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Bsence of YAP1 (clusters 1 and 2). Yap1p also had a slight
Yap1p also had a slight effect on some genes involved in proteolysis (part of cluster 3), possibly indirectly due to the Cinobufagin MedChemExpress significant influence of Yap1p on RPN4 expression (see additional file 6). We detected no significant binding of Pdr1p to the promoter of FLR1, despite using several pairs of Bleomycin sulfate medchemexpress oligonu-Page 5 of(page number not for citation purposes)BMC PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27072691 Genomics 2008, 9:http://www.biomedcentral.com/1471-2164/9/Figure 4 weights of RPN4, PDR1, PDR3 or YAP1 in the selenite response Respective Respective weights of RPN4, PDR1, PDR3 or YAP1 in the selenite response. More surprisingly, the deletion of RPN4 slightly but reproducibly decreased the selenite induction of several Yap1p targets (clusters 1 and 4). The inactivation of PDR1 or PDR3 altered the expression of few genes (less than 20 of the genes in figure 4A), all of which were Yap1p targets (upper parts of clusters 1 and 4) and encoded proteins involved in chemical stress response and xenobiotic export (FLR1, ATR1, FRM2, etc.). Remarkably, these effects were similar to those of the RPN4 deletion on these genes (figure 4C). We carried out chromatin immunoprecipitation (ChIP) analyses, together with real-time quantitative PCR, to investigate the direct binding of Pdr1p to these Pdr1pdependent genes, using a myc-tagged version of Pdr1p [2]. We used the PDR5 promoter as a positive control, as this sequence constitutively binds Pdr1p [2]. We first focused on the FLR1 promoter, which contains a PDRE and is partially controlled by Pdr3p in response to oxidative stress [35]. We detected no significant binding of Pdr1p to the promoter of FLR1, despite using several pairs of oligonu-Page 5 of(page number not for citation purposes)BMC PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/27072691 Genomics 2008, 9:http://www.biomedcentral.com/1471-2164/9/Figure 4 weights of RPN4, PDR1, PDR3 or YAP1 in the selenite response Respective Respective weights of RPN4, PDR1, PDR3 or YAP1 in the selenite response. (A) Hierarchical clustering of the genes dependent on one or several of the four transcription factors studied for selenite induction. DNA microarrays were used to compare gene expression levels between wild-type and rpn4, pdr1, pdr3 or yap1 exposed to selenite (times 40, 60 and 80 minutes) or mock-treated (time 0). The 175 genes displaying an alteration of selenite induction in at least one mutant strain were clustered into 5 groups (see additional files 5 and 6). (B): Schematic representation of the importance of each transcription factor in the regulation of the five clusters defined in (A). The arrows symbolize the positive regulation of each cluster by the transcription factor: the width PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26581802 of the arrows indicates the importance of the regulation (large arrows: strong effect, thin arrows: weak effect). Dashed arrows indicate that the transcription factor controls the expression of only some of the genes present in the cluster. Solid arrows mean that all the genes present in the cluster are regulated. The relevance of the Gene Ontology categories and regulatory relationships in each of the clusters was investigated with the SGD GO term finder and Yeastract tools [33,34].
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