Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera
| dc.contributor.advisor | Clara Isabel, Bermúdez Santana | |
| dc.contributor.author | Rodríguez Riascos, Yamile Andrea | |
| dc.contributor.editor | Reyes Bermúdez, Alejandro | |
| dc.contributor.researchgroup | Grupo de Investigación: RN´omica teórica y computacional | spa |
| dc.date.accessioned | 2023-08-31T16:44:23Z | |
| dc.date.available | 2023-08-31T16:44:23Z | |
| dc.date.issued | 2023 | |
| dc.description | ilustraciones, diagramas | spa |
| dc.description.abstract | Los ARN largos no codificantes (lncRNA) desempeñan funciones reguladoras en una amplia gama de procesos biológicos bien definidos como la regulación génica, la epigenética y el anda- miaje molecular. Sin embargo, para muchas especies de corales, la ausencia de un ensamblaje del genomas y transcriptomas completos, impide la identificación integral de los lncRNA. Gracias a los avances recientes en la tecnologı́a de secuenciación Existe nueva información en datos que respectan a genomas borrares y transcriptomas con niveles de ensamblajes que van hasta cromosomas, sentando las bases para la identificación y caracterización de lncRNA de su expresión en diversos tejidos. El objetivo de este estudio fue entender el papel de los lncRNA en la gastrulación de tres especies del género Acropora incluyendo datos de expre- sión de las fases del desarrollo de Acropora digitifera, Acropora tenuis y anotar los lncRNA resultantes en función de su potencial para la ortologı́a con lncRNA conocidos entre estas especies, además de validar por estructura conservada estas moléculas. Para dar respuesta a esta necesidad y usando el ensamblaje del transcriptoma de novo, se logro identificar 4.326 lncRNA potenciales con expresión diferencial para A. digitifera y 3.375 lncRNA en A. tenuis de los cuales detectaron lncRNAs sobreregulados y especie-especı́ficos para gástrula con un total de 56 en A. digitifera y 21 en A. tenuis, de de lncRNA de alta confianza, 25 se encuentran en homologı́a de secuencia en las dos especies mencinadas anteriormente y 74 tienen ortólogos entre las tres especies de Acropora. Además a estos lncRNA en términos de las relaciones de estabilidad termodinámica y conservación estructural, se detectaron 2258 estructuras, se las cuales se identificaron 56 estructuras en A. digitifera y 21 en A. tenuis que poseen expresión diferencial en la etapa de gástrula, pero que no están en ortologı́a y que son considerados especie-especı́ficos en esta etapa del desarrollo. En conjunto, este trabajo proporciona un recurso valioso para el estudio comparativo, funcional y estructural de los lncRNA lo que facilitarı́a la comprensión del papel de estas moléculas en procesos del desarrollo de corales. (Texto tomado de la fuente) | spa |
| dc.description.abstract | Long non-coding RNAs (lncRNAs) play regulatory roles in a wide range of well-defined bio- logical processes such as gene regulation, epigenetics, and molecular scaffolding. However, for many coral species, the absence of a complete genome and transcriptome assembly prevents the comprehensive identification of lncRNAs. Recent advances in sequencing technology re- veal new information data regarding deletion genomes and transcriptomes with assembly levels ranging up to chromosomes, laying the foundation for lncRNA identification and cha- racterization of their expression in various tissues. This study aimed to understand the role of lncRNAs in the gastrulation of three species of the Acropora genus including expression data from the developmental stages of Acropora digitifera, and Acropora tenuis and to anno- tate the resulting lncRNAs according to their potential for orthology with known lncRNAs among these species, in addition to validating by conserved structure these molecules. In response to this need and using de novo transcriptome assembly, we identified 4,326 diffe- rentially expressed potential lncRNAs for A. digitifera and 3,375 lncRNAs in A. tenuis of which we detected over-regulated and species-specific lncRNAs for gastrula with a total of 56 in A. digitifera and 21 in A. tenuis, of the high-confidence lncRNAs, 25 are in sequen- ce homology in the two species mentioned above and 74 have orthologs among the three Acropora species. In addition to these lncRNAs in terms of thermodynamic stability and structural conservation relationships, 2258 structures were detected, of which 56 structures were identified in A. digitifera and 21 inA. tenuis that possesses differential expression at the gastrula stage, but is not in ortholog and is considered species-specific at this stage of development. Taken together, this work provides a valuable resource for the comparative, functional, and structural study of lncRNAs that will facilitate understanding these mole- cules’ role in coral developmental processes. | eng |
| dc.description.degreelevel | Maestría | spa |
| dc.description.degreename | Magíster en Ciencias - Biología | spa |
| dc.description.researcharea | Genómica Comparativa | spa |
| dc.format.extent | xv, 80 páginas | spa |
| dc.format.mimetype | application/pdf | spa |
| dc.identifier.instname | Universidad Nacional de Colombia | spa |
| dc.identifier.reponame | Repositorio Institucional Universidad Nacional de Colombia | spa |
| dc.identifier.repourl | https://repositorio.unal.edu.co/ | spa |
| dc.identifier.uri | https://repositorio.unal.edu.co/handle/unal/84620 | |
| dc.language.iso | spa | spa |
| dc.publisher | Universidad Nacional de Colombia | spa |
| dc.publisher.branch | Universidad Nacional de Colombia - Sede Bogotá | spa |
| dc.publisher.faculty | Facultad de Ciencias | spa |
| dc.publisher.place | Bogotá, Colombia | spa |
| dc.publisher.program | Bogotá - Ciencias - Maestría en Ciencias - Biología | spa |
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| dc.relation.references | F. Li, Q. Zheng, P. Ryvkin, I. Dragomir, Y. Desai, S. Aiyer, O. Valladares, J. Yang, S. Bambina, L. R. Sabin, et al., “Global analysis of rna secondary structure in two metazoans,” Cell reports, vol. 1, no. 1, pp. 69–82, 2012. | spa |
| dc.relation.references | D. H. Mathews, D. H. Turner, and M. Zuker, “Rna secondary structure prediction,” Current protocols in nucleic acid chemistry, vol. 28, no. 1, pp. 11–2, 2007. | spa |
| dc.relation.references | K. A. Leamy, S. M. Assmann, D. H. Mathews, and P. C. Bevilacqua, “Bridging the gap between in vitro and in vivo rna folding,” Quarterly reviews of biophysics, vol. 49, p. e10, 2016. | spa |
| dc.rights.accessrights | info:eu-repo/semantics/openAccess | spa |
| dc.rights.license | Reconocimiento 4.0 Internacional | spa |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | spa |
| dc.subject.ddc | 570 - Biología | spa |
| dc.subject.decs | Antozoos | spa |
| dc.subject.decs | Anthozoa | eng |
| dc.subject.lemb | Corales | spa |
| dc.subject.proposal | LncRNA | spa |
| dc.subject.proposal | Transcriptoma | spa |
| dc.subject.proposal | Genómica comparativa | spa |
| dc.subject.proposal | Ortología | spa |
| dc.subject.proposal | Estructura secundaria conservada | spa |
| dc.title | Entendiendo el rol del lncRNA durante la gastrulación en las especies de acropora: A. tenuis y A. digitifera | spa |
| dc.title.translated | The role of lncRNA during gastrulation in Acropora species: A. tenuis and A. digitifera | eng |
| dc.type | Trabajo de grado - Maestría | spa |
| dc.type.coar | http://purl.org/coar/resource_type/c_bdcc | spa |
| dc.type.coarversion | http://purl.org/coar/version/c_ab4af688f83e57aa | spa |
| dc.type.content | DataPaper | spa |
| dc.type.driver | info:eu-repo/semantics/masterThesis | spa |
| dc.type.redcol | http://purl.org/redcol/resource_type/TM | spa |
| dc.type.version | info:eu-repo/semantics/acceptedVersion | spa |
| oaire.accessrights | http://purl.org/coar/access_right/c_abf2 | spa |
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