摘要
Pafl复合物(PaflC)是一种在真核生物中非常保守的复合物,目前已获得鉴定的PaflC中,含有Paf1、Cdc73、Ctr9, Leol及Rtfl(最近发现hSki8也是其人源复合物的组分之一)五种蛋白质组分。 PaflC主要的功能是通过与RNA聚合酶Ⅱ (RNApolⅡ)相互作用,共同参与包括转录起始、延伸和终止的全过程。作为Pafl复合物中最早被鉴定出的亚基之一,酿酒酵母Cdc73蛋白参与了很多转录相关的生命过程,包括与RNA Pol Ⅱ的直接相互作用,招募和激活组蛋白修饰相关因子并和其它的一些转录激活因子共同参与转录。酿酒酵母Cdc73蛋白在人源中的同源蛋白Parafibromin被鉴定为一个肿瘤抑制因子,它的突变与乳腺癌,肾癌和胃癌的发生相关。
本文第一部分以酿酒酵母Cdc73蛋白质为研究对象,首次解析了其C-端结构域结构。研究表明Cdc73的C-端氨基酸序列非常保守,其结构是一个由中心6个p折叠片被6个α螺旋包裹的α/β结构,通过Dali在线比对发现其与经典的GTPase的结构非常类似。但序列分析显示Cdc73与GTPase的同源度非常低,且关键区域也不保守。通过等温滴定量热法检测不到Cdc73与GTP明显结合,酶活实验也检测不到Cdc73具有水解GTP的GTPase酶活性,因此Cdc73尽管与GTPase具有类似的折叠方式,但可能不是一个GTP水解酶。该结构的解析为加深人们对Pafl复合物组装的认识提供了重要思路,为Cdc73与RNA Pol Ⅱ相互作用的研究以及人源的Cdc73与疾病相关研究等提供了重要的结构基础。
DNA是生命遗传信息的载体,各种内源性或者外源性的DNA损伤因素会使其受到不同程度的损伤,从而导致基因组不稳定或基因组重排,进而导致一些疾病的发生。DNA损伤包括单链DNA损伤和双链DNA损伤。针对不同的DNA损伤。细胞内有许多不同的修复方式对其进行修复,包括碱基切除修复、核苷酸切除修复、错配修复、同源重组修复等。除了这些精确修复外,还有另外一种在复制叉延滞时进行的绕过损伤的修复方式,叫DNA损伤容限(DNA Damage tolerance, DDT),也叫复制后修复(PRR)。在复制后修复中有一种是无错修复方式(error-free),该过程和同源重组方式很类似,需要Rad51蛋白的参与。酿酒酵母Shu复合物由Csm2、Psy3、Shul和Shu2四个亚基组成,其通过抑制Srs2的活性促进Rad51依赖的同源重组发生。酿酒酵母中Psy3、Shul、Shu2在人源中对应的同源蛋白分别是Rad51D、Xrcc2和Sws1,其中裂殖酵母中Shu2的同源蛋白Sws1与Srs2有直接相互作用。最近发现人源中的Sws1能与一个新发现的蛋白质Swsap1形成稳定的复合物并参与同源重组修复过程。为理解该复合物的形成及相互作用机制,本文第二部分致力于解析人源Sws1-Swsap1复合物的结构。
Pafl complex which contains Pafl, Cdc73, Ctr9, Leol and Rtfl (recently discovered hSki8is one subunit in human Pafl complex) subunits is a conserved complex in eukaryotes. The main function of Pafl complex is taking part in transcription including initiation, elongation and termination together with RNA pol II. As one of the first identified subunits of PaflC, yeast Cdc73(yCdc73) takes part in many transcription-related processes, including binding to RNA polymerase II, recruitment and activation of histonemodification factors and communication with other transcriptional activators. The human homologue of yCdc73, parafibromin, has been identified as a tumour suppressor linked to breast, renal and gastric cancers.
In this work, we targeted yeast Cdc73for structural studies and determined the C-terminal structure of yCdc73. The C-terminal of Cdc73is very conserved and a DALI server search indicates the C-terminal structure of Cdc73is a canonical a6/p6GTPase-like fold, although the primary sequence of it has very low identity to GTPases and is not conservative at the key region. No significant GTP-binding ability and hydrolysis activity were detected by ITC and enzyme activity assay. So Cdc73, with a GTPase-like fold, may not be a GTPase. The determination of the structure of Cdc73has provided further insights into the assembly way of Pafl complex and the structural basis for study on Cdc73-RNA PolⅡ interaction and human related diseases.
DNA, the carrier of genetic information, is always induced a wide range of lesions by exogenous or endogenous DNA damaging agents. The genome will be instabile or re-arrange if the lesions of DNA are not repaired, and then some related diseases will occur. There are many DNA repair pathways to different DNA lesions, including base excision repair, nucleotide excision repair, mismatch repair and homologous recombination repair. In addition to these accurate repair pathways, when presence of replication-blocking lesions, there is another DNA damage tolerance (DDT) mechanism which does not remove DNA damages in the template strand, but bypass the DNA lesions during replication to prevent replication fork collapse, which is also named post-replication repair (PRR). An error-free pathway within PRR is very similar to the Rad51dependent homologous recombination repair (HRR). The yeast Shu complex is comprised of four subunits, Csm2, Psy3, Shu land Shu2, which promotes Rad51dependent homologous recombination via inhibit the activity of Srs2. The human orthologous of yeast Psy3, Shul and Shu2are Rad51D, Xrcc2and Sws1respectively. Sws1, the Shu2orthologous in fission yeast, was reported to have the ability to interact with Srs2. A newly identified human Swsl associate protein, Swsapl can form a stable complex with Swsl and takes part in homologous recombination repair. We are trying to solve the structure of Swsl-Swsapl complex and explain its function mechanism.
引文
Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology.5th edition. New York:W. H. Freeman; 2004.
Tomson, B. N. and K. M. Arndt (2013). "The many roles of the conserved eukaryotic Pafl complex in regulating transcription, histone modifications, and disease states." Biochim Biophys Acta 1829(1) : 116-126.
Adami, S., C. Marcocci, et al. (2002). "Epidemiology of primary hyperparathyroidism in Europe." J Bone Miner Res 17 Suppl 2:N18-23.
Akhtar, M. S., M. Heidemann, et al. (2009). "TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNApolymerase II." Mol Cell 34(3):387-393.
Amrich, C. G, C. P. Davis, et al. (2012). "Cdc73 subunit of Pafl complex contains C-terminal Ras-like domain that promotes association of Pafl complex with chromatin." J Biol Chem 287(14):10863-10875.
Benkert, P., M. Biasini, et al. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics 27(3):343-350.
Bernstein, B. E., E. L. Humphrey, et al. (2002). "Methylation of histone H3 Lys 4 in coding regions of active genes." Proc Natl Acad Sci U S A 99(13):8695-8700.
Boggs, B. A., P. Cheung, et al. (2002). "Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes." Nat Genet 30(1):73-76.
Bradley, K. J., B. M. Cavaco, et al. (2006). "Parafibromin mutations in hereditary hyperparathyroidism syndromes and parathyroid tumours." Clin Endocrinol (Oxf) 64(3): 299-306.
Bradley, K. J., M. R. Hobbs, et al. (2005). "Uterine tumours are a phenotypic manifestation of the hyperparathyroidism-jaw tumour syndrome." J Intern Med 257(1):18-26.
Briggs, S. D., M. Bryk, et al. (2001). "Histone H3 lysine 4 methylation is mediated by Setl and required for cell growth and rDNA silencing in Saccharomyces cerevisiae." Genes Dev 15(24):3286-3295.
Bromberg, J. and T. C. Wang (2009). "Inflammation and cancer:IL-6 and STAT3 complete the link." Cancer Cell 15(2):79-80.
Buratowski, S. (1994). "The basics of basal transcription by RNA polymerase II." Gell 77(1): 1-3.
Burton, Z. F., M. Killeen, et al. (1988). "RAP30/74:a general initiation factor that binds to RNA polymerase II." Mol Cell Biol 8(4):1602-1613.
Cavaco, B. M., L. Barros, et al. (2001). "The hyperparathyroidism-jaw tumour syndrome in a Portuguese kindred." QJM 94(4):213-222.
Chaudhary, K., S. Deb, et al. (2007). "Human RNA polymerase II-associated factor complex: dysregulation in cancer." Oncogene 26(54):7499-7507.
Chen, H., N. Shi, et al. (2012). "Crystallographic analysis of the conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like fold." Acta Crystallogr D Biol Crystallogr 68(Pt 8):953-959.
Chen, J. D., C. Morrison, et al. (2003). "Hyperparathyroidism-jaw tumour syndrome." J Intern Med 253(6):634-642.
Chen, V. B., W. B. Arendall,3rd, et al. (2010). "MolProbity:all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr 66(Pt 1):12-21.
Chen, Y., Y. Yamaguchi, et al. (2009). "DSIF, the Pafl complex, and Tat-SFl have nonredundant, cooperative roles in RNA polymerase II elongation." Genes Dev 23(23):2765-2777.
Chu, Y., R. Simic, et al. (2007). "Regulation of histone modification and cryptic transcription by the Burl and Pafl complexes." EMBOJ 26(22):4646-4656.
Conaway, R. C. and J. W. Conaway (1993). "General initiation factors for RNA polymerase II." Annu Rev Biochem 62:161-190.
Costa, P. J. and K. M. Arndt (2000). "Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtfl protein in transcription elongation." Genetics 156(2): 535-547.
Crisucci, E. M. and K. M. Arndt (2011). "The Pafl complex represses ARG1 transcription in Saccharomyces cerevisiae by promoting histone modifications." Eukarvot Cell 10(6): 712-723.
Daniel, J. A., M. S. Torok, et al. (2004). "Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription." J Biol Chem 279(3):1867-1871.
de Jong, R. N., V. Truffault, et al. (2008). "Structure and DNA binding of the human Rtfl Plus3 domain." Structure 16(1):149-159.
Di Como, C. J., H. Chang, et al. (1995). "Activation of CLN1 and CLN2 Gl cyclin gene expression by BCK2." Mol Cell Biol 15(4):1835-1846.
Ding, L., M. Paszkowski-Rogacz, et al. (2009). "A genome-scale RNAi screen for Oct4 modulators defines a role of the Pafl complex for embryonic stem cell identity." Cell Stem Cell 4(5):403-415.
Ebright, R. H. (2000). "RNA polymerase:structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II." J Mol Biol 304(5):687-698.
Exinger, F. and F. Lacroute (1992). "6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae." Curr Genet 22(1):9-11.
Foreman, P. K. and R. W. Davis (1996). "CDP1, a novel Saccharomyces cerevisiae gene required for proper nuclear division and chromosome segregation." Genetics 144(4):1387-1397.
Formosa, T. (2012). "The role of FACT in making and breaking nucleosomes." Biochim Biophys Acta 1819(3-4):247-255.
Gaspar-Maia, A., A. Alajem, et al. (2009). "Chdl regulates open chromatin and pluripotency of embryonic stem cells." Nature 460(7257):863-868.
Glover-Cutter, K., S. Larochelle, et al. (2009). "TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase II." Mol Cell Biol 29(20):5455-5464.
Grummt, I. (1999). "Regulation of mammalian ribosomal gene transcription by RNA polymerase I." Prog Nucleic Acid Res Mol Biol 62:109-154.
Henry, K. W., A. Wyce, et al. (2003). "Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8." Genes Dev 17(21):2648-2663.
Howell, V. M., C. J. Haven, et al. (2003). "HRPT2 mutations are associated with malignancy in sporadic parathyroid tumours." J Med Genet 40(9):657-663.
Kao, C. F., C. Hillyer, et al. (2004). "Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B." Genes Dev 18(2):184-195.
Kim, J., M. Guermah, et al. (2010). "The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS." Cell 140(4):491-503.
Kim, J. and R. G Roeder (2009). "Direct Brel-Pafl complex interactions and RING finger-independent Brel-Rad6 interactions mediate histone H2B ubiquitylation in yeast." J Biol Chem 284(31):20582-20592.
Kim, K. Y. and D. E. Levin (2011). "Mpkl MAPK association with the Pafl complex blocks Senl-mediated premature transcription termination." Cell 144(5):745-756.
Kim, M., S. H. Ahn, et al. (2004). "Transitions in RNA polymerase II elongation complexes at the 3" ends of genes." EMBOJ 23(2):354-364.
Kim, M., H. Suh, et al. (2009). "Phosphorylation of the yeast Rpbl C-terminal domain at serines 2,5, and 7." J Biol Chem 284(39):26421-26426.
Koch, C., P. Wollmann, et al. (1999). "A role for Ctr9p and Paflp in the regulation Gl cyclin expression in yeast." Nucleic Acids Res 27(10):2126-2134.
Krogan, N. J., J. Dover, et al. (2002). "COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression." J Biol Chem 277(13):10753-10755.
Krogan, N. J., J. Dover, et al. (2003). "The Pafl complex is required for histone H3 methylation by COMPASS and Dotlp:linking transcriptional elongation to histone methylation." Mol Cell 11(3):721-729.
Krogan, N. J., M. Kim, et al. (2002). "RNA polymerase Ⅱ elongation factors of Saccharomyces cerevisiae:a targeted proteomics approach." Mol Cell Biol 22(20):6979-6992.
Kutach, A. K. and J. T. Kadonaga (2000). "The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters." Mol Cell Biol 20(13): 4754-4764.
Laribee, R. N., N. J. Krogan, et al. (2005). "BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex.' Curr Biol 15(16):1487-1493.
Laskowski, R., M. MacArthur, et al. (1993). "PROCHECK:A program to check the stereochemical quality of protein structures." J. Appl. Cryst 26:283-291.
Lee, C. K., Y. Shibata, ct al. (2004). "Evidence for nucleosome depletion at active regulatory regions genome-wide." Nat Genet 36(8):900-905.
Lee, J. S., A. Shukla, et al. (2007). "Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS." Cell 131(6):1084-1096.
Lee, S. H., K. Baek, et al. (2008). "Large nucleotide-dependent conformational change in Rab28." FEBS Lett 582(29):4107-4111.
Lee, Y., M. Kim, et al. (2004). "MicroRNA genes are transcribed by RNA polymerase II." EMBOJ 23(20):4051-4060.
Litt, M. D., M. Simpson, et al. (2001). "Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus." Science 293(5539):2453-2455.
Liu, L., N. M. Oliveira, et al. (2011). "A whole genome screen for HIV restriction factors." Retrovirology 8:94.
Liu, Y, L. Warfield, et al. (2009). "Phosphorylation of the transcription elongation factor Spt5 by yeast Burl kinase stimulates recruitment of the PAF complex." Mol Cell Biol 29(17): 4852-4863.
Magdolen, V, P. Lang, et al. (1994). "The gene LEOl on yeast chromosome XV encodes a non-essential, extremely hydrophilic protein." Biochim Biophvs Acta 1218(2):205-209.
Marazzi, I., J. S. Ho, et al. (2012). "Suppression of the antiviral response by an influenza histone mimic." Nature 483(7390):428-433.
Mayer, A., M. Lidschreiber, et al. (2010). "Uniform transitions of the general RNA polymerase Ⅱ transcription complex." Nat Struct Mol Biol 17(10):1272-1278.
Miller, T., N. J. Krogan, et al. (2001). "COMPASS:a complex of proteins associated with a trithorax-related SET domain protein." Proc Natl Acad Sci U S A 98(23):12902-12907.
Milne, T. A., S. D. Briggs, et al. (2002). "MLL targets SET domain methyltransferase activity to Hox gene promoters." Mol Cell 10(5):1107-1117.
Minakhin, L., S. Bhagat, et al. (2001). "Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly." Proc Natl Acad Sci U S A 98(3):892-897.
Moniaux, N., C. Nemos, et al. (2006). "The human homologue of the RNA polymerase II-associated factor 1 (hPafl), localized on the 19q13 amplicon, is associated with tumorigenesis." Oncogene 25(23):3247-3257.
Mueller, C. L. and J. A. Jaehning (2002). "Ctr9, Rtfl, and Leol are components of the Pafl/RNA polymerase Ⅱ complex." Mol Cell Biol 22(7):1971-1980.
Mueller, C. L., S. E. Porter, et al. (2004). "The Pafl complex has functions independent of actively transcribing RNA polymerase II." Mol Cell 14(4):447-456.
Mutiu, A. I., S. M. Hoke, et al. (2007). "The role of histone ubiquitylation and deubiquirylation in gene expression as determined by the analysis of an HTB1(K123R) Saccharomyces cerevisiae strain." Mol Genet Genomics 277(5):491-506.
Myer, V. E. and R. A. Young (1998). "RNA polymerase Ⅱ holoenzymes and subcomplexes." J Biol Chem 273(43):27757-27760.
Myers, L. C. and R. D. Kornberg (2000). "Mediator of transcriptional regulation." Annu Rev Biochem 69:729-749.
Newey, P. J., M. R. Bowl, et al. (2010). "Cell division cycle protein 73 homolog (CDC73) mutations in the hyperparathyroidism-jaw tumor syndrome (HPT-JT) and parathyroid tumors." Hum Mutat 31(3):295-307.
Newey, P. J., M. R. Bowl, et al. (2009). "Parafibromin-functional insights." J Intern Med 266(1): 84-98.
Ng, H. H., S. Dole, et al. (2003). "The Rtfl component of the Pafl transcriptional elongation complex is required for ubiquitination of histone H2B." J Biol Chem 278(36): 33625-33628.
Ng, H. H., F. Robert, et al. (2003). "Targeted recruitment of Setl histone methylase by elongating Pol Ⅱprovides a localized mark and memory of recent transcriptional activity." Mol Cell 11(3):709-719.
Nordick, K., M. G Hoffman, et al. (2008). "Direct interactions between the Pafl complex and a cleavage and polyadenylation factor are revealed by dissociation of Pafl from RNA polymerase II." Eukaryot Cell 7(7):1158-1167.
Orphanides, G, G LeRoy, et al. (1998). "FACT, a factor that facilitates transcript elongation through nucleosomes." Cell 92(1):105-116.
Pavri, R., B. Zhu, et al. (2006). "Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase Ⅱ." Cell 125(4):703-717.
Penheiter, K. L., T. M. Washburn, et al. (2005). "A posttranscriptional role for the yeast Pafl-RNA polymerase Ⅱ complex is revealed by identification of primary targets." Mol Cell 20(2):213-223.
Peterson, C. L. and J. W. Tamkun (1995). "The SWI-SNF complex:a chromatin remodeling machine?" Trends Biochem Sci 20(4):143-146.
Phatnani, H. P. and A. L. Greenleaf (2006). "Phosphorylation and functions of the RNA polymerase Ⅱ CTD." Genes Dev 20(21):2922-2936.
Piro, A. S., M. K. Mayekar, et al. (2012). "Small region of Rtfl protein can substitute for complete Pafl complex in facilitating global histone H2B ubiquitylation in yeast." Proc Natl Acad Sci U S A 109(27):10837-10842.
Pokholok, D. K., N. M. Hannett, et al. (2002). "Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo." Mol Cell 9(4):799-809.
Ponnusamy, M. P., S. Deb, et al. (2009). "RNA polymerase Ⅱ associated factor 1/PD2 maintains self-renewal by its interaction with Oct3/4 in mouse embryonic stem cells." Stem Cells 27(12):3001-3011.
Qiu, H., C. Hu, et al. (2012). "Pol II CTD kinases Burl and Kin28 promote Spt5 CTR-independent recruitment of Pafl complex." EMBOJ 31(16):3494-3505.
Qiu, H., C. Hu, et al. (2006). "The Spt4p subunit of yeast DSIF stimulates association of the Pafl complex with elongating RNA polymerase II." Mol Cell Biol 26(8):3135-3148.
Reed, S. I., J. Ferguson, et al. (1988). "Isolation and characterization of two genes encoding yeast mating pheromone signaling elements:CDC72 and CDC73." Cold Spring Harb Symp Quant Biol 53 Pt 2:621-627.
Roguev, A., D. Schaft, et al. (2001). "The Saccharomyces cerevisiae Setl complex includes an Ash2 homologue and methylates histone 3 lysine 4." EMBOJ 20(24):7137-7148.
Rozenblatt-Rosen, O., C. M. Hughes, et al. (2005). "The parafibromin tumor suppressor protein is part of a human Pafl complex." Mol Cell Biol 25(2):612-620.
Rozenblatt-Rosen, O., T. Nagaike, et al. (2009). "The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3'mRNA processing factors." Proc Natl Acad Sci U S A 106(3):755-760.
Rubin, M. R. and S. J. Silverberg (2005). "Editorial:HRPT2 in parathyroid cancer:a piece of the puzzle." J Clin Endocrinol Metab 90(9):5505-5507.
Shattuck, T. M., S. Valimaki, et al. (2003). "Somatic and germ-line mutations of the HRPT2 gene in sporadic parathyroid carcinoma." N Engl J Med 349(18):1722-1729.
Sheldon, K. E., D. M. Mauger, et al. (2005). "A Requirement for the Saccharomyces cerevisiae Pafl complex in snoRNA 3 end formation." Mol Cell 20(2):225-236.
Shema, E., I. Tirosh, et al. (2008). "The histone H2B-specific ubiquitin ligase RNF20/hBREl acts as a putative tumor suppressor through selective regulation of gene expression." Genes Dev 22(19):2664-2676.
Shi, X., M. Chang, et al. (1997). "Cdc73p and Paflp are found in a novel RNA polymerase Ⅱ-containing complex distinct from the Srbp-containing holoenzyme." Mol Cell Biol 17(3): 1160-1169.
Shi, X., A. Finkelstein, et al. (1996). "Paflp, an RNA polymerase Ⅱ-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription." Mol Cell Biol 16(2):669-676.
Shilatifard, A. (2008). "Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation." Curr Opin Cell Biol 20(3):341-348.
Sikorski, T. W. and S. Buratowski (2009). "The basal initiation machinery:beyond the general transcription factors." Curr Opin Cell Biol 21(3):344-351.
Smale, S. T. and D. Baltimore (1989). "The "initiator" as a transcription control element." Cell 57(1):103-113.
Sobhian, B., N. Laguette, et al. (2010). "HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP." Mol Cell 38(3):439-451.
Squazzo, S. L., P. J. Costa, et al. (2002). "The Pafl complex physically and functionally associates with transcription elongation factors in vivo." EMBO J 21(7):1764-1774.
Stenmark, H. and V. M. Olkkonen (2001). "The Rab GTPase family." Genome Biol 2(5): REVIEWS3007.
Stolinski, L. A., D. M. Eisenmann, et al. (1997). "Identification of RTF 1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae." Mol Cell Biol 17(8):4490-4500.
Strahl, B. D., R. Ohba, et al. (1999). "Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena." Proc Natl Acad Sci U S A 96(26):14967-14972.
Suzuki, Y., T. Tsunoda, et al. (2001). "Identification and characterization of the potential promoter regions of 1031 kinds of human genes." Genome Res 11(5):677-684.
Takahashi, A., R. Tsutsumi, et al. (2011). "SHP2 tyrosine phosphatase converts parafibromin/Cdc73 from a tumor suppressor to an oncogenic driver." Mol Cell 43(1): 45-56.
Thompson, C. M., A. J. Koleske, et al. (1993). "A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast." Cell 73(7):1361-1375.
Tomson, B. N., C. P. Davis, et al. (2011). "Identification of a role for histone H2B ubiquitylation in noncoding RNA 3'-end formation through mutational analysis of Rtfl in Saccharomyces cerevisiae." Genetics 188(2):273-289.
Wade, P. A., W. Werel, et al. (1996). "A novel collection of accessory factors associated with yeast RNA polymerase II." Protein ExprPurif 8(1):85-90.
Warner, M. H., K. L. Roinick, et al. (2007). "Rtfl is a multifunctional component of the Pafl complex that regulates gene expression by directing cotranscriptional histone modification." Mol Cell Biol 27(17):6103-6115.
Werner, F. (2012). "A nexus for gene expression-molecular mechanisms of Spt5 and NusG in the three domains of life." J Mol Biol 417(1-2):13-27.
Willis, I. M. (1993). "RNA polymerase III. Genes, factors and transcriptional specificity." Eur J Biochem 212(1):1-11.
Wood, A., J. Schneider, et al. (2003). "The Pafl complex is essential for histone monoubiquitination by the Rad6-Brel complex, which signals for histone methylation by COMPASS and Dotlp." J Biol Chem 278(37):34739-34742.
Wood, A., J. Schneider, et al. (2005). "The Burl/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Brel and histone methylation by COMPASS." Mol Cell 20(4): 589-599.
Xiao, T, C. F. Kao, et al. (2005). "Histone H2B ubiquitylation is associated with elongating RNA polymerase Ⅱ." Mol Cell Biol 25(2):637-651.
Yao, S. and G. Prelich (2002). "Activation of the Burl-Bur2 cycl in-dependent kinase complex by Cakl." Mol Cell Biol 22(19):6750-6758.
Yart, A., M. Gstaiger, et al. (2005). "The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase Ⅱ." Mol Cell Biol 25(12):5052-5060.
Youn, M. Y., H. S. Yoo, et al. (2007). "hCTR9, a component of Pafl complex, participates in the transcription of interleukin 6-responsive genes through regulation of STAT3-DNA interactions." J Biol Chem 282(48):34727-34734.
Young, R. A. (1991). "RNA polymerase Ⅱ." Annu Rev Biochem 60:689-715.
Zawel, L. and D. Reinberg (1995). "Common themes in assembly and function of eukaryotic transcription complexes." Annu Rev Biochem 64:533-561.
Zhao, J., A. Yart, et al. (2007). "Sporadic human renal tumors display frequent allelic imbalances and novel mutations of the HRPT2 gene." Oncogene 26(23):3440-3449.
Zhou, K., W. H. Kuo, et al. (2009). "Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5." Proc Natl Acad Sci U S A 106(17):6956-6961.
Zhu, B., S. S. Mandal, et al. (2005). "The human PAF complex coordinates transcription with events downstream of RNA synthesis." Genes Dev 19(14):1668-1673.
Aboussekhra, A., M. Biggerstaff, et al. (1995). "Mammalian DNA nucleotide excision repair reconstituted with purified protein components." Cell 80(6):859-868.
Adami, S., C. Marcocci, et al. (2002). "Epidemiology of primary hyperparathyroidism in Europe." J Bone Miner Res 17 Suppl 2:N18-23.
Akhtar, M. S., M. Heidemann, et al. (2009). "TFIIH kinase places bivalent marks on the carboxy-terminal domain of RNA polymerase II." Mol Cell 34(3):387-393.
Amrich, C. G., C. P. Davis, et al. (2012). "Cdc73 subunit of Pafl complex contains C-terminal Ras-like domain that promotes association of Pafl complex with chromatin." J Biol Chem 287(14): 10863-10875.
Andersen, P. L., F. Xu, et al. (2008). "Eukaryotic DNA damage tolerance and translesion synthesis through covalent modifications of PCNA." Cell Res 18(1):162-173.
Antony, E., E. J. Tomko, et al. (2009). "Srs2 disassembles Rad51 filaments by a protein-protein interaction triggering ATP turnover and dissociation of Rad51 from DNA." Mol Cell 35(1): 105-115.
Araujo, S. J., F. Tirode, et al. (2000). "Nucleotide excision repair of DNA with recombinant human proteins:definition of the minimal set of factors, active forms of TFIIH, and modulation by CAK." Genes Dev 14(3):349-359.
Baker, T. A. and S. P. Bell (1998). "Polymerases and the replisome:machines within machines." Cell 92(3):295-305.
Bakkenist, C. J. and M. B. Kastan (2003). "DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation." Nature 421(6922):499-506.
Ball, L. G., K. Zhang, et al. (2009). "The yeast Shu complex couples error-free post-replication repair to homologous recombination." Mol Microbiol 73(1):89-102.
Baumann, P., F. E. Benson, et al. (1996). "Human Rad51 protein promotes ATP-dependent homologous pairing and strand transfer reactions in vitro." Cell 87(4):757-766.
Benkert, P., M. Biasini, et al. (2011). "Toward the estimation of the absolute quality of individual protein structure models." Bioinformatics 27(3):343-350.
Bernstein, B. E., E. L. Humphrey, et al. (2002). "Methylation of histone H3 Lys 4 in coding regions of active genes." Proc Natl Acad Sci U S A 99(13):8695-8700.
Bernstein, K. A., R. J. D. Reid, et al. (2011). "The Shu complex, which contains Rad51 paralogues, promotes DNA repair through inhibition of the Srs2 anti-recombinase." Molecular Biology of the Cell 22(9):1599-1607.
Boggs, B. A., P. Cheung, et al. (2002). "Differentially methylated forms of histone H3 show unique association patterns with inactive human X chromosomes." Nat Genet 30(1):73-76.
Bradley, K. J., B. M. Cavaco, et al. (2006). "Parafibromin mutations in hereditary hyperparathyroidism syndromes and parathyroid tumours." Clin Endocrinol (Oxf) 64(3):299-306.
Bradley, K. J., M. R. Hobbs, et al. (2005). "Uterine tumours are a phenotypic manifestation of the hyperparathyroidism-jaw tumour syndrome." J Intern Med 257(1):18-26.
Briggs, S. D., M. Bryk, et al. (2001). "Histone H3 lysine 4 methylation is mediated by Setl and required for cell growth and rDNA silencing in Saccharomyces cerevisiae." Genes Dev 15(24): 3286-3295.
Bromberg, J. and T. C. Wang (2009). "Inflammation and cancer:IL-6 and STAT3 complete the link." Cancer Cell 15(2):79-80.
Buratowski, S. (1994). "The basics of basal transcription by RNA polymerase II." Cell 77(1):1-3.
Burton, Z. F., M. Killeen, et al. (1988). "RAP30/74:a general initiation factor that binds to RNA polymerase II." Mol Cell Biol 8(4):1602-1613.
Cavaco, B. M., L. Barros, et al. (2001). "The hyperparathyroidism-jaw tumour syndrome in a Portuguese kindred." QJM 94(4):213-222.
Chaudhary, K., S. Deb, et al. (2007). "Human RNA polymerase Ⅱ-associated factor complex: dysregulation in cancer." Oncogene 26(54):7499-7507.
Chen, H., N. Shi, et al. (2012). "Crystallographic analysis of the conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like fold." Acta Crystallogr D Biol Crvstallogr 68(Pt 8):953-959.
Chen, J. D., C. Morrison, et al. (2003). "Hyperparathyroidism-jaw tumour syndrome." J Intern Med 253(6):634-642.
Chen, P. L., C. F. Chen, et al. (1998). "The BRC repeats in BRCA2 are critical for RAD51 binding and resistance to methyl methanesulfonate treatment." Proc Natl Acad Sci U S A 95(9):5287-5292.
Chen, V. B., W. B. Arendall,3rd, et al. (2010). "MolProbity:all-atom structure validation for macromolecular crystallography." Acta Crystallogr D Biol Crystallogr 66(Pt 1):12-21.
Chen, Y., Y. Yamaguchi, et al. (2009). "DSIF, the Pafl complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation." Genes Dev 23(23):2765-2777.
Chu, Y., R. Simic, et al. (2007). "Regulation of histone modification and cryptic transcription by the Burl and Pafl complexes." EMBOJ 26(22):4646-4656.
Coin, F., V. Oksenych, et al. (2007). "Distinct roles for the XPB/p52 and XPD/p44 subcomplexes of TFIIH in damaged DNA opening during nucleotide excision repair." Mol Cell 26(2):245-256.
Colavito, S., M. Macris-Kiss, et al. (2009). "Functional significance of the Rad51-Srs2 complex in Rad51 presynaptic filament disruption." Nucleic Acids Res 37(20):6754-6764.
Collis, S. J. and S. J. Boulton (2007). "Emerging links between the biological clock and the DNA damage response." Chromosoma 116(4):331-339.
Conaway, R. C. and J. W. Conaway (1993). "General initiation factors for RNA polymerase Ⅱ." Annu Rev Biochem 62:161-190.
Costa, P. J. and K. M. Arndt (2000). "Synthetic lethal interactions suggest a role for the Saccharomyces cerevisiae Rtfl protein in transcription elongation." Genetics 156(2):535-547.
Crisucci, E. M. and K. M. Arndt (2011). "The Pafl complex represses ARG1 transcription in Saccharomyces cerevisiae by promoting histone modifications." Eukaryot Cell 10(6):712-723.
Curtin, N. J. (2012). "DNA repair dysregulation from cancer driver to therapeutic target." Nat Rev Cancer 12(12):801-817.
Daniel, J. A., M. S. Torok, et al. (2004). "Deubiquitination of histone H2B by a yeast acetyltransferase complex regulates transcription." J Biol Chem 279(3):1867-1871.
de Jong, R. N., V. Truffault, et al. (2008). "Structure and DNA binding of the human Rtfl Plus3 domain." Structure 16(1):149-159.
De Vos, M., V. Schreiber, et al. (2012). "The diverse roles and clinical relevance of PARPs in DNA damage repair:current state of the art." Biochem Pharmacol 84(2):137-146.
di Caprio, L. and B. S. Cox (1981). "DNA synthesis in UV-irradiated yeast." Mutat Res 82(1):69-85.
Di Como, C. J., H. Chang, et al. (1995). "Activation of CLN1 and CLN2 G1 cyclin gene expression by BCK2." Mol Cell Biol 15(4):1835-1846.
Ding, L., M. Paszkowski-Rogacz, et al. (2009). "A genome-scale RNAi screen for Oct4 modulators defines a role of the Pafl complex for embryonic stem cell identity." Cell Stem Cell 4(5): 403-415.
Drapkin, R., J. T. Reardon, et al. (1994). "Dual role of TFIIH in DNA excision repair and in transcription by RNA polymerase Ⅱ." Nature 368(6473):769-772.
Duker, N. J. (2002). "Chromosome breakage syndromes and cancer." Am J Med Genet 115(3): 125-129.
Ebright, R. H. (2000). "RNA polymerase:structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase Ⅱ." J Mol Biol 304(5):687-698.
El-Khamisy, S. F., M. Masutani, et al. (2003). "A requirement for PARP-1 for the assembly or stability of XRCC1 nuclear foci at sites of oxidative DNA damage." Nucleic Acids Res 31(19):5526-5533.
Evans, M. D., M. Dizdaroglu, et al. (2004). "Oxidative DNA damage and disease:induction, repair and significance." Mutat Res 567(1):1-61.
Exinger, F. and F. Lacroute (1992). "6-Azauracil inhibition of GTP biosynthesis in Saccharomyces cerevisiae." Curr Genet 22(1):9-11.
Feng, Z., W. Hu, et al. (2003). "Effects of genomic context and chromatin structure on transcription-coupled and global genomic repair in mammalian cells." Nucleic Acids Res 31(20): 5897-5906.
Foreman, P. K. and R. W. Davis (1996). "CDP1, a novel Saccharomyces cerevisiae gene required for proper nuclear division and chromosome segregation." Genetics 144(4):1387-1397.
Formosa, T. (2012). "The role of FACT in making and breaking nucleosomes." Biochim Biophys Acta 1819(3-4):247-255.
Fousteri, M. and L. H. Mullenders (2008). "Transcription-coupled nucleotide excision repair in mammalian cells:molecular mechanisms and biological effects." Cell Res 18(1):73-84.
Garg, P. and P. M. Burgers (2005). "Ubiquitinated proliferating cell nuclear antigen activates translesion DNA polymerases eta and REV1." Proc Natl Acad Sci U S A 102(51):18361-18366.
Gaspar-Maia, A., A. Alajem, et al. (2009). "Chd1 regulates open chromatin and pluripotency of embryonic stem cells." Nature 460(7257):863-868.
Glover-Cutter, K., S. Larochelle, et al. (2009). "TFIIH-associated Cdk7 kinase functions in phosphorylation of C-terminal domain Ser7 residues, promoter-proximal pausing, and termination by RNA polymerase Ⅱ." Mol Cell Biol 29(20):5455-5464.
Godin, S., A. Wier, et al. (2013). "The Shu complex interacts with Rad51 through the Rad51 paralogues Rad55-Rad57 to mediate error-free recombination." Nucleic Acids Res.
Goodman, M. F. (2002). "Error-prone repair DNA polymerases in prokaryotes and eukaryotes." Annu Rev Biochem 71:17-50.
Grummt, Ⅰ. (1999). "Regulation of mammalian ribosomal gene transcription by RNA polymerase I." Prog Nucleic Acid Res Mol Biol 62:109-154.
Harper, J. W. and S. J. Elledge (2007). "The DNA damage response:ten years after." Mol Cell 28(5): 739-745.
Henry, K. W., A. Wyce, et al. (2003). "Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8." Genes Dev 17(21): 2648-2663.
Heyer, W. D. (2007). "Biochemistry of eukaryotic homologous recombination." Top Curr Genet 17: 95-133.
Heyer, W. D., K. T. Ehmsen, et al. (2010). "Regulation of homologous recombination in eukaryotes." Annu Rev Genet 44:113-139.
Hiom, K. (2010). "Coping with DNA double strand breaks." DNA Repair (Amst) 9(12):1256-1263.
Hoege, C., B. Pfander, et al. (2002). "RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO." Nature 419(6903):135-141.
Hoeijmakers, J. H. (2009). "DNA damage, aging, and cancer." N Engl J Med 361(15):1475-1485.
Holloman, W. K. (2011). "Unraveling the mechanism of BRCA2 in homologous recombination." Nat Struct Mol Biol 18(7):748-754.
Holthausen, J. T, C. Wyman, et al. (2010). "Regulation of DNA strand exchange in homologous recombination." DNA Repair (Amst) 9(12):1264-1272.
Howell, V. M., C. J. Haven, et al. (2003). "HRPT2 mutations are associated with malignancy in sporadic parathyroid tumours." J Med Genet 40(9):657-663.
Hsieh, P. and K. Yamane (2008). "DNA mismatch repair:molecular mechanism, cancer, and ageing." Mech Ageing Dev 129(7-8):391-407.
Ito, T., T. Chiba, et al. (2001). "A comprehensive two-hybrid analysis to explore the yeast protein interactome." Proc Natl Acad Sci U S A 98(8):4569-4574.
Jeppesen, D. K., V. A. Bohr, et al. (2011). "DNA repair deficiency in neurodegeneration." Prog Neurobiol 94(2):166-200.
Jiricny, J. (2006). "The multifaceted mismatch-repair system." Nat Rev Mol Cell Biol 7(5):335-346.
Kao, C. F., C. Hillyer, et al. (2004). "Rad6 plays a role in transcriptional activation through ubiquitylation of histone H2B." Genes Dev 18(2):184-195.
Karpenshif, Y. and K. A. Bernstein (2012). "From yeast to mammals:recent advances in genetic control of homologous recombination." DNA Repair (Amst) 11(10):781-788.
Kelman, Z. (1997). "PCNA:structure, functions and interactions." Oncogene 14(6):629-640.
Kim, J., M. Guermah, et al. (2010). "The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS." CeN 140(4):491-503.
Kim, J. and R. G. Roeder (2009). "Direct Bre1-Pafl complex interactions and RING finger-independent Bre1-Rad6 interactions mediate histone H2B ubiquitylation in yeast." J Biol Chem 284(31): 20582-20592.
Kim, K. Y. and D. E. Levin (2011). "Mpk1 MAPK association with the Pafl complex blocks Senl-mediated premature transcription termination." Cell 144(5):745-756.
Kim, M., S. H. Ahn, et al. (2004). "Transitions in RNA polymerase II elongation complexes at the 3' ends of genes." EMBO J 23(2):354-364.
Kim, M., H. Suh, et al. (2009). "Phosphorylation of the yeast Rpbl C-terminal domain at serines 2,5, and 7."J Biol Chem 284(39):26421-26426.
Koch, C., P. Wollmann, et al. (1999). "A role for Ctr9p and Paflp in the regulation Gl cyclin expression in yeast." Nucleic Acids Res 27(10):2126-2134.
Krejci, L., S. Van Komen, et al. (2003). "DNA helicase Srs2 disrupts the Rad51 presynaptic filament." Nature 423(6937):305-309.
Krogan, N. J., J. Dover, et al. (2002). "COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression." J Biol Chem 277(13):10753-10755.
Krogan, N. J., J. Dover, et al. (2003). "The Pafl complex is required for histone H3 methylation by COMPASS and Dotlp:linking transcriptional elongation to histone methylation." Mol Cell 11(3): 721-729.
Krogan, N. J., M. Kim, et al. (2002). "RNA polymerase II elongation factors of Saccharomyces cerevisiae:a targeted proteomics approach." Mol Cell Biol 22(20):6979-6992.
Kumagai, A., J. Lee, et al. (2006). "TopBPl activates the ATR-ATRIP complex." Cell 124(5):943-955.
Kunkel, T. A. (1993). "Nucleotide repeats. Slippery DNA and diseases." Nature 365(6443):207-208.
Kutach, A. K. and J. T. Kadonaga (2000). "The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters." Mol Cell Biol 20(13):4754-4764.
Laribee, R. N., N. J. Krogan, et al. (2005). "BUR kinase selectively regulates H3 K4 trimethylation and H2B ubiquitylation through recruitment of the PAF elongation complex." Curr Biol 15(16): 1487-1493.
Laskowski, R., M. MacArthur, et al. (1993). "PROCHECK:A program to check the stereochemical quality of protein structures." J. Appl. Cryst 26:283-291.
Lee, C. K., Y. Shibata, et al. (2004). "Evidence for nucleosome depletion at active regulatory regions genome-wide." Nat Genet 36(8):900-905.
Lee, J. H. and T. T. Paull (2005). "ATM activation by DNA double-strand breaks through the Mrell-Rad50-Nbsl complex." Science 308(5721):551-554.
Lee, J. S., A. Shukla, et al. (2007). "Histone crosstalk between H2B monoubiquitination and H3 methylation mediated by COMPASS." Cell 131(6):1084-1096.
Lee, S. H., K. Baek, et al. (2008). "Large nucleotide-dependent conformational change in Rab28." FEBS Lett 582(29):4107-4111.
Lee, Y., M. Kim, et al. (2004). "MicroRNA genes are transcribed by RNA polymerase Ⅱ." EMBOJ 23(20): 4051-4060.
Li, G. M. (2008). "Mechanisms and functions of DNA mismatch repair." Cell Res 18(1):85-98.
Lindahl, T. (1993). "Instability and decay of the primary structure of DNA." Nature 362(6422): 709-715.
Litt, M. D., M. Simpson, et al. (2001). "Correlation between histone lysine methylation and developmental changes at the chicken beta-globin locus." Science 293(5539):2453-2455.
Liu, L., N. M. Oliveira, et al. (2011). "A whole genome screen for HIV restriction factors." Retrovirology 8:94.
Liu, T., L. Wan, et al. (2011). "hSWS1.SWSAP1 is an evolutionarily conserved complex required for efficient homologous recombination repair." J Biol Chem 286(48):41758-41766.
Liu, Y, L. Warfield, et al. (2009). "Phosphorylation of the transcription elongation factor Spt5 by yeast Burl kinase stimulates recruitment of the PAF complex." Mol Cell Biol 29(17):4852-4863.
Magdolen, V., P. Lang, et al. (1994). "The gene LE01 on yeast chromosome XV encodes a non-essential, extremely hydrophilic protein." Biochim Biophys Acta 1218(2):205-209.
Majka, J., A. Niedziela-Majka, et al. (2006). "The checkpoint clamp activates Mecl kinase during initiation of the DNA damage checkpoint." Mol Cell 24(6):891-901.
Mankouri, H. W., H.-P. Ngo, et al. (2007). "Shu proteins promote the formation of homologous recombination intermediates that are processed by Sgs1-Rmil-Top3." Molecular Biology of the Cell 18(10):4062-4073.
Marazzi, I., J. S. Ho, et al. (2012). "Suppression of the antiviral response by an influenza histone mimic." Nature 483(7390):428-433.
Martin, V., C. Chahwan, et al. (2006). "Swsl is a conserved regulator of homologous recombination in eukaryoticcells." EMBO J 25(11):2564-2574.
Mayer, A., M. Lidschreiber, et al. (2010). "Uniform transitions of the general RNA polymerase II transcription complex." Nat Struct Mol Biol 17(10):1272-1278.
Miller, T, N. J. Krogan, et al. (2001). "COMPASS:a complex of proteins associated with a trithorax-related SET domain protein." Proc Natl Acad Sci U S A 98(23):12902-12907.
Milne, T. A., S. D. Briggs, et al. (2002). "MLL targets SET domain methyltransferase activity to Hox gene promoters." Mol Cell 10(5):1107-1117.
Minakhin, L., S. Bhagat, et al. (2001). "Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly." Proc Natl Acad Sci U S A 98(3):892-897.
Missura, M., T. Buterin, et al. (2001). "Double-check probing of DNA bending and unwinding by XPA-RPA:an architectural function in DNA repair." EMBO J 20(13):3554-3564.
Moldovan, G. L., D. Dejsuphong, et al. (2012). "Inhibition of homologous recombination by the PCNA-interacting protein PARI." Mol Cell 45(1):75-86.
Moldovan, G. L., B. Pfander, et al. (2007). "PCNA, the maestro of the replication fork." Cell 129(4): 665-679.
Moniaux, N., C. Nemos, et al. (2006). "The human homologue of the RNA polymerase Ⅱ-associated factor 1 (hPaf1), localized on the 19q13 amplicon, is associated with tumorigenesis." Oncogene 25(23):3247-3257.
Moser, J., M. Volker, et al. (2005). "The UV-damaged DNA binding protein mediates efficient targeting of the nucleotide excision repair complex to UV-induced photo lesions." DNA Repair (Amst) 4(5): 571-582.
Mueller, C. L. and J. A. Jaehning (2002). "Ctr9, Rtf1, and Leol are components of the Pafl/RNA polymerase II complex." Mol Cell Biol 22(7):1971-1980.
Mueller, C. L., S. E. Porter, et al. (2004). "The Pafl complex has functions independent of actively transcribing RNA polymerase II." Mol Cell 14(4):447-456.
Mullenders, L. H., H. Vrieling, et al. (1991). "Hierarchies of DNA repair in mammalian cells:biological consequences." Mutat Res 250(1-2):223-228.
Mutiu, A. I., S. M. Hoke, et al. (2007). "The role of histone ubiquitylation and deubiquitylation in gene expression as determined by the analysis of an HTB1(K123R) Saccharomyces cerevisiae strain.' Mol Genet Genomics 277(5):491-506.
Myer, V. E. and R. A. Young (1998). "RNA polymerase Ⅱ holoenzymes and subcomplexes."J Biol Chem 273(43):27757-27760.
Myers, J. S. and D. Cortez (2006). "Rapid activation of ATR by ionizing radiation requires ATM and Mrell." J Biol Chem 281(14):9346-9350.
Myers, L. C. and R. D. Kornberg (2000). "Mediator of transcriptional regulation." Annu Rev Biochem 69:729-749.
Newey, P. J., M. R. Bowl, et al. (2010). "Cell division cycle protein 73 homolog (CDC73) mutations in the hyperparathyroidism-jaw tumor syndrome (HPT-JT) and parathyroid tumors." Hum Mutat 31(3):295-307.
Newey, P. J., M. R. Bowl, et al. (2009). "Parafibromin-functional insights." J Intern Med 266(1):84-98.
Ng, H. H., S. Dole, et al. (2003). "The Rtf1 component of the Paf1 transcriptional elongation complex is required for ubiquitination of histone H2B." J Biol Chem 278(36):33625-33628.
Ng, H. H., F. Robert, et al. (2003). "Targeted recruitment of Setl histone methylase by elongating Pol II provides a localized mark and memory of recent transcriptional activity." Mol Cell 11(3): 709-719.
Nordick, K., M. G. Hoffman, et al. (2008). "Direct interactions between the Pafl complex and a cleavage and polyadenylation factor are revealed by dissociation of Pafl from RNA polymerase Ⅱ." Eukarvot Cell 7(7):1158-1167.
O'Donovan, A., A. A. Davies, et al. (1994). "XPG endonuclease makes the 3'incision in human DNA nucleotide excision repair." Nature 371(6496):432-435.
Ohmori, H., E. C. Friedberg, et al. (2001). "The Y-family of DNA polymerases." Mol Cell 8(1):7-8.
Orphanides, G., G. LeRoy, et al. (1998). "FACT, a factor that facilitates transcript elongation through nucleosomes." Cell 92(1):105-116.
Pavri, R., B. Zhu, et al. (2006). "Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase Ⅱ." Cell 125(4):703-717.
Penheiter, K. L., T. M. Washburn, et al. (2005). "A posttranscriptional role for the yeast Pafl-RNA polymerase II complex is revealed by identification of primary targets." Mol Cell 20(2):213-223.
Peterson, C. L. and J. W. Tamkun (1995). "The SWI-SNF complex:a chromatin remodeling machine?" Trends Biochem Sci 20(4):143-146.
Phatnani, H. P. and A. L. Greenleaf (2006). "Phosphorylation and functions of the RNA polymerase II CTD." Genes Dev 20(21):2922-2936.
Piro, A. S., M. K. Mayekar, et al. (2012). "Small region of Rtfl protein can substitute for complete Pafl complex in facilitating global histone H2B ubiquitylation in yeast." Proc Natl Acad Sci U S A 109(27):10837-10842.
Pokholok, D. K., N. M. Hannett, et al. (2002). "Exchange of RNA polymerase II initiation and elongation factors during gene expression in vivo." Mol Cell 9(4):799-809.
Ponnusamy, M. P., S. Deb, et al. (2009). "RNA polymerase II associated factor 3/PD2 maintains self-renewal by its interaction with Oct3/4 in mouse embryonic stem cells." Stem Cells 27(12): 3001-3011.
Prakash, L (1981). "Characterization of postreplication repair in Saccharomyces cerevisiae and effects of rad6, rad18, rev3 and rad52 mutations." Mol Gen Genet 184(3):471-478.
Prakash, R., D. Satory, et al. (2009). "Yeast Mphl helicase dissociates Rad51-made D-loops: implications for crossover control in mitotic recombination." Genes Dev 23(1):67-79.
Prakash, S., R. E. Johnson, et al. (2005). "Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function." Annu Rev Biochem 74:317-353.
Qiu, H., C. Hu, et al. (2012). "Pol Ⅱ CTD kinases Burl and Kin28 promote Spt5 CTR-independent recruitment of Paf1 complex." EMBO J 31(16):3494-3505.
Qiu, H., C. Hu, et al. (2006). "The Spt4p subunit of yeast DSIF stimulates association of the Paf1 complex with elongating RNA polymerase II." Mol Cell Biol 26(8):3135-3148.
Ralhan, R., J. Kaur, et al. (2007). "Links between DNA double strand break repair and breast cancer: accumulating evidence from both familial and nonfamilial cases." Cancer Lett 248(1):1-17.
Rapic-Otrin, V., M. P. McLenigan, et al. (2002). "Sequential binding of UV DNA damage binding factor and degradation of the p48 subunit as early events after UV irradiation." Nucleic Acids Res 30(11):2588-2598.
Reed, S. I., J. Ferguson, et al. (1988). "Isolation and characterization of two genes encoding yeast mating pheromone signaling elements:CDC72 and CDC73." Cold Spring Harb Symp Quant Biol 53 Pt 2:621-627.
Roguev, A., D. Schaft, et al. (2001). "The Saccharomyces cerevisiae Setl complex includes an Ash2 homologue and methylates histone 3 lysine 4." EMBO J 20(24):7137-7148.
Rothkamm, K., I. Kruger, et al. (2003). "Pathways of DNA double-strand break repair during the mammalian cell cycle." Mol Cell Biol 23(16):5706-5715.
Rozenblatt-Rosen, O., C. M. Hughes, et al. (2005). "The parafibromin tumor suppressor protein is part of a human Pafl complex." Mol Cell Biol 25(2):612-620.
Rozenblatt-Rosen, O., T. Nagaike, et al. (2009). "The tumor suppressor Cdc73 functionally associates with CPSF and CstF 3' mRNA processing factors." Proc Natl Acad Sci U S A 106(3):755-760.
Rubin, M. R. and S. J. Silverberg (2005). "Editorial:HRPT2 in parathyroid cancer:a piece of the puzzle." J Clin Endocrinol Metab 90(9):5505-5507.
Schreiber, V, F. Dantzer, et al. (2006). "Poly(ADP-ribose):novel functions for an old molecule." Nat Rev Mol Cell Biol 7(7):517-528.
Seong, C., S. Colavito, et al. (2009). "Regulation of Rad51 recombinase presynaptic filament assembly via interactions with the Rad52 mediator and the Srs2 anti-recombinase." J Biol Chem 284(36): 24363-24371.
Shattuck, T. M., S. Valimaki, et al. (2003). "Somatic and germ-line mutations of the HRPT2 gene in sporadic parathyroid carcinoma." N Engl J Med 349(18):1722-1729.
She, Z., Z. Q. Gao, et al. (2012). "Structural and SAXS analysis of the budding yeast SHU-complex proteins." FEBS Lett 586(16):2306-2312.
Sheldon, K. E., D. M. Mauger, et al. (2005). "A Requirement for the Saccharomyces cerevisiae Pafl complex in snoRNA 3'end formation." Mol Cell 20(2):225-236.
Shema, E., I. Tirosh, et al. (2008). "The histone H2B-specific ubiquitin ligase RNF20/hBREl acts as a putative tumor suppressor through selective regulation of gene expression." Genes Dev 22(19): 2664-2676.
Shi, X., M. Chang, et al. (1997). "Cdc73p and Paf1p are found in a novel RNA polymerase Ⅱ-containing complex distinct from the Srbp-containing holoenzyme." Mol Cell Biol 17(3):1160-1169.
Shi, X., A. Finkelstein, et al. (1996). "Paflp, an RNA polymerase Ⅱ-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription." Mol Cell Biol 16(2): 669-676.
Shilatifard, A. (2008). "Molecular implementation and physiological roles for histone H3 lysine 4 (H3K4) methylation." Curr Opin Cell Biol 20(3):341-348.
Shim, K. S., C. Schmutte, et al. (2004). "hXRCC2 enhances ADP/ATP processing and strand exchange by hRAD51." J Biol Chem 279(29):30385-30394.
Shor, E., J. Weinstein, et al. (2005). "A genetic screen for top3 suppressors in Saccharomyces cerevisiae identifies SHU1, SHU2, PSY3 and CSM2:four genes involved in error-free DNA repair." Genetics 169(3):1275-1289.
Sijbers, A. M., W. L. de Laat, et al. (1996). "Xeroderma pigmentosum group F caused by a defect in a structure-specific DNA repair endonuclease." Cell 86(5):811-822.
Sikorski, T. W. and S. Buratowski (2009). "The basal initiation machinery:beyond the general transcription factors." Curr Opin Cell Biol 21(3):344-351.
Smale, S. T. and D. Baltimore (1989). "The "initiator" as a transcription control element." Cell 57(1): 103-113.
Sobhian, B., N. Laguette, et al. (2010). "HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP." Mol Cell 38(3):439-451.
Squazzo, S. L, P. J. Costa, et al. (2002). "The Paf1 complex physically and functionally associates with transcription elongation factors in vivo." EMBO J 21(7):1764-1774.
Stelter, P. and H. D. Ulrich (2003). "Control of spontaneous and damage-induced mutagenesis by SUMO and ubiquitin conjugation." Nature 425(6954):188-191.
Stenmark, H. and V. M. Olkkonen (2001). "The Rab GTPase family." Genome Biol 2(5):REVIEWS3007.
Stolinski, L. A., D. M. Eisenmann, et al. (1997). "Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae." Mol Cell Biol 17(8): 4490-4500.
Stracker, T. H., J. W. Theunissen, et al. (2004). "The Mrell complex and the metabolism of chromosome breaks:the importance of communicating and holding things together." DNA Repair (Amst) 3(8-9):845-854.
Strahl, B. D., R. Ohba, et al. (1999). "Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena." Proc Natl Acad Sci U S A 96(26): 14967-14972.
Sugasawa, K., T. Okamoto, et al. (2001). "A multistep damage recognition mechanism for global genomic nucleotide excision repair." Genes Dev 15(5):507-521.
Sugiyama, T. and S. C. Kowalczykowski (2002). "Rad52 protein associates with replication protein A (RPA)-single-stranded DNA to accelerate Rad51-mediated displacement of RPA and presynaptic complex formation." J Biol Chem 277(35):31663-31672.
Suzuki, Y., T. Tsunoda, et al. (2001). "Identification and characterization of the potential promoter regions of 1031 kinds of human genes." Genome Res 11(5):677-684.
Symington, L. S. and J. Gautier (2011). "Double-strand break end resection and repair pathway choice." Annu Rev Genet 45:247-271.
Takahashi, A., R. Tsutsumi, et al. (2011). "SHP2 tyrosine phosphatase converts parafibromin/Cdc73 from a tumor suppressor to an oncogenic driver." Mol Cell 43(1):45-56.
Takata, M., M. S. Sasaki, et al. (2001). "Chromosome instability and defective recombinational repair in knockout mutants of the five Rad51 paralogs." Mol Cell Biol 21(8):2858-2866.
Tao, Y., X. Li, et al. (2012). "Structural analysis of Shu proteins reveals a DNA binding role essential for resisting damage." J Biol Chem 287(24):20231-20239.
Thacker, J. (2005). "The RAD51 gene family, genetic instability and cancer." Cancer Lett 219(2): 125-135.
Thompson, C. M., A. J. Koleske, et al. (1993). "A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast." Cell 73(7):1361-1375.
Tomson, B. N., C. P. Davis, et al. (2011). "Identification of a role for histone H2B ubiquitylation in noncoding RNA 3'-end formation through mutational analysis of Rtfl in Saccharomyces cerevisiae." Genetics 188(2):273-289.
Unk, I., I. Hajdu, et al. (2010). "Role of yeast Rad5 and its human orthologs, HLTF and SHPRH in DNA damage tolerance." DNA Repair (Amst) 9(3):257-267.
Valerie, K. and L. F. Povirk (2003). "Regulation and mechanisms of mammalian double-strand break repair." Oncogene 22(37):5792-5812.
van Loon, B., E. Markkanen, et al. (2010). "Oxygen as a friend and enemy:How to combat the mutational potential of 8-oxo-guanine." DNA Repair (Amst) 9(6):604-616.
Veaute, X., J. Jeusset, et al. (2003). "The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments." Nature 423(6937):309-312.
Vilenchik, M. M. and A. G. Knudson (2003). "Endogenous DNA double-strand breaks:production, fidelity of repair, and induction of cancer." Proc Natl Acad Sci U S A 100(22):12871-12876.
Volker, M., M. J. Mone, et al. (2001). "Sequential assembly of the nucleotide excision repair factors in vivo." Mol Cell 8(1):213-224.
Wade, P. A., W. Werel, et al. (1996). "A novel collection of accessory factors associated with yeast RNA polymerase II." Protein Expr Purif 8(1):85-90.
Wang, Z., S. Buratowski, et al. (1995). "The yeast TFB1 and SSL1 genes, which encode subunits of transcription factor IIH, are required for nucleotide excision repair and RNA polymerase II transcription." Mol Cell Biol 15(4):2288-2293.
Warner, M. H., K. L. Roinick, et al. (2007). "Rtfl is a multifunctional component of the Pafl complex that regulates gene expression by directing cotranscriptional histone modification." Mol Cell Biol 27(17):6103-6115.
Werner, F. (2012). "A nexus for gene expression-molecular mechanisms of Spt5 and NusG in the three domains of life." J Mol Biol 417(1-2):13-27.
Willis, I. M. (1993). "RNA polymerase III. Genes, factors and transcriptional specificity." Eur J Biochem 212(1):1-11.
Wiseman, H. and B. Halliwell (1996). "Damage to DNA by reactive oxygen and nitrogen species:role in inflammatory disease and progression to cancer." Biochem J 313 (Pt 1):17-29.
Wood, A., J. Schneider, et al. (2003). "The Pafl complex is essential for histone monoubiquitination by the Rad6-Brel complex, which signals for histone methylation by COMPASS and Dot1p." J Biol Chem 278(37):34739-34742.
Wood, A., J. Schneider, et al. (2005). "The Bur1/Bur2 complex is required for histone H2B monoubiquitination by RadE/Brel and histone methylation by COMPASS." Mol Cell 20(4): 589-599.
Xiao, T., C. F. Kao, et al. (2005). "Histone H2B ubiquitylation is associated with elongating RNA polymerase II." Mol Cell Biol 25(2):637-651.
Yang, X. H. and L. Zou (2006). "Checkpoint and coordinated cellular responses to DNA damage." Results Probl Cell Differ 42:65-92.
Yao, S. and G. Prelich (2002). "Activation of the Burl-Bur2 cyclin-dependent kinase complex by Cak1." Mol Cell Biol 22(19):6750-6758.
Yart, A., M. Gstaiger, et al. (2005). "The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase Ⅱ." Mol Cell Biol 25(12):5052-5060.
Youn, M. Y, H. S. Yoo, et al. (2007). "hCTR9, a component of Pafl complex, participates in the transcription of interleukin 6-responsive genes through regulation of STAT3-DNA interactions." J Biol Chem 282(48):34727-34734.
Young, R. A. (1991). "RNA polymerase Ⅱ." Annu Rev Biochem 60:689-715.
Zawel, L and D. Reinberg (1995). "Common themes in assembly and function of eukaryotic transcription complexes." Annu Rev Biochem 64:533-561.
Zhao, J., A. Yart, et al. (2007). "Sporadic human renal tumors display frequent allelic imbalances and novel mutations of the HRPT2 gene." Oncogene 26(23):3440-3449.
Zhou, K., W. H. Kuo, et al. (2009). "Control of transcriptional elongation and cotranscriptional histone modification by the yeast BUR kinase substrate Spt5." Proc Natl Acad Sci U S A 106(17): 6956-6961.
Zhu, B., S. S. Mandal, et al. (2005). "The human PAF complex coordinates transcription with events downstream of RNA synthesis." Genes Dev 19(14):1668-1673.
Zou, L. and S. J. Elledge (2003). "Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes." Science 300(5625):1542-1548.