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 e...
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| Main Authors: | , , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
Januar 2024
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| In: |
Genes
Year: 2024, Volume: 15, Issue: 1, Pages: 1-14 |
| ISSN: | 2073-4425 |
| DOI: | 10.3390/genes15010033 |
| Online Access: | Resolving-System, kostenfrei, Volltext: https://doi.org/10.3390/genes15010033 Verlag, kostenfrei, Volltext: https://www.mdpi.com/2073-4425/15/1/33 
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| Author Notes: | Lukas Henn, Aaron Sievers, Michael Hausmann and Georg Hildenbrand |
| Summary: | 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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| Item Description: | Online veröffentlicht: 25. Dezember 2023 Gesehen am 19.08.2024 |
| Physical Description: | Online Resource |
| ISSN: | 2073-4425 |
| DOI: | 10.3390/genes15010033 |