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Gene expression change of M1 and BY-P41K-RPB7 in YPAD (OD600 reached 1) and after 12h Very High Gravity (VHG) fermentation

ABSTRACT: To further study the transcription profile of mutant M1 and its control (BY-P41K-RPB7), we have employed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in YPAD medium under OD600 reached 1 and after 12 VHG fermentation.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE77853 | GEO | 2016/02/12

SECONDARY ACCESSION(S): PRJNA311732

REPOSITORIES: GEO

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Gene expression change of M1 and BY-P41K-RPB7 in YPAD (OD600 reached 1) and after 12h Very High Gravity (VHG) fermentation

Project description:To further study the transcription profile of mutant M1 and its control (BY-P41K-RPB7), we have employed whole genome microarray expression profiling as a discovery platform to identify differentially expressed genes in YPAD medium under OD600 reached 1 and after 12 VHG fermentation. Total cellular RNAs were extracted from both the mutant and the control using RNeasyÂ® Mini Kit and RNase-Free DNase Set (Qiagen,Hilden, Germany) under the following two conditions: i) when cells reached early exponential phase (OD600 ~1.0) in YPAD; ii) after 12h VHG fermentation. RNA quality and integrity was verified by gel electrophoresis, as well as by measuring 260/230 ratios with a NanoDrop 1000 spectrophotometer (Thermo Scientific, MA, USA). Two biological replicates of each sample were sent to Genomax Technologies (Singapore) for DNA microarray assay using Yeast (V2) Gene Expression Microarray, 8Ã?15K Microarrays (Agilent technologies, USA). The obtained data was analyzed by Agilent Genespring GX software and the p-values were calculated by unpaired Student t-test.

2016-02-12 | E-GEOD-77853 | biostudies-arrayexpress

CTDP1 and RPB7 Stabilize Pol II and Permit Reinitiation

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RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChAR-Seq]

Project description:The regulations of transcription process have been extensively investigated, but how RNA Pol II terminates and reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. RPB7 degradation combing knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop-region and dimerization of RPB7 and the phosphorylation state of Pol II CTD. Site-specific cancer mutations in the RPB7 loop-region caused the dysregulations of specific gene expression. Moreover, the loss of RPB7 or CTD phosphatase subunit 1 (CTDP1) result in the defects in Pol II termination-reinitiation recycle. Together, our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

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RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [RNA-Seq]

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RPB7/CTDP1 stabilizes and licenses Pol II termination to reinitiation [ChIP-Seq]

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CTDP1 and RPB7 stabilize and license Pol II termination to reinitiation [PRO-seq]

Project description:The regulations of RNA Pol II initiation, elongation, and termination have been extensively investigated in mammalian cells, but how RNA Pol II terminates and then reinitiates a new round of transcription remains elusive. Here, we found that RPB7 loss triggers the degradation of RNA Pol II. Strikingly, RPB7 degradation combines knock out of E3 ligase Cullin 3 led to the accumulation of phosphorylated Pol II in the soluble fractions and Pol II reinitiation failure. The stability of recycled Pol II is dependent on the loop domain of RPB7 and the dephosphorylation of Pol II CTD. Termination-reinitiation recycling requires RPB7, CTD phosphatase subunit 1 (CTDP1), and stabilization of Pol II. Our study demonstrates that RPB7/CTDP1 controls the dephosphorylation and stabilization of RNA Pol II to permit RNA Pol II termination to reinitiation recycle in mammalian cells.

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CTDP1 and RPB7 stabilize and license Pol II termination to reinitiation [Micro-C]

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2023-12-31 | E-MTAB-13370 | biostudies-arrayexpress

ChIP-seq of RNA Polymerase II (Rpb3) from wild-type and Rpb7-QHF cells

Project description:Our structural and biochemical studies show that S. cerevisiae RNA Polymerase II (RNAPII) homodimerizes through the stalk domain (formed by the Rpb4-Rpb7 subunits). To explore the biological impact of disrupting this interaction we introduced a triple point mutation at the RNAPII dimerization interface in Rpb7 (Q96A, H97A, F109K). To test the impact of the dimerziation mutant on RNAPII occupancy, we performed ChIP-seq using a monoclonal antibody against the Rpb3 subunit (1Y26, abcam) of RNAPII, in WT and Rpb7-QHF cells.

2023-12-31 | E-MTAB-13369 | biostudies-arrayexpress

Genome wide transcriptional response to altered levels of the Rpb7 subunit of RNA polymerase II identifies its role in DNA damage response in Schizosaccharomyces pombe

Project description:RNA Pol II is a highly conserved and multisubunit protein complex composed of 12 different subunits. Rpb4 and Rpb7 are small subunits and uniquely present in RNA Pol II in eukaryotes. Rpb7 is essential and highly conserved protein among all eukaryotes. However, we have a limited understanding of the functions of Rpb7 subunit. Therefore, in the present study, we have used whole genome microarrays to compare the transcriptional response of S. pombe cells expressing low levels of rpb7+ with wild type cells.

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