Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site

Autores
Zambrano Siri, Romina Trinidad; Beati, Maria Paula; Smircich, Pablo; Alonso, Guillermo Daniel; Ocampo, Josefina
Año de publicación
2024
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, and are characterized by having complex life cycles, alternating between a mammal host and an insect vector. 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. Here, we have analyzed the genome-wide chromatin organization for the parasite stage present in the insect vector by chromatin digestion with micrococcal nuclease followed by deep sequencing (MNase-seq) using our own data for T. cruzi and public data for T. brucei and L. major. We have predicted the most likely trans-splicing acceptor sites (TAS) and used them as reference points for genomic analysis. We have made a comparative analysis among TriTryps for comparable extensions of MNase digestion. By representing average nucleosome occupancy, we found that the average chromatin organization is very similar between T. cruzi and T. brucei with a mild nucleosome depletion at the TAS. This depletion at the TAS is also conserved in L. major even for less digested samples. A detailed examination of nucleosome landscapes resulting from different levels of digestion shows that an MNase-sensitive complex is protecting the trans-splicing acceptor site in Trypanosoma brucei. Additionally, by analyzing MNase-ChIP-seq data for histone H3 we uphold that the average MNase protection observed at the TAS for earlier digestion points in T. brucei is mainly due to a non-histone complex, underlining the conserved nucleosome depletion at that genomic point in TriTryps. Moreover, we show that this nucleosome organization is not just an average since the same layout is observed in most of the genome. Furthermore, in T. brucei the nucleosome trough observed at TAS colocalizes with a footprint of DNA-RNA duplex. Here, we show that this reciprocity is not only an average but is conserved in the whole genome and there is a correlation between the intensity of the R-loop signal and the TAS protection from MNase. We are currently making a detailed analysis of the genomic regions that present a faster release of the protective complex observed at the TAS in response to the enzymatic digestion and its relationship with their genomic locations epigenetic marks and DNA accessibility, in T. brucei.A deeper analysis of the chromatin organization and the interacting complexes at TAS might open the road for a better understanding on the processing of the polycistronic transcripts into the mature ARNs.
Fil: Zambrano Siri, Romina Trinidad. 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. Instituto de Investigaciones Biológicas "Clemente Estable"; 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
XXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de Protozoología
Ciudad Autónoma de Buenos Aires
Argentina
Federación Latinoamericana de Parasitología
Sociedad Argentina de Protozoología
Materia
TRYPANOSOMATIDS
NUCLEOSOMES
CHROMATIN
TRANS SPLICING
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:11336/275093
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/275093
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor siteZambrano Siri, Romina TrinidadBeati, Maria PaulaSmircich, PabloAlonso, Guillermo DanielOcampo, JosefinaTRYPANOSOMATIDSNUCLEOSOMESCHROMATINTRANS SPLICINGhttps://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, and are characterized by having complex life cycles, alternating between a mammal host and an insect vector. 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. Here, we have analyzed the genome-wide chromatin organization for the parasite stage present in the insect vector by chromatin digestion with micrococcal nuclease followed by deep sequencing (MNase-seq) using our own data for T. cruzi and public data for T. brucei and L. major. We have predicted the most likely trans-splicing acceptor sites (TAS) and used them as reference points for genomic analysis. We have made a comparative analysis among TriTryps for comparable extensions of MNase digestion. By representing average nucleosome occupancy, we found that the average chromatin organization is very similar between T. cruzi and T. brucei with a mild nucleosome depletion at the TAS. This depletion at the TAS is also conserved in L. major even for less digested samples. A detailed examination of nucleosome landscapes resulting from different levels of digestion shows that an MNase-sensitive complex is protecting the trans-splicing acceptor site in Trypanosoma brucei. Additionally, by analyzing MNase-ChIP-seq data for histone H3 we uphold that the average MNase protection observed at the TAS for earlier digestion points in T. brucei is mainly due to a non-histone complex, underlining the conserved nucleosome depletion at that genomic point in TriTryps. Moreover, we show that this nucleosome organization is not just an average since the same layout is observed in most of the genome. Furthermore, in T. brucei the nucleosome trough observed at TAS colocalizes with a footprint of DNA-RNA duplex. Here, we show that this reciprocity is not only an average but is conserved in the whole genome and there is a correlation between the intensity of the R-loop signal and the TAS protection from MNase. We are currently making a detailed analysis of the genomic regions that present a faster release of the protective complex observed at the TAS in response to the enzymatic digestion and its relationship with their genomic locations epigenetic marks and DNA accessibility, in T. brucei.A deeper analysis of the chromatin organization and the interacting complexes at TAS might open the road for a better understanding on the processing of the polycistronic transcripts into the mature ARNs.Fil: Zambrano Siri, Romina Trinidad. 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; Uruguay. Instituto de Investigaciones Biológicas "Clemente Estable"; 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"; ArgentinaXXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de ProtozoologíaCiudad Autónoma de Buenos AiresArgentinaFederación Latinoamericana de ParasitologíaSociedad Argentina de ProtozoologíaSociedad Argentina de Protozoología2024info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/conferenceObjectCongresoJournalhttp://purl.org/coar/resource_type/c_5794info:ar-repo/semantics/documentoDeConferenciaapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/275093Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site; XXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de Protozoología; Ciudad Autónoma de Buenos Aires; Argentina; 2024; 87-882953-5751CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://protozoologia.org.ar/revista-parasitus/Internacionalinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-12-03T08:51:30Zoai:ri.conicet.gov.ar:11336/275093instacron: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:34982025-12-03 08:51:31.243CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
title Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
spellingShingle Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
Zambrano Siri, Romina Trinidad
TRYPANOSOMATIDS
NUCLEOSOMES
CHROMATIN
TRANS SPLICING
title_short Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
title_full Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
title_fullStr Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
title_full_unstemmed Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
title_sort Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site
dc.creator.none.fl_str_mv Zambrano Siri, Romina Trinidad
Beati, Maria Paula
Smircich, Pablo
Alonso, Guillermo Daniel
Ocampo, Josefina
author Zambrano Siri, Romina Trinidad
author_facet Zambrano Siri, Romina Trinidad
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 TRYPANOSOMATIDS
NUCLEOSOMES
CHROMATIN
TRANS SPLICING
topic TRYPANOSOMATIDS
NUCLEOSOMES
CHROMATIN
TRANS SPLICING
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, and are characterized by having complex life cycles, alternating between a mammal host and an insect vector. 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. Here, we have analyzed the genome-wide chromatin organization for the parasite stage present in the insect vector by chromatin digestion with micrococcal nuclease followed by deep sequencing (MNase-seq) using our own data for T. cruzi and public data for T. brucei and L. major. We have predicted the most likely trans-splicing acceptor sites (TAS) and used them as reference points for genomic analysis. We have made a comparative analysis among TriTryps for comparable extensions of MNase digestion. By representing average nucleosome occupancy, we found that the average chromatin organization is very similar between T. cruzi and T. brucei with a mild nucleosome depletion at the TAS. This depletion at the TAS is also conserved in L. major even for less digested samples. A detailed examination of nucleosome landscapes resulting from different levels of digestion shows that an MNase-sensitive complex is protecting the trans-splicing acceptor site in Trypanosoma brucei. Additionally, by analyzing MNase-ChIP-seq data for histone H3 we uphold that the average MNase protection observed at the TAS for earlier digestion points in T. brucei is mainly due to a non-histone complex, underlining the conserved nucleosome depletion at that genomic point in TriTryps. Moreover, we show that this nucleosome organization is not just an average since the same layout is observed in most of the genome. Furthermore, in T. brucei the nucleosome trough observed at TAS colocalizes with a footprint of DNA-RNA duplex. Here, we show that this reciprocity is not only an average but is conserved in the whole genome and there is a correlation between the intensity of the R-loop signal and the TAS protection from MNase. We are currently making a detailed analysis of the genomic regions that present a faster release of the protective complex observed at the TAS in response to the enzymatic digestion and its relationship with their genomic locations epigenetic marks and DNA accessibility, in T. brucei.A deeper analysis of the chromatin organization and the interacting complexes at TAS might open the road for a better understanding on the processing of the polycistronic transcripts into the mature ARNs.
Fil: Zambrano Siri, Romina Trinidad. 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. Instituto de Investigaciones Biológicas "Clemente Estable"; 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
XXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de Protozoología
Ciudad Autónoma de Buenos Aires
Argentina
Federación Latinoamericana de Parasitología
Sociedad Argentina de Protozoología
description Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, usually known as TriTryps, are the causal agents of animal and human sickness, and are characterized by having complex life cycles, alternating between a mammal host and an insect vector. 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. Here, we have analyzed the genome-wide chromatin organization for the parasite stage present in the insect vector by chromatin digestion with micrococcal nuclease followed by deep sequencing (MNase-seq) using our own data for T. cruzi and public data for T. brucei and L. major. We have predicted the most likely trans-splicing acceptor sites (TAS) and used them as reference points for genomic analysis. We have made a comparative analysis among TriTryps for comparable extensions of MNase digestion. By representing average nucleosome occupancy, we found that the average chromatin organization is very similar between T. cruzi and T. brucei with a mild nucleosome depletion at the TAS. This depletion at the TAS is also conserved in L. major even for less digested samples. A detailed examination of nucleosome landscapes resulting from different levels of digestion shows that an MNase-sensitive complex is protecting the trans-splicing acceptor site in Trypanosoma brucei. Additionally, by analyzing MNase-ChIP-seq data for histone H3 we uphold that the average MNase protection observed at the TAS for earlier digestion points in T. brucei is mainly due to a non-histone complex, underlining the conserved nucleosome depletion at that genomic point in TriTryps. Moreover, we show that this nucleosome organization is not just an average since the same layout is observed in most of the genome. Furthermore, in T. brucei the nucleosome trough observed at TAS colocalizes with a footprint of DNA-RNA duplex. Here, we show that this reciprocity is not only an average but is conserved in the whole genome and there is a correlation between the intensity of the R-loop signal and the TAS protection from MNase. We are currently making a detailed analysis of the genomic regions that present a faster release of the protective complex observed at the TAS in response to the enzymatic digestion and its relationship with their genomic locations epigenetic marks and DNA accessibility, in T. brucei.A deeper analysis of the chromatin organization and the interacting complexes at TAS might open the road for a better understanding on the processing of the polycistronic transcripts into the mature ARNs.
publishDate 2024
dc.date.none.fl_str_mv 2024
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dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/275093
Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site; XXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de Protozoología; Ciudad Autónoma de Buenos Aires; Argentina; 2024; 87-88
2953-5751
CONICET Digital
CONICET
url http://hdl.handle.net/11336/275093
identifier_str_mv Contrasting study among Trypanosomatids reveals singularities in their chromatin landscape but a conserved nucleosome depletion at the trans-splicing acceptor site; XXVII Congreso de la Federación Latinoamericana de Parasitología y XII Congreso de la Sociedad Argentina de Protozoología; Ciudad Autónoma de Buenos Aires; Argentina; 2024; 87-88
2953-5751
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://protozoologia.org.ar/revista-parasitus/
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dc.coverage.none.fl_str_mv Internacional
dc.publisher.none.fl_str_mv Sociedad Argentina de Protozoología
publisher.none.fl_str_mv Sociedad Argentina de Protozoología
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