Only a small portion of the RNAs encoded in any genome are used to make proteins. My lab investigates what these noncoding RNAs (ncRNAs) do within and outside of cells, where regulators of their expression are located in the genome, and how perturbations of ncRNAs and their regulators contribute to disease.
Thomas Gingeras and colleagues study where and how functional information is stored in genomes. These efforts help explain the biological and clinical effects of disease-causing gene mutations in humans and other organisms. Gingeras is a leader of the ENCODE (ENCyclopedia of DNA Elements) and the mouseENCODE and modENCODE (model genome ENCODE) projects of the National Institutes of Health. His research has altered our understanding of the traditional boundaries of genes, revealing that almost the entire lengths of genomes in organisms ranging from bacteria to humans can be transcribed into RNA (pervasive transcription) and that most RNA products made by a cell are not destined to be translated into proteins (noncoding, or ncRNAs). In fact, ncRNAs are proving to be involved in a variety of other important biological functions. Some have been shown to be critical components in the pre- and posttranscriptional and translational processes, as scaffolds upon which large protein complexes are assembled and as extracellular signals. The initial studies that led to these observations have been extended to cover the entire human genome.
Redefining biologists, redefining genes
May 16, 2017
Base Pairs podcast Set aside your notions of how biologists are born, or what the word “gene” means as you listen to our first chat episode. We talk with Assistant Professor Molly Hammell, a genome biologist who started out as an astrophysicist. She tells us what it’s like to peer deep into space using a...
Dark matter of the genome, part 2
April 15, 2017
Base Pairs podcast Did you know? If unwound and tied together, the strands of DNA in one cell would stretch past the entire length of you body (~ 6 ft). Now imagine that among all that, only enough genetic information to run the length of your thumb-nail is of any importance! Soon after the Human...
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Results are part of a comprehensive view of the mouse genome that emerges from the Mouse ENCODE project Cold Spring Harbor, NY – An international team of researchers led by Professor Thomas R. Gingeras of Cold Spring Harbor Laboratory (CSHL) and Roderic Guigo, of the Centre For Genomic Regulation, Barcelona, have identified some 6600 genes...
Scientists looking across human, fly and worm genomes find shared biology
September 8, 2014
Washington, DC and Cold Spring Harbor, NY – Researchers analyzing human, fly, and worm genomes have found that these species have a number of key genomic processes in common, reflecting their shared ancestry. The findings, appearing in the journal Nature, offer fresh insights into embryonic development, gene regulation and other biological processes vital to understanding...
In massive genome analysis ENCODE data suggests ‘gene’ redefinition
August 31, 2012
Cold Spring Harbor, NY — Most people understand genes to bespecific segments of DNA that determine traits or diseases that are inherited. Textbooks suggest that genes are copied (“transcribed”) into RNA molecules, which are then used as templates for making protein—the highly diverse set of molecules that act as building blocks and engines of our...
Podcast: CSHL Prof. Thomas Gingeras on new findings about the fly genome and why they are important
December 23, 2010
CSHL Professor Thomas Gingeras, Ph.D., is a widely recognized genome investigator and developer of pioneering technologies used to probe it, including DNA microarrays. He is a co-principal investigator of ENCODE, The Encyclopedia of DNA Elements, a project launched by the National Genome Research Institute. Its aim: to compile a comprehensive list of functional elements across...
2010 highlights of CSHL awards and honors
December 17, 2010
A runner-up for Science’s “Breakthrough of the Year for 2010 was a Publication of the full nuclear genome of Neandertal December 17, 2010 A runner-up for Science’s “Breakthrough of the Year” for 2010 was publication of the full nuclear genome of Neandertal, based on highly corrupted samples nearly 40,000 years old. The feat was made...
CSHL scientists find a new class of small RNAs and define its function
January 27, 2009
Small, stable RNAs clipped from mature protein-coding RNAs can regulate gene expression Cold Spring Harbor, NY — Researchers at Cold Spring Harbor Laboratory (CSHL) announced today the discovery of a new class of small RNAs. At the same time, they reported that their discovery suggests the presence of a strikingly novel biochemical pathway for RNA...
Batut, P. J. and Gingeras, T. R. (2017) Conserved noncoding transcription and core promoter regulatory code in early Drosophila development. Elife, 6
Lagarde, J. and Uszczynska-Ratajczak, B. and Carbonell, S. and Perez-Lluch, S. and Abad, A. and Davis, C. and Gingeras, T. R. and Frankish, A. and Harrow, J. and Guigo, R. and Johnson, R. (2017) High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing. Nat Genet, 49(12) pp. 1731-1740.
Breschi, A. and Gingeras, T. R. and Guigo, R. (2017) Comparative transcriptomics in human and mouse. Nat Rev Genet, 18(7) pp. 425-440.
Dobin, A. and Davis, C. A. and Schlesinger, F. and Drenkow, J. and Zaleski, C. and Jha, S. and Batut, P. and Chaisson, M. and Gingeras, T. R. (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1) pp. 15-21.
Djebali, S. and Davis, C. A. and Merkel, A. and Dobin, A. and Lassmann, T. and Mortazavi, A. and Tanzer, A. and Lagarde, J. and Lin, W. and Schlesinger, F. and Xue, C. and Marinov, G. K. and Khatun, J. and Williams, B. A. and Zaleski, C. and Rozowsky, J. and Röder, M. and Kokocinski, F. and Abdelhamid, R. F. and Alioto, T. and Antoshechkin, I. and Baer, M. T. and Bar, N. S. and Batut, P. and Bell, K. and Bell, I. and Chakrabortty, S. and Chen, X. and Chrast, J. and Curado, J. and Derrien, T. and Drenkow, J. and Dumais, E. and Dumais, J. and Duttagupta, R. and Falconnet, E. and Fastuca, M. and Fejes-Toth, K. and Ferreira, P. and Foissac, S. and Fullwood, M. J. and Gao, H. and Gonzalez, D. and Gordon, A. and Gunawardena, H. and Howald, C. and Jha, S. and Johnson, R. and Kapranov, P. and King, B. and Kingswood, C. and Luo, O. J. and Park, E. and Persaud, K. and Preall, J. B. and Ribeca, P. and Risk, B. and Robyr, D. and Sammeth, M. and Schaffer, L. and See, L. H. and Shahab, A. and Skancke, J. and Suzuki, A. M. and Takahashi, H. and Tilgner, H. and Trout, D. and Walters, N. and Wang, H. and Wrobel, J. and Yu, Y. and Ruan, X. and Hayashizaki, Y. and Harrow, J. and Gerstein, M. and Hubbard, T. and Reymond, A. and Antonarakis, S. E. and Hannon, G. and Giddings, M. C. and Ruan, Y. and Wold, B. and Carninci, P. and Guig, R. and Gingeras, T. R. (2012) Landscape of transcription in human cells. Nature, 489(7414) pp. 101-108.
Dunham, I. and Kundaje, A. and Aldred, S. F. and Collins, P. J. and Davis, C. and Doyle, F. and Epstein, C. B. and Frietze, S. and Harrow, J. and Kaul, R. and Khatun, J. and Lajoie, B. R. and Landt, S. G. and Lee, B. K. and Pauli, F. and Rosenbloom, K. R. and Sabo, P. and Safi, A. and Sanyal, A. and Shoresh, N. and Simon, J. M. and Song, L. and Trinklein, N. D. and Altshuler, R. C. and Birney, E. and Brown, J. B. and Cheng, C. and Djebali, S. and Dong, X. J. and Ernst, J. and Furey, T. S. and Gerstein, M. and Giardine, B. and Greven, M. and Hardison, R. C. and Harris, R. S. and Herrero, J. and Hoffman, M. M. and Iyer, S. and Kellis, M. and Kheradpour, P. and Lassmann, T. and Li, Q. H. and Lin, X. and Marinov, G. K. and Merkel, A. and Mortazavi, A. and Parker, S. C. J. and Reddy, T. E. and Rozowsky, J. and Schlesinger, F. and Thurman, R. E. and Wang, J. and Ward, L. D. and Whitfield, T. W. and Wilder, S. P. and Wu, W. and Xi, H. L. S. and Yip, K. Y. and Zhuang, J. L. and Bernstein, B. E. and Green, E. D. and Gunter, C. and Snyder, M. and Pazin, M. J. and Lowdon, R. F. and Dillon, L. A. L. and Adams, L. B. and Kelly, C. J. and Zhang, J. and Wexler, J. R. and Good, P. J. and Feingold, E. A. and Crawford, G. E. and Dekker, J. and Elnitski, L. and Farnham, P. J. and Giddings, M. C. and Gingeras, T. R. and Guigo, R. and Hubbard, T. J. and Kent, W. J. and Lieb, J. D. and Margulies, E. H. and Myers, R. M. and Stamatoyannopoulos, J. A. and Tenenbaum, S. A. and Weng, Z. P. and White, K. P. and Wold, B. and Yu, Y. and Wrobel, J. and Risk, B. A. and Gunawardena, H. P. and Kuiper, H. C. and Maier, C. W. and Xie, L. and Chen, X. and Mikkelsen, T. S. and Gillespie, S. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414) pp. 57-74.
Additional materials of the author atCSHL Institutional Repository