title: Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs.
abstract: Transposable elements (TEs) are known to influence the regulation of neighboring genes through a variety of mechanisms. Additionally, it was recently discovered that TEs can regulate non-neighboring genes through the trans-acting nature of small interfering RNAs (siRNAs). When the epigenetic repression of TEs is lost, TEs become transcriptionally active, and the host cell acts to repress mutagenic transposition by degrading TE mRNAs into siRNAs. In this study, we have performed a genome-wide analysis in the model plant Arabidopsis thaliana and found that TE siRNA-based regulation of genic mRNAs is more pervasive than the two formerly characterized proof-of-principle examples. We identified 27 candidate genic mRNAs that do not contain a TE fragment but are regulated through partial complementarity by the accumulation of TE siRNAs and are therefore influenced by TE epigenetic activation. We have experimentally confirmed several gene targets and demonstrated that they respond to the accumulation of specific 21 nucleotide TE siRNAs that are incorporated into the Arabidopsis Argonaute1 protein. Additionally, we found that one TE siRNA specifically targets and inhibits the formation of a host protein that acts to repress TE activity, suggesting that TEs harbor and potentially evolutionarily select short sequences to act as suppressors of host TE repression.
authors.affiliation: Department of Molecular Genetics & Center for RNA Biology; The Ohio State University; Columbus, OH, USA.
authors.forename: Andrea D
authors.initials: AD
authors.lastname: McCue
authors.forename: Saivageethi
authors.initials: S
authors.lastname: Nuthikattu
authors.forename: R Keith
authors.initials: RK
authors.lastname: Slotkin
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D060565:Argonaute Proteins / Q000235:genetics / Q000378:metabolism; D004251:DNA Transposable Elements; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D017343:Genes, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: C117457:AGO1 protein, Arabidopsis; D029681:Arabidopsis Proteins; D060565:Argonaute Proteins; D004251:DNA Transposable Elements; D012333:RNA, Messenger; D018749:RNA, Plant; D034741:RNA, Small Interfering
keywords: Arabidopsis; epigenetics; microRNA; post-transcriptional silencing; small interfering RNA; transposable element; transposon