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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/227698

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spelling 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
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info:eu-repo/semantics/conferenceObject
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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
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