Chromosome specificity of satellite DNAs: short- and long-range organization of a diverged dimeric subset of human alpha satellite from chromosome 3

Chromosoma ◽  
1989 ◽  
Vol 97 (6) ◽  
pp. 475-480 ◽  
Author(s):  
John S. Waye ◽  
Huntington F. Willard
Keyword(s):  
Long Range ◽  
Chromosome 3 ◽  
Alpha Satellite ◽  
Satellite Dnas

Human α-satellite DNAs are not susceptible to undercondensation after 5-azacytidine treatment

1994 ◽  
Vol 65 (1-2) ◽  
pp. 92-94 ◽  
Author(s):  
J.L Fernández ◽  
V. Goyanes ◽  
C. López-Femández ◽  
J. Gosálvez
Keyword(s):  
Alpha Satellite ◽  
Satellite Dnas

scholarly journals Cytogenetic Analysis of the Third Chromosome Heterochromatin of Drosophila melanogaster

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 509-517
Author(s):  
Dmitry E Koryakov ◽  
Igor F Zhimulev ◽  
Patrizio Dimitri
Keyword(s):  
Drosophila Melanogaster ◽  
Mitotic Chromosome ◽  
Essential Genes ◽  
Chromosome 3 ◽  
Cytogenetic Map ◽  
Satellite Dnas ◽  
Genetic Organization ◽  
The Third ◽  
Heterochromatic Genes ◽  
Insight Into

Abstract Previous cytological analysis of heterochromatic rearrangements has yielded significant insight into the location and genetic organization of genes mapping to the heterochromatin of chromosomes X, Y, and 2 of Drosophila melanogaster. These studies have greatly facilitated our understanding of the genetic organization of heterochromatic genes. In contrast, the 12 essential genes known to exist within the mitotic heterochromatin of chromosome 3 have remained only imprecisely mapped. As a further step toward establishing a complete map of the heterochomatic genetic functions in Drosophila, we have characterized several rearrangements of chromosome 3 by using banding techniques at the level of mitotic chromosome. Most of the rearrangement breakpoints were located in the dull fluorescent regions h49, h51, and h58, suggesting that these regions correspond to heterochromatic hotspots for rearrangements. We were able to construct a detailed cytogenetic map of chromosome 3 heterochromatin that includes all of the known vital genes. At least 7 genes of the left arm (from l(3)80Fd to l(3)80Fj) map to segment h49–h51, while the most distal genes (from l(3)80Fa to l(3)80Fc) lie within the h47–h49 portion. The two right arm essential genes, l(3)81Fa and l(3)81Fb, are both located within the distal h58 segment. Intriguingly, a major part of chromosome 3 heterochromatin was found to be “empty,” in that it did not contain either known genes or known satellite DNAs.

scholarly journals Rich polymorphic variants of alpha satellite 34mer higher order repeats in hg38 assembly of human chromosome Y

2019 ◽  
Author(s):  
Ines Vlahović ◽  
Matko Glunčić ◽  
Vladimir Paar
Keyword(s):  
Cell Division ◽  
Y Chromosome ◽  
Tandem Repeats ◽  
Genomic Sequence ◽  
Higher Order ◽  
Alpha Satellite ◽  
Satellite Dnas ◽  
Polymorphic Variants ◽  
Human Y Chromosome

AbstractA challenging problem in human population genetics is related to the unique role of human Y chromosome, with properties that distinguish humans from other species. Centromeres in primate genomes are constituted of tandem repeats of ∼ 171 bp alpha satellite monomers, commonly organized into higher order repats (HORs). Because of gaps in DNA sequencing, HOR regions as genomic “black holes” have been understudied in spite of crucial importance. Only recently the sequencing of more complete satellite DNAs becomes accessible. In human Y chromosome the largest alpha satellite higher order repeat unit 34/36mer was found, but its polymorphic variants were not investigated. Here, we study the human Y chromosome centromeric genomic sequence from hg38 assembly using our novel ALPHAsub algorithm for simple identification of alpha satellite arrays and robust GRM algorithm for HOR identification in repeat sequences. We determine the monomer alignment scheme for alpha satellite HOR array based on canonical 34mer HOR, discovering a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions.Author SummaryThe centromere is important for segregation of chromosomes during cell division in eukaryotes. Its destabilization results in chromosomal missegregation, aneuploidy, hallmarks of cancers and birth defects. In primate genomes centromeres contain tandem repeats of ∼ 171 bp alpha satellite DNA, commonly organized into higher order repeats (HORs). In this work, we used our bioinformatics algorithms to study the human Y chromosome centromeric genomic sequence and we discover a wealth of novel polymorphic variants which include the HOR-type monomer duplications, monomer deletions/insertions or rearrangements and non-HOR insertions. These results could help to understand the role of alpha satellites and alpha HOR structures in centromeric organization and function, in particular their role in creating a functional kinetochore that is crucial for chromosome segregation during cell division.

FOXL2 inactivation by a translocation 171 kb away: analysis of 500 kb of chromosome 3 for candidate long-range regulatory sequences

Genomics ◽  
2004 ◽  
Vol 83 (5) ◽  
pp. 757-764 ◽  
Author(s):  
Laura Crisponi ◽  
Manuela Uda ◽  
Manila Deiana ◽  
Angela Loi ◽  
Ramaiah Nagaraja ◽  
...  
Keyword(s):  
Long Range ◽  
Chromosome 3 ◽  
Regulatory Sequences

scholarly journals Heat Stress Affects H3K9me3 Level at Human Alpha Satellite DNA Repeats

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 663
Author(s):  
Isidoro Feliciello ◽  
Antonio Sermek ◽  
Željka Pezer ◽  
Maja Matulić ◽  
Đurđica Ugarković
Keyword(s):  
Heat Stress ◽  
Satellite Dna ◽  
Constitutive Heterochromatin ◽  
Dna Repeats ◽  
Alpha Satellite ◽  
Satellite Dnas ◽  
Alpha Satellite Dna ◽  
Expression Of Genes ◽  
Insertion Sites ◽  
H3k9me3 Level

Satellite DNAs are tandemly repeated sequences preferentially assembled into large arrays within constitutive heterochromatin and their transcription is often activated by stress conditions, particularly by heat stress. Bioinformatic analyses of sequenced genomes however reveal single repeats or short arrays of satellite DNAs dispersed in the vicinity of genes within euchromatin. Here, we analyze transcription of a major human alpha satellite DNA upon heat stress and follow the dynamics of “silent” H3K9me3 and “active” H3K4me2/3 histone marks at dispersed euchromatic and tandemly arranged heterochromatic alpha repeats. The results show H3K9me3 enrichment at alpha repeats upon heat stress, which correlates with the dynamics of alpha satellite DNA transcription activation, while no change in H3K4me2/3 level is detected. Spreading of H3K9me3 up to 1–2 kb from the insertion sites of the euchromatic alpha repeats is detected, revealing the alpha repeats as modulators of local chromatin structure. In addition, expression of genes containing alpha repeats within introns as well as of genes closest to the intergenic alpha repeats is downregulated upon heat stress. Further studies are necessary to reveal the possible contribution of H3K9me3 enriched alpha repeats, in particular those located within introns, to the silencing of their associated genes.

Alpha satellite DNAs on chromosomes 10 and 12 are both members of the dimeric suprachromosomal subfamily, but display little identity at the nucleotide sequence level

Genomics ◽  
1992 ◽  
Vol 13 (4) ◽  
pp. 1125-1132 ◽  
Author(s):  
L.H.J. Looijenga ◽  
J.W. Oosterhuis ◽  
V.T.H.B.M. Smit ◽  
J.W. Wessels ◽  
P. Mollevanger ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Alpha Satellite ◽  
Satellite Dnas ◽  
Nucleotide Sequence Level
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