"The Sharp Lab focuses on the biology and technology of small RNAs and other types of non-coding RNAs. RNA interference (RNAi) has dramatically expanded the possibilities for genotype/phenotype analysis in cell biology and for therapeutic intervention. MicroRNAs (miRNAs) are encoded by endogenous genes and regulate primarily at the stage of translation over half of all genes in mammalian cells. The Sharp laboratory is working to identify physically the target mRNAs for particular miRNAs. His laboratory has recently discovered a new class of microRNAs that are produced from sequences adjacent to transcription start sites (TSS-miRNAs). The functions of the small RNAs are a subject of investigation. His laboratory is also investigating the relationship between gene regulation by miRNAs and angiogenesis and cellular stress. Most promoters and enhancers in mammalian cells are transcribed divergently with RNA polymerases initiating in both directions. Divergent transcription generates thousands of long non-coding RNAs. The extent of elongation by polymerase in either the sense direction or the antisense direction is controlled by recognition of the nascent RNA by U1 snRNP, a spliceosome component. The function of the divergent non-coding transcripts is being investigated as well as the relationship of RNA splicing, chromatin modifications and transcription."
Phillip A. Sharp is Institute Professor (highest academic rank) at the Massachusetts Institute of Technology and member of the Department of Biology and the Koch Institute for Integrative Cancer Research. He joined the Center for Cancer Research (now the Koch Institute) in 1974 and served as its director for six years, from 1985 to 1991, before taking over as head of the Department of Biology, a position he held for the next eight years. More recently, he was founding director of the McGovern Institute, a position he held from 2000 to 2004. His research interests have centered on the molecular biology of gene expression relevant to cancer and the mechanisms of RNA splicing. His landmark work in 1977 provided the first indications of “discontinuous genes” in mammalian cells. The discovery fundamentally changed scientists’ understanding of gene structure and earned Dr. Sharp the 1993 Nobel Prize in Physiology or Medicine. Dr. Sharp has authored over 400 papers. He is an elected member of the National Academy of Sciences, the Institute of Medicine, the American Academy of Arts and Sciences, the American Philosophical Society, and the Royal Society, UK. Among his many awards are the Gairdner Foundation International Award, the Lasker Basic Medical Research Award and the National Medal of Science. His long list of service includes the presidency of the AAAS (2013) and Chair of the Scientific Advisory Committee, SU2C Project, AACR. A native of Kentucky, Dr. Sharp earned a B.A. degree from Union College, Barbourville, KY, and a Ph.D. in chemistry from the University of Illinois, Champaign-Urbana in 1969. Dr. Sharp is a co-founder of Biogen and Alnylam Pharmaceuticals Inc.
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MicroRNAs (21-22 nt) are processed from hairpin RNAs encoded by cellular DNA and regulate gene expression primarily by inhibiting translation and promoting mRNA degradation. Some 250-350 conserved miRNA genes are encoded in the human genome (see Figure 1). siRNAs function through the miRNA-pathway and these RNAs will inhibit the translation of a reporter gene that contains multiple partially complementary target sites. We have developed methods for identifying the targets of the RNP complex containing miRNAs and we surprisingly found that mRNAs appear to be bound to components of the miRNP in the absence of miRNAs. miRNA regulation is not essential for survival, not even for some tumorigenic properties of mammalian cells. We have recently isolated a sarcoma tumor cell line that is null for dicer, devoid of miRNAs, and yet can produce a tumor in vivo. However this cell line is very sensitive to stresses.
We have recently reported that divergent transcription is common of promoter sites for genes in embryonic stem cells (see Figure 2). These promoters have an RNA polymerase initiated in the sense direction immediately downstream of the transcription start site and a second polymerase initiated in the antisense direction, about 250 base pairs upstream. The evidence for this structure is multifold. It includes the identification of small RNAs from these two regions of many promoters, detection of small RNAs by Northerns and mapping of RNA polymerase and modifications of chromatin in these regions. This research has been done in collaboration with Professor Richard Young. Surprisingly, the anti-sense polymerase is controlled by elongation processes very similar to those of sense polymerase. For example, both require P-TEFb for elongation beyond about 50 nts. The nature of factors or sequences that differentiate the effective elongation of the polymerase in the sense direction as compared to the ineffective elongation in the anti-sense direction remains to be identified.
Long non-coding RNAs (lncRNAs) have been described from analysis of deep RNA sequencing from many types of mammalian cells. Comparable RNA species have also been reported from sequencing data of yeast and Drosophila. Recent analysis of several large data sets of RNA sequences expressed in embryonic stem cells shows that a majority of long non-coding RNAs originated from initiation sites that are divergent from known protein-encoding genes or sites with chromatin marks indicating enhancer elements. Thus, synthesis of some long non-coding RNAs is probably a manifestation of general transcriptional processes. However, these lncRNAs could function in regulation of genes in cis to the site of transcription or in trans at other sites in the genome. In the latter case, the lncRNAs would probably need to be more abundant then the 1-2 copies per cells for most divergent transcripts.
Gene sequences important for accurate splicing of the nuclear precursors to mRNAs are commonly conserved during evolution. We are using computational methods to identify, by comparison of genomic sequences from multiple organisms, intron and exon sequences which are important for accurate splicing and for control of alternative RNA splicing. The cell surface protein CD44 is expressed as a variety of isoforms in tumor and activated cells but is present in a constitutive form in quiescent cells. These isoforms influence the cells’ motility, invasiveness and recognition of extracellular factors. Accordingly, shifts in the prevalence of these isoforms occur as tumor cells become more invasive such as in the epithelial to mesenchymal transition. RNA binding proteins and signaling pathways controlling alternative RNA splicing of CD44 are being investigated using high throughput sequencing methods to define transcriptomes. We are also investigating the relationship between chromatin structure and alternative RNA splicing.
Ravi, A.R.*, Gurtan A.M.*, Kumar, M.S., Chin, C., Jacks, T., and Sharp, P.A. Proliferation and tumorigenesis of a murine sarcoma cell line in the absence of DICER1. Cancer Cell 21, 848-55 (2012). *These authors contributed equally.
Leung, A.K.L., Vyas, S., Rood, J.E., Bhutkar, A., Sharp, P.A., and Chang, P. Poly(ADP-ribose) regulates stress responses and microRNA activity in the cytoplasm. Mol. Cell 42, 489-99 (2011).
Agrawal, A., Min, D.H., Singh, N., Zhu, H., Birjiniuk, A., von Maltzahn, G., Harris, T.J., Xing, D., Woolfenden, S., Sharp, P.A., Charest, A., and Bhatia, S.N. Functional delivery of siRNA in mice using dendriworms. ACS Nano 3, 2495-504 (2009).
Sharp, P.A. The Centrality of RNA (Leading Edge Essay). Cell 136, 577-580 (2009).
Kumar, M.S., Erkeland, S.J., Pester, R.E., Chen, C. Y., Ebert, M.S, Sharp, P.A., Jacks, T. Suppression of non-small cell lung tumor development by the let-7 microRNA family. Proc. Natl. Acad. Sci., USA 105, 3903-3908 (2008). PMCID: PMC2268826
Ventura, A., Young, A.G., Winslow, M.M., Lintault, L., Meissner, A., Erkeland, S.J., Newman, J., Bronson, R.T., Crowley, D., Stone, J.R., Jaenisch, R., Sharp, P.A. and Jacks, T. Targeted deletion reveals essential and overlapping functions of the miR-17~92 family of miRNA clusters. Cell 132, 875-886 (2008). PMCID: PMC2323338
Marson, A., Levine, S.S., Cole, M.F., Frampton, G.M., Brambrink, T., Johnstone, S., Guenther, M.G., Johnston, W.K., Wernig, M., Newman, J., Calabrese, M., Dennis, L.M., Volkert, T.L., Gupta, S., Love, J., Hannett, N., Sharp, P.A., Bartel, D.P., Jaenisch, R., and Young, R.A. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533 (2008). PMCID: PMC2586071
Seila, A.C., Calabrese, J.M., Levine, S.S., Yeo, G.W., Rahl, B., Young, R.A., and Sharp P.A. Divergent transcription from active promoters. Science 322, 1849-1851 (2008). NIHMSID: 94606
Sandberg, R., Neilson, J.R., Sarma, A., Sharp, P.A., and Burge, C. Widespread evasion of posttranscriptional regulation associated with proliferation. Science, 320, 1643-1647 (2008). PMCID: PMC2587246