The identification of putative RNA polymerase II C-terminal domain associated proteins in red and green algae

References

• Allison LA, Moyle M, Shales M, Ingles CJ. Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 1985; 42:599-610; PMID:3896517; http://dx.doi.org/10.1016/0092-8674(85)90117-5
   PubMed Web of Science ®Google Scholar
• Corden JL, Cadena DL, Ahearn JM, Dahmus ME. A Unique Structure at the Carboxyl Terminus of the Largest Subunit of Eukaryotic Rna Polymerase-Ii. Proc Natl Acad Sci U S A 1985; 82:7934-8; PMID:2999785; http://dx.doi.org/10.1073/pnas.82.23.7934
   PubMed Web of Science ®Google Scholar
• Corden JL. RNA polymerase II C-terminal domain: Tethering transcription to transcript and template. Chem Rev 2013; 113:8423-55; PMID:24040939; http://dx.doi.org/10.1021/cr400158h
   PubMed Web of Science ®Google Scholar
• West ML, Corden JL. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics 1995; 140:1223-33; PMID:7498765
   PubMed Web of Science ®Google Scholar
• Nonet M, Sweetser D, Young RA. Functional redundancy and structural polymorphism in the large subunit of RNA polymerase II. Cell 1987; 50:909-15; PMID:3304659; http://dx.doi.org/10.1016/0092-8674(87)90517-4
   PubMedGoogle Scholar
• Bartolomei MS, Halden NF, Cullen CR, Corden JL. Genetic analysis of the repetitive carboxyl-terminal domain of the largest subunit of mouse RNA polymerase II. Mol Cell Biol 1988; 8:330-9; PMID:3275873
   PubMed Web of Science ®Google Scholar
• Liu P, Greenleaf AL, Stiller JW. The essential sequence elements required for RNAP II carboxyl-terminal domain function in yeast and their evolutionary conservation. Mol Biol Evol 2008; 25:719-27; PMID:18209193; http://dx.doi.org/10.1093/molbev/msn017
   PubMed Web of Science ®Google Scholar
• Schwer B, Shuman S. Deciphering the RNA Polymerase II CTD Code in Fission Yeast. Mol Cell 2011; 43:311-8; PMID:21684186; http://dx.doi.org/10.1016/j.molcel.2011.05.024
   PubMed Web of Science ®Google Scholar
• Stiller JW, Cook MS. Functional unit of the RNA polymerase II C-terminal domain lies within heptapeptide pairs. Eukaryot Cell 2004; 3:735-40; PMID:15189994; http://dx.doi.org/10.1128/EC.3.3.735-740.2004
   PubMedGoogle Scholar
• Schwer B, Sanchez AM, Shuman S. Punctuation and syntax of the RNA polymerase II CTD code in fission yeast. Proc Natl Acad Sci U S A 2012; 109:18024-9; PMID:23071310; http://dx.doi.org/10.1073/pnas.1208995109
   PubMed Web of Science ®Google Scholar
• Liu P, Kenney JM, Stiller JW, Greenleaf AL. Genetic organization, length conservation, and evolution of RNA polymerase II carboxyl-terminal domain. Mol Biol Evol 2010; 27:2628-41; PMID:20558594; http://dx.doi.org/10.1093/molbev/msq151
   PubMed Web of Science ®Google Scholar
• Jasnovidova O, Stefl R. The CTD code of RNA polymerase II: a structural view. Wiley Interdiscip Rev RNA 2013; 4:1-16.
   Google Scholar
• Yang C, Stiller JW. Evolutionary diversity and taxon-specific modifications of the RNA polymerase II C-terminal domain. Proc Natl Acad Sci U S A 2014; 111:5920-5; PMID:24711388; http://dx.doi.org/10.1073/pnas.1323616111
   PubMed Web of Science ®Google Scholar
• Das A, Bellofatto V. The Non-Canonical CTD of RNAP-II Is Essential for Productive RNA Synthesis in Trypanosoma brucei. PLoS One 2009; 4.
   Web of Science ®Google Scholar
• Eick D, Geyer M. The RNA polymerase II carboxy-terminal domain (CTD) code. Chem Rev 2013; 113:8456-90; PMID:23952966; http://dx.doi.org/10.1021/cr400071f
   PubMed Web of Science ®Google Scholar
• Zhang DW, Rodriguez-Molina JB, Tietjen JR, Nemec CM, Ansari AZ. Emerging Views on the CTD Code. Genet Res Int 2012; 2012:347214; PMID:22567385
   PubMedGoogle Scholar
• Egloff S, Murphy S. Cracking the RNA polymerase II CTD code. Trends Genet 2008; 24:280-8; PMID:18457900; http://dx.doi.org/10.1016/j.tig.2008.03.008
   PubMed Web of Science ®Google Scholar
• Bartkowiak B, Greenleaf AL. Phosphorylation of RNAPII: To P-TEFb or not to P-TEFb? Transcription 2011; 2:115-9; PMID:21826281; http://dx.doi.org/10.4161/trns.2.3.15004
   PubMedGoogle Scholar
• Carty SM, Greenleaf AL. Hyperphosphorylated C-terminal repeat domain-associating proteins in the nuclear proteome link transcription to DNA/chromatin modification and RNA processing. Mol Cell Proteomics 2002; 1:598-610; PMID:12376575; http://dx.doi.org/10.1074/mcp.M200029-MCP200
   PubMed Web of Science ®Google Scholar
• Phatnani HP, Jones JC, Greenleaf AL. Expanding the functional repertoire of CTD kinase I and RNA polymerase II: novel phosphoCTD-associating proteins in the yeast proteome. Biochemistry 2004; 43:15702-19; PMID:15595826; http://dx.doi.org/10.1021/bi048364h
   PubMed Web of Science ®Google Scholar
• Lee JY. Versatile casein kinase 1: multiple locations and functions. Plant Signal Behav 2009; 4:652-4; PMID:19820321; http://dx.doi.org/10.4161/psb.4.7.8991
   PubMedGoogle Scholar
• Ho Y, Mason S, Kobayashi R, Hoekstra M, Andrews B. Role of the casein kinase I isoform, Hrr25, and the cell cycle-regulatory transcription factor, SBF, in the transcriptional response to DNA damage in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 1997; 94:581-6; PMID:9012827; http://dx.doi.org/10.1073/pnas.94.2.581
   PubMed Web of Science ®Google Scholar
• Payne JM, Laybourn PJ, Dahmus ME. The Transition of Rna Polymerase-Ii from Initiation to Elongation Is Associated with Phosphorylation of the Carboxyl-Terminal Domain of Subunit-Iia. J Biol Chem 1989; 264:19621-9; PMID:2584185
   PubMed Web of Science ®Google Scholar
• Palancade B, Dubois MF, Bensaude O. FCP1 phosphorylation by casein kinase 2 enhances binding to TFIIF and RNA polymerase II carboxyl-terminal domain phosphatase activity. J Biol Chem 2002; 277:36061-7; PMID:12138108; http://dx.doi.org/10.1074/jbc.M205192200
   PubMed Web of Science ®Google Scholar
• Zhou Z, Luo MJ, Straesser K, Katahira J, Hurt E, Reed R. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature 2000; 407:401-5; PMID:11014198; http://dx.doi.org/10.1038/35030160
   PubMed Web of Science ®Google Scholar
• MacKellar AL, Greenleaf AL. Cotranscriptional association of mRNA export factor Yra1 with C-terminal domain of RNA polymerase II. J Biol Chem 2011; 286:36385-95; PMID:21856751; http://dx.doi.org/10.1074/jbc.M111.268144
   PubMed Web of Science ®Google Scholar
• Mangus DA, Evans MC, Jacobson A. Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression. Genome Biol 2003; 4:223; PMID:12844354; http://dx.doi.org/10.1186/gb-2003-4-7-223
   PubMed Web of Science ®Google Scholar
• Dermody JL, Dreyfuss JM, Villen J, Ogundipe B, Gygi SP, Park PJ, Ponticelli AS, Moore CL, Buratowski S, Bucheli ME. Unphosphorylated SR-like protein Npl3 stimulates RNA polymerase II elongation. PLoS One 2008; 3:e3273; PMID:18818768; http://dx.doi.org/10.1371/journal.pone.0003273
   PubMed Web of Science ®Google Scholar
• Morris DP, Greenleaf AL. The splicing factor, Prp40, binds the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 2000; 275:39935-43; PMID:10978320; http://dx.doi.org/10.1074/jbc.M004118200
   PubMed Web of Science ®Google Scholar
• David CJ, Boyne AR, Millhouse SR, Manley JL. The RNA polymerase II C-terminal domain promotes splicing activation through recruitment of a U2AF65-Prp19 complex. Genes Dev 2011; 25:972-83; PMID:21536736; http://dx.doi.org/10.1101/gad.2038011
   PubMed Web of Science ®Google Scholar
• Zhu P, Zhou W, Wang J, Puc J, Ohgi KA, Erdjument-Bromage H, Tempst P, Glass CK, Rosenfeld MG. A histone H2A deubiquitinase complex coordinating histone acetylation and H1 dissociation in transcriptional regulation. Mol Cell 2007; 27:609-21; PMID:17707232; http://dx.doi.org/10.1016/j.molcel.2007.07.024
   PubMed Web of Science ®Google Scholar
• Werner-Allen JW, Lee CJ, Liu P, Nicely NI, Wang S, Greenleaf AL, Zhou P. cis-Proline-mediated Ser(P)5 dephosphorylation by the RNA polymerase II C-terminal domain phosphatase Ssu72. J Biol Chem 2011; 286:5717-26; PMID:21159777; http://dx.doi.org/10.1074/jbc.M110.197129
   PubMed Web of Science ®Google Scholar
• Durocher D, Jackson SP. The FHA domain. FEBS Lett 2002; 513:58-66; PMID:11911881; http://dx.doi.org/10.1016/S0014-5793(01)03294-X
   PubMed Web of Science ®Google Scholar
• Shaiu WL, Hsieh TS. Targeting to transcriptionally active loci by the hydrophilic N-terminal domain of Drosophila DNA topoisomerase I. Mol Cell Biol 1998; 18:4358-67; PMID:9632819
   PubMed Web of Science ®Google Scholar
• Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T. Repair of alkylated DNA: recent advances. DNA Repair (Amst) 2007; 6:429-42; PMID:17112791
   PubMedGoogle Scholar
• Wu J, Phatnani HP, Hsieh TS, Greenleaf AL. The phosphoCTD-interacting domain of Topoisomerase I. Biochem Biophys Res Commun 2010; 397:117-9; PMID:20493173; http://dx.doi.org/10.1016/j.bbrc.2010.05.081
   PubMed Web of Science ®Google Scholar
• Winston F, Carlson M. Yeast SNF/SWI transcriptional activators and the SPT/SIN chromatin connection. Trends Genet 1992; 8:387-91; PMID:1332230; http://dx.doi.org/10.1016/0168-9525(92)90300-S
   PubMed Web of Science ®Google Scholar
• Schwabish MA, Struhl K. The Swi/Snf complex is important for histone eviction during transcriptional activation and RNA polymerase II elongation in vivo. Mol Cell Biol 2007; 27:6987-95; PMID:17709398; http://dx.doi.org/10.1128/MCB.00717-07
   PubMed Web of Science ®Google Scholar
• Euskirchen G, Auerbach RK, Snyder M. SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions. J Biol Chem 2012; 287:30897-905; PMID:22952240; http://dx.doi.org/10.1074/jbc.R111.309302
   PubMed Web of Science ®Google Scholar
• Spain MM, Govind CK. A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics. Transcription 2011; 2:78-81; PMID:21468233; http://dx.doi.org/10.4161/trns.2.2.14638
   PubMedGoogle Scholar
• Joo YJ, Kim JA, Baek JH, Seong KM, Han KD, Song JM, Choi JY, Kim J. Cooperative regulation of ADE3 transcription by Gcn4p and Bas1p in Saccharomyces cerevisiae. Eukaryot Cell 2009; 8:1268-77; PMID:19525417; http://dx.doi.org/10.1128/EC.00116-09
   PubMedGoogle Scholar
• Stracke R, Werber M, Weisshaar B. The R2R3-MYB gene family in Arabidopsis thaliana. Curr Opin Plant Biol 2001; 4:447-56; PMID:11597504; http://dx.doi.org/10.1016/S1369-5266(00)00199-0
   PubMed Web of Science ®Google Scholar
• Conaway RC, Bradsher JN, Conaway JW. Mechanism of Assembly of the Rna Polymerase-Ii Preinitiation Complex - Evidence for a Functional Interaction between the Carboxyl-Terminal Domain of the Largest Subunit of Rna Polymerase-Ii and a High Molecular Mass Form of the Tata Factor. J Biol Chem 1992; 267:8464-7; PMID:1569096
   PubMed Web of Science ®Google Scholar
• Koleske AJ, Buratowski S, Nonet M, Young RA. A Novel Transcription Factor Reveals a Functional Link between the Rna Polymerase-Ii Ctd and Tfiid. Cell 1992; 69:883-94; PMID:1591782; http://dx.doi.org/10.1016/0092-8674(92)90298-Q
   PubMed Web of Science ®Google Scholar
• Kwon I, Kato M, Xiang S, Wu L, Theodoropoulos P, Mirzaei H, Han T, Xie S, Corden JL, McKnight SL. Phosphorylation-regulated binding of RNA polymerase II to fibrous polymers of low-complexity domains. Cell 2013; 155:1049-60; PMID:24267890; http://dx.doi.org/10.1016/j.cell.2013.10.033
   PubMed Web of Science ®Google Scholar
• Morris DP, Phatnani HP, Greenleaf AL. Phospho-carboxyl-terminal domain binding and the role of a prolyl isomerase in pre-mRNA 3'-End formation. J Biol Chem 1999; 274:31583-7; PMID:10531363; http://dx.doi.org/10.1074/jbc.274.44.31583
   PubMed Web of Science ®Google Scholar
• Carty SM, Goldstrohm AC, Sune C, Garcia-Blanco MA, Greenleaf AL. Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. Proc Natl Acad Sci U S A 2000; 97:9015-20; PMID:10908677; http://dx.doi.org/10.1073/pnas.160266597
   PubMed Web of Science ®Google Scholar
• Matsuzaki M, Misumi O, Shin IT, Maruyama S, Takahara M, Miyagishima SY, Mori T, Nishida K, Yagisawa F, Yoshida Y, et al. Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 2004; 428:653-7; PMID:15071595; http://dx.doi.org/10.1038/nature02398
   PubMed Web of Science ®Google Scholar
• Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, et al. The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science 2007; 318:245-50; PMID:17932292; http://dx.doi.org/10.1126/science.1143609
   PubMed Web of Science ®Google Scholar
• Spingola M, Grate L, Haussler D, Ares M Jr. Genome-wide bioinformatic and molecular analysis of introns in Saccharomyces cerevisiae. Rna-a Publication of the Rna Society 1999; 5:221-34; http://dx.doi.org/10.1017/S1355838299981682
   PubMed Web of Science ®Google Scholar
• Csuros M, Rogozin IB, Koonin EV. A detailed history of intron-rich eukaryotic ancestors inferred from a global survey of 100 complete genomes. PLoS Comput Biol 2011; 7:e1002150; PMID:21935348; http://dx.doi.org/10.1371/journal.pcbi.1002150
   PubMedGoogle Scholar
• Butterfield NJ. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 2000; 26:386-404; http://dx.doi.org/10.1666/0094-8373(2000)026%3c0386:BPNGNS%3e2.0.CO;2
   Web of Science ®Google Scholar
• Burton ZF. The Old and New Testaments of gene regulation: Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD. Transcription 2014; 5:e28764. http://dx.doi.org/10.4161/trns.28674
   Google Scholar
• Gorman DS, Levine RP. Cytochrome f and plastocyanin: their sequence in the photosynthetic electron transport chain of Chlamydomonas reinhardi. Proc Natl Acad Sci U S A 1965; 54:1665-9; PMID:4379719; http://dx.doi.org/10.1073/pnas.54.6.1665
   PubMed Web of Science ®Google Scholar
• Minoda A, Sakagami R, Yagisawa F, Kuroiwa T, Tanaka K. Improvement of culture conditions and evidence for nuclear transformation by homologous recombination in a red alga, Cyanidioschyzon merolae 10D. Plant Cell Physiol 2004; 45:667-71; PMID:15215501; http://dx.doi.org/10.1093/pcp/pch087
   PubMed Web of Science ®Google Scholar
• Cao L, Chen F, Yang X, Xu W, Xie J, Yu L. Phylogenetic analysis of CDK and cyclin proteins in premetazoan lineages. BMC Evol Biol 2014; 14:10; PMID:24433236; http://dx.doi.org/10.1186/1471-2148-14-10
   PubMed Web of Science ®Google Scholar
• Guo Z, Stiller JW. Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs. BMC Genomics 2004; 5:69; PMID:15380029; http://dx.doi.org/10.1186/1471-2164-5-69
   PubMed Web of Science ®Google Scholar
• Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-7; PMID:15034147; http://dx.doi.org/10.1093/nar/gkh340
   PubMed Web of Science ®Google Scholar
• Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-52; PMID:10742046; http://dx.doi.org/10.1093/oxfordjournals.molbev.a026334
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17:754-5; PMID:11524383; http://dx.doi.org/10.1093/bioinformatics/17.8.754
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731-9; PMID:21546353; http://dx.doi.org/10.1093/molbev/msr121
   PubMed Web of Science ®Google Scholar