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

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 o...

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Autores principales:	Teresa Szczepińska, Ayatullah Faruk Mollah, Dariusz Plewczynski
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) QH301-705.5 Chemistry QD1-999
Acceso en línea:	https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a
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spelling	oai:doaj.org-article:c70eb61a3c904522890e72ffc4afbe2a2021-11-11T17:04:19ZGenomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows10.3390/ijms2221115911422-00671661-6596https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a2021-10-01T00:00:00Zhttps://www.mdpi.com/1422-0067/22/21/11591https://doaj.org/toc/1661-6596https://doaj.org/toc/1422-0067The 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.Teresa SzczepińskaAyatullah Faruk MollahDariusz PlewczynskiMDPI AGarticle3D genome structurechromatin compartmentsepigenetic modificationsopen chromatinH3K4me1H3K79me2Biology (General)QH301-705.5ChemistryQD1-999ENInternational Journal of Molecular Sciences, Vol 22, Iss 11591, p 11591 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) QH301-705.5 Chemistry QD1-999
spellingShingle	3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) QH301-705.5 Chemistry QD1-999 Teresa Szczepińska Ayatullah Faruk Mollah Dariusz Plewczynski Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
description	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.
format	article
author	Teresa Szczepińska Ayatullah Faruk Mollah Dariusz Plewczynski
author_facet	Teresa Szczepińska Ayatullah Faruk Mollah Dariusz Plewczynski
author_sort	Teresa Szczepińska
title	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
title_short	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
title_full	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
title_fullStr	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
title_full_unstemmed	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
title_sort	genomic marks associated with chromatin compartments in the ctcf, rnapii loop and genomic windows
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a
work_keys_str_mv	AT teresaszczepinska genomicmarksassociatedwithchromatincompartmentsinthectcfrnapiiloopandgenomicwindows AT ayatullahfarukmollah genomicmarksassociatedwithchromatincompartmentsinthectcfrnapiiloopandgenomicwindows AT dariuszplewczynski genomicmarksassociatedwithchromatincompartmentsinthectcfrnapiiloopandgenomicwindows
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Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

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