Role of transposable elements in heterochromatin and epigenetic control
Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and wer...
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| Veröffentlicht in: | Nature (London) 2004-07, Vol.430 (6998), p.471-476 |
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| creator | Lippman, Z Gendrel, A.V Black, M Vaughn, M.W Dedhia, N McCombie, W.R Lavine, K Mittal, V May, B Kasschau, K.D |
| description | Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs. |
| doi_str_mv | 10.1038/nature02651 |
| format | Article |
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Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.</description><identifier>ISSN: 0028-0836</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/nature02651</identifier><identifier>PMID: 15269773</identifier><identifier>CODEN: NATUAS</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>adenosinetriphosphatase ; Arabidopsis ; Arabidopsis - genetics ; Arabidopsis Proteins - genetics ; Arabidopsis thaliana ; Biological and medical sciences ; Cellular Biology ; chromatin remodeling adenosinetriphosphatase ; Chromosomes, Plant - genetics ; Cluster Analysis ; Corn ; Deoxyribonucleic acid ; DNA ; DNA (Cytosine-5-)-Methyltransferases - metabolism ; DNA Methylation ; DNA methyltransferase ; DNA Transposable Elements - genetics ; DNA-Binding Proteins - genetics ; DNA-Binding Proteins - metabolism ; Drosophila ; Epigenesis, Genetic - genetics ; epigenetics ; Flowers & plants ; Fundamental and applied biological sciences. Psychology ; FWA gene ; gene expression regulation ; Gene Expression Regulation, Plant ; Genes ; Genetics ; Genic rearrangement. Recombination. Transposable element ; Genomic Imprinting ; Heterochromatin ; Heterochromatin - genetics ; Homeodomain Proteins - genetics ; Humanities and Social Sciences ; letter ; Life Sciences ; methyltransferases ; microarray technology ; Molecular and cellular biology ; Molecular genetics ; multidisciplinary ; Oligonucleotide Array Sequence Analysis ; repetitive sequences ; RNA ; RNA, Small Interfering - genetics ; RNA, Small Interfering - metabolism ; Science ; small interfering RNA ; Tandem Repeat Sequences - genetics ; Transcription Factors - genetics ; Transcription Factors - metabolism ; transposons ; Zea mays</subject><ispartof>Nature (London), 2004-07, Vol.430 (6998), p.471-476</ispartof><rights>Macmillan Magazines Ltd. 2004</rights><rights>2004 INIST-CNRS</rights><rights>COPYRIGHT 2004 Nature Publishing Group</rights><rights>Copyright Macmillan Journals Ltd. Jul 22, 2004</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c704t-fb7056be94f1352c7bb164749186bacbd4fbd05427dc9f6de6d9d610b33212463</citedby><cites>FETCH-LOGICAL-c704t-fb7056be94f1352c7bb164749186bacbd4fbd05427dc9f6de6d9d610b33212463</cites><orcidid>0000-0002-6382-1610</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/nature02651$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/nature02651$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>230,314,777,781,882,27905,27906,41469,42538,51300</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=15970076$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/15269773$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.inrae.fr/hal-02677166$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Lippman, Z</creatorcontrib><creatorcontrib>Gendrel, A.V</creatorcontrib><creatorcontrib>Black, M</creatorcontrib><creatorcontrib>Vaughn, M.W</creatorcontrib><creatorcontrib>Dedhia, N</creatorcontrib><creatorcontrib>McCombie, W.R</creatorcontrib><creatorcontrib>Lavine, K</creatorcontrib><creatorcontrib>Mittal, V</creatorcontrib><creatorcontrib>May, B</creatorcontrib><creatorcontrib>Kasschau, K.D</creatorcontrib><title>Role of transposable elements in heterochromatin and epigenetic control</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.</description><subject>adenosinetriphosphatase</subject><subject>Arabidopsis</subject><subject>Arabidopsis - genetics</subject><subject>Arabidopsis Proteins - genetics</subject><subject>Arabidopsis thaliana</subject><subject>Biological and medical sciences</subject><subject>Cellular Biology</subject><subject>chromatin remodeling adenosinetriphosphatase</subject><subject>Chromosomes, Plant - genetics</subject><subject>Cluster Analysis</subject><subject>Corn</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA (Cytosine-5-)-Methyltransferases - metabolism</subject><subject>DNA Methylation</subject><subject>DNA methyltransferase</subject><subject>DNA Transposable Elements - genetics</subject><subject>DNA-Binding Proteins - genetics</subject><subject>DNA-Binding Proteins - metabolism</subject><subject>Drosophila</subject><subject>Epigenesis, Genetic - genetics</subject><subject>epigenetics</subject><subject>Flowers & plants</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>FWA gene</subject><subject>gene expression regulation</subject><subject>Gene Expression Regulation, Plant</subject><subject>Genes</subject><subject>Genetics</subject><subject>Genic rearrangement. Recombination. 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metabolism</topic><topic>DNA Methylation</topic><topic>DNA methyltransferase</topic><topic>DNA Transposable Elements - genetics</topic><topic>DNA-Binding Proteins - genetics</topic><topic>DNA-Binding Proteins - metabolism</topic><topic>Drosophila</topic><topic>Epigenesis, Genetic - genetics</topic><topic>epigenetics</topic><topic>Flowers & plants</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>FWA gene</topic><topic>gene expression regulation</topic><topic>Gene Expression Regulation, Plant</topic><topic>Genes</topic><topic>Genetics</topic><topic>Genic rearrangement. Recombination. 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(HAL)</collection><jtitle>Nature (London)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lippman, Z</au><au>Gendrel, A.V</au><au>Black, M</au><au>Vaughn, M.W</au><au>Dedhia, N</au><au>McCombie, W.R</au><au>Lavine, K</au><au>Mittal, V</au><au>May, B</au><au>Kasschau, K.D</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Role of transposable elements in heterochromatin and epigenetic control</atitle><jtitle>Nature (London)</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2004-07-22</date><risdate>2004</risdate><volume>430</volume><issue>6998</issue><spage>471</spage><epage>476</epage><pages>471-476</pages><issn>0028-0836</issn><eissn>1476-4687</eissn><coden>NATUAS</coden><abstract>Heterochromatin has been defined as deeply staining chromosomal material that remains condensed in interphase, whereas euchromatin undergoes de-condensation. Heterochromatin is found near centromeres and telomeres, but interstitial sites of heterochromatin (knobs) are common in plant genomes and were first described in maize. These regions are repetitive and late-replicating. In Drosophila, heterochromatin influences gene expression, a heterochromatin phenomenon called position effect variegation. Similarities between position effect variegation in Drosophila and gene silencing in maize mediated by "controlling elements" (that is, transposable elements) led in part to the proposal that heterochromatin is composed of transposable elements, and that such elements scattered throughout the genome might regulate development. Using microarray analysis, we show that heterochromatin in Arabidopsis is determined by transposable elements and related tandem repeats, under the control of the chromatin remodelling ATPase DDM1 (Decrease in DNA Methylation 1). Small interfering RNAs (siRNAs) correspond to these sequences, suggesting a role in guiding DDM1. We also show that transposable elements can regulate genes epigenetically, but only when inserted within or very close to them. This probably accounts for the regulation by DDM1 and the DNA methyltransferase MET1 of the euchromatic, imprinted gene FWA, as its promoter is provided by transposable-element-derived tandem repeats that are associated with siRNAs.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>15269773</pmid><doi>10.1038/nature02651</doi><tpages>6</tpages><orcidid>https://orcid.org/0000-0002-6382-1610</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0028-0836 |
| ispartof | Nature (London), 2004-07, Vol.430 (6998), p.471-476 |
| issn | 0028-0836 1476-4687 |
| language | eng |
| recordid | cdi_hal_primary_oai_HAL_hal_02677166v1 |
| source | MEDLINE; SpringerLink Journals; Nature Journals Online |
| subjects | adenosinetriphosphatase Arabidopsis Arabidopsis - genetics Arabidopsis Proteins - genetics Arabidopsis thaliana Biological and medical sciences Cellular Biology chromatin remodeling adenosinetriphosphatase Chromosomes, Plant - genetics Cluster Analysis Corn Deoxyribonucleic acid DNA DNA (Cytosine-5-)-Methyltransferases - metabolism DNA Methylation DNA methyltransferase DNA Transposable Elements - genetics DNA-Binding Proteins - genetics DNA-Binding Proteins - metabolism Drosophila Epigenesis, Genetic - genetics epigenetics Flowers & plants Fundamental and applied biological sciences. Psychology FWA gene gene expression regulation Gene Expression Regulation, Plant Genes Genetics Genic rearrangement. Recombination. Transposable element Genomic Imprinting Heterochromatin Heterochromatin - genetics Homeodomain Proteins - genetics Humanities and Social Sciences letter Life Sciences methyltransferases microarray technology Molecular and cellular biology Molecular genetics multidisciplinary Oligonucleotide Array Sequence Analysis repetitive sequences RNA RNA, Small Interfering - genetics RNA, Small Interfering - metabolism Science small interfering RNA Tandem Repeat Sequences - genetics Transcription Factors - genetics Transcription Factors - metabolism transposons Zea mays |
| title | Role of transposable elements in heterochromatin and epigenetic control |
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