Small RNA-mediated chromatin silencing directed to the 3' region of the Arabidopsis gene encoding the developmental regulator, FLC.
Small RNA-mediated chromatin silencing is well characterized for repeated sequences and transposons, but its role in regulating single-copy endogenous genes is unclear. We have identified two small RNAs (30 and 24 nucleotides) corresponding to the reverse strand 3' to the canonical poly(A) site of FLOWERING LOCUS C (FLC), an Arabidopsis gene encoding a repressor of flowering. Genome searches suggest that these RNAs originate from the FLC locus in a genomic region lacking repeats. The 24-nt small RNA, which is most abundant in developing fruits, is absent in mutants defective in RNA polymerase IVa, RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3, components required for RNAi-mediated chromatin silencing. The corresponding genomic region shows histone 3 lysine 9 dimethylation, which was reduced in a dcl2,3,4 triple mutant. Investigations into the origins of the small RNAs revealed a polymerase IVa-dependent spliced, antisense transcript covering the 3' FLC region. Mutation of this genomic region by T-DNA insertion led to FLC misexpression and delayed flowering, suggesting that RNAi-mediated chromatin modification is an important component of endogenous pathways that function to suppress FLC expression.
Swiezewski
Szymon
S
Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom.
Crevillen
Pedro
P
Liu
Fuquan
F
Ecker
Joseph R
JR
Jerzmanowski
Andrzej
A
Dean
Caroline
C
D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation; D012321:DNA-Directed RNA Polymerases / Q000235:genetics / Q000378:metabolism; D026161:MADS Domain Proteins / Q000235:genetics* / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000235:genetics*; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D043244:Ribonuclease III / Q000235:genetics / Q000378:metabolism
D029681:Arabidopsis Proteins; D002843:Chromatin; C418902:At5g10140 protein, Arabidopsis; D026161:MADS Domain Proteins; D034741:RNA, Small Interfering; C499181:RNA polymerase IV, Arabidopsis; D012324:RNA-Dependent RNA Polymerase; D012321:DNA-Directed RNA Polymerases; C519654:DCL3 protein, Arabidopsis; D043244:Ribonuclease III