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Series GSE136847 Query DataSets for GSE136847
Status Public on Jan 23, 2020
Title Polymerase IV Plays a Crucial Role in Pollen Development in Capsella
Organisms Arabidopsis thaliana; Capsella rubella
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Other
Methylation profiling by high throughput sequencing
Summary In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernable pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae species Capsella rubella, caused post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were 2 depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nt and 24-nt siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella rubella compared to Arabidopsis thaliana, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.
 
Overall design 12 small RNA sequencing libraries, 8 RNA-seq libraries, 4 genome-wide cytosine methylation libraries and 6 whole genome sequencing libraries. 4 small RNA libraries were generated from Arabidopsis microspore of Col-0 wt and nrpd1a mutants. 4 small RNA libraries were generated from Capsella microspore of wt and nrpd1a mutants. 4 small RNA libraries were generated from Capsella leaves of wt and nrpd1a mutants. 4 RNA libraries were generated from Arabidopsis microspore of Col-0 wt and nrpd1a mutants. 4 RNA libraries were generated from Capsella microspore of wt and nrpd1a mutants. 4 genome-wide cytosine methylation libraries were generated from Capsella leaves of wt and nrpd1a mutants. 6 whole genome sequencing libraries were generated from Capsella leaves of wt and nrpd1a mutants.
 
Contributor(s) Wang Z, Butel N, Santos-Gonzalez J, Borges F, Yi J, Martienssen RA, Martinez G, Kohler C
Citation(s) 31988265
Submission date Sep 04, 2019
Last update date Apr 23, 2020
Contact name Juan C Santos-González
E-mail(s) juan.santos@slu.se
Organization name SLU
Department Department of Plant Biology and Forest Genetics
Lab Köhler's lab
Street address Almas Allé 5
City Uppsala
State/province Uppsala
ZIP/Postal code 75007
Country Sweden
 
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL25199 Illumina HiSeq 2500 (Capsella rubella)
Samples (32)
GSM4059332 at-microspore.sRNA.nrpd1a-3.replicate1
GSM4059333 at-microspore.sRNA.nrpd1a-3.replicate2
GSM4059334 at-microspore.sRNA.WT.replicate1
Relations
BioProject PRJNA563854
SRA SRP220305

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

Supplementary file Size Download File type/resource
GSE136847_RAW.tar 765.8 Mb (http)(custom) TAR (of TXT)
GSE136847_at.microspore.RNAseq.rpkm.txt.gz 681.6 Kb (ftp)(http) TXT
GSE136847_cr.leaves.TEs_detected_insertions.txt.gz 9.8 Kb (ftp)(http) TXT
GSE136847_cr.microspore.RNAseq.rpkm.txt.gz 862.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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