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Rrd1p, an RNA polymerase II-specific prolyl isomerase and activator of phosphoprotein phosphatase, promotes transcription independently of rapamycin response.

Sen R, Malik S, Frankland-Searby S, Uprety B, Lahudkar S, Bhaumik SR - Nucleic Acids Res. (2014)

Bottom Line: Similarly, inducible, but rapamycin-responsive, non-GAL genes such as CTT1, STL1 and CUP1 are also regulated by Rrd1p.Consistently, transcription of the constitutively active genes is not changed in the Δrrd1 strain.Taken together, our results demonstrate a new function of Rrd1p in stimulation of initial rounds of transcription, but not steady-state/constitutive transcription, of both rapamycin-responsive and non-responsive genes independently of rapamycin treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.

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CUP1, STL1 and CTT1 are rapamycin-responsive genes, and are not regulated by Rrd1p following long transcriptional induction. (A and B) RT-PCR analysis of CUP1, STL1, CTT1 and ACT1 mRNA levels in the presence and absence of rapamycin treatment. (C) ChIP analysis of RNA polymerase II association with STL1, CTT1 and CUP1 following long transcriptional induction (30 min induction for STL1 and CTT1; and 1 h induction for CUP1). (D and E) RT-PCR analysis of CUP1, STL1, CTT1 and ADH1 mRNA levels in the wild-type and Δrrd1 strains following long transcriptional induction. (F) ChIP analysis for TBP recruitment to the core promoters of CUP1, CTT1, STL1 in the wild-type and Δrrd1 strains following short transcriptional induction (i.e. 7 min induction for CTT1 and STL1; and 15 min induction for CUP1).
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Figure 8: CUP1, STL1 and CTT1 are rapamycin-responsive genes, and are not regulated by Rrd1p following long transcriptional induction. (A and B) RT-PCR analysis of CUP1, STL1, CTT1 and ACT1 mRNA levels in the presence and absence of rapamycin treatment. (C) ChIP analysis of RNA polymerase II association with STL1, CTT1 and CUP1 following long transcriptional induction (30 min induction for STL1 and CTT1; and 1 h induction for CUP1). (D and E) RT-PCR analysis of CUP1, STL1, CTT1 and ADH1 mRNA levels in the wild-type and Δrrd1 strains following long transcriptional induction. (F) ChIP analysis for TBP recruitment to the core promoters of CUP1, CTT1, STL1 in the wild-type and Δrrd1 strains following short transcriptional induction (i.e. 7 min induction for CTT1 and STL1; and 15 min induction for CUP1).

Mentions: We find above that Rrd1p promotes transcription of GAL genes independently of rapamycin treatment. To determine whether Rrd1p has similar effects on transcription of non-GAL genes, we analyzed transcription of CUP1, STL1 and CTT1 following transcriptional induction in the presence and absence of Rrd1p. CTT1 and STL1 are induced by NaCl, while Cu2+ induces CUP1. We found that transcription of CUP1, STL1 and CTT1 was impaired following transcriptional induction in the absence of Rrd1p (Figure 7A and B). Consistently, Rrd1p associates with CTT1, STL1 and CUP1 (Figure 7C, Supplementary Figure S1), and the association of RNA polymerase II with CUP1, STL1 and CTT1 was decreased in the Δrrd1 strain in comparison to the wild-type equivalent (Figure 7D and E). Thus, like the results at GAL genes, Rrd1p associates with non-GAL genes and facilitates their transcription in the absence of rapamycin. Intriguingly, transcription of these genes was decreased following rapamycin treatment (Figure 8A and B). Thus, unlike GAL genes, these genes are regulated by rapamycin. Although these genes are controlled by rapamycin, they are positively regulated by Rrd1p in the absence of rapamycin treatment (Figure 7A, B, D and E), similar to the results at the rapamycin non-responsive GAL genes. However, the effect of Rrd1p on the association of RNA polymerase II with CUP1, STL1 and CTT1 following long transcriptional induction was not observed (Figure 8C). Consistently, transcription of these genes was not altered after long transcriptional induction (Figure 8D and E). Thus, similar to the results at GAL genes, Rrd1p promotes initial rounds of transcription of non-GAL genes independently of rapamycin response (or TOR pathway), but has no effect on the steady-state level. However, unlike the results at the GAL genes, the recruitment of TBP to the CUP1 promoter is not altered in the absence of Rrd1p (Figure 8F). Thus, Rrd1p appears to promote transcriptional elongation of CUP1, but not initiation. Consistently, Rrd1p has been recently implicated in regulation of transcriptional elongation, but not initiation, of rapamycin-responsive genes in the presence of rapamycin treatment (10). On the other hand, Rrd1p facilitates TBP recruitment to the core promoters of CTT1 and STL1 (Figure 8F), but has more effect on RNA polymerase II association with the coding sequence, similar to the results at the GAL genes, thus indicating the role of Rrd1p in both transcriptional initiation and elongation of CTT1 and STL1.


Rrd1p, an RNA polymerase II-specific prolyl isomerase and activator of phosphoprotein phosphatase, promotes transcription independently of rapamycin response.

Sen R, Malik S, Frankland-Searby S, Uprety B, Lahudkar S, Bhaumik SR - Nucleic Acids Res. (2014)

CUP1, STL1 and CTT1 are rapamycin-responsive genes, and are not regulated by Rrd1p following long transcriptional induction. (A and B) RT-PCR analysis of CUP1, STL1, CTT1 and ACT1 mRNA levels in the presence and absence of rapamycin treatment. (C) ChIP analysis of RNA polymerase II association with STL1, CTT1 and CUP1 following long transcriptional induction (30 min induction for STL1 and CTT1; and 1 h induction for CUP1). (D and E) RT-PCR analysis of CUP1, STL1, CTT1 and ADH1 mRNA levels in the wild-type and Δrrd1 strains following long transcriptional induction. (F) ChIP analysis for TBP recruitment to the core promoters of CUP1, CTT1, STL1 in the wild-type and Δrrd1 strains following short transcriptional induction (i.e. 7 min induction for CTT1 and STL1; and 15 min induction for CUP1).
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Figure 8: CUP1, STL1 and CTT1 are rapamycin-responsive genes, and are not regulated by Rrd1p following long transcriptional induction. (A and B) RT-PCR analysis of CUP1, STL1, CTT1 and ACT1 mRNA levels in the presence and absence of rapamycin treatment. (C) ChIP analysis of RNA polymerase II association with STL1, CTT1 and CUP1 following long transcriptional induction (30 min induction for STL1 and CTT1; and 1 h induction for CUP1). (D and E) RT-PCR analysis of CUP1, STL1, CTT1 and ADH1 mRNA levels in the wild-type and Δrrd1 strains following long transcriptional induction. (F) ChIP analysis for TBP recruitment to the core promoters of CUP1, CTT1, STL1 in the wild-type and Δrrd1 strains following short transcriptional induction (i.e. 7 min induction for CTT1 and STL1; and 15 min induction for CUP1).
Mentions: We find above that Rrd1p promotes transcription of GAL genes independently of rapamycin treatment. To determine whether Rrd1p has similar effects on transcription of non-GAL genes, we analyzed transcription of CUP1, STL1 and CTT1 following transcriptional induction in the presence and absence of Rrd1p. CTT1 and STL1 are induced by NaCl, while Cu2+ induces CUP1. We found that transcription of CUP1, STL1 and CTT1 was impaired following transcriptional induction in the absence of Rrd1p (Figure 7A and B). Consistently, Rrd1p associates with CTT1, STL1 and CUP1 (Figure 7C, Supplementary Figure S1), and the association of RNA polymerase II with CUP1, STL1 and CTT1 was decreased in the Δrrd1 strain in comparison to the wild-type equivalent (Figure 7D and E). Thus, like the results at GAL genes, Rrd1p associates with non-GAL genes and facilitates their transcription in the absence of rapamycin. Intriguingly, transcription of these genes was decreased following rapamycin treatment (Figure 8A and B). Thus, unlike GAL genes, these genes are regulated by rapamycin. Although these genes are controlled by rapamycin, they are positively regulated by Rrd1p in the absence of rapamycin treatment (Figure 7A, B, D and E), similar to the results at the rapamycin non-responsive GAL genes. However, the effect of Rrd1p on the association of RNA polymerase II with CUP1, STL1 and CTT1 following long transcriptional induction was not observed (Figure 8C). Consistently, transcription of these genes was not altered after long transcriptional induction (Figure 8D and E). Thus, similar to the results at GAL genes, Rrd1p promotes initial rounds of transcription of non-GAL genes independently of rapamycin response (or TOR pathway), but has no effect on the steady-state level. However, unlike the results at the GAL genes, the recruitment of TBP to the CUP1 promoter is not altered in the absence of Rrd1p (Figure 8F). Thus, Rrd1p appears to promote transcriptional elongation of CUP1, but not initiation. Consistently, Rrd1p has been recently implicated in regulation of transcriptional elongation, but not initiation, of rapamycin-responsive genes in the presence of rapamycin treatment (10). On the other hand, Rrd1p facilitates TBP recruitment to the core promoters of CTT1 and STL1 (Figure 8F), but has more effect on RNA polymerase II association with the coding sequence, similar to the results at the GAL genes, thus indicating the role of Rrd1p in both transcriptional initiation and elongation of CTT1 and STL1.

Bottom Line: Similarly, inducible, but rapamycin-responsive, non-GAL genes such as CTT1, STL1 and CUP1 are also regulated by Rrd1p.Consistently, transcription of the constitutively active genes is not changed in the Δrrd1 strain.Taken together, our results demonstrate a new function of Rrd1p in stimulation of initial rounds of transcription, but not steady-state/constitutive transcription, of both rapamycin-responsive and non-responsive genes independently of rapamycin treatment.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.

Show MeSH
Related in: MedlinePlus