| Our lab studies RNA genomics and gene regulationary mechanisms by computational and molecular biology
approaches. We are currently working on the following research topics:
|
| |
|
1. Regulation of
gene expression via alternative polyadenylation (Alt-PA or APA). Regulation of gene transcripts can be
achieved by variable 3' end formation through APA. We are using
bioinformatic methods to map and predict polyadenylation sites in metazoan genomes and
study the evolution of APA. We also use molecular biology
techniques to study the mechanism of APA and its impact on
gene expression. In addition, we are interested in understanding the interplay between
splicing and polyadenylation in gene regulation.
Representative publications:
- Ji, Z., and Tian, B. (2009). Reprogramming of 3' Untranslated Regions of mRNAs by Alternative Polyadenylation in Generation of Pluripotent Stem Cells from Different Cell Types. PLoS ONE 4(12): e8419.
- Ji, Z., Lee, J.Y., Pan, Z., Jiang, B., and Tian, B. (2009). Progressive lengthening of 3' untranslated regions of mRNAs by alternative polyadenylation during mouse embryonic development. Proc. Natl. Acad. Sci. U. S. A. 106:7028-33.
- Lee, J.Y., Ji, Z., and Tian, B. (2008). Phylogenetic analysis of mRNA polyadenylation sites reveals a role of transposable elements in evolution of the 3' end of genes. Nucleic Acids Res. 36:5581-90.
- 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.
- Cheng, Y., Miura, R.M., and Tian, B. (2006). Prediction of mRNA polyadenylation sites by support vector machine. Bioinformatics 22:2320-5.
- 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.
|
|
|
|
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.
- 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.
|
|
|
|
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:
- Qiu, H., Dai, H., Jain, K., Shah, R., Hong, C., Pain, J., Tian, B., Vatner, D.E., Vatner, S.F., and Depre, C. (2008). Characterization of a novel cardiac isoform of the cell cycle-related kinase that is regulated during heart failure. J. Biol. Chem. 283:22157-65.
- 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.
|
