Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site
- Autores
- Zambrano Siri, Romina T.; Beati, Maria Paula; Smircich, Pablo; Alonso, Guillermo Daniel; Ocampo, Josefina
- Año de publicación
- 2022
- Idioma
- inglés
- Tipo de recurso
- documento de conferencia
- Estado
- versión publicada
- Descripción
- Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, usually known as TriTryps, are the causal agents of animal and human sickness. TriTryps are characterized by having complex life cycles, alternating between a mammal host and an insect vector. One peculiarity of these organisms is that their genes are organized in long transcriptional units that give rise to polycistronic transcripts which maturate into mRNA by a process known as trans-splicing. Even though gene expression regulation occurs mainly post-transcriptionally, it has been recently shown that chromatin plays a role in modulation. In this work, we made a comparative analysis of genome-wide chromatin organization and its potential impact on gene expression for the parasite stage present in the insect vector for the TriTryps using MNase-seq and RNAse-seq data, publicly available or generated by our laboratory. To compare average nucleosome positioning and mRNA patterns, we predicted the most likely trans-splicing acceptor sites and used them as reference points to plot average nucleosome or RNA-seq signals. By representing MNase-seq data, we corroborated the presence of a mild nucleosome depleted region (NDR) around trans-splicing acceptor sites (TASs) in T. cruzi and L. major; but not in T. brucei, as previously reported. However, when analyzing H3 ChIP-seq data, we uphold that TAS protection in T. brucei is due to a non-histone complex instead of a well-position nucleosome, as previously claimed. Moreover, we showed that this nucleosome organization around TASs is not just an average, since the same layout is conserved in most of the genome. Furthermore, the strand-specific analysis revealed that the NDR is not exactly at the TAS but a few base pairs upstream of that point. We corroborated that this trough, is coincident with a footprint of DNA-RNA duplex, as previously observed.Additionally, it was previously shown that average nucleosome density around TAS correlates with average RNA-seq signals. To test how strong is that correlation, we performed gene clustering using k-means with either nucleosome occupancy or mRNA signals relative to TAS as predictor variables. From the MNase-seq clustering, we observed a homogenous distribution of average nucleosome density in the three organisms except for a subset of genes with unusually high nucleosome density in T. cruzi. As opposed, from RNA-seq analysis, we obtained well-defined gene clusters for the three organisms supported by high silhouette values. Particularly, we observed that there is a subset of genes with markedly high mRNA levels compared to the rest, but the correspondence between nucleosome density and mRNA signal is only partial. To have a better understanding of the role and conservation of those subsets of genes with unusual characteristics among TriTryps, we are currently performing GO and Metabolic pathway analysis.
Fil: Zambrano Siri, Romina T.. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Smircich, Pablo. Universidad de la República; Uruguay
Fil: Alonso, Guillermo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina
Fil: Ocampo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research
Mendoza
Argentina
Sociedad Argentina de Investigaciones en Bioquímica y Biología Molecular - Materia
-
CHOROMATIN ORGANIZATION
TRYPANOSOMATIDS
CHAGAS DISEASE
LEISHMANIASIS
SLEEPING SICKNESS - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/227698
Ver los metadatos del registro completo
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Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor siteZambrano Siri, Romina T.Beati, Maria PaulaSmircich, PabloAlonso, Guillermo DanielOcampo, JosefinaCHOROMATIN ORGANIZATIONTRYPANOSOMATIDSCHAGAS DISEASELEISHMANIASISSLEEPING SICKNESShttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, usually known as TriTryps, are the causal agents of animal and human sickness. TriTryps are characterized by having complex life cycles, alternating between a mammal host and an insect vector. One peculiarity of these organisms is that their genes are organized in long transcriptional units that give rise to polycistronic transcripts which maturate into mRNA by a process known as trans-splicing. Even though gene expression regulation occurs mainly post-transcriptionally, it has been recently shown that chromatin plays a role in modulation. In this work, we made a comparative analysis of genome-wide chromatin organization and its potential impact on gene expression for the parasite stage present in the insect vector for the TriTryps using MNase-seq and RNAse-seq data, publicly available or generated by our laboratory. To compare average nucleosome positioning and mRNA patterns, we predicted the most likely trans-splicing acceptor sites and used them as reference points to plot average nucleosome or RNA-seq signals. By representing MNase-seq data, we corroborated the presence of a mild nucleosome depleted region (NDR) around trans-splicing acceptor sites (TASs) in T. cruzi and L. major; but not in T. brucei, as previously reported. However, when analyzing H3 ChIP-seq data, we uphold that TAS protection in T. brucei is due to a non-histone complex instead of a well-position nucleosome, as previously claimed. Moreover, we showed that this nucleosome organization around TASs is not just an average, since the same layout is conserved in most of the genome. Furthermore, the strand-specific analysis revealed that the NDR is not exactly at the TAS but a few base pairs upstream of that point. We corroborated that this trough, is coincident with a footprint of DNA-RNA duplex, as previously observed.Additionally, it was previously shown that average nucleosome density around TAS correlates with average RNA-seq signals. To test how strong is that correlation, we performed gene clustering using k-means with either nucleosome occupancy or mRNA signals relative to TAS as predictor variables. From the MNase-seq clustering, we observed a homogenous distribution of average nucleosome density in the three organisms except for a subset of genes with unusually high nucleosome density in T. cruzi. As opposed, from RNA-seq analysis, we obtained well-defined gene clusters for the three organisms supported by high silhouette values. Particularly, we observed that there is a subset of genes with markedly high mRNA levels compared to the rest, but the correspondence between nucleosome density and mRNA signal is only partial. To have a better understanding of the role and conservation of those subsets of genes with unusual characteristics among TriTryps, we are currently performing GO and Metabolic pathway analysis.Fil: Zambrano Siri, Romina T.. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Smircich, Pablo. Universidad de la República; UruguayFil: Alonso, Guillermo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; ArgentinaFil: Ocampo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaLVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology ResearchMendozaArgentinaSociedad Argentina de Investigaciones en Bioquímica y Biología MolecularTech Science Press2022info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectReuniónJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/227698Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site; LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research; Mendoza; Argentina; 2022; 1-20327-95451667-5746CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.techscience.com/biocell/v47nSuppl.1/50703/pdfinfo:eu-repo/semantics/altIdentifier/url/https://saib.org.ar/archivos/biocell-47.pdfInternacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:52:36Zoai:ri.conicet.gov.ar:11336/227698instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:52:36.628CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
title |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
spellingShingle |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site Zambrano Siri, Romina T. CHOROMATIN ORGANIZATION TRYPANOSOMATIDS CHAGAS DISEASE LEISHMANIASIS SLEEPING SICKNESS |
title_short |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
title_full |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
title_fullStr |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
title_full_unstemmed |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
title_sort |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site |
dc.creator.none.fl_str_mv |
Zambrano Siri, Romina T. Beati, Maria Paula Smircich, Pablo Alonso, Guillermo Daniel Ocampo, Josefina |
author |
Zambrano Siri, Romina T. |
author_facet |
Zambrano Siri, Romina T. Beati, Maria Paula Smircich, Pablo Alonso, Guillermo Daniel Ocampo, Josefina |
author_role |
author |
author2 |
Beati, Maria Paula Smircich, Pablo Alonso, Guillermo Daniel Ocampo, Josefina |
author2_role |
author author author author |
dc.subject.none.fl_str_mv |
CHOROMATIN ORGANIZATION TRYPANOSOMATIDS CHAGAS DISEASE LEISHMANIASIS SLEEPING SICKNESS |
topic |
CHOROMATIN ORGANIZATION TRYPANOSOMATIDS CHAGAS DISEASE LEISHMANIASIS SLEEPING SICKNESS |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, usually known as TriTryps, are the causal agents of animal and human sickness. TriTryps are characterized by having complex life cycles, alternating between a mammal host and an insect vector. One peculiarity of these organisms is that their genes are organized in long transcriptional units that give rise to polycistronic transcripts which maturate into mRNA by a process known as trans-splicing. Even though gene expression regulation occurs mainly post-transcriptionally, it has been recently shown that chromatin plays a role in modulation. In this work, we made a comparative analysis of genome-wide chromatin organization and its potential impact on gene expression for the parasite stage present in the insect vector for the TriTryps using MNase-seq and RNAse-seq data, publicly available or generated by our laboratory. To compare average nucleosome positioning and mRNA patterns, we predicted the most likely trans-splicing acceptor sites and used them as reference points to plot average nucleosome or RNA-seq signals. By representing MNase-seq data, we corroborated the presence of a mild nucleosome depleted region (NDR) around trans-splicing acceptor sites (TASs) in T. cruzi and L. major; but not in T. brucei, as previously reported. However, when analyzing H3 ChIP-seq data, we uphold that TAS protection in T. brucei is due to a non-histone complex instead of a well-position nucleosome, as previously claimed. Moreover, we showed that this nucleosome organization around TASs is not just an average, since the same layout is conserved in most of the genome. Furthermore, the strand-specific analysis revealed that the NDR is not exactly at the TAS but a few base pairs upstream of that point. We corroborated that this trough, is coincident with a footprint of DNA-RNA duplex, as previously observed.Additionally, it was previously shown that average nucleosome density around TAS correlates with average RNA-seq signals. To test how strong is that correlation, we performed gene clustering using k-means with either nucleosome occupancy or mRNA signals relative to TAS as predictor variables. From the MNase-seq clustering, we observed a homogenous distribution of average nucleosome density in the three organisms except for a subset of genes with unusually high nucleosome density in T. cruzi. As opposed, from RNA-seq analysis, we obtained well-defined gene clusters for the three organisms supported by high silhouette values. Particularly, we observed that there is a subset of genes with markedly high mRNA levels compared to the rest, but the correspondence between nucleosome density and mRNA signal is only partial. To have a better understanding of the role and conservation of those subsets of genes with unusual characteristics among TriTryps, we are currently performing GO and Metabolic pathway analysis. Fil: Zambrano Siri, Romina T.. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina Fil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina Fil: Smircich, Pablo. Universidad de la República; Uruguay Fil: Alonso, Guillermo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentina Fil: Ocampo, Josefina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research Mendoza Argentina Sociedad Argentina de Investigaciones en Bioquímica y Biología Molecular |
description |
Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, usually known as TriTryps, are the causal agents of animal and human sickness. TriTryps are characterized by having complex life cycles, alternating between a mammal host and an insect vector. One peculiarity of these organisms is that their genes are organized in long transcriptional units that give rise to polycistronic transcripts which maturate into mRNA by a process known as trans-splicing. Even though gene expression regulation occurs mainly post-transcriptionally, it has been recently shown that chromatin plays a role in modulation. In this work, we made a comparative analysis of genome-wide chromatin organization and its potential impact on gene expression for the parasite stage present in the insect vector for the TriTryps using MNase-seq and RNAse-seq data, publicly available or generated by our laboratory. To compare average nucleosome positioning and mRNA patterns, we predicted the most likely trans-splicing acceptor sites and used them as reference points to plot average nucleosome or RNA-seq signals. By representing MNase-seq data, we corroborated the presence of a mild nucleosome depleted region (NDR) around trans-splicing acceptor sites (TASs) in T. cruzi and L. major; but not in T. brucei, as previously reported. However, when analyzing H3 ChIP-seq data, we uphold that TAS protection in T. brucei is due to a non-histone complex instead of a well-position nucleosome, as previously claimed. Moreover, we showed that this nucleosome organization around TASs is not just an average, since the same layout is conserved in most of the genome. Furthermore, the strand-specific analysis revealed that the NDR is not exactly at the TAS but a few base pairs upstream of that point. We corroborated that this trough, is coincident with a footprint of DNA-RNA duplex, as previously observed.Additionally, it was previously shown that average nucleosome density around TAS correlates with average RNA-seq signals. To test how strong is that correlation, we performed gene clustering using k-means with either nucleosome occupancy or mRNA signals relative to TAS as predictor variables. From the MNase-seq clustering, we observed a homogenous distribution of average nucleosome density in the three organisms except for a subset of genes with unusually high nucleosome density in T. cruzi. As opposed, from RNA-seq analysis, we obtained well-defined gene clusters for the three organisms supported by high silhouette values. Particularly, we observed that there is a subset of genes with markedly high mRNA levels compared to the rest, but the correspondence between nucleosome density and mRNA signal is only partial. To have a better understanding of the role and conservation of those subsets of genes with unusual characteristics among TriTryps, we are currently performing GO and Metabolic pathway analysis. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022 |
dc.type.none.fl_str_mv |
info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/conferenceObject Reunión Journal http://purl.org/coar/resource_type/c_5794 info:ar-repo/semantics/documentoDeConferencia |
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http://hdl.handle.net/11336/227698 Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site; LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research; Mendoza; Argentina; 2022; 1-2 0327-9545 1667-5746 CONICET Digital CONICET |
url |
http://hdl.handle.net/11336/227698 |
identifier_str_mv |
Contrasting study among Trypanosomatids reveals conserved chromatin organization around trans splicing-acceptor site; LVIII Annual Meeting of the Argentine Society for Biochemistry and Molecular Biology Research; Mendoza; Argentina; 2022; 1-2 0327-9545 1667-5746 CONICET Digital CONICET |
dc.language.none.fl_str_mv |
eng |
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eng |
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info:eu-repo/semantics/altIdentifier/url/https://www.techscience.com/biocell/v47nSuppl.1/50703/pdf info:eu-repo/semantics/altIdentifier/url/https://saib.org.ar/archivos/biocell-47.pdf |
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Tech Science Press |
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Tech Science Press |
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reponame:CONICET Digital (CONICET) instname:Consejo Nacional de Investigaciones Científicas y Técnicas |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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