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Series GSE146913 Query DataSets for GSE146913
Status Public on Nov 16, 2020
Title Broad non-coding transcription suggests genome surveillance by RNA Polymerase V
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Eukaryotic genomes are pervasively transcribed, yet most transcribed sequences lack conservation or known biological functions. In Arabidopsis thaliana RNA polymerase V (Pol V) produces non-coding transcripts, which base-pair with small interfering RNA (siRNA) and allow specific establishment of RNA-directed DNA methylation (RdDM) on transposable elements. Here, we show that Pol V transcribes much more broadly than previously expected, including subsets of both heterochromatic and euchromatic regions. At already established RdDM targets Pol V and siRNA work together to maintain silencing. In contrast, some euchromatic sequences do not give rise to siRNA but are covered by low levels of Pol V transcription, which is needed to establish RdDM de novo if a transposon is reactivated. We propose a model where Pol V surveils the genome to make it competent to silence newly activated or integrated transposons. This indicates that pervasive transcription of non-conserved sequences may serve an essential role in maintenance of genome integrity.
Overall design Immunoprecipitation followed by Analysis of RNA Ends (IPARE) with an anti-NRPE1 antibody was performed on 24 samples, which include 11 different genotypes (Col-0:6replicates; nrpe1:5replicates; spt5l,ago4,dms5-1,drd3-3: 2replicates each, drd1,dms3,suvh2, suvh9, suvh2/suvh9: 1replicate each)
Contributor(s) Tsuzuki M, Sethuraman S, Coke AN, Rothi MH, Boyle AP, Wierzbicki AT
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Submission date Mar 12, 2020
Last update date Nov 16, 2020
Contact name Shriya Sethuraman
Organization name University of Michigan
Department Bioinformatics
Lab Andrzej Wierzbicki lab
Street address 5164 Biological Sciences Building, 1105 N. University Ave.
City Ann Arbor
State/province MI
ZIP/Postal code 48105
Country USA
Platforms (2)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (28)
GSM4409524 Col-0_IPARE_rep1
GSM4409525 nrpe1_IPARE_rep1
GSM4409526 spt5l_IPARE_rep1
BioProject PRJNA612354
SRA SRP252639

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Supplementary file Size Download File type/resource
GSE146913_200bp_150bp_sliding_windows_allDatasets_coverages.bed.gz 18.7 Mb (ftp)(http) BED
GSE146913_RdDM_PolV_transcribed_HMM_bins.bed.gz 787.1 Kb (ftp)(http) BED
GSE146913_nonPolV_transcribed_HMM_bins.bed.gz 2.1 Mb (ftp)(http) BED
GSE146913_nonRdDM_PolV_transcribed_HMM_bins.bed.gz 1.1 Mb (ftp)(http) BED
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Processed data are available on Series record

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