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

Autor
Szyman, Kinga
DĄBROWSKI, MICHAŁ
Wilczyński, Bartosz
Data publikacji
2021
Abstrakt (EN)

Maps 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.

Słowa kluczowe EN
Hi-C
4-mer
dinucleotide
CpG
S/MAR
embryonic stem cell
Dyscyplina PBN
informatyka
Czasopismo
International Journal of Molecular Sciences
Tom
22
Zeszyt
15
Strony od-do
8067:1-15
ISSN
1422-0067
Data udostępnienia w otwartym dostępie
2021-07-28
Licencja otwartego dostępu
Uznanie autorstwa