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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

ABSTRACT: 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

PROVIDER: PRJNA449932 | 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.

2019-08-08 | GSE113076 | GEO

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.

2019-08-08 | GSE112441 | GEO

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.

2019-08-08 | GSE113078 | GEO

Genome-wide occupancy of BDR1, BDR2 and FPA (ChIP-seq)

Project description:We generated Arabidopsis lines expressing tagged (3X Myc tag) versions of BDR1 or BDR2 driven by their endogenous promoters on a bdrs triple mutant background (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). The genome-wide distribution of BDR1 and BDR2 in 8-day old seedlings were analyzed by ChIP-seq using an anti Myc antibody. We also analyzed by ChIP-seq the genome-wide distribution of FPA (AT2G43410) in wild-type seedlings using a rabbit anti-FPA polyclonal antibody raised against the C-terminal portion (position 536-901) of the FPA protein. Controls include sequencing of input DNA for each sample and a ChIP perfomed in wild-type seedlings with the anti-Myc tag antibody. We found that BDR1 and BDR2 are enriched at the border of a large number of genes in Arabidopsis genome and that FPA localizes mostly at the 3' end of genes.

2019-08-08 | GSE113059 | GEO

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

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

| PRJNA446047 | ENA

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

| PRJNA446046 | ENA

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

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

| PRJNA449936 | ENA

Gene expression profiling (RNA-seq) in wild-type and bdrs triple mutant Arabidopsis seedlings in response to light or to a heat shock

Project description:We analyzed by RNA-seq the modulation of the transcriptome in response to light or a heat shock in wild-type and bdrs triple mutant Arabidopsis thaliana seedlings (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We showed that the overall changes in the transcriptome were very similar in the two genotypes. However, when studying specifically gene pairs organized in tandem and with short intergenic distances, we showed that the rapid and strong regulations of upstream genes was associated with bdrs-dependent changes on the downstream gene expression that are consistent with bdrs-dependent transcriptional interferences.

2019-08-08 | GSE112442 | GEO

Extensive intergenic transcription from loss of Arabidopsis 3’ regulators FCA and FPA

Project description:The Arabidopsis RNA-binding proteins FCA and FPA were initially identified based on their suppression of the flowering time regulator FLC. Recently, however, they have been found to influence expression of a wide range of targets in the Arabidopsis genome. Here, we use whole-genome tiling arrays to determine the extent of their targets at two stages of seedling development. A wide range of genes and transposable elements were mis-expressed in the fcafpa double mutant with a significant bias for mis-regulated genomic segments mapping to the 3’ region of genes. A large number of previously unannotated (UA) genomic segments, which mapped to intergenic regions, were also mis-expressed in the fcafpa double mutant. We characterized a subset of these UA segments in detail and established them as strand-specific and direct targets of FCA and FPA, with a complex interplay between their functions. Only a few of the UA segments also showed regulation by a histone demethylase previously linked to FCA FPA function; however, others were associated with siRNA production and DNA methylation. Our data suggest that FCA/FPA play important roles in terminating transcription at many loci, often via promotion of proximal polyadenylation, and that in their absence, ectopic transcription and/or extensive read-through transcription occurs. These transcriptional products have the potential to interfere with overlapping transcripts and flanking genes and appear to form the basis for how modulation of FCA FPA function triggers RNA-mediated chromatin silencing mechanisms at a variety of loci in the Arabidopsis genome.

2011-07-11 | GSE24364 | GEO

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