Genome-scale portrait and evolutionary significance of human-specific core promoter tri- and tetranucleotide short tandem repeats

While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their...

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Bibliographic Details
Published in:	Human genomics Vol. 12; no. 1; p. 17
Main Authors:	Nazaripanah, N, Adelirad, F, Delbari, A, Sahaf, R, Abbasi-Asl, T, Ohadi, M
Format:	Journal Article
Language:	English
Published:	England BioMed Central 05-04-2018 BMC
Subjects:	Computational Biology Core promoter Evolution, Molecular Genome, Human - genetics Human-specific Humans Microsatellite Repeats - genetics Primary Research Promoter Regions, Genetic Short tandem repeat Species Specificity Tetranucleotide Trinucleotide Human-specific Tetranucleotide Core promoter Short tandem repeat Trinucleotide
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Summary:	While there is an ongoing trend to identify single nucleotide substitutions (SNSs) that are linked to inter/intra-species differences and disease phenotypes, short tandem repeats (STRs)/microsatellites may be of equal (if not more) importance in the above processes. Genes that contain STRs in their promoters have higher expression divergence compared to genes with fixed or no STRs in the gene promoters. In line with the above, recent reports indicate a role of repetitive sequences in the rise of young transcription start sites (TSSs) in human evolution. Following a comparative genomics study of all human protein-coding genes annotated in the GeneCards database, here we provide a genome-scale portrait of human-specific short- and medium-size (≥ 3-repeats) tri- and tetranucleotide STRs and STR motifs in the critical core promoter region between - 120 and + 1 to the TSS and evidence of skewing of this compartment in reference to the STRs that are not human-specific (Levene's test p < 0.001). Twenty-five percent and 26% enrichment of human-specific transcripts was detected in the tri and tetra human-specific compartments (mid-p < 0.00002 and mid-p < 0.002, respectively). Our findings provide the first evidence of genome-scale skewing of STRs at a specific region of the human genome and a link between a number of these STRs and TSS selection/transcript specificity. The STRs and genes listed here may have a role in the evolution and development of characteristics and phenotypes that are unique to the human species.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1479-7364 1473-9542 1479-7364
DOI:	10.1186/s40246-018-0149-3