Document Detail


Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function.
MedLine Citation:
PMID:  12691979     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: Bkm (Banded krait minor) satellite DNA sequences (GATA repeats) have been shown to be associated with the sex determining chromosomes of various eukaryotes and have been implicated in the evolution and differentiation of sex chromosomes in snakes. The objective of the study is to analyze the GATA repeats of human genome specifically, the Y-chromosome, and other model organisms to understand the possible function and potential role in higher order chromatin organization.
RESULTS: Our extensive analysis of GATA repeats in the prokaryotic and eukaryotic genomes, which have been completely sequenced so far, has revealed that GATA repeats are absent in prokaryotes and have been gradually accumulated in higher organisms during the course of evolution. In human, the Y-chromosome has the highest GATA repeat density, which predominantly exists in the Yq centromeric region. Generally, occurrence of repeats in the genomes decreases steadily as the length of the repeat increases. In contrast, we report, that the occurrence of GATA repeats increases as the length of the repeat increases from six tandem repeats onwards and peaks at (GATA)(10-12). This has not been observed with any other simple repeat. Distribution of (GATA)(10-12) along the chromosome and their close proximity to Matrix Associated Regions (GATA-MAR) suggests that it may be demarking chromatin domains for a coordinated expression of genes residing in these domains.
Authors:
Subbaya Subramanian; Rakesh K Mishra; Lalji Singh
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Publication Detail:
Type:  Comparative Study; Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  19     ISSN:  1367-4803     ISO Abbreviation:  Bioinformatics     Publication Date:  2003 Apr 
Date Detail:
Created Date:  2003-04-14     Completed Date:  2003-12-16     Revised Date:  2013-05-20    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  681-5     Citation Subset:  IM    
Affiliation:
Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India.
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MeSH Terms
Descriptor/Qualifier:
Animals
Base Sequence
Biological Evolution*
Bungarus / genetics*
Chromatin / genetics*
Chromosomes, Human, Y / genetics
Gene Expression Regulation / genetics
Genome, Human*
Humans
Microsatellite Repeats / genetics*
Molecular Sequence Data
Sequence Alignment / methods*
Sequence Analysis, DNA / methods
Tandem Repeat Sequences / genetics
Y Chromosome / genetics*
Chemical
Reg. No./Substance:
0/Chromatin

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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