CpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genome

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dc.contributor.authorBartas, Martincs
dc.contributor.authorPetrovič, Michalcs
dc.contributor.authorBrázda, Václavcs
dc.contributor.authorTrenz, Oldřichcs
dc.contributor.authorĎurčanský, Alešcs
dc.contributor.authorŠťastný, Jiřícs
dc.coverage.issue6cs
dc.coverage.volume301cs
dc.date.accessioned2025-07-17T08:59:31Z
dc.date.available2025-07-17T08:59:31Z
dc.date.issued2025-05-21cs
dc.description.abstractWith continuous advances in DNA sequencing methods, accessibility to high-quality genomic information for all living organisms is ever-increasing. However, to interpret this information effectively and formulate hypotheses, users often require higher level programming skills. Therefore, the generation of web-based tools is becoming increasingly popular. CpG island regions in genomes are often found in gene promoters and are prone to DNA methylation, with their methylation status determining if a gene is expressed. Notably, understanding the biological impact of CpX modifications on genomic regulation is becoming increasingly important as these modifications have been associated with diseases such as cancer and neurodegeneration. However, there is currently no easy-to-use, scalable tool to detect and quantify CpX islands in full genomes. We have developed a Java-based web server for CpX island analyses that benefits from the DNA Analyzer Web server environment and overcomes several limitations. For a pilot demonstration study, we selected a well-described model organism Drosophila melanogaster. Subsequent analysis of the obtained CpX islands revealed several interesting and previously undescribed phenomena. One of them is the fact, that nearly half of long CpG islands were located on chromosome X, and that long CpA and CpT islands were significantly overrepresented at the subcentromeric regions of autosomes (chr2 and chr3) and also on chromosome Y. Wide genome overlays of predicted CpX islands revealed their co-occurrence with various (epi)genomics features comprising cytosine methylations, accessible chromatin, transposable elements, or binding of transcription factors and other proteins. CpX Hunter is freely available as a web tool at: https://bioinformatics.ibp.cz/ #/analyse/cpg.en
dc.formattextcs
dc.format.extent1-11cs
dc.format.mimetypeapplication/pdfcs
dc.identifier.citationJOURNAL OF BIOLOGICAL CHEMISTRY. 2025, vol. 301, issue 6, p. 1-11.en
dc.identifier.doi10.1016/j.jbc.2025.108537cs
dc.identifier.issn0021-9258cs
dc.identifier.orcid0000-0003-2837-4226cs
dc.identifier.orcid0000-0003-3724-6357cs
dc.identifier.other197952cs
dc.identifier.researcheridF-9582-2011cs
dc.identifier.researcheridF-8025-2012cs
dc.identifier.scopus57191582635cs
dc.identifier.urihttps://hdl.handle.net/11012/255190
dc.language.isoencs
dc.publisherElseviercs
dc.relation.ispartofJOURNAL OF BIOLOGICAL CHEMISTRYcs
dc.relation.urihttps://www.sciencedirect.com/science/article/pii/S0021925825003862?via%3Dihubcs
dc.rightsCreative Commons Attribution 4.0 Internationalcs
dc.rights.accessopenAccesscs
dc.rights.sherpahttp://www.sherpa.ac.uk/romeo/issn/0021-9258/cs
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/cs
dc.subjectCpA islandsen
dc.subjectCpG islandsen
dc.subjectCpT islandsen
dc.subjectdinucleotideen
dc.subjectDrosophilaen
dc.subjectgenome analysesen
dc.subjectweb serveren
dc.titleCpX Hunter web tool allows high-throughput identification of CpG, CpA, CpT, and CpC islands: A case study in Drosophila genomeen
dc.type.driverarticleen
dc.type.statusPeer-revieweden
dc.type.versionpublishedVersionen
sync.item.dbidVAV-197952en
sync.item.dbtypeVAVen
sync.item.insts2025.07.17 10:59:31en
sync.item.modts2025.07.17 10:33:58en
thesis.grantorVysoké učení technické v Brně. Fakulta strojního inženýrství. Ústav automatizace a informatikycs
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