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Series GSE112441 Query DataSets for GSE112441
Status Public on Aug 08, 2019
Title Gene expression profiling by RNA-seq of wild-type, fpa mutant, bdr1 mutant, bdr2 mutant, bdr3 mutant and bdrs triple mutant Arabidopsis seedlings
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), single mutants for BDR proteins (bdr1/AT5G25520 ; bdr2/AT5G11430 or bdr3/AT2G25640), single mutant for FPA (fpa/AT2G43410, line fpa-7) or a triple mutant of all three BDR proteins (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We identified hundreds of genes differentially expressed between wild-type and bdrs triple mutant and a significant overlap in DE genes with the fpa mutant. We also analyzed the binding of BDR1 and BDR2 as well as RNA polymerase II and histone marks by ChIP-seq in wild-type, bdrs and fpa-deficient seedlings. Our data support a role of BDRs as negative elongation factors. They bind on the gene body and regulate the expression of genes involved in defense response pathways. Strikingly, by modulating 3' pausing of RNA polymerase II and possibly contributing to gene looping, they also protect a number of genes from transcriptional interferences originating from a highly expressed upstream tandem gene. Thus BDRs proteins are negative elongation factors that act as transcriptional "gatekeepers" in the Arabidopsis thaliana genome.
 
Overall design mRNA profiles in 8-day old seedlings from wild-type (Col0), bdr single mutants (bdr1/AT5G25520 ; bdr2/AT5G11430 or bdr3/AT2G25640), fpa single mutant (fpa/AT2G43410) or bdr triple mutant were generated by deep sequencing, in triplicates, on Illumina NextSeq500
 
Contributor(s) Michaels SD, Martin PG, Yu X, Huang J, Ford JB
Citation(s) 31554790
Submission date Mar 28, 2018
Last update date Nov 07, 2019
Contact name Pascal GP Martin
E-mail(s) pascal.martin@inrae.fr
Organization name INRAE
Department UMR1332 BFP
Lab FDFE
Street address 71 avenue Edouard Bourlaux
City Villenave d'Ornon
ZIP/Postal code 33140
Country France
 
Platforms (1)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
Samples (18)
GSM3070160 WT_rep1
GSM3070161 WT_rep2
GSM3070162 WT_rep3
This SubSeries is part of SuperSeries:
GSE112443 RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings
Relations
BioProject PRJNA446046
SRA SRP136640

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Supplementary file Size Download File type/resource
GSE112441_GSF1238_NormalizedCounts_bdrs.txt.gz 2.6 Mb (ftp)(http) TXT
GSE112441_GSF1238_RawCounts_bdrs.txt.gz 718.7 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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