Specific patterns in correlations of super-short tandem repeats (SSTRs) with G+C content, genic and intergenic regions, and retrotransposons on all human chromosomes

• Verfasst von: Henn, Lukas [VerfasserIn]
• Verfasst von: Sievers, Aaron [VerfasserIn]
• Verfasst von: Hausmann, Michael [VerfasserIn]
• Verfasst von: Hildenbrand, Georg Lars [VerfasserIn]
• Titel: Specific patterns in correlations of super-short tandem repeats (SSTRs) with G+C content, genic and intergenic regions, and retrotransposons on all human chromosomes
• Verf.angabe: Lukas Henn, Aaron Sievers, Michael Hausmann and Georg Hildenbrand
• E-Jahr: 2024
• Jahr: Januar 2024
• Umfang: 14 S.
• Fussnoten: Online veröffentlicht: 25. Dezember 2023 ; Gesehen am 19.08.2024
• Titel Quelle: Enthalten in: Genes
• Ort Quelle: Basel : MDPI, 2009
• Jahr Quelle: 2024
• Band/Heft Quelle: 15(2024), 1, Artikel-ID 33, Seite 1-14
• ISSN Quelle: 2073-4425
• DOI: doi:10.3390/genes15010033
• Datenträger: Online-Ressource
• Sprache: eng
• Sach-SW: DNA
• Sach-SW: k-mer
• Sach-SW: SEQUENCE
• Sach-SW: tandem repeats
• Sach-SW: transposons
• K10plus-PPN: 1899127909

Abstract

The specific characteristics of k-mer words (2 <= k <= 11) regarding genomic distribution and evolutionary conservation were recently found. Among them are, in high abundance, words with a tandem repeat structure (repeat unit length of 1 bp to 3 bp). Furthermore, there seems to be a class of extremely short tandem repeats (<= 12 bp), so far overlooked, that are non-random-distributed and, therefore, may play a crucial role in the functioning of the genome. In the following article, the positional distributions of these motifs we call super-short tandem repeats (SSTRs) were compared to other functional elements, like genes and retrotransposons. We found length- and sequence-dependent correlations between the local SSTR density and G+C content, and also between the density of SSTRs and genes, as well as correlations with retrotransposon density. In addition to many general interesting relations, we found that SINE Alu has a strong influence on the local SSTR density. Moreover, the observed connection of SSTR patterns to pseudogenes and -exons might imply a special role of SSTRs in gene expression. In summary, our findings support the idea of a special role and the functional relevance of SSTRs in the genome.