Identification of genes regulated by histone acetylation during root development in Populus trichocarpa.
Identifieur interne : 001823 ( Main/Exploration ); précédent : 001822; suivant : 001824Identification of genes regulated by histone acetylation during root development in Populus trichocarpa.
Auteurs : Xujun Ma [République populaire de Chine] ; Chao Zhang [République populaire de Chine] ; Bing Zhang [République populaire de Chine] ; Chuanping Yang [République populaire de Chine] ; Shujuan Li [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2016.
Descripteurs français
- KwdFr :
- Acides hydroxamiques (métabolisme), Acétylation (MeSH), Analyse de profil d'expression de gènes (MeSH), Biologie informatique (méthodes), Développement des plantes (génétique), Gibbérellines (métabolisme), Gènes de plante (MeSH), Histone (métabolisme), Histone deacetylases (métabolisme), Phénotype (MeSH), Populus (génétique), Populus (métabolisme), Racines de plante (croissance et développement), Racines de plante (génétique), Racines de plante (métabolisme), Reproductibilité des résultats (MeSH), Régulation de l'expression des gènes végétaux (MeSH), Régénération (génétique).
- MESH :
- croissance et développement : Racines de plante.
- génétique : Développement des plantes, Populus, Racines de plante, Régénération.
- métabolisme : Acides hydroxamiques, Gibbérellines, Histone, Histone deacetylases, Populus, Racines de plante.
- méthodes : Biologie informatique.
- Acétylation, Analyse de profil d'expression de gènes, Gènes de plante, Phénotype, Reproductibilité des résultats, Régulation de l'expression des gènes végétaux.
English descriptors
- KwdEn :
- Acetylation (MeSH), Computational Biology (methods), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genes, Plant (MeSH), Gibberellins (metabolism), Histone Deacetylases (metabolism), Histones (metabolism), Hydroxamic Acids (metabolism), Phenotype (MeSH), Plant Development (genetics), Plant Roots (genetics), Plant Roots (growth & development), Plant Roots (metabolism), Populus (genetics), Populus (metabolism), Regeneration (genetics), Reproducibility of Results (MeSH).
- MESH :
- chemical , metabolism : Gibberellins, Histone Deacetylases, Histones, Hydroxamic Acids.
- genetics : Plant Development, Plant Roots, Populus, Regeneration.
- growth & development : Plant Roots.
- metabolism : Plant Roots, Populus.
- methods : Computational Biology.
- Acetylation, Gene Expression Profiling, Gene Expression Regulation, Plant, Genes, Plant, Phenotype, Reproducibility of Results.
Abstract
BACKGROUND
Histone deacetylases (HDACs) are key enzymes catalyzing the removal of acetyl groups from histones. HDACs act in concert with histone acetyltransferases (HATs) to regulate histone acetylation status, which modifies chromatin structure, affecting gene transcription and thus regulating multiple biological processes such as plant growth and development. Over a decade, certain HDACs in herbaceous plants have been deeply studied. However, functions of HDACs in woody plants are not well understood.
RESULTS
Histone deacetylase specific inhibitor trichostatin A (TSA) was used to investigate the role of HDACs in organogenesis of roots and root development in Populus trochocarpa. The adventitious roots were regenerated and grown on medium supplemented with 0, 1, and 2.5 μM TSA. TSA treatment delayed root regeneration and inhibited primary root growth. To examine the genes modified by TSA in the regenerated roots, tag-based digital gene expression (DGE) analysis was performed using Illumina HiSeqTM 2000. Approximately 4.5 million total clean tags were mapped per library. The distinct clean tags for the three libraries corresponding to 0, 1 and 2.5 μM TSA treatment were 166167, 143103 and 153507, from which 38.45%, 31.84% and 38.88% were mapped unambiguously to the unigene database, respectively. Most of the tags were expressed at similar levels, showing a < 5-fold difference after 1 μM and 2.5 μM TSA treatments and the maximum fold-change of the tag copy number was around 20. The expression levels of many genes in roots were significantly altered by TSA. A total of 36 genes were up-regulated and 1368 genes were down-regulated after 1 μM TSA treatment, while 166 genes were up-regulated and 397 genes were down-regulated after 2.5 μM TSA treatment. Gene ontology (GO) and pathway analyses indicated that the differentially expressed genes were related to many kinds of molecular functions and biological processes. The genes encoding key enzymes catalyzing gibberellin biosynthesis were significantly down-regulated in the roots exposed to 2.5 μM TSA and their expression changes were validated by using real-time PCR.
CONCLUSIONS
HDACs were required for de novo organogenesis and normal growth of populus roots. DGE data provides the gene profiles in roots probably regulated by histone acetylation during root growth and development, which will lead to a better understanding of the mechanism controlling root development.
DOI: 10.1186/s12864-016-2407-x
PubMed: 26847576
PubMed Central: PMC4743431
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. cpyang_nefu@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Li, Shujuan" sort="Li, Shujuan" uniqKey="Li S" first="Shujuan" last="Li">Shujuan Li</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry 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wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. fredzhang1990@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Bing" sort="Zhang, Bing" uniqKey="Zhang B" first="Bing" last="Zhang">Bing Zhang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. 903253543@qq.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Yang, Chuanping" sort="Yang, Chuanping" uniqKey="Yang C" first="Chuanping" last="Yang">Chuanping Yang</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. cpyang_nefu@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author><author><name sortKey="Li, Shujuan" sort="Li, Shujuan" uniqKey="Li S" first="Shujuan" last="Li">Shujuan Li</name><affiliation wicri:level="1"><nlm:affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. lishujuan@126.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040</wicri:regionArea><wicri:noRegion>150040</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Acetylation (MeSH)</term><term>Computational Biology (methods)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genes, Plant (MeSH)</term><term>Gibberellins (metabolism)</term><term>Histone Deacetylases (metabolism)</term><term>Histones (metabolism)</term><term>Hydroxamic Acids (metabolism)</term><term>Phenotype (MeSH)</term><term>Plant Development (genetics)</term><term>Plant Roots (genetics)</term><term>Plant Roots (growth & development)</term><term>Plant Roots (metabolism)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Regeneration (genetics)</term><term>Reproducibility of Results (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Acides hydroxamiques (métabolisme)</term><term>Acétylation (MeSH)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Biologie informatique (méthodes)</term><term>Développement des plantes (génétique)</term><term>Gibbérellines (métabolisme)</term><term>Gènes de plante (MeSH)</term><term>Histone (métabolisme)</term><term>Histone deacetylases (métabolisme)</term><term>Phénotype (MeSH)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Racines de plante (croissance et développement)</term><term>Racines de plante (génétique)</term><term>Racines de plante (métabolisme)</term><term>Reproductibilité des résultats (MeSH)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Régénération (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Gibberellins</term><term>Histone Deacetylases</term><term>Histones</term><term>Hydroxamic Acids</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Development</term><term>Plant Roots</term><term>Populus</term><term>Regeneration</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Plant Roots</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Développement des plantes</term><term>Populus</term><term>Racines de plante</term><term>Régénération</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plant Roots</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Acides hydroxamiques</term><term>Gibbérellines</term><term>Histone</term><term>Histone deacetylases</term><term>Populus</term><term>Racines de plante</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Biologie informatique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Acetylation</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genes, Plant</term><term>Phenotype</term><term>Reproducibility of Results</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Acétylation</term><term>Analyse de profil d'expression de gènes</term><term>Gènes de plante</term><term>Phénotype</term><term>Reproductibilité des résultats</term><term>Régulation de l'expression des gènes végétaux</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Histone deacetylases (HDACs) are key enzymes catalyzing the removal of acetyl groups from histones. HDACs act in concert with histone acetyltransferases (HATs) to regulate histone acetylation status, which modifies chromatin structure, affecting gene transcription and thus regulating multiple biological processes such as plant growth and development. Over a decade, certain HDACs in herbaceous plants have been deeply studied. However, functions of HDACs in woody plants are not well understood.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Histone deacetylase specific inhibitor trichostatin A (TSA) was used to investigate the role of HDACs in organogenesis of roots and root development in Populus trochocarpa. The adventitious roots were regenerated and grown on medium supplemented with 0, 1, and 2.5 μM TSA. TSA treatment delayed root regeneration and inhibited primary root growth. To examine the genes modified by TSA in the regenerated roots, tag-based digital gene expression (DGE) analysis was performed using Illumina HiSeqTM 2000. Approximately 4.5 million total clean tags were mapped per library. The distinct clean tags for the three libraries corresponding to 0, 1 and 2.5 μM TSA treatment were 166167, 143103 and 153507, from which 38.45%, 31.84% and 38.88% were mapped unambiguously to the unigene database, respectively. Most of the tags were expressed at similar levels, showing a < 5-fold difference after 1 μM and 2.5 μM TSA treatments and the maximum fold-change of the tag copy number was around 20. The expression levels of many genes in roots were significantly altered by TSA. A total of 36 genes were up-regulated and 1368 genes were down-regulated after 1 μM TSA treatment, while 166 genes were up-regulated and 397 genes were down-regulated after 2.5 μM TSA treatment. Gene ontology (GO) and pathway analyses indicated that the differentially expressed genes were related to many kinds of molecular functions and biological processes. The genes encoding key enzymes catalyzing gibberellin biosynthesis were significantly down-regulated in the roots exposed to 2.5 μM TSA and their expression changes were validated by using real-time PCR.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>HDACs were required for de novo organogenesis and normal growth of populus roots. DGE data provides the gene profiles in roots probably regulated by histone acetylation during root growth and development, which will lead to a better understanding of the mechanism controlling root development.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26847576</PMID><DateCompleted><Year>2016</Year><Month>10</Month><Day>20</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>17</Volume><PubDate><Year>2016</Year><Month>Feb</Month><Day>04</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Identification of genes regulated by histone acetylation during root development in Populus trichocarpa.</ArticleTitle><Pagination><MedlinePgn>96</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-016-2407-x</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Histone deacetylases (HDACs) are key enzymes catalyzing the removal of acetyl groups from histones. HDACs act in concert with histone acetyltransferases (HATs) to regulate histone acetylation status, which modifies chromatin structure, affecting gene transcription and thus regulating multiple biological processes such as plant growth and development. Over a decade, certain HDACs in herbaceous plants have been deeply studied. However, functions of HDACs in woody plants are not well understood.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Histone deacetylase specific inhibitor trichostatin A (TSA) was used to investigate the role of HDACs in organogenesis of roots and root development in Populus trochocarpa. The adventitious roots were regenerated and grown on medium supplemented with 0, 1, and 2.5 μM TSA. TSA treatment delayed root regeneration and inhibited primary root growth. To examine the genes modified by TSA in the regenerated roots, tag-based digital gene expression (DGE) analysis was performed using Illumina HiSeqTM 2000. Approximately 4.5 million total clean tags were mapped per library. The distinct clean tags for the three libraries corresponding to 0, 1 and 2.5 μM TSA treatment were 166167, 143103 and 153507, from which 38.45%, 31.84% and 38.88% were mapped unambiguously to the unigene database, respectively. Most of the tags were expressed at similar levels, showing a < 5-fold difference after 1 μM and 2.5 μM TSA treatments and the maximum fold-change of the tag copy number was around 20. The expression levels of many genes in roots were significantly altered by TSA. A total of 36 genes were up-regulated and 1368 genes were down-regulated after 1 μM TSA treatment, while 166 genes were up-regulated and 397 genes were down-regulated after 2.5 μM TSA treatment. Gene ontology (GO) and pathway analyses indicated that the differentially expressed genes were related to many kinds of molecular functions and biological processes. The genes encoding key enzymes catalyzing gibberellin biosynthesis were significantly down-regulated in the roots exposed to 2.5 μM TSA and their expression changes were validated by using real-time PCR.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">HDACs were required for de novo organogenesis and normal growth of populus roots. DGE data provides the gene profiles in roots probably regulated by histone acetylation during root growth and development, which will lead to a better understanding of the mechanism controlling root development.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Xujun</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. mxj3000@sina.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Chao</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. fredzhang1990@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Bing</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. 903253543@qq.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Chuanping</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. cpyang_nefu@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Shujuan</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Northeast Forestry University, Harbin, 150040, China. lishujuan@126.com.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>02</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005875">Gibberellins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006657">Histones</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D006877">Hydroxamic Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>3X2S926L3Z</RegistryNumber><NameOfSubstance UI="C012589">trichostatin A</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.5.1.98</RegistryNumber><NameOfSubstance UI="D006655">Histone Deacetylases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000107" MajorTopicYN="N">Acetylation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005875" MajorTopicYN="N">Gibberellins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006655" MajorTopicYN="N">Histone Deacetylases</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006657" MajorTopicYN="N">Histones</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D006877" MajorTopicYN="N">Hydroxamic Acids</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D063245" MajorTopicYN="N">Plant Development</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018517" MajorTopicYN="N">Plant Roots</DescriptorName><QualifierName UI="Q000235" 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