Rtr1 Is a Dual Specificity Phosphatase That Dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD

Hsu, Peter L.; Yang, Fan; Smith-Kinnaman, Whitney R.; Yang, Wen; Song, Jae Eun; Mosley, Amber L.; Varani, Gabriele

doi:10.1016/j.jmb.2014.06.010

Cited by 41 publications

(66 citation statements)

References 43 publications

(52 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this study, we show that S. cerevisiae Rtr1 is a regulator of Ser5 phosphorylation in the RNAPII CTD in agreement with previous findings (14,39,41,49,51,52). We show that deletion of RTR1 leads to global increases in Ser5-P CTD occupancy at RNAPII target genes, suggesting that Rtr1 is a general regulator of RNAPII phosphorylation during transcription elongation.…”

supporting

confidence: 92%

“…Ssu72 also participates in gene looping and the suppression of divergent transcription (37,38). Rtr1 is a conserved protein that has been reported by both in vitro and in vivo experimental studies to be a phosphatase responsible for the removal of Ser5-P from the CTD (14,(39)(40)(41)(42). ChIP assays found that the localization of Rtr1 is predominant between the peaks of Ser5-P and Ser2-P.…”

mentioning

confidence: 98%

“…We have previously found that the Rtr1 interaction with RNAPII is dependent on Ctk1 activity and that Rtr1 can interact with RNAPII phosphorylated at Ser2, Ser5, and/or Ser7 (49). In fact, multiple lines of evidence suggest that Rtr1 binds to a multiply phosphorylated form of the RNAPII CTD (40)(41)(42)49). These data suggest that Rtr1 can act as both a reader and an eraser for the CTD code and could function as a potential regulator of Set2 targeting to RNAPII target genes through regulation of Ser5-P RNAPII levels.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation

Hunter

Fox

Smith-Kinnaman

et al. 2016

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

cIn eukaryotes, the C-terminal domain (CTD) of Rpb1 contains a heptapeptide repeat sequence of (Y 1 S 2 P 3 T 4 S 5 P 6 S 7 ) n that undergoes reversible phosphorylation through the opposing action of kinases and phosphatases. Rtr1 is a conserved protein that colocalizes with RNA polymerase II (RNAPII) and has been shown to be important for the transition from elongation to termination during transcription by removing RNAPII CTD serine 5 phosphorylation (Ser5-P) at a selection of target genes. In this study, we show that Rtr1 is a global regulator of the CTD code with deletion of RTR1 causing genome-wide changes in Ser5-P CTD phosphorylation and cotranscriptional histone H3 lysine 36 trimethylation (H3K36me3). Using chromatin immunoprecipitation and high-resolution microarrays, we show that RTR1 deletion results in global changes in RNAPII Ser5-P levels on genes with different lengths and transcription rates consistent with its role as a CTD phosphatase. Although Ser5-P levels increase, the overall occupancy of RNAPII either decreases or stays the same in the absence of RTR1. Additionally, the loss of Rtr1 in vivo leads to increases in H3K36me3 levels genome-wide, while total histone H3 levels remain relatively constant within coding regions. Overall, these findings suggest that Rtr1 regulates H3K36me3 levels through changes in the number of binding sites for the histone methyltransferase Set2, thereby influencing both the CTD and histone codes. R eversible phosphorylation of the C-terminal domain (CTD)of the largest subunit of RNA polymerase II (RNAPII) controls transcription elongation and termination through the orderly recruitment of transcription regulatory factors. These factors are involved in various processes including mRNA processing and cotranscriptional histone modifications (1-3). The CTD is comprised of the heptapeptide repeat of Y 1 S 2 P 3 T 4 S 5 P 6 S 7 that is highly conserved with 26 repeats in Saccharomyces cerevisiae, 42 repeats in Drosophila melanogaster, and 52 repeats in humans and is essential for viability (4-10). The CTD is an unstructured domain that is unique to RNAPII and contains some degenerative repeats that deviate from the canonical sequence (11). Multiple residues within the CTD repeats are phosphorylated (P) at different stages of the transcription cycle; these residues include Ser2, Ser5, Ser7, Tyr1, and Tyr4, which thereby serve as a signaling scaffold for RNAPII transcription machinery (12). The phosphorylation of Ser2, Ser5, and Ser7 in S. cerevisiae has been well characterized by several laboratories (13,14). Phosphorylation of Tyr1 and Thr4 are less characterized but have also been implicated in the regulation of RNAPII transcription (12, 15). Additionally, the proline at position six in the CTD repeats is subject to cis-trans isomerization by Ess1 (16,17). Despite a great deal of research into these modifications, the extent to which these modifications coexist in a phosphorylated and nonphosphorylated state on a single heptapeptide repeat in vivo remains enigmatic.Th...

show abstract

supporting

confidence: 92%

mentioning

confidence: 98%

mentioning

confidence: 99%

See 1 more Smart Citation

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation

Hunter

Fox

Smith-Kinnaman

et al. 2016

Molecular and Cellular Biology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Rtr1p, (regulator of transcription 1), was previously identified as a phosphatase that dephosphorylates Ser5 and Tyr1 of the RNA polymerase II CTD tail, thus establishing a role for this protein in regulating transcription elongation and termination (Gibney et al 2008;Mosley et al 2009;Hsu et al 2014). In this work we show that Rtr1p autoregulates its own mRNA post-transcriptionally and that this degradation pathway involves the 3 ′ -5 ′ exonucleases Rex2p and Rex3p and the Dhh1p helicase.…”

Section: Introductionmentioning

confidence: 58%

The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases

Hodko

Ward

Chanfreau

2016

RNA

View full text Add to dashboard Cite

Rtr1p is a phosphatase that impacts gene expression by modulating the phosphorylation status of the C-terminal domain of the large subunit of RNA polymerase II. Here, we show that Rtr1p is a component of a novel mRNA degradation pathway that promotes its autoregulation through turnover of its own mRNA. We show that the 3 ′ UTR of the RTR1 mRNA contains a cis element that destabilizes this mRNA. RTR1 mRNA turnover is achieved through binding of Rtr1p to the RTR1 mRNP in a manner that is dependent on this cis element. Genetic evidence shows that Rtr1p-mediated decay of the RTR1 mRNA involves the 5 ′ -3 ′ DExD/H-box RNA helicase Dhh1p and the 3 ′ -5 ′ exonucleases Rex2p and Rex3p. Rtr1p and Rex3p are found associated with Dhh1p, suggesting a model for recruiting the REX exonucleases to the RTR1 mRNA for degradation. Rtr1p-mediated decay potentially impacts additional transcripts, including the unspliced BMH2 pre-mRNA. We propose that Rtr1p may imprint its RNA targets cotranscriptionally and determine their downstream degradation mechanism by directing these transcripts to a novel turnover pathway that involves Rtr1p, Dhh1p, and the REX family of exonucleases.

show abstract

“…Although Ssu72 predominantly regulates S5P-CTD at the 39 ends of genes, it may also act at the 59 end of some genes and can stimulate transcription elongation in vitro (Dichtl et al 2002, Reyes-Reyes and. Another S5P-CTD phosphatase, Rtr1/RPAP2, is implicated to regulate the S5P-S2P transition at gene promoters in yeast (Mosley et al 2009), although the ability of Rtr1 to remove Y1P (Hsu et al 2014) is also consistent with a role in termination. A third candidate, the small CTD phosphatase SCP-1, regulates S5P-CTD levels in the promoter region of neuronal genes (Eick and Geyer 2013).…”

mentioning

confidence: 99%

A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation

et al. 2014

View full text Add to dashboard Cite

HIV-1 Tat stimulates transcription elongation by recruiting the P-TEFb (positive transcription elongation factor-b) (CycT1:CDK9) C-terminal domain (CTD) kinase to the HIV-1 promoter. Here we show that Tat transactivation also requires the Ssu72 CTD Ser5P (S5P)-specific phosphatase, which mediates transcription termination and intragenic looping at eukaryotic genes. Importantly, HIV-1 Tat interacts directly with Ssu72 and strongly stimulates its CTD phosphatase activity. We found that Ssu72 is essential for Tat:P-TEFb-mediated phosphorylation of the S5P-CTD in vitro. Interestingly, Ssu72 also stimulates nascent HIV-1 transcription in a phosphatasedependent manner in vivo. Chromatin immunoprecipitation (ChIP) experiments reveal that Ssu72, like P-TEFb and AFF4, is recruited by Tat to the integrated HIV-1 proviral promoter in TNF-a signaling 2D10 T cells and leaves the elongation complex prior to the termination site. ChIP-seq (ChIP combined with deep sequencing) and GROseq (genome-wide nuclear run-on [GRO] combined with deep sequencing) analysis further reveals that Ssu72 predominantly colocalizes with S5P-RNAPII (RNA polymerase II) at promoters in human embryonic stem cells, with a minor peak in the terminator region. A few genes, like NANOG, also have high Ssu72 at the terminator. Ssu72 is not required for transcription at most cellular genes but has a modest effect on cotranscriptional termination. We conclude that Tat alters the cellular function of Ssu72 to stimulate viral gene expression and facilitate the early S5P-S2P transition at the integrated HIV-1 promoter.

show abstract

Rtr1 Is a Dual Specificity Phosphatase That Dephosphorylates Tyr1 and Ser5 on the RNA Polymerase II CTD

Cited by 41 publications

References 43 publications

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation

Phosphatase Rtr1 Regulates Global Levels of Serine 5 RNA Polymerase II C-Terminal Domain Phosphorylation and Cotranscriptional Histone Methylation

The Rtr1p CTD phosphatase autoregulates its mRNA through a degradation pathway involving the REX exonucleases

A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation

Contact Info

Product

Resources

About