Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization
This study explored the relationship between 3D genome organization and RNA–DNA triplex-forming sites of long noncoding RNAs (lncRNAs), a group of RNAs that do not code for proteins but are important factors regulating different aspects of genome activity. The triplex-forming sites of anti-sense car...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-06-01
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| Series: | Non-Coding RNA |
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| Online Access: | https://www.mdpi.com/2311-553X/8/3/41 |
| _version_ | 1827657895213268992 |
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| author | Benjamin Soibam |
| author_facet | Benjamin Soibam |
| author_sort | Benjamin Soibam |
| collection | DOAJ |
| description | This study explored the relationship between 3D genome organization and RNA–DNA triplex-forming sites of long noncoding RNAs (lncRNAs), a group of RNAs that do not code for proteins but are important factors regulating different aspects of genome activity. The triplex-forming sites of anti-sense cardiac lncRNA <i>GATA6-AS1</i> derived from DBD-Capture-Seq were examined and compared to modular features of 3D genome organization called topologically associated domains (TADs) obtained from Hi-C data. It was found that <i>GATA6-AS1</i> triplex-forming sites are positioned non-randomly in TADs and their boundaries. The triplex sites showed a preference for TAD boundaries over internal regions of TADs. Computational prediction analysis indicated that CTCF, the key protein involved in TAD specification, may interact with <i>GATA6-AS1</i>, and their binding sites correlate with each other. Examining locations of repeat elements in the genome suggests that the ability of lncRNA <i>GATA6-AS1</i> to form triplex sites with many genomic locations may be achieved by the rapid expansion of different repeat elements. Some of the triplex-forming sites were found to be positioned in regions that undergo dynamic chromatin organization events such as loss/gain of TAD boundaries during cardiac differentiation. These observed associations suggest that lncRNA–DNA triplex formation may contribute to the specification of TADs in 3D genome organization. |
| first_indexed | 2024-03-09T22:52:19Z |
| format | Article |
| id | doaj.art-6dd7f005a34948d1af40d22cc9d4f57f |
| institution | Directory Open Access Journal |
| issn | 2311-553X |
| language | English |
| last_indexed | 2024-03-09T22:52:19Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Non-Coding RNA |
| spelling | doaj.art-6dd7f005a34948d1af40d22cc9d4f57f2023-11-23T18:18:16ZengMDPI AGNon-Coding RNA2311-553X2022-06-01834110.3390/ncrna8030041Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin OrganizationBenjamin Soibam0Computer Science and Engineering Technology, University of Houston-Downtown, Houston, TX 77002, USAThis study explored the relationship between 3D genome organization and RNA–DNA triplex-forming sites of long noncoding RNAs (lncRNAs), a group of RNAs that do not code for proteins but are important factors regulating different aspects of genome activity. The triplex-forming sites of anti-sense cardiac lncRNA <i>GATA6-AS1</i> derived from DBD-Capture-Seq were examined and compared to modular features of 3D genome organization called topologically associated domains (TADs) obtained from Hi-C data. It was found that <i>GATA6-AS1</i> triplex-forming sites are positioned non-randomly in TADs and their boundaries. The triplex sites showed a preference for TAD boundaries over internal regions of TADs. Computational prediction analysis indicated that CTCF, the key protein involved in TAD specification, may interact with <i>GATA6-AS1</i>, and their binding sites correlate with each other. Examining locations of repeat elements in the genome suggests that the ability of lncRNA <i>GATA6-AS1</i> to form triplex sites with many genomic locations may be achieved by the rapid expansion of different repeat elements. Some of the triplex-forming sites were found to be positioned in regions that undergo dynamic chromatin organization events such as loss/gain of TAD boundaries during cardiac differentiation. These observed associations suggest that lncRNA–DNA triplex formation may contribute to the specification of TADs in 3D genome organization.https://www.mdpi.com/2311-553X/8/3/41<i>GATA6-AS1</i>CTCFtopologically associated domainsRNA–DNA triplex |
| spellingShingle | Benjamin Soibam Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization Non-Coding RNA <i>GATA6-AS1</i> CTCF topologically associated domains RNA–DNA triplex |
| title | Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization |
| title_full | Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization |
| title_fullStr | Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization |
| title_full_unstemmed | Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization |
| title_short | Association between Triplex-Forming Sites of Cardiac Long Noncoding RNA <i>GATA6-AS1</i> and Chromatin Organization |
| title_sort | association between triplex forming sites of cardiac long noncoding rna i gata6 as1 i and chromatin organization |
| topic | <i>GATA6-AS1</i> CTCF topologically associated domains RNA–DNA triplex |
| url | https://www.mdpi.com/2311-553X/8/3/41 |
| work_keys_str_mv | AT benjaminsoibam associationbetweentriplexformingsitesofcardiaclongnoncodingrnaigata6as1iandchromatinorganization |