Study : Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings
Identification
Name
Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings
Identifier
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Source
Description
We analyzed by RNA-seq the transcriptome of 8-day old Arabidopsis thaliana seedlings for wild-type (Col-0), 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 occupy 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 (Col-0), fpa single mutant (fpa/AT2G43410) or bdrs triple mutant (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905) were generated by deep sequencing, in triplicates, on Illumina HiSeq2000
Genotype
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