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

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)...

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Autores principales: Szyman, Kinga, Wilczyński, Bartek, Dąbrowski, Michał
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347099/
https://www.ncbi.nlm.nih.gov/pubmed/34360860
http://dx.doi.org/10.3390/ijms22158067
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author Szyman, Kinga
Wilczyński, Bartek
Dąbrowski, Michał
author_facet Szyman, Kinga
Wilczyński, Bartek
Dąbrowski, Michał
author_sort Szyman, Kinga
collection PubMed
description 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.
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spelling pubmed-83470992021-08-08 K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells Szyman, Kinga Wilczyński, Bartek Dąbrowski, Michał Int J Mol Sci Article 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. MDPI 2021-07-28 /pmc/articles/PMC8347099/ /pubmed/34360860 http://dx.doi.org/10.3390/ijms22158067 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Szyman, Kinga
Wilczyński, Bartek
Dąbrowski, Michał
K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title_full K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title_fullStr K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title_full_unstemmed K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title_short K-mer Content Changes with Node Degree in Promoter–Enhancer Network of Mouse ES Cells
title_sort k-mer content changes with node degree in promoter–enhancer network of mouse es cells
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8347099/
https://www.ncbi.nlm.nih.gov/pubmed/34360860
http://dx.doi.org/10.3390/ijms22158067
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