The short-sequence design of DNA and its involvement in the 3-D structure of the genome
Recent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of ol...
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| Drugi avtorji: | , , |
| Format: | article |
| Jezik: | angleščina |
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2018
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| Online dostop: | https://hdl.handle.net/20.500.12008/22004 |
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Brez oznak, prvi označite!
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| _version_ | 1868890185330065408 |
|---|---|
| author | Lamolle, Guillermo |
| author2 | Sabbia Carriquiry, Victor Manuel Musto, Héctor Bernardi, Giorgio |
| author2_role | author author author |
| author_browse | Bernardi, Giorgio Lamolle, Guillermo Musto, Héctor Sabbia Carriquiry, Victor Manuel |
| author_facet | Lamolle, Guillermo Sabbia Carriquiry, Victor Manuel Musto, Héctor Bernardi, Giorgio |
| author_role | author |
| collection | COLIBRI |
| dc.contributor.none.fl_str_mv | Lamolle, Guillermo. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología Sabbia, Victor. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología Musto, Héctor. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología. |
| dc.creator.none.fl_str_mv | Lamolle, Guillermo Sabbia Carriquiry, Victor Manuel Musto, Héctor Bernardi, Giorgio |
| dc.date.none.fl_str_mv | 2018 2019-10-02T22:08:23Z 2019-10-02T22:08:23Z 20190930 |
| dc.format.none.fl_str_mv | application/pdf |
| dc.identifier.none.fl_str_mv | Lamolle, G., et al. The short-sequence design of DNA and its involvement in the 3-D structure of the genome. Scientific Reports, 2018, 8, art nro. 17820. doi: 10.1038/s41598-018-35864-9 2045-2322 https://hdl.handle.net/20.500.12008/22004 10.1038/s41598-018-35864-9 |
| dc.language.none.fl_str_mv | en eng |
| dc.publisher.none.fl_str_mv | Nature Publishing Group |
| dc.relation.none.fl_str_mv | Scientific Reports, 2018, 8, art. no. 17820 |
| dc.rights.none.fl_str_mv | info:eu-repo/semantics/openAccess Licencia Creative Commons Atribución (CC –BY 4.0) |
| dc.source.none.fl_str_mv | reponame:COLIBRI instname:Universidad de la República instacron:Universidad de la República |
| dc.subject.none.fl_str_mv | Isochores Chromosome 21 Chromatin domains |
| dc.title.none.fl_str_mv | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| dc.type.none.fl_str_mv | Artículo info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion |
| description | Recent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of oligo-Adenines that are intrinsically stiff, curved and unfavorable for nucleosome binding. This leads to a structure of the corresponding chromatin domains, the Lamina Associated Domains, or LADs, which is well suited for interaction with the lamina. In contrast, the high-heterogeneity GC-rich isochores are in the form of compositional peaks and valleys characterized by increasing gradients of oligo-Guanines in the peaks and oligo-Adenines in the valleys that lead to increasing nucleosome depletions in the corresponding chromatin domains, the Topological Associating Domains, or TADs. These results encouraged us to investigate in detail the di- and tri-nucleotide profiles of 100 Kb segments of chromosome 21, as well as those of the di- to octa-Adenines and di- to octa-Guanines in some representative regions of the chromosome. The results obtained show that the 3-D structures of isochores and chromatin domains depend not only upon oligo-Adenines and oligo-Guanines but also, to a lower but definite extent, upon the majority of di- and tri-nucleotides. This conclusion has strong implications for the biological role of non-coding sequences. |
| eu_rights_str_mv | openAccess |
| format | article |
| id | anni_c2b95ec237eb294606505bbfeaeff8e5 |
| identifier_str_mv | Lamolle, G., et al. The short-sequence design of DNA and its involvement in the 3-D structure of the genome. Scientific Reports, 2018, 8, art nro. 17820. doi: 10.1038/s41598-018-35864-9 2045-2322 10.1038/s41598-018-35864-9 |
| instacron_str | Universidad de la República |
| institution | Universidad de la República |
| instname_str | Universidad de la República |
| language | eng |
| language_invalid_str_mv | en |
| network_acronym_str | anni |
| network_name_str | oai-lr-anni |
| oai_identifier_str | oai:colibri.udelar.edu.uy:20.500.12008/22004 |
| publishDate | 2018 |
| publishDateSort | 2018 |
| publisher.none.fl_str_mv | Nature Publishing Group |
| reponame_str | COLIBRI |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | Licencia Creative Commons Atribución (CC –BY 4.0) |
| spelling | The short-sequence design of DNA and its involvement in the 3-D structure of the genomeLamolle, GuillermoSabbia Carriquiry, Victor ManuelMusto, HéctorBernardi, GiorgioIsochoresChromosome 21Chromatin domainsRecent investigations have shown that isochores are characterized by a 3-D structure which is primarily responsible for the topology of chromatin domains. More precisely, an analysis of human chromosome 21 demonstrated that low-heterogeneity, GC-poor isochores are characterized by the presence of oligo-Adenines that are intrinsically stiff, curved and unfavorable for nucleosome binding. This leads to a structure of the corresponding chromatin domains, the Lamina Associated Domains, or LADs, which is well suited for interaction with the lamina. In contrast, the high-heterogeneity GC-rich isochores are in the form of compositional peaks and valleys characterized by increasing gradients of oligo-Guanines in the peaks and oligo-Adenines in the valleys that lead to increasing nucleosome depletions in the corresponding chromatin domains, the Topological Associating Domains, or TADs. These results encouraged us to investigate in detail the di- and tri-nucleotide profiles of 100 Kb segments of chromosome 21, as well as those of the di- to octa-Adenines and di- to octa-Guanines in some representative regions of the chromosome. The results obtained show that the 3-D structures of isochores and chromatin domains depend not only upon oligo-Adenines and oligo-Guanines but also, to a lower but definite extent, upon the majority of di- and tri-nucleotides. This conclusion has strong implications for the biological role of non-coding sequences.Nature Publishing GroupLamolle, Guillermo. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de BiologíaSabbia, Victor. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de BiologíaMusto, Héctor. Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.2019-10-02T22:08:23Z2019-10-02T22:08:23Z201820190930Artículoinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfLamolle, G., et al. The short-sequence design of DNA and its involvement in the 3-D structure of the genome. Scientific Reports, 2018, 8, art nro. 17820. doi: 10.1038/s41598-018-35864-92045-2322https://hdl.handle.net/20.500.12008/2200410.1038/s41598-018-35864-9reponame:COLIBRIinstname:Universidad de la Repúblicainstacron:Universidad de la RepúblicaenengScientific Reports, 2018, 8, art. no. 17820Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad De La República. (Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. Nº 16 de C.D.C. de 07/10/2014)info:eu-repo/semantics/openAccessLicencia Creative Commons Atribución (CC –BY 4.0)oai:colibri.udelar.edu.uy:20.500.12008/220042026-04-14T10:09:14Z |
| spellingShingle | The short-sequence design of DNA and its involvement in the 3-D structure of the genome Lamolle, Guillermo Isochores Chromosome 21 Chromatin domains |
| status_str | publishedVersion |
| title | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| title_full | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| title_fullStr | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| title_full_unstemmed | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| title_short | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| title_sort | The short-sequence design of DNA and its involvement in the 3-D structure of the genome |
| topic | Isochores Chromosome 21 Chromatin domains |
| url | https://hdl.handle.net/20.500.12008/22004 |