Phillip A. Sharp

"MicroRNAs (miRNAs) are encoded by endogenous genes and regulate over half of all genes in mammalian cells. They regulate gene expression at the stages of translation and mRNA stability. Developing methods to physically identify the target mRNAs for particular miRNAs is on going. RNA interference (RNAi) has dramatically expanded the possibilities for genotype/phenotype analyses in cell biology. Investigations into the mechanisms responsible for the activities of short interfering RNAs (siRNAs) are underway with the objective of increasing their effectiveness in gene silencing. High throughput sequencing of RNA populations revealed the generation of small RNAs from divergent transcription in mammalian cells. The role of this pervasive transcription from the anti-sense strand is under investigation. It is likely that these anti-sense transcripts are unstable because, in contrast to the sense transcript, they are not adequately recognized by certain RNA splicing factors. However, some of the non-coding RNAs generated by divergent transcription are processed by splicing and polyadenylation and are sufficiently abundant to be considered long non-coding RNAs (lncRNAs). The same high throughput technology allows definition of alternatively spliced isoforms. Shifts in isoforms are common in cancer versus normal cells. Also, recent results from other labs have suggested that chromatin structure is related to control of alternative splicing. We are investigating these processes and, in particular, the relationship between elongation of transcription, RNA splicing and chromatin modifications."

Phillip A. Sharp, Institute Professor (highest academic rank) at MIT and faculty member of the Koch Institute for Integrative Cancer Research and Department of Biology, has made fundamental contributions to cancer biology and to understanding gene structure and regulation.  Sharp’s seminal discovery of ‘split genes’ in eukaryotic cells and the associated mechanism of pre-mRNA splicing resulted in numerous awards and honors, including the Nobel Prize in Physiology or Medicine (1993), the Lasker Prize (1988), the Gairdner Foundation International Award (1986) and the 2004 National Medal of Science.   In addition, he holds numerous honorary degrees from universities here and abroad and serves on many advisory boards for the government, academic institutions, scientific societies, and companies.  He is elected member of the National Academy of Sciences, the Institute of Medicine, the American Academy of Arts and Sciences, and the Royal Society of the UK.   His MIT career spans over 39 years where he served as Director of the Center for Cancer Research (now the Koch Institute), Head of the Department of Biology and, later, was Founding Director of the McGovern Institute for Brain Research.  A native of Kentucky, Dr. Sharp earned a B.A. degree from Union College, KY in 1966, and a PhD in chemistry from the University of Illinois, Champaign-Urbana in 1969.  He did his postdoctoral training at the California Institute of Technology, where he studied the molecular biology of plasmids from bacteria in Professor Norman Davidson's laboratory.   Prior to joining MIT, he was Senior Scientist at Cold Spring Harbor Laboratory.  He has published over 390 papers.  In 1978 Dr. Sharp co-founded Biogen (now Biogen Idec) and in 2002 he co-founded Alnylam Pharmaceuticals.

Further Information

Research Summary

Non-coding RNAs

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.

RNA Splicing

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.

Selected Publications

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

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