Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis.
Intergenic transcription by RNA Polymerase II (Pol II) is widespread in plant and animal genomes, but the functions of intergenic transcription or the resulting noncoding transcripts are poorly understood. Here, we show that Arabidopsis Pol II is indispensable for endogenous siRNA-mediated transcriptional gene silencing (TGS) at intergenic low-copy-number loci, despite the presence of two other polymerases-Pol IV and Pol V-that specialize in TGS through siRNAs. We show that Pol II produces noncoding scaffold transcripts that originate outside of heterochromatic, siRNA-generating loci. Through these transcripts and physical interactions with the siRNA effector protein ARGONAUTE4 (AGO4), Pol II recruits AGO4/siRNAs to homologous loci to result in TGS. Meanwhile, Pol II transcription also recruits Pol IV and Pol V to different locations at heterochromatic loci to promote siRNA biogenesis and siRNA-mediated TGS, respectively. This study establishes that intergenic transcription by Pol II is required for siRNA-mediated TGS, and reveals an intricate collaboration and division of labor among the three polymerases in gene silencing.
Zheng
Binglian
B
Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California at Riverside, Riverside, California 92521, USA.
Wang
Zhengming
Z
Li
Shengben
S
Yu
Bin
B
Liu
Jin-Yuan
JY
Chen
Xuemei
X
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology* / Q000235:genetics*; D002843:Chromatin / Q000378:metabolism; D021901:DNA, Intergenic / Q000235:genetics*; D012321:DNA-Directed RNA Polymerases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D008969:Molecular Sequence Data; D009154:Mutation; D012319:RNA Polymerase II / Q000378:metabolism*; D034741:RNA, Small Interfering / Q000378:metabolism*; D016415:Sequence Alignment
D002843:Chromatin; D021901:DNA, Intergenic; D034741:RNA, Small Interfering; D012319:RNA Polymerase II; D012321:DNA-Directed RNA Polymerases