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CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events
BACKGROUND: The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regio...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157658/ https://www.ncbi.nlm.nih.gov/pubmed/34039269 http://dx.doi.org/10.1186/s12859-021-04191-8 |
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author | Scala, Giovanni Federico, Antonio Greco, Dario |
author_facet | Scala, Giovanni Federico, Antonio Greco, Dario |
author_sort | Scala, Giovanni |
collection | PubMed |
description | BACKGROUND: The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regions has been shown to have a crucial role in the maintenance and establishment of methylation statuses. This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region. Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena. RESULTS: Here we present a novel computational strategy based on short DNA motif discovery in order to characterize sequence patterns related to aberrant CpG methylation events. We provide our framework as a user-friendly, shiny-based application, CpGmotifs, to easily retrieve and characterize DNA patterns related to CpG methylation in the human genome. Our tool supports the functional interpretation of deregulated methylation events by predicting transcription factors binding sites (TFBS) encompassing the identified motifs. CONCLUSIONS: CpGmotifs is an open source software. Its source code is available on GitHub https://github.com/Greco-Lab/CpGmotifs and a ready-to-use docker image is provided on DockerHub at https://hub.docker.com/r/grecolab/cpgmotifs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04191-8. |
format | Online Article Text |
id | pubmed-8157658 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-81576582021-05-28 CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events Scala, Giovanni Federico, Antonio Greco, Dario BMC Bioinformatics Software BACKGROUND: The investigation of molecular alterations associated with the conservation and variation of DNA methylation in eukaryotes is gaining interest in the biomedical research community. Among the different determinants of methylation stability, the DNA composition of the CpG surrounding regions has been shown to have a crucial role in the maintenance and establishment of methylation statuses. This aspect has been previously characterized in a quantitative manner by inspecting the nucleotidic composition in the region. Research in this field still lacks a qualitative perspective, linked to the identification of certain sequences (or DNA motifs) related to particular DNA methylation phenomena. RESULTS: Here we present a novel computational strategy based on short DNA motif discovery in order to characterize sequence patterns related to aberrant CpG methylation events. We provide our framework as a user-friendly, shiny-based application, CpGmotifs, to easily retrieve and characterize DNA patterns related to CpG methylation in the human genome. Our tool supports the functional interpretation of deregulated methylation events by predicting transcription factors binding sites (TFBS) encompassing the identified motifs. CONCLUSIONS: CpGmotifs is an open source software. Its source code is available on GitHub https://github.com/Greco-Lab/CpGmotifs and a ready-to-use docker image is provided on DockerHub at https://hub.docker.com/r/grecolab/cpgmotifs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-021-04191-8. BioMed Central 2021-05-26 /pmc/articles/PMC8157658/ /pubmed/34039269 http://dx.doi.org/10.1186/s12859-021-04191-8 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Software Scala, Giovanni Federico, Antonio Greco, Dario CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title | CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title_full | CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title_fullStr | CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title_full_unstemmed | CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title_short | CpGmotifs: a tool to discover DNA motifs associated to CpG methylation events |
title_sort | cpgmotifs: a tool to discover dna motifs associated to cpg methylation events |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8157658/ https://www.ncbi.nlm.nih.gov/pubmed/34039269 http://dx.doi.org/10.1186/s12859-021-04191-8 |
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