title: An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs.
abstract: BACKGROUND
  Small RNAs generated by RNA polymerase IV (Pol IV) are the most abundant class of small RNAs in flowering plants. In Arabidopsis thaliana Pol IV-dependent short interfering (p4-si)RNAs are imprinted and accumulate specifically from maternal chromosomes in the developing seeds. Imprinted expression of protein-coding genes is controlled by differential DNA or histone methylation placed in gametes. To identify epigenetic factors required for maternal-specific expression of p4-siRNAs we analyzed the effect of a series of candidate mutations, including those required for genomic imprinting of protein-coding genes, on uniparental expression of a representative p4-siRNA locus.
  
  
  RESULTS
  Paternal alleles of imprinted genes are marked by DNA or histone methylation placed by DNA METHYLTRANSFERASE 1 or the Polycomb Repressive Complex 2. Here we demonstrate that repression of paternal p4-siRNA expression at locus 08002 is not controlled by either of these mechanisms. Similarly, loss of several chromatin modification enzymes, including a histone acetyltransferase, a histone methyltransferase, and two nucleosome remodeling proteins, does not affect maternal expression of locus 08002. Maternal alleles of imprinted genes are hypomethylated by DEMETER DNA glycosylase, yet expression of p4-siRNAs occurs irrespective of demethylation by DEMETER or related glycosylases.
  
  
  CONCLUSIONS
  Differential DNA methylation and other chromatin modifications associated with epigenetic silencing are not required for maternal-specific expression of p4-siRNAs at locus 08002. These data indicate that there is an as yet unknown epigenetic mechanism causing maternal-specific p4-siRNA expression that is distinct from the well-characterized mechanisms associated with DNA methylation or the Polycomb Repressive Complex 2.
authors: Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom. rmosher@cals.arizona.edu
authors: Rebecca A
authors: RA
authors: Mosher
authors: Ek Han
authors: EH
authors: Tan
authors: Juhyun
authors: J
authors: Shin
authors: Robert L
authors: RL
authors: Fischer
authors: Craig S
authors: CS
authors: Pikaard
authors: David C
authors: DC
authors: Baulcombe
mesh_terms: D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000378:metabolism; D032461:Chromosomes, Plant / Q000235:genetics; D045647:DNA Glycosylases / Q000378:metabolism; D019175:DNA Methylation / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D056625:Endosperm / Q000201:enzymology / Q000235:genetics / Q000378:metabolism; D044127:Epigenesis, Genetic / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D056426:Genetic Loci / Q000235:genetics; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D008239:Lysine; D034741:RNA, Small Interfering / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D006657:Histones; D034741:RNA, Small Interfering; C499181:RNA polymerase IV, Arabidopsis; D012321:DNA-Directed RNA Polymerases; D045647:DNA Glycosylases; D008239:Lysine