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. This is particularly important in cancer. Our laboratory works on endometrial cancer and its relationship to age and obesity.
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. The initial studies that led to these observations have been extended to cover the entire human genome. The maps of where and what types of RNA are transcribed serves as a foundation by many areas of disease diagnosis and treatment. In particular non-protein coding (nc)RNAs are responsible for the expression of the regulatory gene, PTEN. In endometrial cancer dysregulation of PTEN via overexpression of a lncRNA (HOTAIR) binding to PTEN. Such overexpression of HOTAIR occurs in obese individuals due to dysregulation of adipogenesis and lipid metabolism leading to endometrial cancer.
ENCODE3: Interpreting the human and mouse genomes
July 29, 2020
Researchers report on 900,000 regulatory elements in our genomes that could influence our health.
CSHL investigators rank among world’s most highly cited
December 11, 2019
Seven researchers affiliated with CSHL are among the scientists producing the top 1 percent of the most highly-cited research in the world.
Base Pairs Episode 9.5: Redefining biologists, redefining genes
May 16, 2017
We talk with Molly Hammell about peering into deep space using a high-tech telescope, we also talk to Tom Gingeras about redefining the gene.
Redefining biologists, redefining genes
May 16, 2017
Drs. Molly Hammell and Thomas Gingeras talk about redefining what a biologist is and what genes are.
Base Pairs Episode 9: Dark matter of the genome, part 2
April 15, 2017
In this episode of Base Pairs, we question the mythos that is “junk DNA” and explore the mysterious non-coding portions of the genome.
Dark matter of the genome, part 2
April 15, 2017
This episode of Base Pairs deals with the myth of "junk DNA" and why scientists are interested in non-coding portions of the genome.
Variation in expression of thousands of genes is kept under tight constraint in mice and humans, in all cells and tissues
November 19, 2014
Researchers have identified some 6600 genes whose level of expression varies within a comparatively restricted range in humans and mice
Scientists looking across human, fly and worm genomes find shared biology
September 8, 2014
Researchers found that human, fly, and worm genomes have a number of key genomic processes in common, reflecting their shared ancestry.
In massive genome analysis ENCODE data suggests ‘gene’ redefinition
August 31, 2012
Potentially far-ranging implications for complex disease.
Podcast: CSHL Prof. Thomas Gingeras on new findings about the fly genome and why they are important
December 23, 2010
New findings about the fly genome and why they are important
3 Jan 2023 | Nature Reviews Molecular Cell Biology
Mattick, John, Amaral, Paulo, Carninci, Piero, Carpenter, Susan, Chang, Howard, Chen, Ling-Ling, Chen, Runsheng, Dean, Caroline, Dinger, Marcel, Fitzgerald, Katherine, Gingeras, Thomas, Guttman, Mitchell, Hirose, Tetsuro, Huarte, Maite, Johnson, Rory, Kanduri, Chandrasekhar, Kapranov, Philipp, Lawrence, Jeanne, Lee, Jeannie, Mendell, Joshua, Mercer, Timothy, Moore, Kathryn, Nakagawa, Shinichi, Rinn, John, Spector, David, Ulitsky, Igor, Wan, Yue, Wilusz, Jeremy, Wu, Mian
May 2022 | Nature | 605(7909):E3
ENCODE Project Consortium, Moore, Jill, Purcaro, Michael, Pratt, Henry, Epstein, Charles, Shoresh, Noam, Adrian, Jessika, Kawli, Trupti, Davis, Carrie, Dobin, Alexander, Kaul, Rajinder, Halow, Jessica, Van Nostrand, Eric, Freese, Peter, Gorkin, David, Shen, Yin, He, Yupeng, Mackiewicz, Mark, Pauli-Behn, Florencia, Williams, Brian, Mortazavi, Ali, Keller, Cheryl, Zhang, Xiao-Ou, Elhajjajy, Shaimae, Huey, Jack, Dickel, Diane, Snetkova, Valentina, Wei, Xintao, Wang, Xiaofeng, Rivera-Mulia, Juan, Rozowsky, Joel, Zhang, Jing, Chhetri, Surya, Zhang, Jialing, Victorsen, Alec, White, Kevin, Visel, Axel, Yeo, Gene, Burge, Christopher, Lécuyer, Eric, Gilbert, David, Dekker, Job, Rinn, John, Mendenhall, Eric, Ecker, Joseph, Kellis, Manolis, Klein, Robert, Noble, William, Kundaje, Anshul, Guigó, Roderic, Farnham, Peggy, Cherry, J, Myers, Richard, Ren, Bing, Graveley, Brenton, Gerstein, Mark, Pennacchio, Len, Snyder, Michael, Bernstein, Bradley, Wold, Barbara, Hardison, Ross, Gingeras, Thomas, Stamatoyannopoulos, John, Weng, Zhiping
May 2022 | Nature | 605(7909):E4
ENCODE Project Consortium, Snyder, Michael, Gingeras, Thomas, Moore, Jill, Weng, Zhiping, Gerstein, Mark, Ren, Bing, Hardison, Ross, Stamatoyannopoulos, John, Graveley, Brenton, Feingold, Elise, Pazin, Michael, Pagan, Michael, Gilchrist, Daniel, Hitz, Benjamin, Cherry, J, Bernstein, Bradley, Mendenhall, Eric, Zerbino, Daniel, Frankish, Adam, Flicek, Paul, Myers, Richard
3 Dec 2021 | Science | 374(6572):1247-1252
Ortiz-Ramírez, Carlos, Guillotin, Bruno, Xu, Xiaosa, Rahni, Ramin, Zhang, Sanqiang, Yan, Zhe, Coqueiro Dias Araujo, Poliana, Demesa-Arevalo, Edgar, Lee, Laura, Van Eck, Joyce, Gingeras, Thomas, Jackson, David, Gallagher, Kimberly, Birnbaum, Kenneth
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
2 Jun 2021 | Nature Communications | 12(1)
Grapotte, M, Saraswat, M, Bessière, C, Menichelli, C, Ramilowski, J, Severin, J, Hayashizaki, Y, Itoh, M, Tagami, M, Murata, M, Kojima-Ishiyama, M, Noma, S, Noguchi, S, Kasukawa, T, Hasegawa, A, Suzuki, H, Nishiyori-Sueki, H, Frith, M, Abugessaisa, I, Aitken, S, Aken, B, Alam, I, Alam, T, Alasiri, R, Alhendi, A, Alinejad-Rokny, H, Alvarez, M, Andersson, R, Arakawa, T, Araki, M, Arbel, T, Archer, J, Archibald, A, Arner, E, Arner, P, Asai, K, Ashoor, H, Astrom, G, Babina, M, Baillie, J, Bajic, V, Bajpai, A, Baker, S, Baldarelli, R, Balic, A, Bansal, M, Batagov, A, Batzoglou, S, Beckhouse, A, Beltrami, A, Beltrami, C, Bertin, N, Bhattacharya, S, Bickel, P, Blake, J, Blanchette, M, Bodega, B, Bonetti, A, Bono, H, Bornholdt, J, Bttcher, M, Bougouffa, S, Boyd, M, Breda, J, Brombacher, F, Brown, J, Bult, C, Burroughs, A, Burt, D, Busch, A, Caglio, G, Califano, A, Cameron, C, Cannistraci, C, Carbone, A, Carlisle, A, Carninci, P, Carter, K, Cesselli, D, Chang, J, Chen, J, Chen, Y, Chierici, M, Christodoulou, J, Ciani, Y, Clark, E, Coskun, M, Dalby, M, Dalla, E, Daub, C, Davis, C, de Hoon, M, de Rie, D, Denisenko, E, Deplancke, B, Detmar, M, Deviatiiarov, R, Di Bernardo, D, Diehl, A, Dieterich, L
26 Apr 2021 | bioRxiv
Rozowsky, Joel, Drenkow, Jorg, Yang, Yucheng, Gursoy, Gamze, Galeev, Timur, Borsari, Beatrice, Epstein, Charles, Xiong, Kun, Xu, Jinrui, Gao, Jiahao, Yu, Keyang, Berthel, Ana, Chen, Zhanlin, Navarro, Fabio, Liu, Jason, Sun, Maxwell, Wright, James, Chang, Justin, Cameron, Christopher, Shoresh, Noam, Gaskell, Elizabeth, Adrian, Jessika, Aganezov, Sergey, Balderrama-Gutierrez, Gabriela, Banskota, Samridhi, Corona, Guillermo, Chee, Sora, Chhetri, Surya, Martins, Gabriel, Danyko, Cassidy, Davis, Carrie, Farid, Daniel, Farrell, Nina, Gabdank, Idan, Gofin, Yoel, Gorkin, David, Gu, Mengting, Hecht, Vivian, Hitz, Benjamin, Issner, Robbyn, Kirsche, Melanie, Kong, Xiangmeng, Lam, Bonita, Li, Shantao, Li, Bian, Li, Tianxiao, Li, Xiqi, Lin, Khine, Luo, Ruibang, Mackiewicz, Mark, Moore, Jill, Mudge, Jonathan, Nelson, Nicholas, Nusbaum, Chad, Popov, Ioann, Pratt, Henry, Qiu, Yunjiang, Ramakrishnan, Srividya, Raymond, Joe, Salichos, Leonidas, Scavelli, Alexandra, Schreiber, Jacob, Sedlazeck, Fritz, See, Lei, Sherman, Rachel, Shi, Xu, Shi, Minyi, Sloan, Cricket, Strattan, Seth, Tan, Zhen, Tanaka, Forrest, Vlasova, Anna, Wang, Jun, Werner, Jonathan, Williams, Brian, Xu, Min, Yan, Chengfei, Yu, Lu, Zaleski, Christopher, Zhang, Jing, Cherry, Michael, Mendenhall, Eric, Noble, William, Weng, Zhiping, Levine, Morgan, Dobin, Alexander, Wold, Barbara, Mortazavi, Ali, Ren, Bing, Gillis, Jesse, Myers, Richard, Snyder, Michael, Choudhary, Jyoti, Milosavljevic, Aleksandar, Schatz, Michael, Guigo, Roderic, Bernstein, Bradley, Gingeras, Thomas, Gerstein, Mark
Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain.
23 Mar 2021 | Scientific Reports | 11(1):6078
Dachet, Fabien, Brown, James, Valyi-Nagy, Tibor, Narayan, Kunwar, Serafini, Anna, Boley, Nathan, Gingeras, Thomas, Celniker, Susan, Mohapatra, Gayatry, Loeb, Jeffrey
Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery
30 Dec 2020 | Developmental Cell | S1534-(20):31021-31022
Xu, X, Crow, M, Rice, B, Li, F, Harris, B, Liu, L, Demesa-Arevalo, E, Lu, Z, Wang, L, Fox, N, Wang, X, Drenkow, J, Luo, A, Char, S, Yang, B, Sylvester, A, Gingeras, T, Schmitz, R, Ware, D, Lipka, A, Gillis, J, Jackson, D
Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment
20 Aug 2020 | Nucleic Acids Research | 48(14):8035-8049
Nechooshtan, G, Yunusov, D, Chang, K, Gingeras, T
Jul 2020 | Nature | 583(7818):699-710
Moore, J, Purcaro, M, Pratt, H, Epstein, C, Shoresh, N, Adrian, J, Kawli, T, Davis, C, Dobin, A, Kaul, R, Halow, J, Van Nostrand, E, Freese, P, Gorkin, D, Shen, Y, He, Y, Mackiewicz, M, Pauli-Behn, F, Williams, B, Mortazavi, A, Keller, C, Zhang, X, Elhajjajy, S, Huey, J, Dickel, D, Snetkova, V, Wei, X, Wang, X, Rivera-Mulia, J, Rozowsky, J, Zhang, J, Chhetri, S, Zhang, J, Victorsen, A, White, K, Visel, A, Yeo, G, Burge, C, Lécuyer, E, Gilbert, D, Dekker, J, Rinn, J, Mendenhall, E, Ecker, J, Kellis, M, Klein, R, Noble, W, Kundaje, A, Guigó, R, Farnham, P, Cherry, J, Myers, R, Ren, B, Graveley, B, Gerstein, M, Pennacchio, L, Snyder, M, Bernstein, B, Wold, B, Hardison, R, Gingeras, T, Stamatoyannopoulos, J, Weng, Z