GSE113078
Genome-wide profiling (ChIP-seq) of RNA polymerase II in wild-type, fpa mutant and bdrs triple mutant
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. Overall design: ChIP-seq profiles in 7 or 8-day old seedlings of RNAPII (ab817, unphosphorylated repeats), S2P (ab5095, Ser2-phosphorylated repeats) or S5P RNAPII (ab5131, Ser5-phosphorylated repeats) in wild-type, fpa single mutant (fpa-7) or bdrs triple mutant were generated by deep sequencing on an Illumina NextSeq500. Biological duplicates or triplicates (independent experiments) were obtained for ChIPs on wild-type and  bdrs triple mutant. Sequencing duplicates (same library, different sequencing runs) were obtained for a ChIP with ab817 for one wild-type and one bdrs sample. Controls include input samples and a ChIP performed with a non-specific IgG.