Publications

1.     Hippocampal subfield transcriptome analysis in schizophrenia psychosis.

Jessica Marie Perez, Stefano BertoKelly GleasonSubroto GhoseChunfeng TanTae-Kyung Kim
Genevieve Konopka and Carol A Tamminga 
Molecular Psychiatry. 2020 March 9; 47:777-780

2.    Emerging themes in neuronal activity-dependent gene expression.

       Madabhushi R, Tae-Kyung Kim

       Molecular and Cellular Neurosciences. 2018; 87:27-34

3.    HDAC5 and Its Target Gene, Npas4, Function in the Nucleus Accumbens to Regulate Cocaine-Conditioned Behaviors.

       Taniguchi M, Carreira MB, Cooper YA, Bobadilla AC, Heinsbroek JA, Koike N, Larson EB, Balmuth EA, Hughes BW, Penrod          RD, Kumar J, Smith LN, Guzman D, Takahashi JS, Tae-Kyung Kim, Kalivas PW, Self DW, Lin Y, Cowan CW.

       Neuron. 2017 Sep 27;96(1):130-144.e6.

4.    An intrinsic transcriptional program underlying synaptic scaling during activity suppression.

       Schaukowitch K, Reese AL, Kim SK, Kilaru G, Joo JY, Kavalali ET, and Tae-Kyung Kim

       Cell Reports 2017 Feb 7;18(6):1512-1526

5.    Stimulus-specific combinatorial functionality of neuronal c-fos enhancers.

       Joo JY, Schaukowitch K, Farbiak L, Kilaru G, Tae-Kyung Kim.

       Nature Neuroscience. 2016; 19(1):75-83.

6.    Architectural and functional commonalities between enhancers and promoters.

       Tae-Kyung Kim and Ramin Shiekhattar (co-corresponding author)

       Cell, 2015; 162(5):948-59

 

7.    Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers.

       Tae-Kyung Kim, Gray JM, Hemberg M, Greenberg ME,

       Cold Spring Harb Perspect Biol. 2015 Jan 5;7(1)

8.    Emerging epigenetic mechanisms of long non-coding RNAs.

       Katie Schaukowitch and Tae-Kyung Kim

       Neuroscience, 264:25-38, 2014

 

9.    SET7/9 methylation of the pluripotency factor LIN28A is a nucleolar localization mechanism that blocks let-7 biogenesis in             human ESCs

       Kim SK, Lee H, Han K, Kim SC, Choi Y, Park SW, Bak G, Lee Y, Choi JK, Tae-Kyung Kim, Han YM, Lee D

       Cell Stem Cell. 15(6):735-49, 2014

 

10.  Enhancer RNA facilitates NELF release from immediate early genes

       Schaukowitch K, Joo J-Y, Liu X, and Tae-Kyung Kim

       Mol. Cell 56(1):29-42, 2014

11.  Usf1, a Suppressor of the Circadian Clock Mutant, Reveals the Nature of the

       DNA-binding of the CLOCK:BMAL1 complex

       Shimomura K, Kumar V, Koike N, Tae-Kyung Kim, Chong J, Buhr ED, Whiteley AR, Low SS, Omura C, Fenner D, Owens JR,             Richards M, Yoo SH, Hong HK, Vitaterna MH, Bass J, Pletcher MT, Wiltshire T, Hogenesch JB, Lowrey PL & Takahashi JS.

       eLife 2, e00426, doi:10.7554/eLife.00426 (2013)

 

12.  Transcriptional Architecture and Chromatin Landscape of the Core Circadian Clock in Mammals

       Koike N, Yoo SH, Huang HC, Kumar V, Lee C, Tae-Kyung Kim, Takahashi JS.

       Science (Article) 338(6105):349-54, 2012

13.  Systematic evaluation of factors influencing ChIP-seq fidelity using ultra-deep sequencing

       Chen Y, Negre N, Mieczkowska JO, Li Q, Zhang Y, He H, Tae-Kyung Kim, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ,           White KP, Lieb JD, Liu XS.

       Nat Methods. 9(6):609-14, 2012

14.  Bhlhb5 and Prdm8 form a repressor complex involved in neuronal circuit assembly.

       Ross SE, McCord AE, Jung C, Atan D, Mok SI, Hemberg M, Tae-Kyung Kim, Hu L, Cohen S, Lin Y, Harrar D, McInnes RR, and         Greenberg ME. 

       Neuron. 73(2):292-303, 2012

15.  Widespread transcription at neuronal activity-regulated enhancers.

       Tae-Kyung Kim, Hemberg M, Gray JM, Costa AM, Bear DM, Wu J, Harmin DA, Laptewicz M, Barbara-Haley K, Kuersten S,           Markenscoff-Papadimitriou E, Kuhl D, Bito H, Worley PF, Kreiman G, Greenberg ME. 

       Nature (Article) 465:182-7, 2010

16.  Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling           pathways.

       Pfenning AR, Tae-Kyung Kim, Spotts JM, Hemberg M, Su D, West AE. 

       PLoS One 27;5(5):e10870, May 2010

17.  Restriction of excitatory synapse number by the Angelman Syndrome-associated ubiquitin ligase, Ube3A.

       Greer PL, Hanayama R, Bloodgood BL, Mardinly AR, Lipton DM, Flavell SW, Tae-Kyung Kim, Griffith EC, Waldon Z, Maehr           R, Ploegh HL, Chowdhury S, Worley PF, Steen J, Greenberg ME. 

       Cell 140(5):704-716, 2010

 

18.  Mef2-mediated transcription of the miR379-410 cluster regulates activity-dependent dendritogenesis by fine-tuning Pumilio2             protein levels.

       Fiore R, Khudayberdiev S, Christensen M, Siegel G, Flavell SW, Tae-Kyung Kim, Greenberg ME, Schratt G. 

       EMBO J. 28(6): 697-710, 2009

 

19.  A retrograde neuronal survival response: target-derived neurotrophins regulate MEF2D and bcl-w. Pazyra-Murphy MF, Hans A,         Karch C, Courchesne S, Heerssen HM,  Watson FL, Tae-Kyung Kim, Greenberg ME, Segal RA. 

       J. Neurosci. 29(20): 6700-6709, 2009

20.  Genome-wide analysis of the target genes of MEF2, a transcription factor that coordinates synapse development.

       Flavell SW*, Tae-Kyung Kim*, GRAY JD, Harmin D, Bear D, Markenscoff-Papadimitriou E, HU LS, Greenberg ME. (* equal             contribution) 

       Neuron 60(6):1022-38, 2008

 

22.  Activity-dependent regulation of GABAergic synapse development by Npas4.

       Lin Y, Hauser JL, Bloodgood BL, Lapan AD, Koon AC, Tae-Kyung Kim, Hu LS, Malik AN, Greenberg ME. 

       Nature (Article), 455(7217):1198-204, 2008

23.  Identifying autism loci and genes by tracing recent shared ancestry.

       Morrow EM, Yoo SY, Flavell SW, Tae-Kyung Kim, Lin Y, Hill RS, Mukaddes NM, Balkhy S, Gascon G, Hashmi A, Al-Saad S,         Ware J, Joseph RM, Greenblatt R, Gleason D, Ertelt JA, Apse KA, Bodell A, Partlow JN, Barry B, Yao H, Markianos K, Ferland         RJ, Greenberg ME, Walsh CA. 

       Science (Article), 321(5886):218-23, 2008

23.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

       Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Tae-Kyung Kim, Koche RP, Lee           W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES,                 Bernstein BE. 

       Nature (Article), 448(7153):553-60, 2007

24.  START: an automated tool for serial analysis of chromatin occupancy data.

       Marinescu VD, Kohane IS, Tae-Kyung Kim, Harmin DA, Greenberg ME, Riva A.

       Bioinformatics, 22(8):999-1001, 2006

25.  Activity-dependent regulation of MEF2 transcription factors suppresses excitatory synapse number.

       Flavell SW, Cowan CW, Tae-Kyung Kim, Paradis S, Griffith EC, Hu, LS, Chen, C, Greenberg ME 

       Science, 311:1008-12, 2006

26.  PARP-1 determines specificity in a retinoid signaling pathway via direct modulation of mediator.

       Pavri R, Lewis B, Tae-Kyung Kim, Dilworth FJ, Erdjument-Bromage H, Tempst P, de Murcia G, Evans R, Chambon P, Reinberg D.

       Mol Cell., 18:83-96, 2005

27.  Site-Specific Protein-DNA Photocrosslinking.

       Tae-Kyung Kim, Thierry Lagrange, Nikolai Naryshkin, Danny Reinberg, Richard Ebright

       Protein-DNA Interactions: A Practical Approach pp.319-334 (Eds. A. Travers, M. Buckle), IRL Press, Oxford, 2000

28.  A Novel Downstream Element in the Human -globin Promoter: Evidence of Extended Sequence-Specific Transcription Factor           IID Contacts.

       Lewis BA, Tae-Kyung Kim, Orkin SH. 

       Proc. Natl. Acad. Sci. USA, 97, 7172-7177, 2000

 

29.  Mechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH.

       Tae-Kyung Kim, Richard H. Ebright, and Danny Reinberg. 

       Science, 288, 1418-1421, 2000

30.  A Protein Phosphatase Functions To Recycle RNA Polymerase II.

       Cho, H., Tae-Kyung Kim, Mancebo, H., Lane, W., Flores, O., Reinberg, D. 

       Genes Dev., 13, 1540-1552, 1999

 

31.  The RNA Polymerase II General Transcription Factors: Past, Present, and Future. 

       Reinberg, D., Orphanides, G., Ebright, R., Akoulitchev, S., Carcamo, J., Cho, H., Cortes, P., Drapkin, R., Flores, O., Ha, I.,           Inostroza, J., Kim, S., Tae-Kyung Kim, Kumar, P., Lagrange, T., Leroy, G., Lu, H., Ma, D.-M., Maldonado, E., Merino, A.,               Mermelstein, F., Olave, I., Sheldon, M., Shiekhattar, R., Stone, N., Sun, X., Weis, L., Yeung, K., and Zawel, L. 

       Cold Spring Harbor Symposia on Quantitative Biology, 58, 83-103, 1998

32.  Trajectory of DNA in the RNA Polymerase II Transcription Preinitiation Complex.

       Tae-Kyung Kim, Thierry Lagrange, Yuh-Hwa Wang, Jack D. Griffith, Danny Reinberg, and Richard Ebright. 

       Proc. Natl. Acad. Sci. USA, 94, 12268-12273, 1997

33.  High-Resolution Mapping of Nucleoprotein Complexes by Site-Specific Protein-DNA Photocrosslinking: Organization of the             Human TBP-TFIIA-TFIIB-DNA Quaternary Complex.  Thierry Lagrange, Tae-Kyung Kim, George Orphanides, Yon W. Ebright,             Richard Ebright, and Danny Reinberg. 

       Proc. Natl. Acad. Sci. USA, 93, 10620-10625, 1996