Dr. Ann-Bin Shyu, Professor and Jesse H. Jones Chair in Molecular Biology
Department of Biochemistry and Molecular Biology
Program in Biochemistry and Molecular Biology
The University of Texas Medical School at Houston
P.O. Box 20708
Houston, Texas 77225
(713) 500-6068 Fax (713)500-0575
Ph.D, Indiana Univeristy, Bloomington
American Cancer Society Postdoctoral Fellow, Harvard Medical School
Junior Faculty Research Award, American Cancer Society
Established Investigator Award, American Heart Association
Senior Investigator Award, Sandler Foundation for Asthma Research
mRNA Turnover; Translational Control; MicroRNA-Mediated Gene Silencing; RNA-binding Proteins in gene regulation;
1. Mechanisms of mammalian mRNA turnover
Airway Inflammation; Cell Transformation
Our laboratory is interested in post-transcriptional regulation of mammalian gene expression. In particular, we are investigating the mechanisms responsible for mRNA turnover in mammalian cells, including elucidation of microRNA-mediated gene silencing and its regulation, the relationship between translation and mRNA degradation, and their roles in regulating gene expression. Both the translation and the stability of mRNAs are affected by deadenylation (i.e., shortening of the mRNA 3’ poly(A) tail), which begins when mRNAs arrive in the cytoplasm. Deadenylation is often a rate-limiting step for mRNA decay and translational silencing and is thus a critical control point in both processes. Two recent developments in eukaryotic mRNA turnover underscore the importance of deadenylation in regulation of gene expression. First, microRNAs (miRNAs) promote rapid decay of their mRNA targets by accelerating deadenylation as a major means of achieving gene silencing. Second, non-translatable mRNA-protein complexes (mRNPs) are found in RNA processing bodies (P-bodies), cytoplasmic domains implicated in mRNA turnover, storage of non-translatable mRNPs, and translation repression. One major consequence of deadenylation is the formation of non-translatable mRNPs. We hypothesized and subsequently demonstrated a close link between deadenylation and P-body formation in mammalian cells.
When deadenylation is impaired, there is no P-body formation. (A) Puromycin treatment of NIH3T3 cells enhances P-body formation (top panel) but when deadenylation is compromised by knocking down a major deadenylase Caf1, it does not induce P-body formation (bottom panel). P-bodies are marked by immuno-staining of two different P-body components, GW182 and Pan2. (B) Puromycin treatment does not induce P-body formation in NIH3T3 cells overexpressing a catalytic inactive mutant of Caf1 (bottom panel, dashed line), which blocks deadenylation. In contrast, cells overexpressing wild-type Caf1 show may P-bodies (top panel).
To provide a framework for studying the mechanisms and regulation of P-body formation, maintenance and disassembly, we recently compiled a list of P-body proteins found in various species and further grouped both reported and predicted human P-body proteins according to their functions. By analyzing protein-protein interactions of human P-body components, we found that many P-body proteins form complex interaction networks with each other and with other cellular proteins that are not recognized as P-body components. The observation suggests that these other cellular proteins may play important roles in regulating P-body dynamics and functions. We further used siRNA-mediated gene knockdown and immunofluorescence microscopy to demonstrate the validity of our in silico analyses. Our combined approach identifies new P-body components and suggests that protein ubiquitination and protein phosphorylation involving14-3-3 proteins may play critical roles for post-translational modifications of P-body components in regulating P-body dynamics.
Research on this line focuses on addressing the following fundamental questions: 1) What are the mechanisms by which deadenylation is regulated and how does regulation of deadenylation affect the fate of mRNA? 2) What trans-acting factors are involved in miRNA-mediated deadenylation and decay? 3) How is miRNA-mediated mRNA decay regulated? 4) What changes does deadenylation trigger in mRNA-protein or mRNP complexes and how do these changes influence the fate of an mRNA? 5) What is the functional link between deadenylation and P-bodies? How P-body dynamics are regulated via protein ubiquitination-deubiquitination? What are the roles played by 14-3-3 proteins in regulating P-bodies? Answers to these questions will reveal fundamental principles that govern mammalian mRNA turnover and translation and provide crucial new insights into several key issues related to the dynamic relationship between mRNA decay, translational control, mRNP remodeling and P-bodies.
2. Roles of post-transcriptional mechanisms in controlling airway inflammation
Another research area focuses on the post-transcriptional mechanisms controlling the inflammatory response of human bronchial epithelial cells—in health and in airway disease —particularly in the context of RNA biology. Currently, our work along this line has focused on miRNA, the predominant small regulatory RNA subtype in humans (and in all animals). The study of small regulatory RNAs is a relatively new and unexplored research field with much potential. miRNAs serve fundamental biological functions in all animals studied. Our research aim is to analyze and manipulate these small molecules in order to learn how miRNA biology is altered in inflammatory airway diseases and how miRNAs help control decay and translation of mRNAs coding for inflammatory mediators and tissue remodeling factors. We seek both to understand how miRNAs contribute to disease pathogenesis, and as a long-term goal to explore how specially designed RNAs may be applied for therapeutic strategies.
- Ezzeddine, N., Chen, C.-Y., Shyu, A.-B. Evidence providing new insights into TOB-promoted deadenylation and supporting a link between TOB's deadenylation-enhancing and anti-proliferative activities. Mol Cell Biol. 32:1089-98, 2012.
- Zheng, D., Chen, C.-Y. A. and Shyu, A.-B. Unraveling regulation and new components of human P-bodies through a protein interaction framework and experimental validation. RNA, 17: 1619-34, 2011.
- Chen, F, Shyu, A-B. and Shneider, B.L. Hu antigen R and tristetraprolin - counter-regulators of rat apical sodium dependent bile acid transporter via effects on mRNA stability. Hepatology, 2011 Jun 17. doi: 10.1002/hep.24496. [Epub ahead of print]
- Chen, C-Y A and Shyu, A-B. Mechanisms of Deadenylation-Dependant Decay. Wiley Interdisciplinary Reviews (WIREs) RNA, 2: 167-183, 2011.
- Chen, C-Y A and Shyu, A-B. HuD Stimulates Translation via eIF4A. Mol Cell. 36: 920-921, 2009.
- Chen, C-Y A, Zheng, D, Xia, Z, and Shyu, A-B. Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nature Struct Mol Biol, 16:1160-1166, 2009.
- Mauxion, F, Chen, C-Y A, Seraphin, B, and Shyu, A-B. BTG/Tob factors impact deadenylases. Trends Biochem Sci, 34: 640-647, 2009.
- Fabian, MR, Mathonnet, G, Sundermeier, T, Mathys, H, Zipprich, JT, Svitkin, YV, Rivas, F, Jenik, M, Wohlschlegel, J, Doudna, JA, Chen, C-Y A, Shyu, A-B, Yates III, JR, Hannon, GJ, Filipowicz, W, Duchaine, TF, Sonenberg, N. Mammalian miRNA RISC recruits CAF1 and PABP to affect PABP-dependent deadenylation. Mol Cell, 35:868-80, 2009.
- Chen C-Y A, Ezzeddine N, Shyu A-B. Messenger RNA half-life measurements in mammalian cells. Methods Enzymol. 448:335-357, 2008.
- Martineau Y, Derry MC, Wang X, Yanagiya A, Berlanga JJ, Shyu A-B, Imataka H, Gehring K, Sonenberg N. Poly(A)-binding protein-interacting protein 1 binds to eukaryotic translation initiation factor 3 to stimulate translation. Mol Cell Biol. 28:6658-6667, 2008.
- Zhai, Y, Zhong, Z, Chen, C-Y A, Xia, Z, Song, L, Blackburn, MR, Shyu, A-B. Coordinated changes in mRNA turnover, translation, and RNA processing bodies in bronchial epithelial cells following inflammatory stimulation. Mol Cell Biol. 28:7414-7426, 2008.
- Zheng, D, Ezzeddine, N, Chen, C-Y A , Zhu, W, He, X, and Shyu, A-B. Deadenylation is prerequisite for P-body formation and mRNA decay in mammalian cells. J Cell Biol 182:89-101, 2008.
- Shyu, A-B, Wilkinson, M, and van Hoof, A. Messenger RNA regulation: To translate or to degrade. EMBO J, 27: 471-481, 2008.
- Ezzeddine, N, Chang, T-C, Yamshita, A, Chen, C-Y A, Zhu, W, Zhong, Z, Yamashita, Y, Zheng, D. and Shyu, A-B. Human TOB, an anti-proliferative transcription factor, is a PABP-dependent positive regulator of cytoplasmic mRNA deadenylation. Mol Cell Biol, 27: 7791-7801, 2007.
- Chen, C-Y A, Yamashita, Y, Chang, T-C, Yamshita, A, Zhu, W, Zhong, Z, and Shyu, A-B. Versatile applications of transcriptional pulsing to study of mRNA turnover in mammalian cells. RNA, 13: 1775-86, 2007.
- Siddiqui, N, Mangus, D A, Chang, T-C, Palermino, J-M, Shyu, A-B, and Gehring, K. Poly(A)-nuclease interacts with the PABC domain from poly(A)-binding protein. J Biol Chem. 282: 25067-75, 2007.
- Lim NS, Kozlov G, Chang TC, Groover O, Siddiqui N, Volpon L, De Crescenzo G, Shyu A-B, Gehring K. Comparative peptide-binding studies of PABC domains from the E3 ubiquitin ligase HYD and poly(A)-binding protein: Implications for HYD function. J Biol Chem. 281: 14376-14382, 2006.
- Shyu, A-B. UNRaveling the regulation of dosage compensation. Nature Struct & Mol Biol, 13: 189-190, 2006.
- Yamashita, A., Chang, T-C, Yamashita, Y, Zhong, Z, Zhu, W, Chen, C-Y A, and Shyu, A-B. Concerted action of poly(A) nucleases and decapping enzyme in mammalian mRNA turnover. Nature Struct & Mol Biol, 12: 1054-1063, 2005. (*Featured in News & Views by the Journal, see pp. 1024-25)
- Chen, C-Y A, Xu, N, Zhu, W, and Shyu, A-B. Functional Dissection of hnRNP D Suggests that Nuclear Import Is Necessary Before hnRNP D Can Modulate mRNA Turnover in the Cytoplasm. RNA, 10:669-680, 2004.
- Chang, T-C, Yamashita, A., Chen, C-Y A., Yamashita, Y, Zhu, W, Durdan, S, Kahvejian, A, Sonenberg, S, and Shyu, A-B. UNR, a new partner of poly(A)-binding protein, plays a key role in translationally coupled mRNA turnover mediated by the c-fos major coding-region determinant. Genes & Dev., 18: 2010-2023, 2004. (*Selected for Journal Research Highlights in Nature Structural and Molecular Biology, 11:811, 2004.
- Chen, C-Y A, and Shyu, A-B. Rapid Deadenylation Triggered by Nonsense Codon Precedes Decay of the RNA Body in a Mammalian Cytoplasmic Nonsense-Mediated-Decay Pathway. Mol. Cell. Biol. 23: 4805-4813, 2003.
- Atasoy, U, Curry, S L, de Silanes, I L, Shyu, A-B, Casolaro, V, Gorospe, M, and Stellato, C. Regulation of eotaxin gene expression by TNFα and IL-4 through messenger RNA stabilization. J Immunology. 171:4369-4378, 2003.
- Wilkinson, M.F. and Shyu, A-B. "RNA surveillance by nuclear scanning?" Nature Cell Biol, 4: E144-E147, 2002.
- Chen, C-Y A, Xu, N, and Shyu, A-B. Highly Selective Actions of HuR in Antagonizing AU-Rich Element-Mediated mRNA Destabilization. Mol. Cell. Biol. 22: 7268-7278, 2002.
- Xu, N, Chen, C-Y A, Shyu, A-B. A versatile role for hnRNP D isoforms in the differential regulation of cytoplasmic mRNA turnover. Mol. Cell. Biol. 21: 6960-6971, 2001.
- Wilkinson, M F and Shyu, A-B. Bifunctional regulatory proteins that control gene expression in both the nucleus and the cytoplasm. BioEssays 23:775-787, 2001.
- Grosset, C, Chen, C.-Y. A., Xu, N., Jacquemin-Sablon, H., Sonenberg, N. and Shyu, A.-B. A mechanism for translationally-coupled mRNA turnover: interaction between the poly(A) tail and an RNA stability determinant in the c-fos coding region via a novel protein complex. Cell, 103: 29-40, 2000.
- Shyu, A-B and Wilkinson, M. The double lives of shuttling RNA-binding proteins. Cell 102: 135-138, 2000.