Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum
- Autores
- Veluchamy, Alaguraj; Lin, Xin; Maumus, Florian; Rivarola, Maximo Lisandro; Bhavsar, Jaysheel; Creasy, Todd; O'Brien, Kimberly; Sengamalay, Naomi A.; Tallon, Luke J.; Smith, Andrew D.; Rayko, Edda; Ahmed, Ikhlak; Crom, Stéphane Le; Farrant, Gregory K.; Sgro, Jean-Yves; Olson, Sue A.; Bondurant, Sandra Splinter; Allen, Andrew; Rabinowicz, Pablo D.; Sussman, Michael R.; Bowler, Chris; Tirichine, Leïla
- Año de publicación
- 2013
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.
Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; Francia
Fil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; China
Fil: Maumus, Florian.
Fil: Rivarola, Maximo Lisandro.
Fil: Bhavsar, Jaysheel.
Fil: Creasy, Todd.
Fil: O'Brien, Kimberly.
Fil: Sengamalay, Naomi A..
Fil: Tallon, Luke J..
Fil: Smith, Andrew D..
Fil: Rayko, Edda.
Fil: Ahmed, Ikhlak.
Fil: Crom, Stéphane Le.
Fil: Farrant, Gregory K..
Fil: Sgro, Jean-Yves.
Fil: Olson, Sue A..
Fil: Bondurant, Sandra Splinter.
Fil: Allen, Andrew.
Fil: Rabinowicz, Pablo D..
Fil: Sussman, Michael R..
Fil: Bowler, Chris.
Fil: Tirichine, Leïla. - Materia
-
Bioinformatics
Genomics
Epigenomics
DNA methylation - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
.jpg)
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/96250
Ver los metadatos del registro completo
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Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutumVeluchamy, AlagurajLin, XinMaumus, FlorianRivarola, Maximo LisandroBhavsar, JaysheelCreasy, ToddO'Brien, KimberlySengamalay, Naomi A.Tallon, Luke J.Smith, Andrew D.Rayko, EddaAhmed, IkhlakCrom, Stéphane LeFarrant, Gregory K.Sgro, Jean-YvesOlson, Sue A.Bondurant, Sandra SplinterAllen, AndrewRabinowicz, Pablo D.Sussman, Michael R.Bowler, ChrisTirichine, LeïlaBioinformaticsGenomicsEpigenomicsDNA methylationhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; FranciaFil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; ChinaFil: Maumus, Florian.Fil: Rivarola, Maximo Lisandro.Fil: Bhavsar, Jaysheel.Fil: Creasy, Todd.Fil: O'Brien, Kimberly.Fil: Sengamalay, Naomi A..Fil: Tallon, Luke J..Fil: Smith, Andrew D..Fil: Rayko, Edda.Fil: Ahmed, Ikhlak.Fil: Crom, Stéphane Le.Fil: Farrant, Gregory K..Fil: Sgro, Jean-Yves.Fil: Olson, Sue A..Fil: Bondurant, Sandra Splinter.Fil: Allen, Andrew.Fil: Rabinowicz, Pablo D..Fil: Sussman, Michael R..Fil: Bowler, Chris.Fil: Tirichine, Leïla.Nature2013-07info: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/11336/96250Veluchamy, Alaguraj; Lin, Xin; Maumus, Florian; Rivarola, Maximo Lisandro; Bhavsar, Jaysheel; et al.; Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum; Nature; Nature Communications; 4; 2091; 7-2013; 1-92041-1723CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.nature.com/articles/ncomms3091info:eu-repo/semantics/altIdentifier/doi/10.1038/ncomms3091info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-03T09:44:19Zoai:ri.conicet.gov.ar:11336/96250instacron: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 09:44:20.22CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
| dc.title.none.fl_str_mv |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| title |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| spellingShingle |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum Veluchamy, Alaguraj Bioinformatics Genomics Epigenomics DNA methylation |
| title_short |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| title_full |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| title_fullStr |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| title_full_unstemmed |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| title_sort |
Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum |
| dc.creator.none.fl_str_mv |
Veluchamy, Alaguraj Lin, Xin Maumus, Florian Rivarola, Maximo Lisandro Bhavsar, Jaysheel Creasy, Todd O'Brien, Kimberly Sengamalay, Naomi A. Tallon, Luke J. Smith, Andrew D. Rayko, Edda Ahmed, Ikhlak Crom, Stéphane Le Farrant, Gregory K. Sgro, Jean-Yves Olson, Sue A. Bondurant, Sandra Splinter Allen, Andrew Rabinowicz, Pablo D. Sussman, Michael R. Bowler, Chris Tirichine, Leïla |
| author |
Veluchamy, Alaguraj |
| author_facet |
Veluchamy, Alaguraj Lin, Xin Maumus, Florian Rivarola, Maximo Lisandro Bhavsar, Jaysheel Creasy, Todd O'Brien, Kimberly Sengamalay, Naomi A. Tallon, Luke J. Smith, Andrew D. Rayko, Edda Ahmed, Ikhlak Crom, Stéphane Le Farrant, Gregory K. Sgro, Jean-Yves Olson, Sue A. Bondurant, Sandra Splinter Allen, Andrew Rabinowicz, Pablo D. Sussman, Michael R. Bowler, Chris Tirichine, Leïla |
| author_role |
author |
| author2 |
Lin, Xin Maumus, Florian Rivarola, Maximo Lisandro Bhavsar, Jaysheel Creasy, Todd O'Brien, Kimberly Sengamalay, Naomi A. Tallon, Luke J. Smith, Andrew D. Rayko, Edda Ahmed, Ikhlak Crom, Stéphane Le Farrant, Gregory K. Sgro, Jean-Yves Olson, Sue A. Bondurant, Sandra Splinter Allen, Andrew Rabinowicz, Pablo D. Sussman, Michael R. Bowler, Chris Tirichine, Leïla |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Bioinformatics Genomics Epigenomics DNA methylation |
| topic |
Bioinformatics Genomics Epigenomics DNA methylation |
| 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 cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes. Fil: Veluchamy, Alaguraj. Institut de Biologie de l'École Normale Supérieure; Francia Fil: Lin, Xin. Institut de Biologie de l'École Normale Supérieure; Francia. Xiamen University; China Fil: Maumus, Florian. Fil: Rivarola, Maximo Lisandro. Fil: Bhavsar, Jaysheel. Fil: Creasy, Todd. Fil: O'Brien, Kimberly. Fil: Sengamalay, Naomi A.. Fil: Tallon, Luke J.. Fil: Smith, Andrew D.. Fil: Rayko, Edda. Fil: Ahmed, Ikhlak. Fil: Crom, Stéphane Le. Fil: Farrant, Gregory K.. Fil: Sgro, Jean-Yves. Fil: Olson, Sue A.. Fil: Bondurant, Sandra Splinter. Fil: Allen, Andrew. Fil: Rabinowicz, Pablo D.. Fil: Sussman, Michael R.. Fil: Bowler, Chris. Fil: Tirichine, Leïla. |
| description |
DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes. |
| publishDate |
2013 |
| dc.date.none.fl_str_mv |
2013-07 |
| 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/11336/96250 Veluchamy, Alaguraj; Lin, Xin; Maumus, Florian; Rivarola, Maximo Lisandro; Bhavsar, Jaysheel; et al.; Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum; Nature; Nature Communications; 4; 2091; 7-2013; 1-9 2041-1723 CONICET Digital CONICET |
| url |
http://hdl.handle.net/11336/96250 |
| identifier_str_mv |
Veluchamy, Alaguraj; Lin, Xin; Maumus, Florian; Rivarola, Maximo Lisandro; Bhavsar, Jaysheel; et al.; Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum; Nature; Nature Communications; 4; 2091; 7-2013; 1-9 2041-1723 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://www.nature.com/articles/ncomms3091 info:eu-repo/semantics/altIdentifier/doi/10.1038/ncomms3091 |
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info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-sa/2.5/ar/ |
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openAccess |
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Nature |
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Nature |
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