Gene-specific RNA polymerase II phosphorylation and the CTD code.

Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA.
Nature Structural & Molecular Biology (Impact Factor: 11.63). 10/2010; 17(10):1279-86. DOI: 10.1038/nsmb.1913
Source: PubMed

ABSTRACT Phosphorylation of the RNA polymerase (Pol) II C-terminal domain (CTD) repeats (1-YSPTSPS-7) is coupled to transcription and may act as a 'code' that controls mRNA synthesis and processing. To examine the code in budding yeast, we mapped genome-wide CTD Ser2, Ser5 and Ser7 phosphorylations and the CTD-associated termination factors Nrd1 and Pcf11. Phospho-CTD dynamics are not scaled to gene length and are gene-specific, with highest Ser5 and Ser7 phosphorylation at the 5' ends of well-expressed genes with nucleosome-occupied promoters. The CTD kinases Kin28 and Ctk1 markedly affect Pol II distribution in a gene-specific way. The code is therefore written differently on different genes, probably under the control of promoters. Ser7 phosphorylation is enriched on introns and at sites of Nrd1 accumulation, suggesting links to splicing and Nrd1 recruitment. Nrd1 and Pcf11 frequently colocalize, suggesting functional overlap. Unexpectedly, Pcf11 is enriched at centromeres and Pol III-transcribed genes.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Prolyl isomerases (PPIases) induce conformational changes in target proteins•PPIases control transcription in eukaryotes at multiple levels.•PPIases regulate transcription factor stability, localization, and activity•PPIases coordinate binding of RNA-processing factors to RNA polymerase II•PPIases regulate recruitment and activity of histone modifying enzymes
    Biochimica et Biophysica Acta (BBA) - General Subjects 10/2014; · 3.83 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Arsenic ROS Dimethoxycurcumin NADPH oxidase Apoptosis Nrf2/Keap1 signaling a b s t r a c t NADPH oxidase mediated ROS generation plays a decisive role in the pathogenesis of arsenic (As) hep-atotoxicity. Antioxidant phytochemicals, like dimethoxycurcumin (DiMC) has a tremendous scope in attenuating the ROS mediated hepatic injury. Hence, the present study has been designed to inves-tigate the hepatoprotective action of DiMC by analysing the markers of hepatic oxidative stress, pro-inflammatory cytokines, apoptotic markers and antioxidant competence in As (5 mg/kg BW) induced hepatotoxic rats. Oral administration of DiMC (80 mg/kg BW) to As intoxicated rats showed a significant amelioration in the levels of serum hepatic markers, pro-inflammatory cytokines and the expression of NADPH oxidase subunits (Nox2, Nox4, and p47phox) in liver. The elevated levels of hepatic oxidative stress markers lipid peroxides, hydroperoxides, protein carbonyls and conjugated dienes and decreased levels of enzymatic and non-enzymatic antioxidants status were also reverted back to near normalcy by DiMC when compared with As treated rats. In addition, mRNA and protein expression analysis also con-firms that DiMC pre-treatment significantly downregulates the NOX subunits and upregulates the Nrf2 and its related enzymes in the liver. Studies on the mechanism of apoptosis showed that As accelerated the markers of mitochondrial dependent apoptotic pathway (enhanced cytochrome c release in cytosol from mitochondria, altered the expression of Bax, Bcl-2, Bad, caspase-9, caspase-3). However, DiMC pre-treatment effectively restored the As-induced alterations in liver. Histological and immunohistochemical results were also evidenced that DiMC potentially protects the liver from As-induced oxidative stress, inflammation and apoptosis. These findings encourage the use of DiMC as a prospective salutary entity for As hepatotoxicty through the suppression of NADPH oxidase and Nrf2 activation.
    biomedicine and preventive nutrition. 10/2014; 4:561-577.
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin modifying enzymes and RNA Pol II. Here, we examine the involvement of Mediator subunit MED25 in the epigenetic regulation of human cytochrome P450 2C9 (CYP2C9)2. MED25 is recruited to the CYP2C9 promoter through association with liver-enriched HNF4α, and we show that MED25 influences the H3K27 status of the HNF4α binding region. This region was enriched for the activating marker H3K27ac and histone acetyltransferase CREBBP after MED25 overexpression, but was trimethylated when MED25 expression was silenced. The epigenetic regulator Polycomb repressive complex (PRC2), which represses expression by methylating H3K27, plays an important role in target gene regulation. Silencing MED25 correlated with increased association of PRC2 with not only the promoter region chromatin but HNF4α itself. We confirmed the involvement of MED25 for fully functional preinitiation complex recruitment and transcriptional output in vitro. Formaldehyde-assisted isolation of regulatory elements (FAIRE) revealed chromatin conformation changes that are reliant on MED25, indicating MED25 induced a permissive chromatin state that reflected increases in CYP2C9 mRNA. For the first time, we show evidence that a functionally relevant human gene is transcriptionally regulated by HNF4α via MED25 and PRC2. CYP2C9 is important for the metabolism of many exogenous chemicals including pharmaceutical drugs as well as endogenous substrates. Thus, MED25 is important for regulating the epigenetic landscape resulting in transcriptional activation of a highly inducible gene, CYP2C9.
    Journal of Biological Chemistry 11/2014; · 4.60 Impact Factor

Full-text (2 Sources)

Available from
Jun 4, 2014

Similar Publications