Specific Patterns in Correlations of Super-Short Tandem Repeats (SSTRs) with G+C Content, Genic and Intergenic Regions, and Retrotransposons on All Human Chromosomes

  • 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.

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Metadaten
Author:Lukas Henn, Aaron Sievers, Michael HausmannORCiD, Georg HildenbrandORCiD
DOI:https://doi.org/https://doi.org/10.3390/genes15010033
ISSN:2073-4425
Parent Title (English):Genes
Publisher:MDPI AG
Document Type:Article
Language:English
Year of Completion:2023
Release Date:2024/11/14
GND Keyword:Genom; Genexpression
Volume:15
Issue:1
Article Number:33
Institutes:Fakultät Ingenieurwissenschaften und Informatik / Studiengänge / Medical Engineering and Data Science (Bachelor)
Research Focuses / Research Horizons:Intelligent Systems / Artifical Intelligence and Data Science
Materials / Material Testing & Sensor Technology
Reviewed:ja
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