241 human active and 13 inactive phosphatases in total;
194 phosphatases have substrate data;
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336 protein substrates;
83 non-protein substrates;
1215 dephosphorylation interactions;
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299 KEGG pathways;
876 Reactome pathways;
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last update: 11 Mar, 2019
Nucleus Cytoplasm, cytoskeleton, microtubule organizing center, centrosome Cytoplasm, cytoskeleton, spindlepole Midbody Note=Found at centrosomes inprometaphase, at spindle and spindle poles in metaphase and atspindle midzone and midbody in anaphase and telophase-G1respectively
Function (UniProt annotation)
Processively dephosphorylates 'Ser-2' and 'Ser-5' of theheptad repeats YSPTSPS in the C-terminal domain of the largest RNApolymerase II subunit This promotes the activity of RNApolymerase II Plays a role in the exit from mitosis bydephosphorylating crucial mitotic substrates (USP44, CDC20 andWEE1) that are required for M-phase-promoting factor (MPF)/CDK1inactivation
TFIIS is a transcription factor involved in different phases of transcription, occurring in a major ubiquitous form and other tissue specific forms. TFIIS stimulates RNA Pol II complex out of elongation arrest. Other transcription factors like ELL, Elongin family members and TFIIF interact directly with elongating Pol II and increase its elongation rate. These factors have been observed to act on naked DNA templates by suppressing transient pausing by the enzyme at all or most steps of nucleotide addition. In Drosophila, ELL is found at a large number of transcriptionally active sites on polytene chromosomes. In general, ELL is suspected to have more unidentified functions. Elongin is a heterotrimeric protein complex that stimulates the overall rate of elongation. In addition, Elongin may act as an E3 Ubiquitin ligase. Ubiquitylation of RNA Pol II occurs rapidly after genotoxic assault by UV light or chemicals, and results in degradation by proteasome. The FACT complex appears to promote elongation by facilitating passage of polymerase through chromatin. All these factors contribute to the formation of a processive elongation complex centered around the RNA Pol II complex positioned on the DNA:RNA hybrid. This enables the RNA Pol II elongation complex to function as a platform that coordinates mRNA processing and export (Reviewed by Shilatifard et al., 2003)
Transcription elongation by RNA polymerase II (RNAPII) is controlled by a number of trans-acting transcription elongation factors as well as by cis-acting elements. Transcription elongation is a rate-limiting step for proper mRNA production in which the phosphorylation of Pol II CTD is a crucial biochemical event. The role of CTD phosphorylation in transcription by Pol II is greatly impaired by protein kinase inhibitors such as 5,6-dichloro-1- ribofuranosylbenzimidazole (DRB), which block CTD phosphorylation and induce arrest of elongating Pol II. DRB-sensitive activation Pol II CTD during elongation has enabled the isolation of two sets of factors -Negative Elongation Factors (NELF) and DRB sensitivity inducing factor (DSIF). P-Tefb is a DRB-sensitive, cyclin-dependent CTD kinase composed of Cdk9 that carries out Serine-2 phosphorylation of Pol II CTD during elongation. The mechanism by which DSIF, NELF and P-TEFb act together in Pol II-regulated elongation is yet to be fully understood. Various biochemical evidences point to a model in which DSIF and NELF negatively regulate elongation through interactions with polymerase containing a hypophosphorylated CTD. Subsequent phosphorylation of the Pol II CTD by P-Tefb might promote elongation by inhibiting interactions of DSIF and NELF with the elongation complex
During the formation of the HIV elongation complex in the absence of HIV Tat, eongation factors are recruited to form the HIV-1 elongation complex (Hill and Sundquist 2013) and P-TEFb complex hyperphosphorylates RNA Pol II CTD (Hermann and Rice, 2005, Zhou et al., 2000)
This HIV-1 event was inferred from the corresponding human RNA Poll II transcription event. The details relevant to HIV-1 are described below. Formation of the early elongation complex involves hypophosphorylation of RNA Pol II CTD by FCP1P protein, association of the DSIF complex with RNA Pol II, and formation of DSIF:NELF:HIV-1 early elongation complex as described below (Mandal et al 2002; Kim et al 2003; Yamaguchi et al 2002)
This HIV-1 event was inferred from the corresponding human RNA Poll II transcription event in Reactome. The details relevant to HIV-1 are described below. For a more detailed description of the general mechanism, see the link to the corresponding RNA Pol II transcription event below. \nThe formation of the HIV-1 elongation complex involves Tat mediated recruitment of P-TEFb(Cyclin T1:Cdk9) to the TAR sequence (Wei et al, 1998) and P-TEFb(Cyclin T1:Cdk9) mediated phosphorylation of the RNA Pol II CTD as well as the negative transcriptional elongation factors DSIF and NELF (Herrmann, 1995; Ivanov et al. 2000; Fujinaga et al. 2004; Zhou et al., 2004)
This event was inferred from the corresponding Reactome human Poll II transcription elongation event. The details specific to HIV-1 transcription elongation are described below. In the absence of the HIV-1 Tat protein, the RNA Pol II complexes associated with the HIV-1 template are non-processive. RNA Pol II is arrested after promoter clearance by the negative transcriptional elongation factors DSIF and NELF as occurs during early elongation of endogenous templates (Wada et al, 1998; Yamaguchi et al. 1999). This arrest cannot be overcome by P-TEFb mediated phosphorylation in the absence of Tat however, and elongation aborts resulting in the accumulation of short transcripts (Kao et al., 1987)
RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. TFIIS reactivates arrested RNA Pol II by promoting the excision of nascent transcript ~7-14 nucleotides upstream of the 3' end
The Tat protein is a viral transactivator protein that regulates HIV-1 gene expression by controlling RNA Pol II-mediated elongation (reviewed in Karn 1999; Taube et al. 1999; Liou et al. 2004; Barboric and Peterlin 2005). Tat appears to be required in order to overcome the arrest of RNA Pol II by the negative transcriptional elongation factors DSIF and NELF (Wada et al. 1998; Yamaguchi et al. 1999; Yamaguchi et al 2002; Fujinaga et al. 2004). While Pol II can associate with the proviral LTR and initiate transcription in the absence of Tat, these polymerase complexes are non-processive and dissociate from the template prematurely producing very short transcripts (Kao et al. 1987). Tat associates with the RNA element, TAR, which forms a stem loop structure in the leader RNA sequence (Dingwall et al. 1989). Tat also associates with the cellular kinase complex P-TEFb(Cyclin T1:Cdk9) and recruits it to the TAR stem loop structure (Herrmann, 1995) (Wei et al. 1998). This association between Tat, TAR and P-TEFb(Cyclin T1:Cdk9) is believed to bring the catalytic subunit of this kinase complex (Cdk9) in close proximity to Pol II where it hyperphosphorylates the CTD of RNA Pol II (Zhou et al. 2000). The RD subunits of NELF and the SPT5 subunit of DSIF, which associate through RD with the bottom stem of TAR, are also phosphorylated by P-TEFb(Cyclin T1:Cdk9) (Yamaguchi et al. 2002; Fujinaga et al. 2004; Ivanov et al. 2000). Phosphorylation of RD results in its dissociation from TAR. Thus, Tat appears to facilitate transcriptional elongation of the HIV-1 transcript by hyperphosphorylating the RNA Poll II CTD and by removing the negative transcription elongation factors from TAR. In addition, there is evidence that the association of Tat with P-TEFb(Cyclin T1:Cdk9) alters the substrate specificity of P-TEFb enhancing phosphorylation of ser5 residues in the CTD of RNA Pol II (Zhou et al. 2000)
RNA Pol II arrest is believed to be a result of irreversible backsliding of the enzyme by ~7-14 nucleotides. TFIIS reactivates arrested RNA Pol II by promoting the excision of nascent transcript ~7-14 nucleotides upstream of the 3' end
For initiation, Pol II assembles with the general transcription factors TFIIB, TFIID, TFIIE, TFIIF and TFIIH, which are collectively known as the general transcription factors, at promoter DNA to form the pre-initiation complex (PIC). Until the nascent transcript is about 15 nucleotides long, the early transcribing complex is functionally unstable. In the beginning, short RNAs are frequently released and Pol II has to restart transcription (abortive cycling)
Several DNA repair genes contain p53 response elements and their transcription is positively regulated by TP53 (p53). TP53-mediated regulation probably ensures increased protein level of DNA repair genes under genotoxic stress.
TP53 directly stimulates transcription of several genes involved in DNA mismatch repair, including MSH2 (Scherer et al. 2000, Warnick et al. 2001), PMS2 and MLH1 (Chen and Sadowski 2005). TP53 also directly stimulates transcription of DDB2, involved in nucleotide excision repair (Tan and Chu 2002), and FANCC, involved in the Fanconi anemia pathway that repairs DNA interstrand crosslinks (Liebetrau et al. 1997). Other p53 targets that can influence DNA repair functions are RRM2B (Kuo et al. 2012), XPC (Fitch et al. 2003), GADD45A (Amundson et al. 2002), CDKN1A (Cazzalini et al. 2010) and PCNA (Xu and Morris 1999). Interestingly, the responsiveness of some of these DNA repair genes to p53 activation has been shown in human cells but not for orthologous mouse genes (Jegga et al. 2008, Tan and Chu 2002). Contrary to the positive modulation of nucleotide excision repair (NER) and mismatch repair (MMR), p53 can negatively modulate base excision repair (BER), by down-regulating the endonuclease APEX1 (APE1), acting in concert with SP1 (Poletto et al. 2016).
Expression of several DNA repair genes is under indirect TP53 control, through TP53-mediated stimulation of cyclin K (CCNK) expression (Mori et al. 2002). CCNK is the activating cyclin for CDK12 and CDK13 (Blazek et al. 2013). The complex of CCNK and CDK12 binds and phosphorylates the C-terminal domain of the RNA polymerase II subunit POLR2A, which is necessary for efficient transcription of long DNA repair genes, including BRCA1, ATR, FANCD2, FANCI, ATM, MDC1, CHEK1 and RAD51D. Genes whose transcription is regulated by the complex of CCNK and CDK12 are mainly involved in the repair of DNA double strand breaks and/or the Fanconi anemia pathway (Blazek et al. 2011, Cheng et al. 2012, Bosken et al. 2014, Bartkowiak and Greenleaf 2015, Ekumi et al. 2015)
The mechanisms governing the process of elongation during eukaryotic mRNA synthesis are being unraveled by recent studies. These studies have led to the expected discovery of a diverse collection of transcription factors that directly regulate the activities of RNA Polymerase II and unexpected discovery of roles for many elongation factors in other basic processes like DNA repair, recombination, etc. The transcription machinery and structural features of the major RNA polymerases are conserved across species. The genes active during elongation fall under different classes like, housekeeping, cell-cycle regulated, development and differentiation specific genes etc. The list of genes involved in elongation has been growing in recent times, and include: -TFIIS,DSIF, NELF, P-Tefb etc. that are involved in drug induced or sequence-dependent arrest - TFIIF, ELL, elongin, elongator etc. that are involved in increasing the catalytic rate of elongation by altering the Km and/or the Vmax of Pol II -FACT, Paf1 and other factors that are involved chromatin modification - DNA repair proteins, RNA processing and export factors, the 19S proteasome and a host of other factors like Spt5-Spt5, Paf1, and NELF complexes, FCP1P etc. (Arndt and Kane, 2003). Elongation also represents processive phase of transcription in which the activities of several mRNA processing factors are coupled to transcription through their binding to RNA polymerase (Pol II). One of the key events that enables this interaction is the differential phosphorylation of Pol II CTD. Phosphorylation pattern of CTD changes during transcription, most significantly at the beginning and during elongation process. TFIIH-dependent Ser5 phosphorylation is observed primarily at promoter regions while P-Tefb mediated Ser2 phosphorylation is seen mainly in the coding regions, during elongation. Experimental evidence suggests a dynamic association of RNA processing factors with differently modified forms of the polymerase during the transcription cycle. (Komarnitsky et al., 2000)
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