Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation

Autores
Chereji, Razvan V.; Eriksson, Peter R.; Ocampo, Josefina; Prajapati, Hemant Kumar; Clark, David
Año de publicación
2019
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.
Fil: Chereji, Razvan V.. National Institutes of Health; Estados Unidos
Fil: Eriksson, Peter R.. National Institutes of Health; Estados Unidos
Fil: Ocampo, Josefina. National Institutes of Health; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Prajapati, Hemant Kumar. National Institutes of Health; Estados Unidos
Fil: Clark, David. National Institutes of Health; Estados Unidos
Materia
CHROMATIN
ACCESSIBILITY
RESTRICTION ENZYME
GENE REGULATION
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:11336/105280
Acceder
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network_acronym_str CONICETDig
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network_name_str CONICET Digital (CONICET)
spelling Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulationChereji, Razvan V.Eriksson, Peter R.Ocampo, JosefinaPrajapati, Hemant KumarClark, DavidCHROMATINACCESSIBILITYRESTRICTION ENZYMEGENE REGULATIONhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.Fil: Chereji, Razvan V.. National Institutes of Health; Estados UnidosFil: Eriksson, Peter R.. National Institutes of Health; Estados UnidosFil: Ocampo, Josefina. National Institutes of Health; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Prajapati, Hemant Kumar. National Institutes of Health; Estados UnidosFil: Clark, David. National Institutes of Health; Estados UnidosCold Spring Harbor Laboratory Press2019-08info: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/11336/105280Chereji, Razvan V.; Eriksson, Peter R.; Ocampo, Josefina; Prajapati, Hemant Kumar; Clark, David; Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation; Cold Spring Harbor Laboratory Press; Genome Research; 29; 12; 8-2019; 1985-19951088-90511549-5469CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1101/gr.249326.119info:eu-repo/semantics/altIdentifier/url/https://genome.cshlp.org/content/29/12/1985.longinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:03:11Zoai:ri.conicet.gov.ar:11336/105280instacron: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 10:03:12.077CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
title Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
spellingShingle Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
Chereji, Razvan V.
CHROMATIN
ACCESSIBILITY
RESTRICTION ENZYME
GENE REGULATION
title_short Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
title_full Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
title_fullStr Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
title_full_unstemmed Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
title_sort Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
dc.creator.none.fl_str_mv Chereji, Razvan V.
Eriksson, Peter R.
Ocampo, Josefina
Prajapati, Hemant Kumar
Clark, David
author Chereji, Razvan V.
author_facet Chereji, Razvan V.
Eriksson, Peter R.
Ocampo, Josefina
Prajapati, Hemant Kumar
Clark, David
author_role author
author2 Eriksson, Peter R.
Ocampo, Josefina
Prajapati, Hemant Kumar
Clark, David
author2_role author
author
author
author
dc.subject.none.fl_str_mv CHROMATIN
ACCESSIBILITY
RESTRICTION ENZYME
GENE REGULATION
topic CHROMATIN
ACCESSIBILITY
RESTRICTION ENZYME
GENE REGULATION
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.
Fil: Chereji, Razvan V.. National Institutes of Health; Estados Unidos
Fil: Eriksson, Peter R.. National Institutes of Health; Estados Unidos
Fil: Ocampo, Josefina. National Institutes of Health; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina
Fil: Prajapati, Hemant Kumar. National Institutes of Health; Estados Unidos
Fil: Clark, David. National Institutes of Health; Estados Unidos
description DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.
publishDate 2019
dc.date.none.fl_str_mv 2019-08
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/11336/105280
Chereji, Razvan V.; Eriksson, Peter R.; Ocampo, Josefina; Prajapati, Hemant Kumar; Clark, David; Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation; Cold Spring Harbor Laboratory Press; Genome Research; 29; 12; 8-2019; 1985-1995
1088-9051
1549-5469
CONICET Digital
CONICET
url http://hdl.handle.net/11336/105280
identifier_str_mv Chereji, Razvan V.; Eriksson, Peter R.; Ocampo, Josefina; Prajapati, Hemant Kumar; Clark, David; Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation; Cold Spring Harbor Laboratory Press; Genome Research; 29; 12; 8-2019; 1985-1995
1088-9051
1549-5469
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1101/gr.249326.119
info:eu-repo/semantics/altIdentifier/url/https://genome.cshlp.org/content/29/12/1985.long
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
publisher.none.fl_str_mv Cold Spring Harbor Laboratory Press
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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score 13.070432

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