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Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

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cris.lastimport.scopus2024-02-12T20:19:34Z
dc.abstract.en<jats:p>The nature of genome organization into two basic structural compartments is as yet undiscovered. However, it has been indicated to be a mechanism of gene expression regulation. Using the classification approach, we ranked genomic marks that hint at compartmentalization. We considered a broad range of marks, including GC content, histone modifications, DNA binding proteins, open chromatin, transcription and genome regulatory segmentation in GM12878 cells. Genomic marks were defined over CTCF or RNAPII loops, which are basic elements of genome 3D structure, and over 100 kb genomic windows. Experiments were carried out to empirically assess the whole set of features, as well as the individual features in classification of loops/windows, into compartment A or B. Using Monte Carlo Feature Selection and Analysis of Variance, we constructed a ranking of feature importance for classification. The best simple indicator of compartmentalization is DNase-seq open chromatin measurement for CTCF loops, H3K4me1 for RNAPII loops and H3K79me2 for genomic windows. Among DNA binding proteins, this is RUNX3 transcription factor for loops and RNAPII for genomic windows. Chromatin state prediction methods that indicate active elements like promoters, enhancers or heterochromatin enhance the prediction of loop segregation into compartments. However, H3K9me3, H4K20me1, H3K27me3 histone modifications and GC content poorly indicate compartments.</jats:p>
dc.affiliationUniwersytet Warszawski
dc.contributor.authorSzczepińska, Teresa
dc.contributor.authorMollah, Ayatullah Faruk
dc.contributor.authorPlewczyński, Dariusz
dc.date.accessioned2024-01-25T02:05:40Z
dc.date.available2024-01-25T02:05:40Z
dc.date.issued2021
dc.description.financePublikacja bezkosztowa
dc.description.number21
dc.description.volume22
dc.identifier.doi10.3390/IJMS222111591
dc.identifier.issn1422-0067
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/107849
dc.identifier.weblinkhttps://www.mdpi.com/1422-0067/22/21/11591
dc.languageeng
dc.relation.ispartofInternational Journal of Molecular Sciences
dc.relation.pages11591
dc.rightsClosedAccess
dc.sciencecloudnosend
dc.titleGenomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
dc.typeJournalArticle
dspace.entity.typePublication