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Thomas Gingeras

Thomas Gingeras

Professor
Cancer Center Member

Ph.D., New York University, 1976

gingeras@cshl.edu | 516-422-4105

Faculty Profile

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.

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All Publications

Long non-coding RNAs: definitions, functions, challenges and recommendations

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

Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes.

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

Author Correction: Perspectives on ENCODE.

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

Ground tissue circuitry regulates organ complexity in maize and Setaria

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

Multi-tissue integrative analysis of personal epigenomes

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

Expanded encyclopaedias of DNA elements in the human and mouse genomes

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

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