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Verfasst von:Hikmat, Wisam Mohammed [VerfasserIn]   i
 Sievers, Aaron [VerfasserIn]   i
 Hausmann, Michael [VerfasserIn]   i
 Hildenbrand, Georg Lars [VerfasserIn]   i
Titel:Peculiar k-mer spectra are correlated with 3D contact frequencies and breakpoint regions in the human genome
Verf.angabe:Wisam Mohammed Hikmat, Aaron Sievers, Michael Hausmann and Georg Hildenbrand
E-Jahr:2024
Jahr:25 September 2024
Umfang:17 S.
Illustrationen:Illustrationen
Fussnoten:Gesehen am 31.03.2025
Titel Quelle:Enthalten in: Genes
Ort Quelle:Basel : MDPI, 2009
Jahr Quelle:2024
Band/Heft Quelle:15(2024), 10, Artikel-ID 1247, Seite 1-17
ISSN Quelle:2073-4425
Abstract:Background: It is widely accepted that the 3D chromatin organization in human cell nuclei is not random and recent investigations point towards an interactive relation of epigenetic functioning and chromatin (re-)organization. Although chromatin organization seems to be the result of self-organization of the entirety of all molecules available in the cell nucleus, a general question remains open as to what extent chromatin organization might additionally be predetermined by the DNA sequence and, if so, if there are characteristic differences that distinguish typical regions involved in dysfunction-related aberrations from normal ones, since typical DNA breakpoint regions involved in disease-related chromosome aberrations are not randomly distributed along the DNA sequence. Methods: Highly conserved k-mer patterns in intronic and intergenic regions have been reported in eukaryotic genomes. In this article, we search and analyze regions deviating from average spectra (ReDFAS) of k-mer word frequencies in the human genome. This includes all assembled regions, e.g., telomeric, centromeric, genic as well as intergenic regions. Results: A positive correlation between k-mer spectra and 3D contact frequencies, obtained exemplarily from given Hi-C datasets, has been found indicating a relation of ReDFAS to chromatin organization and interactions. We also searched and found correlations of known functional annotations, e.g., genes correlating with ReDFAS. Selected regions known to contain typical breakpoints on chromosomes 9 and 5 that are involved in cancer-related chromosomal aberrations appear to be enriched in ReDFAS. Since transposable elements like ALUs are often assigned as major players in 3D genome organization, we also studied their impact on our examples but could not find a correlation between ALU regions and breakpoints comparable to ReDFAS. Conclusions: Our findings might show that ReDFAS are associated with instable regions of the genome and regions with many chromatin contacts which is in line with current research indicating that chromatin loop anchor points lead to genomic instability.
DOI:doi:10.3390/genes15101247
URL:Bitte beachten Sie: Dies ist ein Bibliographieeintrag. Ein Volltextzugriff für Mitglieder der Universität besteht hier nur, falls für die entsprechende Zeitschrift/den entsprechenden Sammelband ein Abonnement besteht oder es sich um einen OpenAccess-Titel handelt.

kostenfrei: Volltext: https://doi.org/10.3390/genes15101247
 kostenfrei: Volltext: https://www.mdpi.com/2073-4425/15/10/1247
 DOI: https://doi.org/10.3390/genes15101247
Datenträger:Online-Ressource
Sprache:eng
Sach-SW:<i>k</i>-mer
 3D genomics
 Hi-C
 sequence analysis
K10plus-PPN:1920845720
Verknüpfungen:→ Zeitschrift

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