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Genes Dec 2022The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our... (Review)
Review
The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our understanding of the genetic architecture and epigenetic properties of human centromeric DNA have advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex, saltatory mutational changes organized around distinct evolutionary layers. Pockets of regional hypomethylation within higher-order α-satellite DNA, termed centromere dip regions, appear to define the site of kinetochore attachment in all human chromosomes, although such epigenetic features can vary even within the same chromosome. Sequence resolution of satellite DNA is providing new insights into centromeric function with potential implications for improving our understanding of human biology and health.
Topics: Humans; DNA, Satellite; Centromere; Kinetochores; DNA; Heterochromatin
PubMed: 36672831
DOI: 10.3390/genes14010092 -
Cold Spring Harbor Perspectives in... Jun 2010Nuclear stress bodies (nSBs) are unique subnuclear organelles which form in response to heat shock. They are initiated through a direct interaction between heat shock... (Review)
Review
Nuclear stress bodies (nSBs) are unique subnuclear organelles which form in response to heat shock. They are initiated through a direct interaction between heat shock transcription factor 1 (HSF1) and pericentric tandem repeats of satellite III sequences and correspond to active transcription sites for noncoding satellite III transcripts. Given their unusual features, nSBs are distinct from other known transcription sites. In stressed cells, they are thought to participate in rapid, transient, and global reprogramming of gene expression through different types of mechanisms including chromatin remodeling and trapping of transcription and splicing factors. The analysis of these atypical and intriguing structures uncovers new facets of the relationship between nuclear organization and nuclear function.
Topics: Animals; DNA, Satellite; Intranuclear Space; Organelles; Stress, Physiological; Transcription, Genetic
PubMed: 20516127
DOI: 10.1101/cshperspect.a000695 -
American Journal of Human Genetics May 1979In reviewing the properties of heterochromatin and satellite DNA in man, it is clear that the human genome does not readily lend itself to experimental tests of the... (Comparative Study)
Comparative Study Review
In reviewing the properties of heterochromatin and satellite DNA in man, it is clear that the human genome does not readily lend itself to experimental tests of the postulated functions for satellite DNA. Since the spectrum of known structural properties of vertebrate and invertebrate satellite DNAs are broadly overlapping, an alternative avenue is to experimentally manipulate the heterochromatin of an organism, and then evaluate the generality of the results. When this is done in Drosophila melanogaster, the one organism where such an experimental approach is indeed possible, the results provide no support for most of the popular hypotheses concerning satellite DNA function. They do, however, reveal an important effect on the meiotic system, namely that the position of crossover events can be markedly altered in the presence of heterochromatin known to be rich in satellite DNAs. This effect is not peculiar to Drosophila, since supporting data are readily available from natural situations in both mammals and grasshoppers. In all such cases, the effects are most easily discernible where the heterochromatic blocks are substantial in size, and non-centric in location, situations which do not apply in man. The human system, however, offers other potentials. The ubiquity of naturally occurring heterochromatic polymorphisms, coupled with the extreme sensitivity of the human genome to perturbation, offers some scope for assessing the possible somatic effects of alterations in the amount of satellite DNA.
Topics: Animals; Chromosome Banding; Chromosomes, Human; Crossing Over, Genetic; DNA; DNA, Satellite; Drosophila melanogaster; Female; Grasshoppers; Heterochromatin; Humans; Male; Meiosis; Mice
PubMed: 111544
DOI: No ID Found -
Genes May 2019The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional... (Review)
Review
The central goal of medical genomics is to understand the inherited basis of sequence variation that underlies human physiology, evolution, and disease. Functional association studies currently ignore millions of bases that span each centromeric region and acrocentric short arm. These regions are enriched in long arrays of tandem repeats, or satellite DNAs, that are known to vary extensively in copy number and repeat structure in the human population. Satellite sequence variation in the human genome is often so large that it is detected cytogenetically, yet due to the lack of a reference assembly and informatics tools to measure this variability, contemporary high-resolution disease association studies are unable to detect causal variants in these regions. Nevertheless, recently uncovered associations between satellite DNA variation and human disease support that these regions present a substantial and biologically important fraction of human sequence variation. Therefore, there is a pressing and unmet need to detect and incorporate this uncharacterized sequence variation into broad studies of human evolution and medical genomics. Here I discuss the current knowledge of satellite DNA variation in the human genome, focusing on centromeric satellites and their potential implications for disease.
Topics: Centromere; DNA, Satellite; Genetic Predisposition to Disease; Genetic Variation; Genome, Human; Humans
PubMed: 31072070
DOI: 10.3390/genes10050352 -
International Journal of Molecular... Apr 2021(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on... (Review)
Review
(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.
Topics: DNA, Satellite; Evolution, Molecular; Genome, Human; Genomics; Humans; Sequence Analysis, DNA; Time Factors
PubMed: 33946766
DOI: 10.3390/ijms22094707 -
Chromosome Research : An International... Sep 2018Repetitive 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... (Review)
Review
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.
Topics: Animals; DNA, Satellite; Genome, Human; Humans; Kinetochores; RNA, Untranslated; Transcriptome
PubMed: 29974361
DOI: 10.1007/s10577-018-9582-3 -
Genes Mar 2023According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in... (Review)
Review
According to the established classical view, satellite DNAs are defined as abundant non-coding DNA sequences repeated in tandem that build long arrays located in heterochromatin. Advances in sequencing methodologies and development of specialized bioinformatics tools enabled defining a collection of all repetitive DNAs and satellite DNAs in a genome, the repeatome and the satellitome, respectively, as well as their reliable annotation on sequenced genomes. Supported by various non-model species included in recent studies, the patterns of satellite DNAs and satellitomes as a whole showed much more diversity and complexity than initially thought. Differences are not only in number and abundance of satellite DNAs but also in their distribution across the genome, array length, interspersion patterns, association with transposable elements, localization in heterochromatin and/or in euchromatin. In this review, we compare characteristic organizational features of satellite DNAs and satellitomes across different animal and plant species in order to summarize organizational forms and evolutionary processes that may lead to satellitomes' diversity and revisit some basic notions regarding repetitive DNA landscapes in genomes.
Topics: Animals; DNA, Satellite; Heterochromatin; Base Sequence; DNA Transposable Elements; Biological Evolution
PubMed: 36981013
DOI: 10.3390/genes14030742 -
Cells Dec 2021Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain...
Although the pericentromeric regions of chromosomes that are enriched in tandemly repeated satellite DNA represent a significant part of eukaryotic genomes, they remain understudied, which is mainly due to interdisciplinary knowledge gaps. Recent studies suggest their important role in genome regulation, karyotype stability, and evolution. Thus, the idea of satellite DNA as a junk part of the genome has been refuted. The integration of data regarding molecular composition, chromosome behaviour, and the details of the in situ organization of pericentromeric regions is of great interest. The objective of this work was a cytogenetic analysis of the interactions between pericentromeric regions from non-homologous chromosomes in mouse spermatocytes using immuno-FISH. We analysed two events: the associations between centromeric regions of the X chromosome and autosomes and the associations between the centromeric regions of the autosomal bivalents that form chromocenters. We concluded that the X chromosome forms temporary synaptic associations with different autosomes in early meiotic prophase I, which can normally be found until the pachytene-diplotene, without signs of pachytene arrest. These associations are formed between the satellite-DNA-rich centromeric regions of the X chromosome and different autosomes but do not involve the satellite-DNA-poor centromeric region of the Y chromosome. We suggest the hypothetical model of X chromosome competitive replacement from such associations during synaptic correction. We showed that the centromeric region of the X chromosome in association remains free of γH2Ax-dependent chromatin inactivation, while the Y chromosome is completely inactivated. This finding highlights the predominant role of associations between satellite DNA-rich regions of different chromosomes, including the X chromosome. We suppose that X-autosomal transient associations are a manifestation of an additional synaptic disorder checkpoint. These associations are normally corrected before the late diplotene stage. We revealed that the intense spreading conditions that were applied to the spermatocyte I nuclei did not lead to the destruction of stretched chromatin fibers of elongated chromocenters enriched in satellite DNA. The tight associations that we revealed between the pericentromeric regions of different autosomal bivalents and the X chromosome may represent the basis for a mechanism for maintaining the repeats stability in the autosomes and in the X chromosome. The consequences of our findings are discussed.
Topics: Animals; Centromere; Chromosomes, Mammalian; DNA; DNA, Satellite; Histones; Meiosis; Mice, Inbred BALB C; Mice, Inbred CBA; X Chromosome; Mice
PubMed: 34943883
DOI: 10.3390/cells10123375 -
Genes Apr 2022Subpolar and polar ecotypes of (Popl.) Roshev, (L.) P. Beauv, and E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants...
Subpolar and polar ecotypes of (Popl.) Roshev, (L.) P. Beauv, and E. Desv. are well adapted to stressful environmental conditions, which make them useful model plants for genetic research and breeding. For the first time, the comparative repeatome analyses of subpolar and polar , , and was performed using RepeatExplorer/TAREAN pipelines and FISH-based chromosomal mapping of the identified satellite DNA families (satDNAs). In the studied species, mobile genetic elements of class 1 made up the majority of their repetitive DNA; interspecific variations in the total amount of Ty3/Gypsy and Ty1/Copia retroelements, DNA transposons, ribosomal, and satellite DNA were revealed; 12-18 high confident and 7-9 low confident putative satDNAs were identified. According to BLAST, most satDNAs demonstrated sequence similarity with satDNAs of and indicating their common origin. Chromosomal mapping of 45S rDNA, 5S rDNA, and satDNAs of allowed us to construct the species karyograms and detect new molecular chromosome markers important for species. Our findings confirmed that genomes of and were more closely related compared to according to repeatome composition and patterns of satDNA chromosomal distribution.
Topics: Antarctic Regions; Chromosomes, Plant; DNA, Ribosomal; DNA, Satellite; Plant Breeding; Poaceae
PubMed: 35627148
DOI: 10.3390/genes13050762 -
Experimental Cell Research Sep 2020We are entering into an exciting era of genomics where truly complete, high-quality assemblies of human chromosomes are available end-to-end, or from... (Review)
Review
We are entering into an exciting era of genomics where truly complete, high-quality assemblies of human chromosomes are available end-to-end, or from 'telomere-to-telomere' (T2T). This technological advance offers a new opportunity to include endogenous human centromeric regions in high-resolution, sequence-based studies. These emerging reference maps are expected to reveal a new functional landscape in the human genome, where centromere proteins, transcriptional regulation, and spatial organization can be examined with base-level resolution across different stages of development and disease. Such studies will depend on innovative assembly methods of extremely long tandem repeats (ETRs), or satellite DNAs, paired with the development of new, orthogonal validation methods to ensure accuracy and completeness. This review reflects the progress in centromere genomics, credited by recent advancements in long-read sequencing and assembly methods. In doing so, I will discuss the challenges that remain and the promise for a new period of scientific discovery for satellite DNA biology and centromere function.
Topics: Centromere; DNA, Satellite; Genomics; Humans; Reproducibility of Results; Tandem Repeat Sequences; Telomere
PubMed: 32504677
DOI: 10.1016/j.yexcr.2020.112127