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| Our lab studies RNA genomics and gene regulationary mechanisms by computational and molecular biology
approaches. We are working on the following research areas:
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1. Regulation of
gene expression via alternative polyadenylation. Regulation of gene transcripts can be
achieved by variable 3' end formation through alternative polyadenylation. We are using
bioinformatic methods to map and predict polyadenylation sites in metazoan genomes and
study the evolution of alternative polyadenylation. We also use molecular biology
techniques to study the mechanism of alternative polyadenylation and its impact on
gene expression. In addition, we are interested in understanding the interplay between
splicing and polyadenylation in gene regulation.
Representative publications:
- Lee, J. Y., Park, J. Y., and Tian, B. (2008). Identification of mRNA polyadenylation sites in genomes using cDNA sequences, expressed sequence tags and Trace. Methods Mol. Biol. 419:23-37.
- Tian, B., Pan, Z., and Lee, J.Y. (2007). Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing. Genome Res.
17:156-65.
- Lee, J.Y., Yeh, I., Park, J.Y., and Tian, B. (2007). PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic Acids Res. 37:D165-8.
- D'mello, V., Lee, J.Y., Macdonald, C.C., and Tian, B. (2006) Alternative mRNA Polyadenylation Can Potentially Affect Detection of Gene Expression by Affymetrix GeneChip((R)) Arrays. Appl. Bioinformatics 5:249-53.
- Cheng, Y., Miura, R.M., and Tian, B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5.
- Pan, Z., Zhang,
H., Hague, L.K., Lee, J.Y., Lutz, C.S., and Tian, B. (2006). An intronic polyadenylation site in human and mouse CstF-77 genes suggests an evolutionarily conserved regulatory mechanism.
Gene 366:325-334.
- Zhang, H., Lee,
J.Y., and Tian, B. (2005). Biased alternative polyadenylation in human
tissues. Genome Biol. 6:R100.
- Hu, J., Lutz, C.S.,
Wilusz, J., and Tian, B. (2005). Bioinformatic identification of candidate
cis-regulatory elements involved in human mRNA polyadenylation. RNA 11:
1485-1493.
- Tian,
B., Hu, J., Zhang, H., and Lutz, C.S. (2005). A large-scale analysis of
mRNA polyadenylation of human and mouse genes. Nucleic Acids Res. 33:201-212.
- Zhang,
H., Hu, J., Recce, M., and Tian, B. (2005). PolyA_DB: a database for
mammalian mRNA polyadenylation. Nucleic Acids Res. 33:D116-20.
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2. RNA sequence and structure
elements in post-transcriptional gene regulation. One of the daunting tasks facing biologists
in the post-genomic era is to uncover functional elements in genomes.
We are developing methods to identify RNA sequence and structure
elements that play regulatory roles in post-transcriptional gene
regulation, e.g., splicing, polyadenylation, RNA localization, translation,
and RNA stability.
Representative publications:
- Khaladkar, M., Liu, J., Wen, D., Wang, J.T. L., and Tian, B. (2008) Mining Structural Elements in Human and Mouse Untranslated Regions of mRNAs using Structure-based Alignment. BMC Genomics 9:189.
- Khaladkar, M., Bellofatto, V., Wang, J.T.L., Tian, B., and Shapiro, B.A. (2007). RADAR: A Web Server for RNA Data Analysis and Research. Nucleic Acids Res. 35 (Web Server issue): W300-4.
- Tian, B., Mukhopadhyay, R. and Mathews, M.B. (2005). Polymorphic CUG repeats in human mRNAs and their effects on gene expression. RNA Biol. 2:149-156.
- Duttagupta1, R., Tian, B., Wilusz, C.J., Khounh, D.T., Soteropoulos, P., Ouyang, M., Dougherty, J.P., and Peltz, S.W. (2005). Global Analysis of Pub1p targets reveals a coordinate control of gene expression through modulation of binding and stability. Mol. Cell. Biol. 25:5499-5513.
- Hu, J., Lutz, C.S., Wilusz, J., and Tian, B. (2005). Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation. RNA 11:1485-1493.
- Liu, J., Wang, T.L., Hu, J., and Tian, B. (2005). A method for aligning RNA secondary structures and its application to RNA motif detection. BMC Bioinformatics 6:89.
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3.
Transcriptional and post-transcriptional gene regulatory programs in the heart. We are trying to understand how genes are regulated at various developmental and disease stages of the heart. Our approach involves global analysis of different levels of gene expression and building regulatory modules and networks.
Representative publications:
- Alcendor, R.R., Gao, S., Zhai, P., Zablocki, D., Holle, E., Yu, X., Tian, B., Wagner, T., Vatner, S.F., and Sadoshima, J. (2007). Sirt1 Regulates Aging and Resistance to Oxidative Stress in the Heart. Circ. Res. 100:1512-21.
- Qiu, H., Tian, B., Resuello, R.G., Natividad, F.F., Peppas, A., Shen, Y.-T., Vatner, D.E., Vatner, S.F. and Depre, C. (2007) Gender-specific regulation of gene expression in the aging monkey aorta. Physiol. Genomics. 29:169-80.
- Ago, T., Yeh, I., Yamamoto, M., Schinke-Braun, M., Brown, J.A., Tian, B., and Sadoshima, J. (2006). Thioredoxin1 Upregulates Mitochondrial Proteins Related to Oxidative Phosphorylation and TCA Cycle in the Heart. Antioxid. Redox. Signal. 8:1635-50.
- Usui, S., Yeh, I., Tian, B., and Sadoshima, J. (2006). Global changes in gene expression during cardiac hypertrophy: A new direction of cardiac signaling research. J. Mol. Cell. Cardiol. 41:219-22.
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