Publications - NeuroepigeneticsLab

Publications

Enhancer RNAs stimulate Pol II pause release by harnessing multivalent interactions to NELF

Vladyslava Gorbovytska, Seung-Kyoon Kim, Filiz Kuybu, Michael Götze, Dahun Um, Keunsoo Kang, Andreas Pittroff, Theresia Brennecke, Lisa-Marie Schneider, Alexander Leitner, Tae-Kyung Kim, Claus-D. Kuhn. nature communications (2022)

NPAS4 regulates the transcriptional response of the suprachiasmatic nucleus to light and circadian behavior

Pin Xu, Stefano Berto,Ashwinikumar Kulkarni, ...,Tae-Kyung Kim, Genevieve Konopka,Joseph S. Takahashi. neuron (2021)

Identification and Functional Characterization of Two Noncoding RNAs Transcribed from Putative Active Enhancers in Hepatocellular Carcinoma

Ye-Eun Lee, Jiyeon Lee, Yong Sun Lee, Jiyoung Joan Jang, Hyeonju Woo, Hae In Choi, Young Gyu Chai, Tae-Kyung Kim, TaeSoo Kim, Lark Kyun Kim, and Sun Shim Choi. Molecules and cells (2021)

Maternal exposure to polystyrene nanoplastics causes brain abnormalities in progeny

Bohyeon Jeong, Jeong Yeob Baek, Jahong Koo, Subin Park, Young-Kyoung Ryu, Kyoung-Shim Kim, Seungjae Zhang, ChiHye Chung, Rumeysa Dogan, Hyung-Seok Choi, Dahun Um, Tae-Kyung Kim, Wang Sik Lee, Jinyoung Jeong, Won-Ho Shin, Jae-Ran Lee, Nam-Soon Kim, Da Yong Lee. j of hazardous materials (2021)

Functional coordination of BET family proteins underlies altered transcription associated with memory impairment in fragile X syndrome

SEUNG-KYOON KIM, XIHUI LIU, JONGMIN PARK, DAHUN UM, GOKHUL KILARU, CHENG-MING CHIANG, MINGON KANG, KIMBERLY M. HUBER, KEUNSOO KANG, TAE-KYUNG KIM. Science advances (2021)

Advances in higher-order chromatin architecture: the move towards 4D genome

Namyoung jung and Tae-Kyung Kim. BMB reports (2021)

Hippocampal subfield transcriptome analysis in schizophrenia psychosis

Jessica Marie Perez, Stefano Berto, Kelly Gleason, Subroto Ghose, Chunfeng Tan, Tae-Kyung Kim, Genevieve Konopka and Carol A Tamminga. Molecular Psychiatry (2020)

Emerging themes in neuronal activity-dependent gene expression

Madabhushi Ram, Tae-Kyung Kim. Molecular and Cellular Neurosciences (2018)

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)

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)

Stimulus-specific combinatorial functionality of neuronal c-fos enhancers

Joo JY, Schaukowitch K, Farbiak L, Kilaru G, Tae-Kyung Kim. nature neuroscience (2016)

Architectural and functional commonalities between enhancers and promoters

Tae-Kyung Kim and Ramin Shiekhattar. Cell (2015)

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)

Emerging epigenetic mechanisms of long non-coding RNAs

Katie Schaukowitch and Tae-Kyung Kim. neuroscience (2014)

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

Kim Seung-Kyoon, 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 (2014)

Enhancer RNA facilitates NELF release from immediate early genes

Schaukowitch K, Joo J-Y, Liu X, and Tae-Kyung Kim. molecular cell (2014)

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 (2013)

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 (2012)

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 (2012)

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 (2012)

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 (2010)

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 (2010)

The Angelman Syndrome Protein Ube3A Regulates Synapse Development by Ubiquitinating Arc

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 (2010)

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 Journal (2009)

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. Journal of Neuroscience (2009)

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. neuron (2008)

Activity-dependent regulation of inhibitory synapse development by Npas4

Lin Y, Hauser JL, Bloodgood BL, Lapan AD, Koon AC, Tae-Kyung Kim, Hu LS, Malik AN, Greenberg ME. Nature (2008)

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 (2008)

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 (2007)

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 (2006)

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 (2006)

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. Molecular Cell (2005)

Site-Specific Protein-DNA Photocrosslinking

Tae-Kyung Kim, Thierry Lagrange, Nikolai Naryshkin, Danny Reinberg, Richard Ebright. Protein-DNA Interactions: A Practical Approach, oxford (2000)

A downstream element in the human β-globin promoter: Evidence of extended sequence-specific transcription factor IID contacts

Lewis BA, Tae-Kyung Kim, Orkin SH. Proceedings of National academy of sciences. (2000)

Mechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH

Tae-Kyung Kim, Richard H. Ebright, Danny Reinberg. Science (2000)

A Protein Phosphatase Functions To Recycle RNA Polymerase II

Cho, H., Tae-Kyung Kim, Mancebo, H., Lane, W., Flores, O., Reinberg, D. Genes Dev. (1999)

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

D Reinberg, G Orphanides, R Ebright, S Akoulitchev, J Carcamo, H Cho, P Cortes, R Drapkin, O Flores, I Ha, J A Inostroza, S Kim, T K Kim, P Kumar, T Lagrange, G LeRoy, H Lu, D M Ma, E Maldonado, A Merino, F Mermelstein, I Olave, M Sheldon, R Shiekhattar, L Zawel, et al. Cold Spring Harbor Symposia on Quantitative Biology (1998)

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. PROCEEDINGS OF NATIONAL ACADEMY OF SCIENCES. (1997)

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. proceedings of national academy of science. (1996)