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

Yupeng Chen, Lirong Zhang, Conchi Estarás, Seung H. Choi, Luis Moreno, Jonathan Karn, James J. Moresco, John R. Yates, Katherine A. Jones

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)2261-2275
Number of pages15
JournalGenes and Development
Volume28
Issue number20
DOIs
StatePublished - Oct 15 2014
Externally publishedYes

Fingerprint

Phosphoric Monoester Hydrolases
Transcriptional Activation
HIV-1
Peptide Elongation Factors
Chromatin Immunoprecipitation
Genes
High-Throughput Nucleotide Sequencing
Transcription Factors
Genetic Terminator Regions
Viral Genes
RNA Polymerase II
Phosphotransferases
Phosphorylation
Genome
T-Lymphocytes
Gene Expression

Keywords

  • CTD phosphatase
  • Elongation
  • HIV-1 Tat
  • Ssu72

ASJC Scopus subject areas

  • Genetics
  • Developmental Biology

Cite this

Chen, Y., Zhang, L., Estarás, C., Choi, S. H., Moreno, L., Karn, J., ... Jones, K. A. (2014). A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. Genes and Development, 28(20), 2261-2275. https://doi.org/10.1101/gad.250449.114

A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. / Chen, Yupeng; Zhang, Lirong; Estarás, Conchi; Choi, Seung H.; Moreno, Luis; Karn, Jonathan; Moresco, James J.; Yates, John R.; Jones, Katherine A.

In: Genes and Development, Vol. 28, No. 20, 15.10.2014, p. 2261-2275.

Research output: Contribution to journalArticle

Chen, Y, Zhang, L, Estarás, C, Choi, SH, Moreno, L, Karn, J, Moresco, JJ, Yates, JR & Jones, KA 2014, 'A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation', Genes and Development, vol. 28, no. 20, pp. 2261-2275. https://doi.org/10.1101/gad.250449.114
Chen, Yupeng ; Zhang, Lirong ; Estarás, Conchi ; Choi, Seung H. ; Moreno, Luis ; Karn, Jonathan ; Moresco, James J. ; Yates, John R. ; Jones, Katherine A. / A gene-specific role for the Ssu72 RNAPII CTD phosphatase in HIV-1 Tat transactivation. In: Genes and Development. 2014 ; Vol. 28, No. 20. pp. 2261-2275.
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AU - Moreno, Luis

AU - Karn, Jonathan

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AB - 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.

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