats [ 24 , 34 ]. MaSat is the most abundant mouse satellite comprising ~10% of the genome and is present at pericentric regions of all chromosomes.…”

Section: Satellite Dna Sequencesmentioning

confidence: 99%

“…MaSat is the most abundant mouse satellite comprising ~10% of the genome and is present at pericentric regions of all chromosomes. The MaSat repeat unit is 234 bp long, is composed of four different 58-60 bp simple repeats, and exhibits monomer variability of up to 30% [ 24 , 34 , 116 ]. While the MaSat satellite is confined to the pericentric regions in M. musculus , it is also present in the chromosomal arms in M spretus and M. caroli [ 20 ].…”

Section: Satellite Dna Sequencesmentioning

confidence: 99%

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Sequence, Chromatin and Evolution of Satellite DNA

Thakur

Packiaraj

Henikoff

2021

IJMS

152

116

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Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.

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Section: Satellite Dna Sequencesmentioning

confidence: 99%

Section: Satellite Dna Sequencesmentioning

confidence: 99%

Section: Satellite Dna Sequencesmentioning

confidence: 99%

Section: Satellite Dna Sequencesmentioning

confidence: 99%

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Sequence, Chromatin and Evolution of Satellite DNA

Thakur

Packiaraj

Henikoff

2021

IJMS

152

116

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“…However, transcripts from repetitive sequences and modified noncoding RNAs are difficult to determine by BLAST searches (11), so the RepeatMasker program (release, open-3.2.9; A. F. A. Smit, R. Hubley, and P. Green, Institute for Systems Biology [http://www.repeatmasker.org]) was employed to search mouse and human genome databases (genome plus transcripts), and similarities were identified with RNAs from diverse genomic repeats, snRNAs, and tRNAs (data not shown). It is noteworthy that some of these RNAs, of approximately the same size as the srRNAs, are derived from heterochromatic satellite sequences at pericentromeric regions of chromosomes, and these RNAs are enriched in human and murine cancer cells, especially by DNA stressors and inducers of apoptosis (3,22,53). Table 1).…”

Section: Inhibitory Activities For Bkv Replication In Mouse Cell Extrmentioning

confidence: 99%

Inhibition of Human BK Polyomavirus Replication by Small Noncoding RNAs

Tikhanovich

Liang

Seoighe

et al. 2011

J Virol

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Small noncoding RNAs regulate a variety of cellular processes, including genomic imprinting, chromatin remodeling, replication, transcription, and translation. Here, we report small replication-regulating RNAs (srRNAs) that specifically inhibit DNA replication of the human BK polyomavirus (BKV) in vitro and in vivo. srRNAs from FM3A murine mammary tumor cells were enriched by DNA replication assay-guided fractionation and hybridization to the BKV noncoding control region (NCCR) and synthesized as cDNAs. Selective mutagenesis of the cDNA sequences and their putative targets suggests that the inhibition of BKV DNA replication is mediated by srRNAs binding to the viral NCCR, hindering early steps in the initiation of DNA replication. Ectopic expression of srRNAs in human cells inhibited BKV DNA replication in vivo. Additional srRNAs were designed and synthesized that specifically inhibit simian virus 40 (SV40) DNA replication in vitro. These observations point to novel mechanisms for regulating DNA replication and suggest the design of synthetic agents for inhibiting replication of polyomaviruses and possibly other viruses.Small noncoding RNAs (ncRNAs) have important roles in eukaryotic gene expression determining developmental processes and growth and differentiation (reviewed in references 1, 8, 20, 27, 30, and 49). In addition, certain ncRNAs (e.g., Y-RNAs) are required for chromosomal DNA replication and proliferation of mammalian cells (5, 23); however, the mechanisms by which these act are not yet understood. Roles for ncRNAs in regulating viral infections of mammalian cells were uncovered with the discovery of virus-and host-encoded RNAs controlling viral gene expression (reviewed in references 10 and 41) and with the recognition that recruitment of the cellular origin recognition complex (ORC) to the viral origin of replication (OriP) by Epstein-Barr virus (EBV) nuclear antigen 1 (EBNA1) and initiation of EBV DNA replication are RNA dependent (38).BK virus (BKV) infects nearly the entire human population but generally is innocuous unless viral replication is activated following kidney transplantation and immune suppression, when it may cause polyomavirus-associated nephropathy (PVAN) and allograft loss (14,19). Polyomavirus DNA replication in vitro and in vivo requires one viral protein, the large T antigen (TAg), with other factors supplied by the host cell (25, 28). Polyomavirus DNA replication initiates with TAg binding at the viral origin of replication (39, 44) and recruitment of host factors such as replication protein A (RPA), DNA polymerase ␣-primase (Pol-primase), and topoisomerase I (2, 45), followed by Pol-primase catalyzed de novo synthesis of nascent primers for DNA replication. Early initiation products, the nascent DNA primers, are then extended by DNA polymerase ␦ and proliferating cell nuclear antigen (PCNA) and the loading factor replication factor C on the leading and lagging strands (37,54). Although the DNA replication machineries are conserved between primates and rodents, BKV does not...

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