Gene capture by transposable elements leads to epigenetic conflict in maize  

作　　者：Aline Muyle Danelle Seymour Nikos Darzentas Elias Primetis Brandon S.Gaut Alexandros Bousios 

机构地区：[1]Department of Ecology and Evolutionary Biology,UC Irvine,Irvine,CA 92697,USA [2]Department of Botany and Plant Sciences,UC Riverside,Riverside,CA 92521,USA [3]Central European Institute of Technology,Masaryk University,Brno,Czech Republic [4]School of Life Sciences,University of Sussex,Brighton,UK

出　　处：《Molecular Plant》2021年第2期237-252,共16页分子植物（英文版）

基　　金：A.M.is supported by an EMBO Postdoctoral Fellowship ALTF 775-2017 and by HFSPO Fellowship LT000496/2018-L;D.K.S.is supported by a Postdoctoral Fellowship from the National Science Foundation(NSF)Plant Genome Research Program(1609024);B.S.G.is supported by an NSF grant 1655808;A.B.is supported by The Royal Society(award nos.UF160222 and RGF/R1/180006).

摘　　要：Transposable elements(TEs)regularly capture fragments of genes.When the host silences these TEs,siRNAs homologous to the captured regions may also target the genes.This epigenetic crosstalk establishes an intragenomic conflict:silencing the TEs has the cost of silencing the genes.If genes are important,however,natural selection may maintain function by moderating the silencing response,which may also advantage the TEs.In this study,we examined this model by focusing on Helitrons,Pack-MULEs,and Sirevirus LTR retrotransposons in the maize genome.We documented 1263 TEs containing exon fragments from 1629 donor genes.Consistent with epigenetic conflict,donor genes mapped more siRNAs and were more methylated than genes with no evidence of capture.However,these patterns differed between syntelog versus translocated donor genes.Syntelogs appeared to maintain function,as measured by gene expression,consistent with moderation of silencing for functionally important genes.Epigenetic marks did not spread beyond their captured regions and 24nt crosstalk siRNAs were linked with CHH methylation.Translocated genes,in contrast,bore the signature of silencing.They were highly methylated and less expressed,but also overrepresented among donor genes and located away from chromosomal arms,which suggests a link between capture and gene movement.Splitting genes into potential functional categories based on evolutionary constraint supported the synteny-based findings.TE families captured genes in different ways,but the evidence for their advantage was generally less obvious;nevertheless,TEs with captured fragments were older,mapped fewer siRNAs,and were slightly less methylated than TEs without captured fragments.Collectively,our results argue that TE capture triggers an intragenomic conflict that may not affect the function of important genes but may lead to the pseudogenization of less-constrained genes.

关 键 词：transposable elements intragenomic conflict gene capture epigenetic silencing METHYLATION SYNTENY 

分 类 号：S513[农业科学—作物学]