Abstract
The exosome functions throughout eukaryotic RNA metabolism and has a prominent role in gene silencing in yeast. In Arabidopsis, exosome regulates expression of a “hidden” transcriptome layer from centromeric, pericentromeric, and other heterochromatic loci that are also controlled by small (sm)RNA-based de novo DNA methylation (RdDM). However, the relationship between exosome and smRNAs in gene silencing in Arabidopsis remains unexplored. To investigate whether exosome interacts with RdDM, we profiled Arabidopsis smRNAs by deep sequencing in exosome and RdDM mutants and also analyzed RdDM-controlled loci. We found that exosome loss had a very minor effect on global smRNA populations, suggesting that, in contrast to fission yeast, in Arabidopsis the exosome does not control the spurious entry of RNAs into smRNA pathways. Exosome defects resulted in decreased histone H3K9 dimethylation at RdDM-controlled loci, without affecting smRNAs or DNA methylation. Exosome also exhibits a strong genetic interaction with RNA Pol V, but not Pol IV, and physically associates with transcripts produced from the scaffold RNAs generating region. We also show that two Arabidopsis rrp6 homologues act in gene silencing. Our data suggest that Arabidopsis exosome may act in parallel with RdDM in gene silencing, by epigenetic effects on chromatin structure, not through siRNAs or DNA methylation.
Highlights
High-throughput analyses have revealed that eukaryotic genomes are pervasively transcribed [1,2,3,4], and the majority of the transcriptional activity takes place outside of protein-coding genes, producing non-coding RNAs derived from genome regions once thought to be transcriptionally silent, including intergenic and heterochromatic regions [1,2,3,5]
Conserved from archaea to humans, the exosome is a stable complex of RNase-like and RNA binding proteins that plays a central role in RNA metabolism in eukaryotes
We found that exosome depletion has only minor effects on smRNA populations that are acting in the main silencing mechanism in Arabidopsis, siRNAs–dependent DNA methylation RNA-based de novo DNA methylation (RdDM)
Summary
High-throughput analyses have revealed that eukaryotic genomes are pervasively transcribed [1,2,3,4], and the majority of the transcriptional activity takes place outside of protein-coding genes, producing non-coding RNAs (ncRNAs) derived from genome regions once thought to be transcriptionally silent, including intergenic and heterochromatic regions [1,2,3,5]. Many of the ncRNA transcripts earned the term ‘‘hidden’’ because they remain invisible unless RNA degradation is prevented, for example, by inactivation of the degradation machinery [1,3,4,10,11,12,13,14], raising the important question of how these ncRNAs are regulated
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
