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K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells

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dc.abstract.enMaps of Hi-C contacts between promoters and enhancers can be analyzed as networks, with cis-regulatory regions as nodes and their interactions as edges. We checked if in the published promoter–enhancer network of mouse embryonic stem (ES) cells the differences in the node type (promoter or enhancer) and the node degree (number of regions interacting with a given promoter or enhancer) are reflected by sequence composition or sequence similarity of the interacting nodes. We used counts of all k-mers (k = 4) to analyze the sequence composition and the Euclidean distance between the k-mer count vectors (k-mer distance) as the measure of sequence (dis)similarity. The results we obtained with 4-mers are interpretable in terms of dinucleotides. Promoters are GC-rich as compared to enhancers, which is known. Enhancers are enriched in scaffold/matrix attachment regions (S/MARs) patterns and depleted of CpGs. Furthermore, we show that promoters are more similar to their interacting enhancers than vice-versa. Most notably, in both promoters and enhancers, the GC content and the CpG count increase with the node degree. As a consequence, enhancers of higher node degree become more similar to promoters, whereas higher degree promoters become less similar to enhancers. We confirmed the key results also for human keratinocytes.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorSzyman, Kinga
dc.contributor.authorDĄBROWSKI, MICHAŁ
dc.contributor.authorWilczyński, Bartosz
dc.date.accessioned2024-01-25T04:47:55Z
dc.date.available2024-01-25T04:47:55Z
dc.date.copyright2021-07-28
dc.date.issued2021
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.number15
dc.description.versionFINAL_PUBLISHED
dc.description.volume22
dc.identifier.doi10.3390/IJMS22158067
dc.identifier.issn1422-0067
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/110407
dc.identifier.weblinkhttps://www.mdpi.com/1422-0067/22/15/8067/pdf
dc.languageeng
dc.pbn.affiliationcomputer and information sciences
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.relation.pages8067:1-15
dc.rightsCC-BY
dc.sciencecloudnosend
dc.subject.enHi-C
dc.subject.en4-mer
dc.subject.endinucleotide
dc.subject.enCpG
dc.subject.enS/MAR
dc.subject.enembryonic stem cell
dc.titleK-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
dc.typeJournalArticle
dspace.entity.typePublication