Eriksson, P.R., Mendiratta, G., McLaughlin, N.B., Wolfsberg, T.G., Marino-Ramírez, L., Pompa, T.A., Jainerin, M., Landsman, D., Shen, C.H., and Clark, D.J. (2005) Global regulation by the yeast Spt10 protein is mediated through chromatin structure and the histone upstream activating sequence elements. Mol. Cell. Biol. 25, 9127-9137.
 Chang, M., French-Cornay, D., Fan, H.-Y., Klein, H., Denis, C.L., and Jaehning, J.A. (1999) A complex containing RNA polymerase II, Paflp, Cdc73p, Hprlp, and Ccr4p plays a role in protein kinase C signaling. Mol. Cell. Biol 19, 1056-1067.
 Liu, H.-Y., Toyn, J. H., Chiang, Y.-C., Draper, M. P., Johnston, L. H., and Denis, C. L.(1997) DBF2, a cell-cycle regulated protein kinase, is physically and functionally associated with the CCR4 transcriptional regulatory complex. EMBO J. 16, 5289-5298.
 Liu, H.-Y., Badarinarayana, V., Audino, D.C., Rappsilber, J., Mann, M., and Denis, C.L. (1998) The NOT proteins are part of the CCR4 transcriptional complex and affect gene expression both positively and negatively. EMBO J. 17, 1097-1106.
 McKenzie, E.A., Kent, N.A., Dowell, S.J., Moreno, F., Bird, L.E., and Mellor, J. (1993) The centromere and promoter factor, 1, CPF1, of Sacchaomyces cerevisiae modulates gene activity through a family of factors including SPT21, RPD1, (SIN3), RPD3 and CCR4. Mol Gen Genet 240, 374-86.
 Chen, J., Rappsilber, J., Chiang, Y.-C., Russell, P., Mann, M., and Denis, C.L. (2001) Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J. Mol. Biol. 314, 683-694.
 Cui, Y., Ramnarain, D.B., Chiang, Y.-C., Ding, L.-H., McMahon, J.S., and Denis, C.L. (2008) Genome wide expression analysis of the CCR4-NOT complex indicates that it consists of three modules with the NOT module controlling SAGA-responsive genes. Mol. Genet. Genomics 279, 323-337.
 Draper, M.P., C. Salvadore, and C.L. Denis (1995) Identification of a mouse protein whose homolog in yeast is a component of the CCR4 transcriptional regulatory complex. Mol. Cell. Biol. 15, 3487-95.
 Collart, M.A. and K. Struhl (1993) CDC39, an essential nuclear protein that negatively regulates transcription and differentially affects the constitutive and inducible HIS3 promoters [published erratum appears in EMBO J. 1993 12, 2990]. EMBO J. 12, 177-186.
 Collart, M. A., and K. Struhl, (1994) NOT1 (CDC39), NOT2 (CDC36), NOT3, and NOT4 encode a global-negative regulator of transcription that differentially affects TATA-element utilization. Genes Dev. 8, 525-537.
 Badarinarayana, V., Y.-C. Chiang, and C. L. Denis, (2000) Functional interaction of CCR4-NOT proteins with TATAA-binding protein (TBP) and its associated factors in yeast. Genetics 155, 1045-1054.
 Tucker, M., R.R. Staples, M.A.Valencia-Sanchez, D. Muhlrad, and R. Parker (2002) CCR4p is the catalytic sub-unit of Ccr4p/Pop2p/Notp mRNA deadenylasecomplex in Saccharomyces cerevisiae. EMBO J. 21, 1427-1436.
 Tucker, M., M.A. Valencia-Sanchez, R. Staples, J. Chen, C.L. Denis, and R. Parker (2001) The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104, 377-386.
 Liu, H.-Y., Chiang, Y.-C., Pan, J., Salvadore, C., Chen, J., Audino, D.C., Badarinarayana, V., Palaniswamy, V., Anderson, B., and Denis, C.L. (2001) Characterization of CAF4 and CAF16 reveal a functional connection between the CCR4-NOT complex and a subset of SRB proteins of the RNA polymerase II holoenzyme. J. Biol. Chem. 276, 7541-7548.
 Bai, Y., Salvadore, C., Chiang, Y.-C., Collart, M., Liu H.-Y, and Denis, C.L. (1999) The CCR4 and CAF1 proteins of the CCR4-NOT complex are physically and functionally separated from NOT2, NOT4,and NOT5. Mol. Cell. Biol. 19, 6642-6651.
 Cui, Y., and C.L. Denis, (2003) In vivo evidence that defects in the transcriptional elongation factors RPB2, TFIIS, and SPT5 enhance upstream poly (A) site utilization. Mol. Cell Biol. 23, 7887-7901.
 Noble, K.N., Tran, E.J., Alcazar-Roman, A.R., Hodge, C.A., Cole, C.N., and Wente, S.R. (2011) The Dbp5 cycle at the nuclear pore complex during mRNA export II: nucleotide cycling and mRNP remodeling by Dbp5 are controlled by Nup159 and Gle1. Genes Dev. 25, 1065-1077.
 Luke, B., Azzalin, C.M., Hug, N. Deplazes, A., Peter, M., and Lingner, J. (2007) Saccharomyces cerevisiae Ebs1p is a putative ortholog of human Smg7 and promotes nonsense-mediated mRNA decay. Nucl. Acids Res. 35, 7688-7697.
 Ford, A.S., Guan, Q., Neeno-Eckwall, E., and Culbertson, M.R. (2006) Ebs1p, a negative regulatory of gene expression controlled by the Upf proteins in the yeast Saccharomyces cerevisiae. Eukaryot. Cell 5, 301-312.
 Uetz, P., Giot, L., Cagney, G., Mansfield, T.A., Judson, R.S., Knight, J.R., Lockshorn, D., Narayan, V.,Srinivasan, M., Pochart, P., Gureshi-Emili, A., Li, Y., Goodwin, B., Conover, D., Kalbfleishch, T., Vijayadamodar, G., Yang, M., Johnston, M., Field, S., and Rothberg, J.M., (2000) A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
 Ohn, T., Chiang, Y.-C., Lee, D.J., Yao, G., Zhang, C., and Denis, C.L. (2007) CAF1 plays an important role in mRNA deadenylation separate from its contact to CCR4. Nucl. Acids Res. 35, 3002-3015.
 Cui, Y., Chiang, Y.-C., Viswanathan, P., Lee, D.J., and Denis, C.L. (2012) SPT5 physically interacts with CCR4 and affects mRNA degradation but does not control mRNA deadenylation. Amer. J. Mol. Biol. In Press.
 Lee, D., Ohn, T., Chiang, Y.-C., Liu, Y, Quigley, G., Yao, G., and Denis, C.L. (2010) PUF3 acceleration of deadenylation in vivo can operate independently of CCR4 activity, possibly involving effects on the PAB1-mRNP structure. J. Mol. Biol. 399, 562-575.
 Shen, C.-H., Leblanc, B.P., Neal, C., Akhavan, R., and Clark, D.J., (2002). Targeted histone acetylation at the yeast CUP1 promoter requires the transcriptional activator, the TATA boxes, and the putative histone acetylase encoded by SPT10. Mol. Cell. Biol. 22, 6406-6416.
 Gaillard, H., Tous, C., Botet, J., Gonzalez-Aguilera, C., Quintero, M.J., Viladevall, L., Garcia-Rubio, M.L., Rodriguez-Gil, A., Marin, A., Anno, J., revuelta, J.L., Chavez, S., and Aguilera, A. (2009) Genome-wide analysis of factors affecting transcription elongation and DNA repair: a new role for PAF and Ccr4-Not in transcription-coupled repair. PLoS Genet. 5, e1000364.
 Hartzog, G.A., Wada, T., Handa, H., and Winston, F. (1998). Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12, 357-369.
 Squazzo, S.L., Costa, P.J., Lindstrom,D.L., Kumer, K.E., Simic, R., Jennings, J., Link, A.J., Arndt, K.M., and Hartzog, G.A., (2002) The Paf1 complex physically and functionally associates with transcription elongation factors in vivo. EMBO 21, 764-1774.
 Strasser, K., S. Masuda, Mason, P., Pfannstiel, J., Oppizzi, M., Rodriguez-Navarro, S., Rondon,, A., Aguilera, A., Struhl, K., Reed, R., and E. Hurt (2002) TREX is a conserved complex coupling transcription with messenger RNA export. Nature 417, 304-307.
 Wada, T., Takagi, T., Yamaguchi, Y., Ferdous, A., Imai, T., Hirose, S., Sugimoto, S., Yano, K., Hartzog, G.A., Winston,F., Buratowski, S., and Handa, H. (1998). DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes & Dev. 12, 343-356.
 Cook, W.J., Mosley, S., Audino, D.C., Rovelli, A., Mullaney, D., Stewart, G., and Denis, C.L.(1994) Mutations in the zinc-finger region of the yeast regulatory protein ADR1 affect both DNA binding and transcriptional activation. J. Biol. Chem. 269, 9374-9379.