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Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica).
Mol Biol Evol. 2012 Oct; 29(10):3193-203.MB

Abstract

In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual elements. Our analyses uncover three strong trends: long LTR-RTs are more highly methylated, the insertion times of LTR-RTs are negatively correlated with methylation, and young LTR-RTs tend to be closer to genes than older insertions. Additionally, a phylogenetic examination of the gypsy-like LTR-RT superfamily revealed that methylation is phylogenetically correlated. Given these observations, we present a model suggesting that the phylogenetic correlation among related LTR-RTs is a primary mechanism driving methylation. In this model, bursts of transposition produce new elements with high sequence similarity. The host machinery identifies proliferating elements as well as closely related LTR-RTs through cross-homology. In addition, our data are consistent with previous hypotheses that methylated LTR-RT elements are removed preferentially from regions near genes, explaining some of the observed age distribution.

Authors+Show Affiliations

Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA. bvonhold@uci.eduNo affiliation info availableNo affiliation info available

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

22593226

Citation

Vonholdt, Bridgett M., et al. "Recent Retrotransposon Insertions Are Methylated and Phylogenetically Clustered in Japonica Rice (Oryza Sativa Spp. Japonica)." Molecular Biology and Evolution, vol. 29, no. 10, 2012, pp. 3193-203.
Vonholdt BM, Takuno S, Gaut BS. Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Mol Biol Evol. 2012;29(10):3193-203.
Vonholdt, B. M., Takuno, S., & Gaut, B. S. (2012). Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). Molecular Biology and Evolution, 29(10), 3193-203.
Vonholdt BM, Takuno S, Gaut BS. Recent Retrotransposon Insertions Are Methylated and Phylogenetically Clustered in Japonica Rice (Oryza Sativa Spp. Japonica). Mol Biol Evol. 2012;29(10):3193-203. PubMed PMID: 22593226.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Recent retrotransposon insertions are methylated and phylogenetically clustered in japonica rice (Oryza sativa spp. japonica). AU - Vonholdt,Bridgett M, AU - Takuno,Shohei, AU - Gaut,Brandon S, Y1 - 2012/05/15/ PY - 2012/5/18/entrez PY - 2012/5/18/pubmed PY - 2013/2/7/medline SP - 3193 EP - 203 JF - Molecular biology and evolution JO - Mol Biol Evol VL - 29 IS - 10 N2 - In plants, the genome of the host responds to the amplification of transposable elements (TEs) with DNA methylation. However, neither the factors involved in TE methylation nor the dynamics of the host-TE interaction are well resolved. Here, we identify 5,522 long terminal repeat retrotransposons (LTR-RT) in the genome of Oryza sativa ssp. japonica and then assess methylation for individual elements. Our analyses uncover three strong trends: long LTR-RTs are more highly methylated, the insertion times of LTR-RTs are negatively correlated with methylation, and young LTR-RTs tend to be closer to genes than older insertions. Additionally, a phylogenetic examination of the gypsy-like LTR-RT superfamily revealed that methylation is phylogenetically correlated. Given these observations, we present a model suggesting that the phylogenetic correlation among related LTR-RTs is a primary mechanism driving methylation. In this model, bursts of transposition produce new elements with high sequence similarity. The host machinery identifies proliferating elements as well as closely related LTR-RTs through cross-homology. In addition, our data are consistent with previous hypotheses that methylated LTR-RT elements are removed preferentially from regions near genes, explaining some of the observed age distribution. SN - 1537-1719 UR - https://www.unboundmedicine.com/medline/citation/22593226/Recent_retrotransposon_insertions_are_methylated_and_phylogenetically_clustered_in_japonica_rice__Oryza_sativa_spp__japonica__ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/mss129 DB - PRIME DP - Unbound Medicine ER -