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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
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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.
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Overall design |
45 smRNA-seq libraries were sequenced
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Contributor(s) |
Zhou M, Law J |
Citation(s) |
29736015, 35017514 |
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Submission date |
Jun 05, 2017 |
Last update date |
Jan 28, 2022 |
Contact name |
Julie Law |
E-mail(s) |
jlaw@salk.edu
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Phone |
8584534100
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Organization name |
Salk Institute for Biological Studies
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Lab |
Julie Law lab
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Street address |
10010 N Torrey Pines Rd, La Jolla
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City |
San Diego |
State/province |
CALIFORNIA |
ZIP/Postal code |
92037 |
Country |
USA |
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Platforms (1) |
GPL17639 |
Illumina HiSeq 2500 (Arabidopsis thaliana) |
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Samples (45)
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GSM2650251 |
clsy1-7_rep1_smRNA-seq |
GSM2650252 |
clsy2-2_rep1_smRNA-seq |
GSM2650253 |
clsy3-1_rep1_smRNA-seq |
GSM2650254 |
clsy4-1_rep1_smRNA-seq |
GSM2650255 |
clsy1-7,2-2_rep1_smRNA-seq |
GSM2650256 |
clsy1-7,3-1_rep1_smRNA-seq |
GSM2650257 |
clsy1-7,4-1_rep1_smRNA-seq |
GSM2650258 |
clsy2-2,3-1_rep1_smRNA-seq |
GSM2650259 |
clsy2-2,4-1_rep1_smRNA-seq |
GSM2650260 |
clsy3-1,4-1_rep1_smRNA-seq |
GSM2650261 |
clsy1-7,2-1,3-1,4-1_rep1_smRNA-seq |
GSM2650262 |
clsy1-7,2-2,3-1,4-1_rep1_smRNA-seq |
GSM2650263 |
shh1-1_rep1_smRNA-seq |
GSM2650264 |
shh1-1,clsy1-7_rep1_smRNA-seq |
GSM2650265 |
shh1-1,clsy1-7,2-1_rep1_smRNA-seq |
GSM2650266 |
shh1-1,clsy3-1,4-1_rep1_smRNA-seq |
GSM2650267 |
nrpd1-4_rep1_smRNA-seq |
GSM2650268 |
drm1-2,2-2_rep1_smRNA-seq |
GSM2650269 |
cmt2-7_rep1_smRNA-seq |
GSM2650270 |
cmt3-11_rep1_smRNA-seq |
GSM2650271 |
MET1-3wt_rep1_smRNA-seq |
GSM2650272 |
MET1-3wt_rep2_smRNA-seq |
GSM2650273 |
met1-3_rep1_smRNA-seq |
GSM2650274 |
met1-3_rep2_smRNA-seq |
GSM2650275 |
ddm1-2_rep1_smRNA-seq |
GSM2650276 |
atxr5,6_rep1_smRNA-seq |
GSM2650277 |
suvh4,5,6_rep1_smRNA-seq |
GSM2650278 |
WT_4_rep2_smRNA-seq |
GSM2650279 |
WT_5_rep2_smRNA-seq |
GSM2650280 |
clsy1-7_rep2_smRNA-seq |
GSM2650281 |
clsy2-2_rep2_smRNA-seq |
GSM2650282 |
clsy3-1_rep2_smRNA-seq |
GSM2650283 |
clsy4-1_rep2_smRNA-seq |
GSM2650284 |
nrpd1-4_rep2_smRNA-seq |
GSM2892116 |
clsy1-7,2-1_rep1_smRNA-seq |
GSM2892117 |
clsy2-1_rep2_smRNA-seq |
GSM2892118 |
WT_6_rep3_smRNA-seq |
GSM2892119 |
WT_7_rep3_smRNA-seq |
GSM2892120 |
clsy1-10_rep3_smRNA-seq |
GSM2892121 |
clsy3-2_rep3_smRNA-seq |
GSM2892122 |
clsy4-2_rep3_smRNA-seq |
GSM2892123 |
clsy3-2,4-2_rep3_smRNA-seq |
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This SubSeries is part of SuperSeries: |
GSE99694 |
Locus-specific control of the de novo DNA methylation pathway |
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Relations |
BioProject |
PRJNA389307 |
SRA |
SRP108635 |
Supplementary file |
Size |
Download |
File type/resource |
GSE99692_RAW.tar |
425.8 Mb |
(http)(custom) |
TAR (of BEDGRAPH) |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data are available in SRA |
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