Associate ProfessorOffice: MRB 283Phone: 970-492-4116Website: http://yaocohenlab.bmb.colostate.eduEducation: Ph.D., University of IowaEmail: Tingting.Yao@Colostate.eduResearch Title: Regulation of Gene Expression and Chromatin Dynamics by Ubiquitin Conjugation & Deconjugation
Our lab studies the interface between the ubiquitin-proteasome pathway and transcriptional regulation. Modification of components of the transcription machinery by ubiquitin can serve as a regulatory switch that both activate and limit gene expression. We are using a variety of biochemical and genetic approaches to define the molecular mechanisms that underlie these seemingly opposite processes. Ubiquitin (Ub) is a small protein of 76 amino acids. It is ubiquitous among all eukaryotes and it is highly conserved from yeast to man. The covalent attachment of Ub to other proteins, i.e., ubiquitination, is used as a regulatory signal in a broad spectrum of biological processes. These include targeting proteins for proteasomal degradation, intracellular trafficking, transcription activation, DNA damage repair, and chromatin remodeling. These different outcomes are due in part to the versatility of the Ub modification, which can vary in the number of Ub molecules attached and, if polyubiquitin chains are formed, the linkage between ubiquitins in the chain. Moreover, like phosphorylation, ubiquitination is reversible. Proteins are subject to ubiquitination and deubiquitination, and the balance between these competing processes determines the fate of the substrate. For most genes, transcription has long been regarded as the dominant regulatory process for production of a functional protein. Rather unexpectedly, recent discoveries have indicated that the Ub-proteasome pathway (UPP) is intimately involved in transcriptional regulation. Studies from many laboratories revealed that a variety of transcription activators are mono- or polyubiquitinated, and in some cases, their regulation involves a transition from one state to the other. Furthermore, although histones were among the first proteins found to be ubiquitinated, it was demonstrated only recently that ubiquitinated histone H2A is a hallmark of repressed chromatin, and that dynamic ubiquitination and deubiquitination of histone H2B is required for gene activation. An understanding of the mechanisms that link ubiquitination with transcription has been hindered by our very limited knowledge of the machinery that establishes and maintains specific (poly)Ub signals; moreover, the Ub receptors that recognize ubiquitinated transcription activators and histones are largely unknown. Our long-term interest is to understand how Ub and Ub-proteasome pathways interface with transcriptional regulation. Currently we are studying functions of a particularly interesting deubiquitinating enzyme called Uch37. We discovered that Uch37 is a shared subunit of both the proteasome and the INO80 chromatin remodeling complex, providing a unique link between these two processes. In addition, we are using a combination of genetics and proteomics approaches to identify new players at the crossroads of UPP and transcription. These studies will provide mechanistic insights into activation and inactivation of some of the most tightly controlled transcription factors, such as c-Myc and Estrogen Receptor α.
Tatavosian, R., Kent, S., Brown, K., Yao, T., Duc, H.N., Huynh, T.N., Zhen, C.Y., Ma, B., Wang, H., Ren, X. (2019) “Nuclear condensates of the Polycomb protein chromobox 2 (CBX2) assemble through phase separation”. J Biol. Chem.249: 1451-1463.
Tatavosian, R., Duc, H.N., Huynh, T.N., Fang, D., Schmitt, B., Shi, X., Deng, Y., Phiel, C., Yao, T., Zhang, Z., Wang, H., Ren, X. (2018) “Live-cell single-molecule dynamics of PcG proteins imposed by the DIPG H3.3K27M mutation.” Nat. Commun. 9:2080.
Zukowski, A., Al-Afaleq, N.O., Duncan, E.D., Yao, T., Johnson, A.M. (2018) “Recruitment and allosteric stimulation of a histone deubiquitinating enzyme during heterochromatin assembly.” J. Biol. Chem. 293(7):2498-2509.
Vanderlinden, R.T., Hemmis, C.W., Robinson., Yao, T., and Hill C.P. (2017) “Structure and energetics of pairwise interactions between proteasome subunits RPN2, RPN13, and ubiquitin clarify a substrate recruitment mechanism.” J. Biol. Chem. 292(23):9493-9504.
Zhen, C.Y., Tatavosian, R., Huynh, T.N., Duc, H.N., Das, R., Kokotovid, M., Grimm, J.B., Lavis, L.D., Lee, J., Mejia, F.J., Li, Y., Yao, T., Ren, X. (2016) “Live-cell single-molecule tracking reveals co-recognition of H3K27Me3 and DNA targets polycomb Cbx7-PRC1 to chromatin.” Elife, 5: e17667.
Yao, T. (2015) “A Timer to Coordinate Substrate Processing by the 26S Proteasome.” Nat. Struct. Mol. Biol. 22: 652-3.
VanderLinden, R.T., Hemmis C.W., Schmitt B., Ndoja A., Whitby, F.G., Robinson H., Cohen, R.E., Yao, T.* and Hill C.P.* (2015) "Structural Basis for the Activation and Inhibition of the Uch37 Deubiquitylase". Mol. Cell 57(5):901-11 *co-corresponding authors
Muthurajan, U., Hepler, M.R.D., Hieb, A.R., Clark, N.J., Kramer, M., Yao, T., and Luger, K. (2014) "Automodification switches PARP-1 function from chromatin architectural protein to histone chaperone." Proc. Natl. Acad. Sci. USA 111:12752-7.
Ndoja, A., and Yao, T. (2014) “A non-proteolytic function of ubiquitin in transcription repression.” Microb. Cell 1: 253-255.
Long, L., Furgason, M., and Yao, T. (2014) “Non-hydrolyzable ubiquitin-histone mimics.” Methods 70: 134-8.
Long, L., Thelen, J.P., Furgason, M., Haj-Yahya M., Brik A., Cheng, D., Peng, J. and Yao, T. (2014) “The U4/U6 recycling factor SART3 has histone chaperone activity and associates with USP15 to regulate H2B deubiquitination.” J. Biol. Chem. 289: 8916-30.
Ndoja, A., Cohen, R.E., and Yao, T. (2014) “Ubiquitin signals proteolysis-independent stripping of transcription factors.” Mol. Cell 53: 893-903.
Yao, T. (2013) “Ubiquitin Carboxyl-terminal Hydrolase 37.” Handbook of Proteolytic Enzymes
Ndoja, A. and Yao, T. (2012) “Regulation of gene expression by the ubiquitin-proteasome system.” Sem. Cell Dev. Biol 23: 523-9.
Samara, N.L., Datta, A.B., Berndsen, C.E., Zhang, X., Yao, T., Cohen, R.E., and Wolberger C. (2010) “Structural insights into the assembly and function of the SAGA deubiquitinating module.” Science 328: 1025-9
Yao, T., Song, L., Jin, J., Cai, Y., Takahashi, H., Swanson, S.K., Washburn, M.P., Florens, L., Conaway, R.C., Cohen, R.E., and Conaway, J.W. (2008) "Distinct modes of regulation of the Uch37 deubiquitinating enzyme in the proteasome and the INO80 chromatin remodeling complex." Mol Cell 31: 909-17.
Cai, Y., Jin, J., Yao, T., Gottschalk, A.J., Swanson, S.K., Wu, S., Shi, Y., Washburn, M.P., Florens, L., Conaway, R.C., and Conaway, J.W. (2007) "Ubiquitous transcriptional regulator YY1 functions with the human INO80 chromatin remodeler to activate transcription." Nat. Struct. Mol. Biol. 14: 872-4.
Cai, Y., Jin, J., Gottschalk, A.J., Yao, T., Conaway, J.W., Conaway, R.C. (2006) "Purification and assay of the human INO80 and SRCAP chromatin remodeling complexes." Methods 40(4):312-7.
Abmayr, S., Yao, T., Parmely, T., and Workman, J.L. (2006) Preparation of nuclear and cytoplasmic extracts from mammalian cells. Curr. Protocols Mol. Biol. Unit 12.1.1-12.1.10
Yao, T., Song, L., Xu, W., DeMartino, G.N., Florens, L., Swanson, S.K., Washburn, M.P., Conaway, R.C., Conaway, J.W., and Cohen, R.E. (2006) "Proteasome recruitment and activation of the Uch37 deubiquitinating enzyme by Adrm1." Nat. Cell Biol. 8: 994-1002.
Yao, T., and Cohen, R.E. (2005) "Ubiquitin-ovomucoid fusion proteins as model substrates for monitoring degradation and deubiquitination by proteasomes." Methods Enzymol. 398: 522-540.
Jin, J., Cai, Y., Yao, T., Gottschalk, A.J., Florens, L., Swanson, S.K., Gutierrez, J.L., Coleman, M.K., Workman, J.L., Mushegian, A., Washburn, M.P., Conaway, R.C, and Conaway, J.W. (2005) "A mammalian chromatin remodeling complex with similarities to the yeast INO80 complex." J. Biol. Chem. 280: 41207-41212.
Conaway, R.C., Sato, S., Tomomori-Sato, C., Yao, T., Conaway, J.W. (2005) "The mammalian Mediator complex and its role in transcriptional regulation." Trends Biochem. Sci. 30: 250-255.
Conaway, J.W., Florens, L., Sato, S., Tomomori-Sato, C., Parmely, T.J., Yao, T., Swanson, S.K., Banks, C.A., Washburn, M.P., Conaway, R.C. (2005) "The mammalian Mediator complex." FEBS Lett. 579: 904-908.
Yao, T., and Cohen, R.E. (2002) "A cryptic protease couples deubiquitination and degradation by the proteasome." Nature 419: 403-407.
Hu, M., Li, P., Li, M., Li, W., Yao, T., Wu, J.W., Gu, W., Cohen, R.E., Shi, Y. (2002) "Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde." Cell 111: 1041-1054.
Yao, T., and Cohen, R.E. (2000) "Cyclization of polyubiquitin by the E2-25K ubiquitin-conjugating enzyme." J. Biol. Chem. 275: 36862-36868.
Yao, T., and Cohen, R.E. (1999) "Giant proteases: beyond the proteasome." Curr. Biol. 9: R551-R553.