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Series GSE55402 Query DataSets for GSE55402
Status Public on Mar 24, 2014
Title Kin28 Regulates the Transient Association of Mediator with Core Promoters
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Mediator is an essential, broadly utilized eukaryotic transcriptional co-activator. How and what it communicates from activators to RNA polymerase II remains an open question. Here we performed genome-wide location profiling of yeast Mediator subunits. Mediator is not found at core promoters but rather occupies the upstream activating sequence (UAS), upstream of the pre-initiation complex. In the absence of Kin28/CDK7 kinase activity, or in cells where the CTD is mutated to replace Ser5 with alanines, however, Mediator accumulates at core promoters together with RNAPII. We propose that Mediator is quickly released from promoters upon Ser5 phosphorylation by Kin28/CDK7, which also allows for RNAPII to escape from the promoter.
 
Overall design We took a systematic approach to examine the genome-wide distribution (using ChIP-chip) of the various Mediator subunits. Mediator occupancy was also assayed in mutants for most of the CTD kinases and in strains where some CTD serines had been replaced by alanines. Mediator ChIPs were performed with Myc-tagged subunits, except in some preliminary experiments where polyclonal antibodies were used. Most ChIPs (in Cy5) were hybridyzed against a control ChIP sample from an isogenic non-tagged strain (in Cy3). In some of the preliminary experiments, non immunoprecipitated DNA (input) was used as the control. In addition to Mediator ChIPs, the project includes TFIIB and RNAPII (Rpb3) ChIP-chip datasets. All ChIP-chip experiments were done in duplicates except for the preliminary experiments that were done in monoplicat for the most part. Each microarray was normalized using the Lima Loess and replicates were combined using a weighted average method as previously described (Pokholok et al., 2005).
 
Contributor(s) Jeronimo C, Robert F
Citation(s) 24704787
Submission date Feb 26, 2014
Last update date Aug 30, 2018
Contact name Francois Robert
E-mail(s) francois.robert@ircm.qc.ca
Organization name IRCM
Lab Chromatin and Genomic Expression
Street address 110 av des Pins Ouest
City Montreal
State/province QC
ZIP/Postal code H2W 1R7
Country Canada
 
Platforms (1)
GPL18340 Agilent-034462 Yeast_4x180K
Samples (90)
GSM1335367 yFR119vsyFR116_18Myc-Rox3-Med19vsUntagged_rep1
GSM1335368 yFR119vsyFR116_18Myc-Rox3-Med19vsUntagged_rep2
GSM1335369 yFR167vsyFR116_9Myc-Srb11vsUntagged_rep1
Relations
BioProject PRJNA239629

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE55402_RAW.tar 3.9 Gb (http)(custom) TAR (of GPR)
GSE55402_yFR116_WT_Rpb3vsInput_30minRapa_Rep1-2_S.cerevisiaeApr11_14509.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR116_WT_Rpb3vsInput_noRapa_Rep1-2_S.cerevisiaeApr11_497876.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR116_newAbTFIIBvsInput_rep1-2_minusMockIP_IgGvsInput_smooth.bed.gz 8.4 Mb (ftp)(http) BED
GSE55402_yFR117_Srb4-5uLvsInput_S.cerevisiaeApr11_926936.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_MockIgGvsInput_rep1-2_S.cerevisiaeApr11_233775.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_Rpb3vsInput_Rep1-2_20130731_S.cerevisiaeApr11_728777.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb10vsInput_rep1_S.cerevisiaeApr11_169853.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb11vsInput_rep1_S.cerevisiaeApr11_410110.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb2vsInput_rep1_S.cerevisiaeApr11_330889.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb4vsInput_rep1_S.cerevisiaeApr11_631894.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb5vsInput_rep1_S.cerevisiaeApr11_570383.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb6vsInput_rep1_S.cerevisiaeApr11_83171.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb7vsInput_rep1_S.cerevisiaeApr11_565566.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb8vsInput_rep1_S.cerevisiaeApr11_848706.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR117_WT_anti-Srb9vsInput_rep1_S.cerevisiaeApr11_769492.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR119_18Myc-MED19vsInput_rep1_S.cerevisiaeApr11_864357.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR119vsyFR116_18Myc-Rox3-Med19vsUntagged_rep1-2_S.cerevisiaeApr11_787250.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR121_9Myc-MED8vsInput_rep1_S.cerevisiaeApr11_268705.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR1321_WT-AA_rapamycin_TFIIBvsInput_rep1-2_MinusMock.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR1325_Srb5-AA_rapamycin_TFIIBvsInput_rep1-2_MinusMock.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR1499_MockvsInput_90minRapamycin_rep1-2_S.cerevisiaeApr11_516361.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR1499_MockvsInput_noRapamycin_rep1-2_S.cerevisiaeApr11_250300.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR1499_endoRPB1-AAvsInput_90minRapa_20131216_rep1-2_S.cerevisiaeApr11_22031_minusMock.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR1499_endoRPB1-AAvsInput_noRapa_20131216_rep1-2_S.cerevisiaeApr11_594792_MinusMock.bed.gz 8.4 Mb (ftp)(http) BED
GSE55402_yFR1499_exoCTDwt-FLAGvsInput_90minRapa_20131216_rep1-2_S.cerevisiaeApr11_319947.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR1499_exoCTDwt-FLAGvsInput_90minRapa_rep3-4_S.cerevisiaeApr11_602223.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR1499_exoCTDwt-FLAGvsInput_noRapa_20131216_rep1-2_S.cerevisiaeApr11_292602.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR1503_exoCTD-S5A-FLAGvsInput_90minRapa_rep1-2_S.cerevisiaeApr11_487767.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR150_18Myc-MED6vsInput_rep1_S.cerevisiaeApr11_976893.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR1526_exoCTD-S7A-FLAGvsInput_90minRapa_rep1-2_S.cerevisiaeApr11_126595.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR1544_Srb4-AA_rapamycin_TFIIBvsInput_rep1-2_MinusMock.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR1636vsyFR762-WT_Gal11-9xMYCvsUntagged_rep1-2_S.cerevisiaeApr11_477340.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR1638vsyFR763-kin28as_Gal11-9xMYCvsUntagged_rep1-2_S.cerevisiaeApr11_429187.bed.gz 8.4 Mb (ftp)(http) BED
GSE55402_yFR1640vsyFR999-srb10D_Gal11-9MYCvsUntagged_rep1-2_S.cerevisiaeApr11_450233.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR1645vsyFR1499_ExoCTDwt-FLAG_Gal11-18MYCvsUntagged_90minRapa_rep1-2_S.cerevisiaeApr11_217790.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR1649vsyFR1503_ExoCTDS5A-FLAG_Gal11-18MYCvsUntagged_90minRapa_rep1-2_S.cerevisiaeApr11_1845.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR1651vsyFR1526_ExoCTDS7A-FLAG_Gal11-18MYCvsUntagged_90minRapa_rep1-2_S.cerevisiaeApr11_208956.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR1658vsyFR117-WT_Gal11-18MYCvsUntagged_rep1-2_S.cerevisiaeApr11_983768.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR1660vsyFR551-ctk1D_Gal11-18MYCvsUntagged_rep1-2_S.cerevisiaeApr11_468734.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR1662vsyFR682-bur2D_Gal11-18MYCvsUntagged_rep1-2_S.cerevisiaeApr11_466215.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR167_9Myc-SRB11vsInput_rep1_S.cerevisiaeApr11_103309.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR167vsyFR116_9Myc-Srb11vsUntagged_rep1-2_S.cerevisiaeApr11_897213.bed.gz 8.1 Mb (ftp)(http) BED
GSE55402_yFR169_18Myc-MED16vsInput_rep1_S.cerevisiaeApr11_753616.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR169vsyFR116_18Myc-Sin4-Med16vsUntagged_rep1-2_S.cerevisiaeApr11_667356.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR178_9Myc-SRB10vsInput_rep1_S.cerevisiaeApr11_663109.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR178vsyFR116_9Myc-Srb10vsUntagged_rep1-2_S.cerevisiaeApr11_333613.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR399_9Myc-MED15vsInput_rep1_S.cerevisiaeApr11_719472.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR399vsyFR116_9Myc-Gal11-Med15vsUntagged_rep1-2_S.cerevisiaeApr11_59675.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR399vsyFR116_Gal11-9MYCvsUntagged_30minRapa_Rep1-2_S.cerevisiaeApr11_99151.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR399vsyFR116_Gal11-9MYCvsUntagged_noRapa_Rep1-2_S.cerevisiaeApr11_614284.bed.gz 8.2 Mb (ftp)(http) BED
GSE55402_yFR401_9Myc-Srb4vsInput_rep1_S.cerevisiaeApr11_477784.bed.gz 8.3 Mb (ftp)(http) BED
GSE55402_yFR762_WT-KIN28_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_898345.bed.gz 8.5 Mb (ftp)(http) BED
GSE55402_yFR763_kin28as_Rpb3vsInput_rep1-2_S.cerevisiaeApr11_242304.bed.gz 8.5 Mb (ftp)(http) BED
Processed data included within Sample table
Processed data are available on Series record
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