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Spreading of heterochromatin is limited to specific families of maize retrotransposons

Eichten, Steven R.; Ellis, Nathanael A.; Makarevitch, Irina; Yeh, Cheng-Ting; Gent, Jonathan I.; Guo, Lin; McGinnis, Karen M.; Zhang, Xiaoyu; Schnable, Patrick S.; Vaughn, Matthew W.; Dawe, R. Kelly; Springer, Nathan M.

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Transposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs...[Show more]

dc.contributor.authorEichten, Steven R.
dc.contributor.authorEllis, Nathanael A.
dc.contributor.authorMakarevitch, Irina
dc.contributor.authorYeh, Cheng-Ting
dc.contributor.authorGent, Jonathan I.
dc.contributor.authorGuo, Lin
dc.contributor.authorMcGinnis, Karen M.
dc.contributor.authorZhang, Xiaoyu
dc.contributor.authorSchnable, Patrick S.
dc.contributor.authorVaughn, Matthew W.
dc.contributor.authorDawe, R. Kelly
dc.contributor.authorSpringer, Nathan M.
dc.date.accessioned2015-10-20T22:54:12Z
dc.date.available2015-10-20T22:54:12Z
dc.identifier.issn1553-7404
dc.identifier.urihttp://hdl.handle.net/1885/15985
dc.description.abstractTransposable elements (TEs) have the potential to act as controlling elements to influence the expression of genes and are often subject to heterochromatic silencing. The current paradigm suggests that heterochromatic silencing can spread beyond the borders of TEs and influence the chromatin state of neighboring low-copy sequences. This would allow TEs to condition obligatory or facilitated epialleles and act as controlling elements. The maize genome contains numerous families of class I TEs (retrotransposons) that are present in moderate to high copy numbers, and many are found in regions near genes, which provides an opportunity to test whether the spreading of heterochromatin from retrotransposons is prevalent. We have investigated the extent of heterochromatin spreading into DNA flanking each family of retrotransposons by profiling DNA methylation and di-methylation of lysine 9 of histone 3 (H3K9me2) in low-copy regions of the maize genome. The effects of different retrotransposon families on local chromatin are highly variable. Some retrotransposon families exhibit enrichment of heterochromatic marks within 800-1,200 base pairs of insertion sites, while other families exhibit very little evidence for the spreading of heterochromatic marks. The analysis of chromatin state in genotypes that lack specific insertions suggests that the heterochromatin in low-copy DNA flanking retrotransposons often results from the spreading of silencing marks rather than insertion-site preferences. Genes located near TEs that exhibit spreading of heterochromatin tend to be expressed at lower levels than other genes. Our findings suggest that a subset of retrotransposon families may act as controlling elements influencing neighboring sequences, while the majority of retrotransposons have little effect on flanking sequences.
dc.description.sponsorshipThe research was supported by grants from the National Science Foundation (DBI-0607123 and IOS-0922095). JIG is funded by an NIH fellowship (NIGMS F32GM095223). This work was created in part using resources or cyberinfrastructure provided by iPlant Collaborative. The iPlant Collaborative is funded by a grant from the National Science Foundation (#DBI-0735191) (www.iplantcollaborative.org).
dc.format12 pages
dc.publisherPublic Library of Science
dc.rights© 2012 Eichten et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.sourcePLoS Genetics
dc.subjectbase sequence
dc.subjectdna methylation
dc.subjectgene silencing
dc.subjectgenome, plant
dc.subjectheterochromatin
dc.subjecthistones
dc.subjectretroelements
dc.subjectsequence analysis, dna
dc.subjectzea mays
dc.subjectgene expression regulation, plant
dc.titleSpreading of heterochromatin is limited to specific families of maize retrotransposons
dc.typeJournal article
local.description.notesImported from ARIES
local.identifier.citationvolume8
dcterms.dateAccepted2012-10-15
dc.date.issued2012-12
local.identifier.absfor060705
local.identifier.ariespublicationu4956746xPUB396
local.publisher.urlhttps://www.plos.org/
local.type.statusPublished Version
local.contributor.affiliationEichten, Steven, College of Medicine, Biology and Environment, CMBE Research School of Biology, Division of Plant Sciences, The Australian National University
local.contributor.affiliationEllis, Nathanael A., University of Georgia, United States of America
local.contributor.affiliationMakarevitch, Irina, Hamline University, United States of America
local.contributor.affiliationYeh, Cheng-Ting, Iowa State University, United States of America
local.contributor.affiliationGent, Jonathan I , University of Georgia, United States of America
local.contributor.affiliationGuo, Lin, University of Georgia, United States of America
local.contributor.affiliationMcGinnis, Karen M., Florida State University,, United States of America
local.contributor.affiliationZhang, Xiaoyu, University of Georgia, United States of America
local.contributor.affiliationSchnable, Patrick S., Iowa State University, United States of America
local.contributor.affiliationVaughn, Matthew W, University of TexasÔÇôAustin, United States of America
local.contributor.affiliationDawe, R Kelly, University of Georgia, United States of America
local.contributor.affiliationSpringer, Nathan M, University of Minnesota, United States of America
local.identifier.essn1553-7404
local.bibliographicCitation.issue12
local.bibliographicCitation.startpagee1003127
local.identifier.doi10.1371/journal.pgen.1003127
local.identifier.absseo970106
dc.date.updated2015-12-09T10:54:25Z
local.identifier.scopusID2-s2.0-84872051484
CollectionsANU Research Publications

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