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Department of Biochemistry and Molecular Biology

Houston, Texas

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Verna and Marrs McLean Department of Biochemistry and Molecular Biology
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Jun Qin, Ph.D.

Photograph of Dr. Qin

Department of Biochemistry and Molecular Biology
Department of Molecular and Cellular Biology

Director, Center for Molecular Discovery


  • Ph.D., Life Science, 1996, The Rockefeller University

Network Analysis Proteomics

Our laboratory is interested in understanding several intriguing biological processes, with a special emphasis on the development and application of cutting-edge mass spectrometry-based proteomics toolkits to untangle challenging biological problems.

1. Protein interaction landscape
We have a long standing interest on a concept of "network analysis proteomics." Proteins tend to assemble into multi-subunit protein complexes as the minimal biologically functional units. The execution of biological processes in the cell can be viewed as a network of ordered interactions between different protein complexes. Thus, the understanding of the basic mechanisms of cellular homeostasis relies on our ability to determine the composition of protein complexes and to decipher the interactions between these protein complex modules. Likewise, the understanding of pathogenesis ultimately depends on the knowledge of global perturbations in the protein ‘complexome’, or a cellular network of protein complex interactions during disease development. Specifically, we are analyzing the endogenous protein complexome by immunoprecipitation (IP) with primary antibody and mass spectrometry. We aim at constructing a complete human protein interactome.

2. Method development for biological mass spectrometry
As an important part of our research, we are continuously developing novel MS-based proteomic methods that will enable us to analyze dynamic changes of complex biological processes in a quantitative manner.

3. Proteomic analysis of protein ubiquitination
Protein ubiquitination is one of the major post translational modifications (PTMs) that regulate a very broad spectrum of cellular functions. Deregulation of ubiquitination is associated with many human diseases such as cancer and human neurodegenerative disorders. We are developing novel proteomics strategies to systematically profile ubiquitin proteome, and to study the regulation of such system in the biological contexts.

4. Sister chromatid cohesion in genome maintenance
The cohesin complex plays a central role in genome maintenance by regulating chromosome segregation in mitosis and DNA damage response (DDR) in other phases of the cell cycle. Checkpoint kinas ATM/ATR phosphorylates SMC1 and SMC3, two core components of the cohesin complex. In addition, SMC3 is acetylated at two critical lysine residues and this modification is critical for sister chromatid cohesion and genome instability in both yeast and human. We recently showed that genome-wide binding of SMC1 and SMC3 after ionizing radiation (IR) is enhanced by reinforcing pre-existing cohesin binding sites in human cancer cells. We are now vigorously investigating the functions of sister chromatid cohesion using a combination of mass spectrometry, biochemistry and genetic manipulations.

Selected Publications

  • Shi Y, Chan DW, Jung SY, Malovannaya A, Wang Y, Qin J. A data set of human endogenous protein ubiquitination sites. Mol Cell Proteomics. 2011 May;10(5):M110.002089. [PubMed]
  • Shi Y, Xu P, Qin J. Ubiquitinated proteome: ready for global? Mol Cell Proteomics. 2011 May;10(5):R110.006882. [PubMed]
  • Malovannaya A, Li Y, Bulynko Y, Jung SY, Wang Y, Lanz RB, O'Malley BW, Qin J. Streamlined analysis schema for high-throughput identification of endogenous protein complexes. Proc Natl Acad Sci U S A. 2010 Feb 9;107(6):2431-6. [PubMed]
  • Zhang J, Shi X, Li Y, Kim BJ, Jia J, Huang Z, Yang T, Fu X, Jung SY, Wang Y, Zhang P, Kim ST, Pan X, Qin J. Acetylation of Smc3 by Eco1 is required for S phase sister chromatid cohesion in both human and yeast. Mol Cell. 2008 Jul 11;31(1):143-51. [PubMed]
  • Mu JJ, Wang Y, Luo H, Leng M, Zhang J, Yang T, Besusso D, Jung SY, Qin J. A proteomic analysis of ataxia telangiectasia-mutated (ATM)/ATM-Rad3-related (ATR) substrates identifies the ubiquitin-proteasome system as a regulator for DNA damage checkpoints. J Biol Chem. 2007 Jun 15;282(24):17330-4. [PubMed]
  • Jacinto E, Facchinetti V, Liu D, Soto N, Wei S, Jung SY, Huang Q, Qin J, Su B. SIN1/MIP1 maintains rictor-mTOR complex integrity and regulates Akt phosphorylation and substrate specificity. Cell. 2006 Oct 6;127(1):125-37. [PubMed]
  • Jung SY, Malovannaya A, Wei J, O'Malley BW, Qin J. Proteomic analysis of steady-state nuclear hormone receptor coactivator complexes. Mol Endocrinol. 2005 Oct;19(10):2451-65. [PubMed]
  • Luo H, Chan DW, Yang T, Rodriguez M, Chen BP, Leng M, Mu JJ, Chen D, Songyang Z, Wang Y, Qin J. A new XRCC1-containing complex and its role in cellular survival of methyl methanesulfonate treatment. Mol Cell Biol. 2004 Oct;24(19):8356-65. [PubMed]
  • Wang Y, Cortez D, Yazdi P, Neff N, Elledge SJ, Qin J. BASC, a super complex of BRCA1-associated proteins involved in the recognition and repair of aberrant DNA structures. Genes Dev. 2000 Apr 15;14(8):927-39. [PubMed]
  • Ogryzko VV, Kotani T, Zhang X, Schiltz RL, Howard T, Yang XJ, Howard BH, Qin J, Nakatani Y. Histone-like TAFs within the PCAF histone acetylase complex. Cell. 1998 Jul 10;94(1):35-44. [PubMed]

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