Abstract
BackgroundThough interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. Herein, totally 540 maps were established, which could clearly display SSR landscape in every bin of 1 k base pairs (Kbp) along the sequenced part of human reference Y-DNA (NC_000024.10), by our developed differential method for improving the existing method to reveal SSR distributional characteristics in large genomic sequences.ResultsThe maps show that SSRs accumulate significantly with forming density peaks in at least 2040 bins of 1 Kbp, which involve different coding, noncoding and intergenic regions of the Y-DNA, and 10 especially high density peaks were reported to associate with biological significances, suggesting that the other hundreds of especially high density peaks might also be biologically significant and worth further analyzing. In contrast, the maps also show that SSRs are extremely sparse in at least 207 bins of 1 Kbp, including many noncoding and intergenic regions of the Y-DNA, which is inconsistent with the widely accepted view that SSRs are mostly rich in these regions, and these sparse distributions are possibly due to powerfully regional selection. Additionally, many regions harbor SSR clusters with same or similar motif in the Y-DNA.ConclusionsThese 540 maps may provide the important information of clearly position-related SSR distributional features along the human reference Y-DNA for better understanding the genome structures of the Y-DNA. This study may contribute to further exploring the biological significance and distribution law of the huge numbers of SSRs in human Y-DNA.
Highlights
Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous Simple sequence repeat (SSR) in human Y-DNA at chromosomal level
The exact distributional features of the SSRs were investigated in the reference sequence of human Y-DNA (NC_000024.10), and this well reviewed Y-DNA is still incompletely sequenced with sequenced segments and gaps (Fig. 1a and Table S1)
The sizes of 55 sequenced segments are in range of 1604 ~ 8,533,670 bp, which can be grouped into large (≥100 k base pairs (Kbp)) and small (< 100 Kbp) size segments; the large sequenced segments are totally 25,805,216 bp representing about 97.65% of the sequenced part of the reference Y-DNA, and the other 45 small segments represent only 2.35% of the sequenced part (Fig. 1b and Table S1)
Summary
Though interest in human simple sequence repeats (SSRs) is increasing, little is known about the exact distributional features of numerous SSRs in human Y-DNA at chromosomal level. SSRs have been reported to nonrandomly occur in genomes and associate with different biological significances, which have been gradually recognized as important elements [2, 6, 7]. They have been discovered in both coding and noncoding regions with important roles in modifying morphological features [8], regulating gene expression [9], protecting sequence structures [7], acting as essential boundaries [10], modulating RNA structure and function [11], creating available variants to survive in the host [12] and contributing to genomic evolution [13]. Rough SSR distributional features have been investigated in human genome [18, 19], and the Genome Browser provides chance for surveying part of the elementary position of relatively longer SSRs in full human genome [20]
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