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Series GSE99692 Query DataSets for GSE99692
Status Public on Apr 14, 2018
Title Locus-specific control of the de novo DNA methylation pathway [smRNA-seq]
Organism Arabidopsis thaliana
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Abstract: Cytosine DNA methylation plays crucial roles in gene regulation, transposon silencing, and diverse developmental processes. While methylation patterns are known to differ between cell-types, tissues, and disease states, how these differences arise remains poorly understood. In plants, DNA methylation is established via the RNA-directed DNA methylation pathway (RdDM), wherein 24-nucleotide small interfering RNAs (siRNAs) guide methylation at cognate genomic loci1. RNA POLYMERASE-IV (Pol-IV), a plant-specific polymerase, initiates the biogenesis of these methylation-targeting RNAs, thus understanding how Pol-IV is regulated is critical in determining how specific patterns of DNA methylation are generated. Here we show roles for four Pol-IV-associated factors, CLASSY (CLSY) 1-42,3, in both locus-specific and global regulation of Pol-IV function. Individually, each CLSY protein controls siRNA production and Pol-IV chromatin association at unique set of loci. This translates into locus-specific DNA methylation losses and the release of silencing. In addition to locus-specific effects, several layers of redundancy were identified: The clsy1,2 and clsy3,4 mutants act synergistically, regulating thousands more siRNA loci than the single mutants. Furthermore, the clsy1,2- and clsy3,4-dependent loci are mutually exclusive and geographically distinct, revealing a striking division of labor amongst the CLSY family. Finally, the clsy quadruple mutant causes global siRNA losses, demonstrating that Pol-IV is completely dependent on the CLSY family. Investigation into the mechanisms underlying the CLSY specificity revealed connections between clsy1,2- and clsy3,4-dependent loci and either SAWADEE HOMEODOMAIN HOMOLOG 1 or DNA METHYLTRANSFERASE 1, demonstrating a reliance on different chromatin modifications, H3K9 or CG DNA methylation, respectively4,5. Together, these findings not only shed light on Pol-IV function, but also reveal an additional layer of complexity to the RdDM pathway that enables the locus-specific control of DNA methylation patterns. Given the parallels between methylation systems in plants and mammals1, these findings will be informative for analogous processes in a broad range of organisms.
 
Overall design 45 smRNA-seq libraries were sequenced
 
Contributor(s) Zhou M, Law J
Citation(s) 29736015, 35017514
Submission date Jun 05, 2017
Last update date Jan 28, 2022
Contact name Julie Law
E-mail(s) jlaw@salk.edu
Phone 8584534100
Organization name Salk Institute for Biological Studies
Lab Julie Law lab
Street address 10010 N Torrey Pines Rd, La Jolla
City San Diego
State/province CALIFORNIA
ZIP/Postal code 92037
Country USA
 
Platforms (1)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
Samples (45)
GSM2650248 WT_1_rep1_smRNA-seq
GSM2650249 WT_2_rep1_smRNA-seq
GSM2650250 WT_3_rep1_smRNA-seq
This SubSeries is part of SuperSeries:
GSE99694 Locus-specific control of the de novo DNA methylation pathway
Relations
BioProject PRJNA389307
SRA SRP108635

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE99692_RAW.tar 425.8 Mb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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