Genome-wide analysis of Bkm sequences (GATA repeats): Predominant association with sex chromosomes and potential role in higher order chromatin organization and function

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 analyse the GATA repeats of human genome specifically, the Y chromosome, and other model organisms to understand the possible function and potential role they have in higher order chromatin organization.Our extensive analysis of GATA repeats in the prokaryotic and eukaryotic genomes, including human, 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. We report, for the first time, that this is not the case with perfect GATA repeats. The occurrence of GATA repeats increases as the length of the repeat increases from 6 tandem repeats onwards and peaks at (GATA)10-12. This has not been observed with any other closely related tetrameric simple repeats. Distribution of such longer GATA repeats along the chromosome and their close proximity to Matrix Associated Regions (GATA-MAR) may be demarking chromatin domains for a coordinated expression of genes residing in these domains. We further propose, based on the absence of GATA repeats in the newly recruited AZFc regions of the Y-chromosome, that these repeats may serve as a land mark in tracing the evolution of sex chromosomes. We suggest that unequal distribution of simple sequence repeats may have emerged during the course of evolution as a component of mechanism of regulating expression of genes located in the specific chromatin domains by modulating the higher order chromatin organization in response to specific signals.

Supplementary Figures and Data

Supplementary Figures 1 to 4: (Fig1, Fig2a, Fig2b, Fig2c, Fig3, Fig4 )

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