Cold Spring Harbor Laboratory  
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Ph.D., New York University, 1976

Genome-wide organization of transcription and the functional roles of non-protein coding RNAs

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The RNA repertoire found in each cell is composed of short RNAs and long polyadenylated and non-polyadenylated transcripts. RNA profiles are highly cell type specific and compartmentalized into sub-cellular compartments. Genic and intergenic regions are characterized by overlapping transcription by which the same sequences can be encoded in both protein coding and non-coding transcripts. Characterization of the transcriptomes from many species of organisms in our laboratory has revealed several common features. These include: (1) the copy number of most coding transcripts out number non-coding RNAs but the sequence complexity of non-coding transcripts is greater (2)  non-polyadenylated antisense and intergenic transcripts are most prevalent in the nucleus and are a growing class of regulatory molecules encoded by a genome,  (3) the fate of most transcripts is to be processed into capped and uncapped short RNAs, (4) recapping of 5' ends of cleavage derived long and short RNAs is common, (5) inter-cellular communication is achieved by selectively recruiting specific short RNAs into micro-vesicles, released and taken up by neighboring cells  (6) the intergenic regions of genomes are shrinking resulting in the merging of genic boundaries , (7) the merging of genic regions prompts a reconsideration of the definition of a gene. How information encoded in genomes is organized and regulated is essential in understanding the perturbations underlying the causes of all complex diseases.


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Selected Publications

Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29: 15–21.

The ENCODE Consortium Project 2012. An integrated Encyclopedia of DNA Elements in the Human Genome. Nature 489: 57-74.

Djebali, S.*, Davis, C.A. *, Merkel, A., Dobin, A., Lassmann, T., Mortazavi5, A. M., Tanzer, A., Lagarde, J.,  Lin, W., Schlesinger,F.,  Xue, C.,  Marinov, G. K., Khatun, J.,. Williams, B. A., Zaleski, C.,  Rozowsky, J.,  Röder, M., Kokocinski, F.,  Abdelhamid, R. F., Alioto, T., Antoshechkin, I., Baer, M. T., Bar, N. S., Batut, P. Bell, K., Bell, I., Chakrabortty, S., Chen, X., Chrast, J., Curado, J., Derrien, T., Drenkow, J., Dumais, E., Dumais, J., Duttagupta, R., Falconnet, E., Fastuca, M., Fejes-Toth, K., Ferreira, P.,  Foissac, S., Fullwood, M. J., Gao, H., Gonzalez, D., Gordon, A., Gunawardena, H., Howald, C., Jha, S., Johnson, R., Kapranov, P., King, B., Kingswood, C., Luo, O. C., Park, E., Persaud, K., Preall, J. B., Ribeca, P., Risk, B.,  Robyr, D., Sammeth, M.,  Schaffer, L., See, L.-H., Shahab, A., Skancke, J.,  Suzuki, A. M., Takahashi, H., Tilgner, H., Trout, D., Walters,N.,  Wang, H., Wrobel, J.,  Yu, Y., Ruan, X., Hayashizaki, Y., Harrow, J.,  Gerstein, M., Hubbard, T., Reymond, A., Antonarakis, S.E., Hannon, G., Giddings, M .C., Ruan, Y., Wold, B., Carninci, P., Guigó, R., Gingeras, T. R. (2012) Landscape of Transcription in Human Cells. Nature 489: 101-108.

Li, G., Ruan, X.,Auerbach, R. K., Sandhu, S. K., Wang, P.,  Me, H., Poh, M., Zheng, M., Goh, Y., Lim. J., Zhang, J.,Sim, H. S. Peh, S. Q., Mulawadi, F. H., Ong, C. T., Orlov, Y., Hong, S.,  Zhang, Z., Landt, S., Raha, D., Euskirchen, G.,Wei C-L., Ge, W., Wang, H., Davis, C., Fisher K., Mortazavi, A., Gerstein, M., Gingeras, T., Wold, B., Sun, Y.,Fullwood, M. J., Cheung, E., Liu, E., Sung, W.-K., Snyder, M., Ruan, Y. 2012. Extensive promoter-centered chromatin interactions provide topological basis to enhance transcription regulation. Cell 148: 84-98.

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., Ruiz de los Mozos, I., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penadés, Valle, J. R., Solano, C., Gingeras, T. R. 2011. Genome-wide antisense transcription regulates mRNA processing in bacteria.  PNAS USA 108: 20172-20177.