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Full-Time

Shih-Peng Chan Associate Professor

聯絡電話:23123456 ext. 88286

E-mail: shihpengchan@ntu.edu.tw

Personal File

Field:

microRNA-mediated gene regulation, C. elegans development, RNA biology

Education:

Ph.D., Inst. of Microbiology and Immunology, National Yang-Ming University
M.S., Inst. of Microbiology and Immunology, National Yang-Ming University
B.S., Dept. of Botany, National Taiwan University

Title:

Associate Professor, Dept. of Microbiology, National Taiwan University (2016/8~present)
Assistant Professor, Dept. of Microbiology, National Taiwan University (2010/8~2016/7)
Postdoctoral Associate, Dept. of Molecular, Cellular and Developmental Biology, Yale University, U.S.A. (2004/11~2010/6)
Postdoctoral Fellow, Inst. of Molecular Biology, Academia Sinica (2003/9~2004/10)

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Current Research

(Please visit our Lab Website for more details.) 

MicroRNAs (miRNAs) are ~22-nucleotide small RNAs that regulate gene expression at the post-transcriptional level. In animals, miRNAs are involved in multiple biological functions, including development, apoptosis, metabolism and signaling pathways. Over a thousand miRNAs have been found in nematode, fly, and mammalian genomes by cloning and bioinformatics approaches. miRNA genes are transcribed by RNA polymerase II or III, and the primary miRNA transcripts (pri-miRNAs) are processed in the nucleus by the RNase III enzyme Drosha. The processed products, ~70-nt hairpin precursor miRNAs (pre-miRNAs), are transported to the cytoplasm and cleaved by another RNase III enzyme Dicer to produce short miRNA duplexes. One strand of the duplex is assembled into the miRNA-induced silencing complex (miRISC), which contains the mature miRNA, Argonaute protein and other co-factors. Through base-pairings between miRNAs and their target sequences, miRISCs associate with the target mRNAs and trigger translational repression or mRNA degradation.

It has been estimated that about 30% of human genes are regulated by miRNAs. Therefore, miRNA-based regulation directly or indirectly affects most, if not all, cellular pathways. A number of miRNAs, called oncomirs, play a role in carcinogenesis due to their ability to regulate cancer-related and apoptosis-related genes. For example, miR-21, an oncogene, has anti-apoptotic abilities and has been frequently found to be overexpressed in many types of tumors, including neuroblastoma, glioblastoma, colorectal, lung, breast and pancreatic cancers. Conversely, let-7, which controls the timing of cell cycle exit and terminal differentiation in Caenorhabditis elegans and has been experimentally demonstrated to repress the oncogene RAS in C. elegans and higher animals, plays a critical role as a tumor suppressor in lung cancer and breast cancer. Hence, the study of miRNAs and their functional modulators, as well as their targets, has become important to cancer research and has showed great promises for prognosis, diagnosis and therapies of cancer.  

My laboratory will employ biochemical and genetic approaches to identify novel factors that play roles in miRNA function and to identify miRNA targets, especially in cancer. Our research will focus on two specific aims:

(1)   miRNA function modulators:

Currently, we are using the C. elegnas let-7 miRNA as a model molecule to identify novel proteins that modulate miRNA function. The complete cell lineage map and the powerful genetic tools in C. elegans have made the nematode a successful model to investigate miRNA biology. let-7, as a heterochronic gene, controls the timing of cell cycle exit and terminal differentiation hence to be an excellent model miRNA in screening or reverse genetics of its functional co-factors. The large abundance of let-7 also eases biochemical approaches such like affinity selection or immunoprecipitation. We have found that certain ribosomal proteins and DEAD-box RNA helicases are involved in let-7 regulation and may function as modulators of miRNAs.    

         (2)   miRNA targets and their regulation in cancer

We will eventually extend the investigation to miRNA-mediated gene regulation in cancer. We have started to develop comprehensive and experimental approaches, including UV-crosslinking, sequence-dependent affinity selection and high throughput sequencing, to identify miRNA targets. We will establish these approaches in the C. elegans system and then apply to human cancer cell lines or tissues. The goal is to understand the regulation patterns of miRNAs in carcinogenesis, which will potentially contribute to future clinical applications of miRNAs in prognosis, diagnosis and therapies of cancer.

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Staff members

碩士研究生:羅尉庭、王于箴、張傑盛、鄭庭葦、秦國璽
博士研究生:陳巧儂
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Selected publications

Selected Publications
1.Ma, T.H., Lee, L.W., Lee, C.C., Yi, Y.H., Chan, S.P., Tan, B.C., Lo, S.J. (2016) Genetic control of nucleolar size: an evolutionary perspective. Nucleus. 25, 112-20 (co-corresponding author).
2.Chu, Y.D., Chen, H.K., Huang, T., Chan, S.P. (2016) A novel function for the DEAD-box RNA helicase DDX-23 in primary microRNA processing in Caenorhabditis elegans. Dev Biol 409, 459-472.
3.Yi, Y.H., Ma, T.H., Lee, L.W., Chiou, P.T., Chen, P.H., Lee, C.M., Chu, Y.D., Yu, H., Hsiung, K.C., Tsai, Y.T., Lee, C.C., Chan, S.P., Tan, B.C., Lo, S.J. (2015) A genetic cascade of let-7-ncl-1-fib-1 modulates nucleolar size and rRNA pool in Caenorhabditis elegans. PLoS Genet 11, e005580 (co-corresponding author).
4.Chu, Y.D., Wang, W.C., Chen, S.A., Hsu, Y.T., Yeh, M.W., Slack, F.J., Chan, S.P. (2014) RACK-1 regulates let-7 microRNA expression and terminal cell differentiation in Caenorhabditis elegans. Cell Cycle 13, 1995-2009.
5.Van Wynsberghe, P.M., Chan, S.P., Slack, F.J., Pasquinelli, A.E. (2011) Analysis of microRNA expression and function. Methods Cell Biol 106, 219-52 (co-first author).
6.Chan, S.P., and Slack, F.J. (2009) Ribosomal protein RPS-14 modulates let-7 function in Caenorhabditis elegans. Dev Biol 334, 152-60.
7.Chan, S.P., Ramaswamy, G., Choi, E.Y., and Slack, F.J. (2008). Identification of specific let-7 microRNA binding complexes in Caenorhabditis elegans. RNA 14, 2104-2114.
8.Chan, S.P., and Slack, F.J. (2007). And now introducing mammalian mirtrons. Dev Cell 13, 605-607.
9.Chan, S.P., and Slack, F.J. (2006). microRNA-mediated silencing inside P-bodies. RNA Biol 3, 97-100.
10.Chen, C.H., Kao, D.I., Chan, S.P., Kao, T.C., Lin, J.Y., and Cheng, S.C. (2006). Functional links between the Prp19-associated complex, U4/U6 biogenesis, and spliceosome recycling. RNA 12, 765-774.
11.Chan, S.P., and Cheng, S.C. (2005). The Prp19-associated complex is required for specifying interactions of U5 and U6 with pre-mRNA during spliceosome activation. J Biol Chem 280, 31190-31199.
12.Chan, S.P., Kao, D.I., Tsai, W.Y., and Cheng, S.C. (2003). The Prp19p-associated complex in spliceosome activation. Science 302, 279-282.
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