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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Autor*in:	Teresa Szczepińska [verfasserIn] Ayatullah Faruk Mollah [verfasserIn] Dariusz Plewczynski [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2021

Schlagwörter:	3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2

Übergeordnetes Werk:	In: International Journal of Molecular Sciences - MDPI AG, 2003, 22(2021), 21, p 11591
Übergeordnetes Werk:	volume:22 ; year:2021 ; number:21, p 11591

Links:	Link aufrufen Link aufrufen Link aufrufen Journal toc Journal toc

DOI / URN:	10.3390/ijms222111591

Katalog-ID:	DOAJ075980126

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spelling	10.3390/ijms222111591 doi (DE-627)DOAJ075980126 (DE-599)DOAJc70eb61a3c904522890e72ffc4afbe2a DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Teresa Szczepińska verfasserin aut Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. 3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) Chemistry Ayatullah Faruk Mollah verfasserin aut Dariusz Plewczynski verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 21, p 11591 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:21, p 11591 https://doi.org/10.3390/ijms222111591 kostenfrei https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a kostenfrei https://www.mdpi.com/1422-0067/22/21/11591 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 21, p 11591
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allfieldsGer	10.3390/ijms222111591 doi (DE-627)DOAJ075980126 (DE-599)DOAJc70eb61a3c904522890e72ffc4afbe2a DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Teresa Szczepińska verfasserin aut Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. 3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) Chemistry Ayatullah Faruk Mollah verfasserin aut Dariusz Plewczynski verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 21, p 11591 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:21, p 11591 https://doi.org/10.3390/ijms222111591 kostenfrei https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a kostenfrei https://www.mdpi.com/1422-0067/22/21/11591 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 21, p 11591
allfieldsSound	10.3390/ijms222111591 doi (DE-627)DOAJ075980126 (DE-599)DOAJc70eb61a3c904522890e72ffc4afbe2a DE-627 ger DE-627 rakwb eng QH301-705.5 QD1-999 Teresa Szczepińska verfasserin aut Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows 2021 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier 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. 3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2 Biology (General) Chemistry Ayatullah Faruk Mollah verfasserin aut Dariusz Plewczynski verfasserin aut In International Journal of Molecular Sciences MDPI AG, 2003 22(2021), 21, p 11591 (DE-627)316340715 (DE-600)2019364-6 14220067 nnns volume:22 year:2021 number:21, p 11591 https://doi.org/10.3390/ijms222111591 kostenfrei https://doaj.org/article/c70eb61a3c904522890e72ffc4afbe2a kostenfrei https://www.mdpi.com/1422-0067/22/21/11591 kostenfrei https://doaj.org/toc/1661-6596 Journal toc kostenfrei https://doaj.org/toc/1422-0067 Journal toc kostenfrei GBV_USEFLAG_A SYSFLAG_A GBV_DOAJ GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 22 2021 21, p 11591
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callnumber-first	Q - Science
author	Teresa Szczepińska
spellingShingle	Teresa Szczepińska misc QH301-705.5 misc QD1-999 misc 3D genome structure misc chromatin compartments misc epigenetic modifications misc open chromatin misc H3K4me1 misc H3K79me2 misc Biology (General) misc Chemistry Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
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topic_title	QH301-705.5 QD1-999 Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows 3D genome structure chromatin compartments epigenetic modifications open chromatin H3K4me1 H3K79me2
topic	misc QH301-705.5 misc QD1-999 misc 3D genome structure misc chromatin compartments misc epigenetic modifications misc open chromatin misc H3K4me1 misc H3K79me2 misc Biology (General) misc Chemistry
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title	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
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title_full	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
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title_sort	genomic marks associated with chromatin compartments in the ctcf, rnapii loop and genomic windows
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title_auth	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
abstract	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.
abstractGer	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.
abstract_unstemmed	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.
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title_short	Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows
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Genomic Marks Associated with Chromatin Compartments in the CTCF, RNAPII Loop and Genomic Windows

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