Rapid advances in computational biology and bioinformatics are providing new approaches to complex biological systems. Advances in systems biology and molecular medicine require combined efforts of bioinformaticists and molecular biologists in order to characterize mathematical models of underlying biological processes and the knowledgeable discovery of highly complex data sets. Such integrative approaches hold promise for elucidating gene function and RNA-based regulation of gene expressions, knowledgeable discovery of highly complex data sets, as well as for identifying potential therapeutic targets. RNA Folding and Modeling at MMC provides flexible and powerful interfaces between disciplines and stimulates scientific cooperation and interaction between theoretical and experimental research within CCR and NIH and with outside. Current collaborations have emphasized on post-transcriptional gene regulation, RNA-based regulation of gene expressions, and discoveries of the regulated targets of miRNAs, FSRs and RNA structure motifs involved in gene expression.
Ongoing Collabrating Projects
- siRNA and shRNA Approaches to Gene Silencing of the cellular cofactors required for HIV and other retroviruses.
We collaborated on studies of induction and suppression of RNA interference by HIV-1, and identification of virus-encoded miRNAs and potential regulated targets of miRNAs with Dr. Jeang's Lab. (Mol. Virol. Section, Lab of Mol. Microbio., NIAID, NIH).
Our recent results indicate that although short interfering RNAs have been used artificially to silence viral infections, no direct evidence exist that natural viral sequences provoke such immunity in mammalian cells. Our computation discovers a series of dsRNAs of 19 base-pairs in about 500 HIV and their related sequences. The conserved, naturally occurring 19 base-pairs dsRNA elicits antiviral RNA interference in human cells. Interestingly, HIV has evolved a suppressor of RNA silencing embodied in its Tat protein to combat this induced RNA interference. And Tat suppresses RNA silencing through a functional abrogation of Dicer activity. Our results suggest it is the pre-processed short interfering siRNA, but not processing-requiring long interfering liRNA nor short hairpin shRNA, that should be the preferred consideration for inhibiting HIV-1 infections.
Publication:
Yeung M.L., Bennasser, Y., Le, Shu-Yun, Jeang, K.-T. RNA interference and HIV-1. Adv. Pharmacol. 55: 427-438, 2007.
Bennasser, Y., Le, Shu-Yun, Yeung M.L., and Jeang, K.-T. MicroRNAs in human immunodeficiency virus-1 infection. Methods Mol. Biol. 342: 241-253, 2006.
Yeung M.L., Bennasser, Y., Le, Shu-Yun, and Jeang, K.-T. siRNA, miRNA and HIV: promises and challenges. Cell Res. 15: 935-946, 2005
Yamina Bennasser, Shu-Yun Le, M. Benkirane and Kuan-Teh Jeang. Evidence that HIV-1 encodes a siRNA and a suppressor of RNA silencing. Immunity, 22: 607-619, 2005.
Yamina Bennasser, Shu-Yun Le, M.L. Yeung and Kuan-Teh Jeang. HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology, 1:43, 2004, ISSN 1742-4690.
- Determination of Functional Structured RNA (FSR) in MS2 Gene
MS2 gene of the ciliated protozoan Paramecium teraurelia shows enhanced expression in the course of aging and also autogamy, so that it is supposed to be involved in determining the life span of this organism. Several evidence indicates that the gene express an mRNA-like non-coding RNA of about 4kb in size. In collaboration with Dr. Hiroyuki Tanabe's Lab (Department of Biochemistry, Kinki University, Japan) we would like to determine the molecular function of MS2 through structural analysis.
Publication:
Tanabe, H. and Le, Shu-Yun Prediction of structural homologs to functional RNAs involved in determination of life span of Paramecium tetraurelia. Jpn. J. Protozool, 39: 151-156, 2006.
- Discovery of FSRs in 3'UTR
It is well known that functional RNA elements and FSRs are actively involved in regulation of mRNA stability, translational control, mRNA transport and localization. We collaborated on studies of identifying functional RNA elements in the 3'UTR with bench scientists.
We identify an unstructured functional AU-rich element in the 3'UTR of parathyroid hormone mRNA with Naveh-Many's Lab (The Hebrew Univ. Medical School, Jerusalem, Israel). The detected 3'-UTR cis-acting element is an open region that utilize the distinct sequence pattern to determine mRNA stability by its interaction with trans-acting factors.
Publication:
R. Kilav, O. Bell, S.-Y. Le, J. Silver and T. Naveh-Many:
The parathyroid hormone mRNA 3'-untranslated region AU-rich element is an unstructured functional element. The Journal of Biological Chemistry, 279: 2109-2116, 2004).We identify a FSR in the 3'UTR of the cytotoxic ribonuclease mRNA with Rybak's Lab (Lab. of Biochemical Physiology, CCR, NCI-FCRDC). The FSR has a long size of dsRNA structure that may suppress the mRNA translation.
Publication:
S. Chen, S.-Y. Le, D.L. Newton, J.V. Maizel, jr. and S.M. Rybak:
A gender-specific mRNA encoding a cytotoxic ribonuclease contains a 3' UTR of unusual length and structure. Nucleic Acids Res 28:(12) 2375-2382, 2000.- Discovery of FSRs in 5'UTR
Experimental study revealed that a special region in 5'-untranslated regions (UTRs) called the internal ribosome entry segment (IRES) allowed the translational machinery to skip over the upstream AUGs. Translational control involving IRES elements is a distinct mechanism in cap-independent translation. In collaboration with various laboratories outside of NIH we have been identified viral IRES in picornavirus, HCV, and pestivirus, as well as cellular IRES in platelet-derived growth factor B (PDGF2/c-sis) mRNA, VEGF, c-myc, and ALM1/RUNX1. Our research indicated that there are homologue core structural motif among the viral and cellular IRES. For cellular IRES, the conservered structural core is a Y-shaped stem-loop followed by a complementary sequence to the 3'-end sequence of 18 S rRNA.
Publication:
1. S. Cencig, C. Nanbru, S.-Y. Le, C. Gueydan, G. Huez, and V. Kruys:
Mapping and characterization of the minimal internal ribosome entry segment in the human c-myc mRNA 5' untranslated region. Oncogene, 23: 267-277, 2004.2. A. Pozner, D. Goldenberg, V. Negreanu, S.-Y. Le, O. Elroy-Stein, D. Levanon, and Y. Groner:
Transcription-coupled translation control of AML1/RUNX1 is mediated by cap- and internal ribosome entry site-dependent mechanisms. Mol. Cell Biol. 20:(7) 2297-2307, 2000.3. Sella, O., G. Gerlitz, S.-Y. Le and Elroy-Stein, O.:
Differentiation-induced internal translation of c-sis mRNA: Analysis of the cis elements and their differentiation-linked binding to the hnRNP C protein. Mol. Cell Biol. 19:(8) 5429-5440, 1999.4. J. Bernstein, O. Sella, S.-Y. Le and O. Elroy-Stein:
PDGF2/c-sis mRNA leader contains a differentiation-linked internal ribosomal entry site (D-IRES). J. Biol. Chem., 272: 9356--9362, 1997.5. G. Akiri, O. Elroy-Stein, D. Nahari, Y. Finkelstein, S.-Y. Le and B.Z. Levi:
The 5' Untranslated region (5'UTR) of vascular endothelial growth factor (VEGF) contains an internal ribosome entry site (IRES) and promoter activity. Oncogene, 17: 227-236, 1998.6. S.-Y. Le, A. Siddiqui and Jacob V. Maizel: A common structural core in the internal ribosome entry sites of picornavirus, hepatitis C virus, and pestivirus. Virus Genes, 12: 135--147, 1996.
7. C. Wang, S.-Y. Le, N. Ali and A. Siddiqui: An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5' noncoding region. RNA 1: 526--537, 1995.
8. S.-Y. Le, W.-m. Liu, and J.V. Maizel Jr.,: Phylogenetic evidence for the improved RNA higher-order structure n internal ribosome entry sequences of HCV and pestiviruses. Virus Genes 1998; 17:279-295.
9. S.-Y. Le, N. Sonenberg, and J.V. Maizel Jr.,: Unusual folding regions and ribosome landing pad within hepatitis C virus and pestivirus RNAs. Gene 1995; 154:137-143.
10. S.-Y. Le, N. Sonenberg, and J.V. Maizel Jr.,: Distinct structural elements and internal entry of ribosomes in mRNA3 encoded by infectious bronchitis virus. Virology, 198: 405--411, 1994.
11. S.-Y. Le, J.-H. Chen, N. Sonenberg, and J.V. Maizel Jr.,: Conserved tertiary structure elements in the 5' nontranslated region of cardiovirus, aphthovirus and hepatitis A virus RNAs. Nucl Acids Res, 21: 2445--2451, 1993.
12. S.-Y. Le, J.-H. Chen, N. Sonenberg, and Jacob V. Maizel Jr.,: Conserved tertiary structure elements in the 5' untranslated region of human enteroviruses and rhinoviruses. Virology, 191: 858--866, 1992.
13. R. Nicholson, J. Pelletier, S.-Y. Le, and N. Sonenberg:
Structural and functional analysis of the ribosome landing pad of polioviruses: in vivo translation studies. J. of Virology, 65: 5886--5894, 1991.- Discovery of cis-acting Elements in Retroviruses
Nucleo-cytoplasmic transport of RNA is one of many cellular pathways. HIV export to the cytoplasm not only full length genomic and structural gene-encoding RNA species, but also partially and fully spliced RNAs. The partially spliced and unspliced RNAs require the interaction of the HIV-1 Rev protein with the cis-acting, viral RRE (Rev responsive element). In collaboration with Cullen's laboratories (Dept. of Genetics and Howard Hughes Medical Institute, Duke Univ. Medical Center), we found Rev responsive element in HIV-1. The functional structured cis-acting elements were also found in HIV-2, SIV, Visna, HTLV-1 and human endogenous retrovirus.
Publication:
1. J. Young, H. Bogerd, S.-Y. Le and B.R. Cullen:
The human endogenous retrovirus K Rev response element coincides with a conserved RNA folding region. RNA 6:1551-1564, 2000.2. L.S. Tiley, P.H. Brown, S.-Y. Le, J.V. Maizel, J.E. Clements and B.R. Cullen:
Visna virus encodes a post-transcriptional regulator of viral structural gene expression, Proc. Natl. Acad. Sci. USA, 87: 7497--7501, 1990.3. M.H. Malim, J. Hauber, S.-Y. Le, Jacob V. Maizel and B.R. Cullen:
The HIV-1 rev trans-activator acts through a structured target sequence to activate nuclear export of unspliced viral mRNA. Nature, 338: 254--257, 1989.4. M.H. Malim, S. Bohnlein, R. Fenrick, S.-Y. Le, Jacob V. Maizel and B.R. Cullen:
Functional comparison of the Rev trans-activators encoded by different primate immunodeficiency virus species, Proc. Natl. Acad. Sci. USA, 86: 8222--8226, 1989.5. R. Fenrick, M.H. Malim, J. Hauber, S.-Y. Le, J.V. Maizel and B.R. Cullen:
Functional analysis of the Tat trans-activator of the human immunodeficiency virus type 2, J. of Virology, 63: 5006--5012, 1989.6. S.M. Hanly, L.T. Rimsky, M.H. Malim, J.H. Kim, J. Hauber, S.-Y. Le, J.V. Maizel, B.R. Cullen and W.C. Greene: Comparison of the HTLV-1 Rex and HIV-1 Rev trans-regulatory proteins and their RNA response elements, Genes and Development, 3: 1534--1544, 1989.
7. S.-Y. Le, M.H. Malim, B.R. Cullen and J.V. Maizel: A highly conserved RNA folding region adjacent to the cleavage site of OMP/TMP in the envelope gene of primate immunodeficiency viruses, Nucl Acids Res, 18: 1613--1623, 1990.
8. S.-Y. Le, J.-H. Chen, M.J. Braun, M.A. Gonda and Jacob V. Maizel: Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-1) Nucl. Acids Res., 16: 5153--5168, 1988.
Please send questions or suggestions on this page to shuyun@ncifcrf.gov
May 16, 2004