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RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings

ABSTRACT: RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings

PROVIDER: PRJNA446041 | ENA |

REPOSITORIES: ENA

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Genome-wide profiling of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP-seq) in wild-type, fpa mutant and bdrs triple mutant

Project description:We used an MNase digestion of chromatin from Arabidopsis seedlings, combined or not with ChIP (native ChIP), to analyze by high-throughput sequencing the genome-wide profiles of nucleosomes (MNase-seq), and of total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIPs) in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and 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 found that BDR proteins occupy regions of low nucleosome density. We also observed that genes upregulated in bdrs triple mutant display high levels of RNA polymerase II on their gene bodies but low levels of H3K4me3 and H3K36me3 in wild-type seedlings. For genes with the highest levels of BDR occupancy in wild-type, increased mRNA expression in bdrs mutant is associated with reduced RNA polymerase II density profile and increased H3K4me3 and H3K36me3 levels.

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Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings

Project 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.

2019-08-08 | GSE112440 | GEO

Gene expression profiling by RNA-seq of wild-type, fpa mutant, bdr1 mutant, bdr2 mutant, bdr3 mutant and bdrs triple mutant Arabidopsis seedlings

Project description: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.

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Genome-wide profiling (ChIP-seq) of RNA polymerase II in wild-type, fpa mutant and bdrs triple mutant

Project description:We used 3 different antibodies targeting the YSPTSPS repeats of the C-terminal domain (CTD) of the Rpb1 subunit of RNA polymerase II (ab817: non phosphorylated repeats, ab5095: phospho Ser2 repeats and ab5131: phospho Ser5 repeats) to obtain genome-wide profiles by ChIP-seq of the localization of RNA polymerase II in wild-type (Col-0), fpa mutant (fpa/AT2G43410, line fpa-7) and 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 found that BDR proteins are involved in RNA polymerase II 3' pausing and that their deletion generates transcriptional interferences in closely spaced, tandemly organized, gene pairs.

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Project description:Gene expression profiling in wild-type, fpa mutant and bdrs triple mutant Arabidopsis seedlings

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Project description:Genome-wide profiling of nucleosomes (MNase-seq), total H3, H3K4me2, H3K4me3 and H3K36me3 (native ChIP-seq) in wild-type, fpa mutant and bdrs triple mutant

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MNase-seq and RNA-seq of linker histone H1 mutant

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RNA-seq, ChIP-seq and MNase-seq in WT, fpa mutant and bdr1,2,3 mutant Arabidopsis seedlings

Project description:This SuperSeries is composed of the SubSeries listed below.

2019-08-08 | GSE112443 | GEO