Improving genome-wide mapping of nucleosomes in Trypanosome cruzi

Autores
Beati, Maria Paula; Massimino Stepñicka, Milena; Vilchez Larrea, Salomé Catalina; Smircich, Pablo; Alonso, Guillermo Daniel; Ocampo, Josefina
Año de publicación
2023
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
In Trypanosoma cruziDNA is packaged into chromatin by octamers of histone proteins that form nucleosomes. Transcription of protein coding genes in trypanosomes is constitutive producing polycistronic units and gene expression is primarily regulated post-transcription- ally. However, chromatin organization influences DNA dependent processes. Hence, deter- mining nucleosome position is of uppermost importance to understand the peculiarities found in trypanosomes. To map nucleosomes genome-wide in several organisms, digestion of chromatin with micrococcal nuclease followed by deep sequencing has been applied. Nonetheless, the special requirements for cell manipulation and the uniqueness of the chro- matin organization in trypanosomes entails a customized analytical approach. In this work, we adjusted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we implemented an exhaustive and thorough computational workflow to overcome the diffi- culties imposed by this complex genome. We tested the performance of two aligners, Bow tie2 and HISAT2, and discuss their advantages and caveats. Specifically, we highlight the relevance of using the whole genome as a reference instead of the commonly used Esmer- aldo-like haplotype to avoid spurious alignments. Additionally, we show that using the whole genome refines the average nucleosome representation, but also the quality of mapping for every region represented. Moreover, we show that the average nucleosome organization around trans-splicing acceptor site described before, is not just an average since the same chromatin pattern is detected for most of the represented regions. In addition, we extended the study to a non-hybrid strain applying the experimental and analytical approach to Sylvio- X10 strain. Furthermore, we provide a source code for the construction of 2D plots and heat- maps which are easy to adapt to any T. cruzi strain.
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: Massimino Stepñicka, Milena. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Vilchez Larrea, Salomé Catalina. 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: Smircich, Pablo. 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
Materia
CHROMATIN
NUCLEOSOME MAPPING
TRYPANOSOMA CRUZI
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/231113
Acceder
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Improving genome-wide mapping of nucleosomes in Trypanosome cruziBeati, Maria PaulaMassimino Stepñicka, MilenaVilchez Larrea, Salomé CatalinaSmircich, PabloAlonso, Guillermo DanielOcampo, JosefinaCHROMATINNUCLEOSOME MAPPINGTRYPANOSOMA CRUZIhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1In Trypanosoma cruziDNA is packaged into chromatin by octamers of histone proteins that form nucleosomes. Transcription of protein coding genes in trypanosomes is constitutive producing polycistronic units and gene expression is primarily regulated post-transcription- ally. However, chromatin organization influences DNA dependent processes. Hence, deter- mining nucleosome position is of uppermost importance to understand the peculiarities found in trypanosomes. To map nucleosomes genome-wide in several organisms, digestion of chromatin with micrococcal nuclease followed by deep sequencing has been applied. Nonetheless, the special requirements for cell manipulation and the uniqueness of the chro- matin organization in trypanosomes entails a customized analytical approach. In this work, we adjusted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we implemented an exhaustive and thorough computational workflow to overcome the diffi- culties imposed by this complex genome. We tested the performance of two aligners, Bow tie2 and HISAT2, and discuss their advantages and caveats. Specifically, we highlight the relevance of using the whole genome as a reference instead of the commonly used Esmer- aldo-like haplotype to avoid spurious alignments. Additionally, we show that using the whole genome refines the average nucleosome representation, but also the quality of mapping for every region represented. Moreover, we show that the average nucleosome organization around trans-splicing acceptor site described before, is not just an average since the same chromatin pattern is detected for most of the represented regions. In addition, we extended the study to a non-hybrid strain applying the experimental and analytical approach to Sylvio- X10 strain. Furthermore, we provide a source code for the construction of 2D plots and heat- maps which are easy to adapt to any T. cruzi strain.Fil: Beati, Maria Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Massimino Stepñicka, Milena. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Vilchez Larrea, Salomé Catalina. 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: Smircich, Pablo. 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"; ArgentinaPublic Library of Science2023-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/231113Beati, Maria Paula; Massimino Stepñicka, Milena; Vilchez Larrea, Salomé Catalina; Smircich, Pablo; Alonso, Guillermo Daniel; et al.; Improving genome-wide mapping of nucleosomes in Trypanosome cruzi; Public Library of Science; Plos One; 18; 11; 11-2023; 1-161932-6203CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0293809info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0293809info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T10:09:02Zoai:ri.conicet.gov.ar:11336/231113instacron: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:34982025-09-03 10:09:02.417CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
title Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
spellingShingle Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
Beati, Maria Paula
CHROMATIN
NUCLEOSOME MAPPING
TRYPANOSOMA CRUZI
title_short Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
title_full Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
title_fullStr Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
title_full_unstemmed Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
title_sort Improving genome-wide mapping of nucleosomes in Trypanosome cruzi
dc.creator.none.fl_str_mv Beati, Maria Paula
Massimino Stepñicka, Milena
Vilchez Larrea, Salomé Catalina
Smircich, Pablo
Alonso, Guillermo Daniel
Ocampo, Josefina
author Beati, Maria Paula
author_facet Beati, Maria Paula
Massimino Stepñicka, Milena
Vilchez Larrea, Salomé Catalina
Smircich, Pablo
Alonso, Guillermo Daniel
Ocampo, Josefina
author_role author
author2 Massimino Stepñicka, Milena
Vilchez Larrea, Salomé Catalina
Smircich, Pablo
Alonso, Guillermo Daniel
Ocampo, Josefina
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv CHROMATIN
NUCLEOSOME MAPPING
TRYPANOSOMA CRUZI
topic CHROMATIN
NUCLEOSOME MAPPING
TRYPANOSOMA CRUZI
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv In Trypanosoma cruziDNA is packaged into chromatin by octamers of histone proteins that form nucleosomes. Transcription of protein coding genes in trypanosomes is constitutive producing polycistronic units and gene expression is primarily regulated post-transcription- ally. However, chromatin organization influences DNA dependent processes. Hence, deter- mining nucleosome position is of uppermost importance to understand the peculiarities found in trypanosomes. To map nucleosomes genome-wide in several organisms, digestion of chromatin with micrococcal nuclease followed by deep sequencing has been applied. Nonetheless, the special requirements for cell manipulation and the uniqueness of the chro- matin organization in trypanosomes entails a customized analytical approach. In this work, we adjusted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we implemented an exhaustive and thorough computational workflow to overcome the diffi- culties imposed by this complex genome. We tested the performance of two aligners, Bow tie2 and HISAT2, and discuss their advantages and caveats. Specifically, we highlight the relevance of using the whole genome as a reference instead of the commonly used Esmer- aldo-like haplotype to avoid spurious alignments. Additionally, we show that using the whole genome refines the average nucleosome representation, but also the quality of mapping for every region represented. Moreover, we show that the average nucleosome organization around trans-splicing acceptor site described before, is not just an average since the same chromatin pattern is detected for most of the represented regions. In addition, we extended the study to a non-hybrid strain applying the experimental and analytical approach to Sylvio- X10 strain. Furthermore, we provide a source code for the construction of 2D plots and heat- maps which are easy to adapt to any T. cruzi strain.
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: Massimino Stepñicka, Milena. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Vilchez Larrea, Salomé Catalina. 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: Smircich, Pablo. 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
description In Trypanosoma cruziDNA is packaged into chromatin by octamers of histone proteins that form nucleosomes. Transcription of protein coding genes in trypanosomes is constitutive producing polycistronic units and gene expression is primarily regulated post-transcription- ally. However, chromatin organization influences DNA dependent processes. Hence, deter- mining nucleosome position is of uppermost importance to understand the peculiarities found in trypanosomes. To map nucleosomes genome-wide in several organisms, digestion of chromatin with micrococcal nuclease followed by deep sequencing has been applied. Nonetheless, the special requirements for cell manipulation and the uniqueness of the chro- matin organization in trypanosomes entails a customized analytical approach. In this work, we adjusted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we implemented an exhaustive and thorough computational workflow to overcome the diffi- culties imposed by this complex genome. We tested the performance of two aligners, Bow tie2 and HISAT2, and discuss their advantages and caveats. Specifically, we highlight the relevance of using the whole genome as a reference instead of the commonly used Esmer- aldo-like haplotype to avoid spurious alignments. Additionally, we show that using the whole genome refines the average nucleosome representation, but also the quality of mapping for every region represented. Moreover, we show that the average nucleosome organization around trans-splicing acceptor site described before, is not just an average since the same chromatin pattern is detected for most of the represented regions. In addition, we extended the study to a non-hybrid strain applying the experimental and analytical approach to Sylvio- X10 strain. Furthermore, we provide a source code for the construction of 2D plots and heat- maps which are easy to adapt to any T. cruzi strain.
publishDate 2023
dc.date.none.fl_str_mv 2023-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/231113
Beati, Maria Paula; Massimino Stepñicka, Milena; Vilchez Larrea, Salomé Catalina; Smircich, Pablo; Alonso, Guillermo Daniel; et al.; Improving genome-wide mapping of nucleosomes in Trypanosome cruzi; Public Library of Science; Plos One; 18; 11; 11-2023; 1-16
1932-6203
CONICET Digital
CONICET
url http://hdl.handle.net/11336/231113
identifier_str_mv Beati, Maria Paula; Massimino Stepñicka, Milena; Vilchez Larrea, Salomé Catalina; Smircich, Pablo; Alonso, Guillermo Daniel; et al.; Improving genome-wide mapping of nucleosomes in Trypanosome cruzi; Public Library of Science; Plos One; 18; 11; 11-2023; 1-16
1932-6203
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://journals.plos.org/plosone/article?id=10.1371/journal.pone.0293809
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0293809
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Public Library of Science
publisher.none.fl_str_mv Public Library of Science
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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