Selected Peer-reviewed Publications (selected from 300)

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates
Guo, Y.E., Manteiga, J.C., Henninger, J.E., Sabari, B.R., Dall'Agnese, A., Hannett, N.M., Spille, J., Afeyan, L.K., Zamudio, A.V., Shrinivas, K., Abraham, B.J., Boija, A., Decker, T., Rimel, J.K., Fant, C.B., Lee, T.I., Cisse, I.I., Sharp, P.A., Taatjes, D.J., Young, R.A. Nature 7 August 2019.


Enhancer Features that Drive Formation of Transcriptional Condensates
Shrinivas, K., Sabari, B.R., Coffey, E.L., Klein, I.A., Boija, A., Zamudio, A.V., Schuijers, J., Hannett, N.M., Sharp, P.A., Young, R.A., Chakraborty, A.K. Molecular Cell 8 August 2019.


Transcription Factors Activate Genes through Phase-Separation Capacity of their Activation Domains
Boija, A., Klein, I.A., Sabari, B., Dall'Agnese, A., Coffey, E.L., Zamudio, A.V., Li, C.H., Shrinivas, K., Manteiga, J.C., Hannett, N.M., Abraham, B.J., Afeyan, L.K., Guo, Y.E., Rimel, J.K., Fant, C.B., Schuijers, J., Lee, T.I., Taatjes, D.J., Young, R.A. Cell ePub 13 December 2018.


Coactivator condensation at super-enhancers links phase separation and gene control
Sabari, B.R., Dall'Agnese, A., Boija, A., Klein, I.A., Coffey, E.L., Shrinivas, K., Abraham, B.J., Hannett, N.M., Zamudio, A.V., Manteiga, J.C., Li, C.H., Guo, Y.E., Day, D.S., Schuijers, J., Vasile, E., Malik, S., Hnisz, D., Lee, T.I., Cisse, I.I., Roeder, R.G., Sharp, P.A., Chakraborty, A.K., Young, R.A. Science ePub 21 June 2018.


YY1 Is a Structural Regulator of Enhancer-Promoter Loops
Weintraub, A.S., Li, C.H., Zamudio, A.V., Sigova, A.A., Hannett, N.M., Day, D.S., Abraham, B.J., Cohen, M.A., Nabet, B., Buckley, D.L., Guo, Y.E., Hnisz, D., Jaenisch, R., Bradner, J.E., Gray, N.S., Young, R.A. Cell Vol. 171, Issue 7, p1573-1588 (2017).


A Phase Separation Model for Transcriptional Control
Hnisz, D., Shrinivas, K., Young, R.A., Chakraborty, A.K., Sharp, P.A. Cell Vol. 169, Issue 1, p13-23 (2017).


Transcriptional Addiction in Cancer
Bradner, J.E., Hnisz, D., Young, R.A. Cell Vol. 168, Issue 4, p629-643 (2017).


Small genomic insertions form enhancers that misregulate oncogenes
Abraham, B.J., Hnisz, D., Weintraub, A.S., Kwiatkowski, N., Li, C.H., Li, Z., Weicher-Leahey, N., Rahman, S., Liu, Y., Etchin, J., Li, B., Shen, S., Lee, T.I., Zhang, J., Look, T.A., Mansour, M.R., Young, R.A. Nature Communications 8:14385 (2017).


Insulated Neighborhoods: Structural and Functional Units of Mammalian Gene Control
Hnisz, D., Day, D.S., Young, R.A. Cell Vol. 167, Issue 5, p1188-1200 (2016).


Activation of proto-oncogenes by disruption of chromosome neighborhoods
Hnisz, D., Weintraub, A.S., Day, D.S., Valton, A.L., Bak, R.O., Li, C.H., Goldmann, J., Lajoie, B.R., Fan, Z.P., Sigova, A.A., Reddy, J., Borges-Rivera D., Lee, T.I., Jaenisch, R., Porteus, M.H., Dekkar, J., Young, R.A. Science Epub March 3 (2016)


3D Chromosome Regulatory Landscape of Human Pluripotent Cells
Ji, X., Dadon, D.B. Powell, B.E.,Fan, Z.P, Borges-Rivera, D., Shachar, S., Weintraub, A.S., Hnisz, D., Pegoraro, G., Lee, T.I., Misteli, T., Jaenisch, R., Young, R.A. Cell Stem Cell Vol. 18, Issue 2, p262-275, (2016)


Transcription factor trapping by RNA in gene regulatory elements
Sigova, A.A., Abraham, B.J., Ji, X., Molinie, B., Hannett, N.M., Guo, Y.E., Jangi, M., Giallourakis, C.C., Sharp, P.A., Young, R.A. Science Epub October 29 (2015)


CDK7-Dependent Transcriptional Addiction in Triple-Negative Breast Cancer
Wang, Y., Zhang, T., Kwiatkowski, N., Abraham, B.J., Lee, T.I., Xie, S., Yuzugullu, H., Von, T., Li, H., Lin, Z., Stover, D.G., Lim, E., Wang, Z.C., Iglehart, J.D., Young, R.A., Gray, N.S., Zhao, J.J. Cell Vol. 163, Issue 1, p174-186 (2015).


Convergence of Developmental and Oncogenic Signaling Pathways at Transcriptional Super-Enhancers
Hnisz, D., Schuijers, J., Lin, C.Y., Weintraub, A.S., Abraham, B.J., Lee, T.I., Bradner, J.E., and Young, R.A. Molecular Cell Epub March 19 (2015).


An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element
Mansour, M.R., Abraham, B.J., Anders, L., Berezovskaya, A., Gutierrez, A., Durbin, A.D., Etchin, J., Lawton, L., Sallan, S.E., Silverman, L.B., Loh, M.L., Hunger, S.P., Sanda, T., Young, R.A. and Look, A.T. Science Epub Nov 13 (2014).


Control of Cell Identity Genes Occurs in Insulated Neighborhoods in Mammalian Chromosomes
Dowen, J.M., Fan, Z.P., Hnisz, D., Ren, G., Abraham, B.J., Zhang, L.N., Weintraub, A.S., Schuijers, J., Lee, T.I., Zhao, K., Young, R.A. Cell Vol. 159, Issue 2, p374-387 (2014).


Targeting transcription regulation in cancer with a covalent CDK7 inhibitor
Kwiatkowski, N., Zhang, T., Rahl, P.B., Abraham, B.J., Reddy, J., Ficarro, S.B., Dastur, A., Amzallag, A., Ramaswamy, S., Tesar, B., Jenkins, C.E., Hannett, N.M., McMillin, D., Sanda, T., Sim, T., Kim, N.D., Look, T., Mitsiades, C.S., Weng, A.P., Brown, J.R., Benes, C.H., Marto, J.A., Young, R.A., and Gray, N.S. Nature 511: 616-620 (2014).


Genome-wide localization of small molecules
Anders, L., Guenther, M.G., Jun, Q., Fan, Z.P., Marineau, J.J, Rahl, P.B., Lovén,J., Sigova,A.A., Smith,W.B., Lee,T.I, Bradner,J.E., and Young, R.A. Nature Biotechnology 32: 92-96 (2014).


Super-Enhancers in the Control of Cell Identity and Disease
Hnisz, D., Abraham, B.J., Lee, T.I., Lau, A., Saint-André, V., Sigova, A.A., Hoke, H.A., and Young, R.A. Cell 155: 937-937 (2013).


Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes
Whyte, W.A., Orlando, D.A., Hnisz, D, Abraham, B.J., Lin, C.Y., Kagey, M.H., Rahl, P.B., Lee,T.I., and Young, R.A. Cell 153: 307-319 (2013).


Selective Inhibition of Tumor Oncogenes by Disruption of Super-enhancers
Lovén, J., Hoke, H.A., Lin, C.Y., Lau, A., Orlando, D.A., Vakoc, C.R., Bradner, J.E., Lee, T.I., and Young, R.A. Cell 153, 320-334 (2013).


Transcriptional Regulation and Its Misregulation in Disease
Lee, T.I., and Young, R.A. Cell 152, 1237-1251 (2013).


Revisiting Global Gene Expression Analysis
Lovén, J., Orlando, D.A., Sigova, A.A., Lin, C.Y., Rahl, P.B., Burge, C.B., Levens, D.L., Lee, T.I., and Young, R.A. Cell 151: 476-482 (2012).


Transcriptional Amplification in Tumor Cells with Elevated c-Myc
Lin, C.Y., Lovén, J., Rahl, P.B., Paranal, R.M., Burge, C.B., Bradner, J.E., Lee, T.I., and Young, R.A. Cell 151: 56-67 (2012).


Enhancer decommissioning by LSD1 during embryonic stem cell differentiation
Whyte, W.A., Bilodeau, S., Orlando,D.A., Hoke, H.A., Frampton, G.M., Foster, C.T., Cowley, S.M., and Young, R.A. Nature 482: 221-225 (2012).


Master transcription factors determine the gene targets of the TGF-B pathway.
Mullen, A.C., Orlando,D.A., Newman, J.J., Lovén, J., Kumar, R.M., Bilodeau, S., Guenther, M.G., DeKoter, R., and Young, R.A. Cell 147: 565-576 (2011).


Control of the Embryonic Stem Cell State
Young, R.A. Cell 144: 940-954 (2011).


Repressive transcription
Guenther, M.G. and Young, R.A. Science 329: 150-151 (2010).


Mediator and cohesin connect gene expression and chromatin architecture
Kagey, M.H., Newman, J.J., Bilodeau S., Zhan, Y., Orlando, D.A., van Berkum, N.L., Ebmeier, C.C., Goossens, J., Rahl, P.B., Levine, S.S., Taatjes, D.J., Dekker, J., and Young, R.A. Nature (2010).


Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells
Guenther, M.G., Frampton, G.M., Soldner, F., Hockemeyer, D., M, M., Jaenisch, R., and Young, R.A. Cell Stem Cell 7: 249–257 (2010).


c-Myc Regulates Transcriptional Pause Release
Rahl, P.B., Lin, C.Y., Seila, A.C., Flynn, R.A., McCuine, S., Burge, C.B., Sharp, P.A., and Young, R.A. Cell 141: 432–445 (2010).


SetDB1 Contributes to Repression of Genes Encoding Developmental Regulators and Maintenance of ES Cell State
Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B., and Young, R.A. Genes & Development 23: 2484-2489 (2009).


Divergent Transcription from Active Promoters
Seila, A.C., Calabrese, J.M., Levine, S.S., Yeo, G.W., Rahl, P.B., Flynn, R.A., Young, R.A. and Sharp, P.A. Science 322: 1849-1851 (2008).


Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells
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, J.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. Cell 134: 521-533 (2008).


Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming
Jaenisch, R. and Young, R.A. Cell 132: 567-582 (2008).


Tcf3 is an Integral Component of the Core Regulatory Circuitry of Embryonic Stem Cells
Cole, M.F., Johnstone, S. E., Newman, J.J., Kagey, M.H. and Young, R.A. Genes & Development 22: 746-755 (2008).


RNA Polymerase Stalling at Developmental Control Genes in the Drosophila Embryo
Zeitlinger, J., Stark, A., Kellis, M., Hong, J.-W., Nechaev, S., Adelman, K., Levine, M. and Young, R.A. Nature Genetics 39: 1512-1516 (2007).


Foxp3 Occupancy and Regulation of Key Target Genes during T-cell Stimulation
Marson, A., Kretschmer, K., Frampton, G.M., Jacobsen, E.S., Polansky, J. MacIsaac, K.D., Levine, S.S., Fraenkel, E., von Boehmer, H., Young, R.A. Nature 445: 931-935 (2007).


A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M., Levine, S.S., Boyer, L.A., Jaenisch, R. and Young, R.A. Cell 130: 77-88 (2007).


Activated Signal Transduction Kinases Frequently Occupy Target Genes
Pokholok, D.K., Zeitlinger, J., Hannett, N., Reynolds, D., and Young, R.A. Science 313: 533-536 (2006).


Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T.I., Jenner, R.G., Boyer, L.A., Guenther, M.G., Chevalier, B., Levine, S.S., Kumar, R.M., Johnstone, S.E., Murray, H.L., Zucker, J.P., Yuan, B., Bell, G.W., Herbolsheimer, E., Hannett, N.M., Cole, M.F., Sun, K., Odom, D.T., Volkert, T.L., Bartel, D.P., Gifford, D.K., Melton, D.A., Jaenisch, R. and Young, R.A. Cell 125: 301-313 (2006).


Polycomb Complexes Repress Developmental Regulators in Murine Embryonic Stem Cells
Boyer, L.A., Plath, K., Zeitlinger, J., Brambrink, T., Medeiros, L.A., Lee, T.I., Levine, S.S., Wernig, M., Tajonar, A., Ray, M.K., Otte, A.P., Vidal, M., Gifford, D.K., Young, R.A. and Jaenisch, R. Nature 441: 349-353 (2006).


Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast
Pokholok, D.K., Harbison, C.T., Levine, S., Cole, M., Hannett, N.M., Lee, T.I., Walker, K., Lewitter, F., Rolfe, P.A., Herbolsheimer, E., Bell, G.W., Zeitlinger, J., Gifford, D.K., Young, R.A. Cell 122: 517-527 (2005).


Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells
Boyer, L.A., Lee, T.I., Cole, M.F., Johnstone, S.E., Levine, S.S., Zucker, J.P., Guenther, M.G., Kumar, R.M., Murray, H.L., D.P., Melton, D.A., Gifford, D.K., Jaenisch, R. and Young, R.A. Cell 122: 947-956 (2005).


Control of Pancreas and Liver Gene Expression by HNF Transcription Factors
Odom, D.T., Zizlsperger, N., Gordon, D.B., Bell, G.W., Rinaldi, N.J., Murray, H.L., Volkert, T.L., Schreiber, J., Rolfe, P.A., Gifford, D.K., Fraenkel, E., Bell, G.I., and Young, R.A. Science 303: 1378-81 (2004).


Transcriptional Regulatory Code of a Eukaryotic Genome
Harbison, C.T., Gordon, D.B., Lee, T.I., Rinaldi, N., Macisaac, K.D., Danford, T.D., Hannett, N.M., Tagne, J-B., Reynolds, D.B., Yoo, J., Jennings, E.G., Zeitlinger, J., Pokholok, D.K., Kellis, M., Rolfe, P.A., Takusagawa, K.T., Lander, E.S., Gifford, D.K., Fraenkel, E. and Young, R.A. Nature 431: 99-104 (2004).


Genome-wide Location and Function of DNA-binding Proteins
Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett N., Kanin, E., Volkert, T.L., Wilson, C., Bell, S.P. & Young, R.A. Science 290: 2306-2309 (2000).


[publications (pubmed database)]

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