Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome.

2.50
Hdl Handle:
http://hdl.handle.net/2336/238422
Title:
Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome.
Authors:
Sigurdsson, Martin I; Smith, Albert V; Bjornsson, Hans T; Jonsson, Jon J
Citation:
Gene 2012, 492(1):104-9
Issue Date:
15-Jan-2012
Abstract:
A potential relationship between transposon-derived repeats (TDR) and human germline methylation is of biological importance since many genes are flanked by TDR and methylation could affect the expression of nearby genes. Furthermore, DNA methylation has been suggested as a global defense mechanism against genome instability threatened by TDR. We studied the correlation between the density of HapMap methyl-associated SNPs (mSNPs), a marker of germline methylation, and proportion of TDR. After correcting for confounding variables, we found a negative correlation between proportion of Alu repeats and mSNP density for 125-1000 kb windows. Similar results were found for the most active subgroup of repeats. In contrast, a negative correlation between proportion of L1 repeats and mSNP density was found only in the larger 1000 kb windows. Using methylation data on germ cells (sperm) from the Human Epigenome Project, we found a lower proportion of Alu repeats adjacent (3-15 kb) to hypermethylated amplicons. On the contrary, there was a higher proportion of L1 repeats in the 3-5 kb of sequence flanking hypermethylated amplicons but not in the 10-15 kb flanks. Our data indicate a differential response to the major repeat families and that DNA methylation is unlikely to be a uniform global defense system against all TDR. It appears to play a role for the L1 subgroup, with sequences adjacent to L1 repeats methylated in response to their proximity. In contrast, sequences adjacent to Alu repeats appear to be hypomethylated, arguing against a role of methylation in germline defense against those elements.
Description:
To access publisher full text version of this article. Please click on the hyperlink in Additional Links field.
Additional Links:
http://dx.doi.org/10.1016/j.gene.2011.10.046
Rights:
Archived with thanks to Gene

Full metadata record

DC FieldValue Language
dc.contributor.authorSigurdsson, Martin Ien_GB
dc.contributor.authorSmith, Albert Ven_GB
dc.contributor.authorBjornsson, Hans Ten_GB
dc.contributor.authorJonsson, Jon Jen_GB
dc.date.accessioned2012-08-14T11:12:51Z-
dc.date.available2012-08-14T11:12:51Z-
dc.date.issued2012-01-15-
dc.identifier.citationGene 2012, 492(1):104-9en_GB
dc.identifier.issn1879-0038-
dc.identifier.pmid22093876-
dc.identifier.doi10.1016/j.gene.2011.10.046-
dc.identifier.urihttp://hdl.handle.net/2336/238422-
dc.descriptionTo access publisher full text version of this article. Please click on the hyperlink in Additional Links field.en_GB
dc.description.abstractA potential relationship between transposon-derived repeats (TDR) and human germline methylation is of biological importance since many genes are flanked by TDR and methylation could affect the expression of nearby genes. Furthermore, DNA methylation has been suggested as a global defense mechanism against genome instability threatened by TDR. We studied the correlation between the density of HapMap methyl-associated SNPs (mSNPs), a marker of germline methylation, and proportion of TDR. After correcting for confounding variables, we found a negative correlation between proportion of Alu repeats and mSNP density for 125-1000 kb windows. Similar results were found for the most active subgroup of repeats. In contrast, a negative correlation between proportion of L1 repeats and mSNP density was found only in the larger 1000 kb windows. Using methylation data on germ cells (sperm) from the Human Epigenome Project, we found a lower proportion of Alu repeats adjacent (3-15 kb) to hypermethylated amplicons. On the contrary, there was a higher proportion of L1 repeats in the 3-5 kb of sequence flanking hypermethylated amplicons but not in the 10-15 kb flanks. Our data indicate a differential response to the major repeat families and that DNA methylation is unlikely to be a uniform global defense system against all TDR. It appears to play a role for the L1 subgroup, with sequences adjacent to L1 repeats methylated in response to their proximity. In contrast, sequences adjacent to Alu repeats appear to be hypomethylated, arguing against a role of methylation in germline defense against those elements.en_GB
dc.description.sponsorshipUniversity of Iceland, Icelandic Student Innovation Fund, Landspitali University Hospital, Memorial Fund of Bergpora Magnusdottir and Jakob Bjarnason,en_GB
dc.language.isoenen
dc.publisherElsevier Scienceen_GB
dc.relation.urlhttp://dx.doi.org/10.1016/j.gene.2011.10.046en_GB
dc.rightsArchived with thanks to Geneen_GB
dc.subject.meshAlu Elementsen_GB
dc.subject.meshDNA Methylationen_GB
dc.subject.meshDNA Transposable Elementsen_GB
dc.subject.meshGenome, Humanen_GB
dc.subject.meshHapMap Projecten_GB
dc.subject.meshHumansen_GB
dc.subject.meshMaleen_GB
dc.subject.meshPolymorphism, Single Nucleotideen_GB
dc.subject.meshRepetitive Sequences, Nucleic Aciden_GB
dc.subject.meshSpermatozoaen_GB
dc.titleDistribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome.en
dc.typeArticleen
dc.contributor.departmentDepartment of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, IS-101, and Department of Genetics and Molecular Medicine, Landspitali-University Hospital, Reykjavik, IS-101, Iceland.en_GB
dc.identifier.journalGeneen_GB
dc.rights.accessNational Consortium - Landsaðganguren
dc.type.categorySameinda, Hjartavernden_GB

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