RNA-mediated transcriptional silencing prevents deleterious effects of transposon activity and controls the expression of protein-coding genes. It involves long non-coding RNAs (lncRNAs)1, which in Arabidopsis thaliana are produced by a specialized RNA Polymerase V (Pol V)2. lncRNAs guide Argonaute-siRNA complexes to specific genomic loci and mediate the establishment of DNA methylation3,4. The mechanism by which lncRNAs affect chromatin structure and mRNA production remains mostly unknown. Here we identify the SWI/SNF nucleosome remodeling complex as a component of the RNA-mediated transcriptional silencing pathway. We found that SWI3, an essential subunit of the SWI/SNF complex, physically interacts with a lncRNA-binding IDN2 protein5,6. RNA-mediated DNA methylation and transcriptional silencing was compromised in the swi3 mutant. Moreover, targets of SWI/SNF significantly overlapped with genes controlled by Pol V, which shows that the physical interaction reflects a functional relationship. We further found that non-coding transcription by Pol V affects nucleosome positioning on silenced regions. We propose that lncRNAs mediate transcriptional silencing by guiding the SWI/SNF complex and establishing positioned nucleosomes on specific genomic loci. We further propose that guiding ATP-dependent chromatin remodeling complexes may be a more general function of lncRNAs. RNA-seq of 3 samples (Col-0, nrpe1 [a mutant defective in the largest subunit of Pol V and unable to produce lncRNA], swi3b, idn2) with 3 biological replicates.
ANAC003 UP in 'nrpe1' vs 'wild type genotype'
AT1G49500 UP in 'idn2-1' vs 'wild type genotype'
DML1 DOWN in 'idn2-1' vs 'wild type genotype'
AT2G07733 DOWN in 'idn2-1' vs 'wild type genotype'
AT4G04223 UP in 'idn2-1' vs 'wild type genotype'
AT1G56090 DOWN in 'nrpe1' vs 'wild type genotype'
AT5G27845 UP in 'nrpe1' vs 'wild type genotype'
GRXS5 UP in 'idn2-1' vs 'wild type genotype'
GRXS4 UP in 'idn2-1' vs 'wild type genotype'
AT3G29644 UP in 'idn2-1' vs 'wild type genotype'
Analysis of 'idn2-1' vs 'wild type genotype'
AT1G33840 UP in 'nrpe1' vs 'wild type genotype'
SEN1 DOWN in 'idn2-1' vs 'wild type genotype'
AT2G35382 UP in 'idn2-1' vs 'wild type genotype'
GRXS3 UP in 'idn2-1' vs 'wild type genotype'
AT4G04293 UP in 'nrpe1' vs 'wild type genotype'
AT2G06002 DOWN in 'nrpe1' vs 'wild type genotype'
AT1G33850 UP in 'nrpe1' vs 'wild type genotype'
AT3G59765 UP in 'idn2-1' vs 'wild type genotype'
PSBE DOWN in 'idn2-1' vs 'wild type genotype'
MYR1 DOWN in 'idn2-1' vs 'wild type genotype'
GRXS13 UP in 'idn2-1' vs 'wild type genotype'
AT1G12730 DOWN in 'nrpe1' vs 'wild type genotype'
Analysis of 'swi3b +/-' vs 'wild type genotype'
AT5G35207 UP in 'nrpe1' vs 'wild type genotype'
AT1G11785 UP in 'idn2-1' vs 'wild type genotype'
ATMRU1 UP in 'idn2-1' vs 'wild type genotype'
RSU1 UP in 'nrpe1' vs 'wild type genotype'
AT3G29644 UP in 'nrpe1' vs 'wild type genotype'
AT5G28300 DOWN in 'idn2-1' vs 'wild type genotype'
ATPF DOWN in 'idn2-1' vs 'wild type genotype'
AT5G61190 DOWN in 'idn2-1' vs 'wild type genotype'
AT1G62310 DOWN in 'idn2-1' vs 'wild type genotype'
AT2G05200 UP in 'nrpe1' vs 'wild type genotype'
NRPD1B DOWN in 'nrpe1' vs 'wild type genotype'
AT1G13650 UP in 'nrpe1' vs 'wild type genotype'
AT3G54730 UP in 'idn2-1' vs 'wild type genotype'
DML1 DOWN in 'nrpe1' vs 'wild type genotype'
GRXS10 UP in 'idn2-1' vs 'wild type genotype'
AT2G16310 UP in 'nrpe1' vs 'wild type genotype'
Analysis of 'nrpe1' vs 'wild type genotype'
AT3G48131 UP in 'nrpe1' vs 'wild type genotype'
AT3G54770 UP in 'idn2-1' vs 'wild type genotype'
AT3G29644 UP in 'swi3b +/-' vs 'wild type genotype'
(Factor value) GENOTYPE/wild type genotype