Publications

*Co-first authors; **Co-corresponding authors

Yoo, W., Song, Y.W., Kim, J., Ahn, J., Kim, J., Shin, Y., Ryu, J.K., and Kim K.K. (2023). Molecular basis for SOX2-dependent regulation of super-enhancer activity. Nucleic Acids Res. 51, 11999-12019.

Ahn, M.*, Park, S.E.*, Choi, J.*, Choi, J., Choi, D., An, D., Jeon, H., Oh, S., Lee, K., Kim, J., Jang, J.**, Kim, S.**, and Byun, Y.** (2023). Synthesis and biological evaluation of flavonoid-based IP6K2 inhibitors. J. Enzyme Inhib. Med. Chem. 38, 2193866.

Crump, N.T.*, Smith, A.L.*, Godfrey, L., Dopico-Fernandez, A.M., Denny, N., Harman, J.R., Hamley, J.C., Jackson, N.E., Chahrour, C., Riva, S., Rice, S., Kim, J., Basrur, V., Fermin, D., Elenitoba-Johnson, K., Roeder, R.G., Allis, C.D., Roberts, I., Roy, A., Geng, H., Davies, J.O.J., and Milne, T.A. (2023). MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia. Nat. Commun. 14, 5208.

Cho, G., Hyun, K., Choi, J., Shin, E., Kim, B., Kim, H., Kim, J.**, and Han, Y.M.** (2023). Arginine 65 methylation of Neurogenin 3 by PRMT1 is required for pancreatic endocrine development of hESCs. Exp. Mol. Med. 55, 1506-1519.

Park, A.*, Kim, K.E.*, Park, I., Lee, S.H., Park, K.Y., Jung, M., Li, X., Sleiman, M.B., Lee, S.J., Kim, D.S., Kim, J., Lim, D.S., Woo, E.J., Lee, E.W., Han, B.S., Oh, K.J., Lee, S.C., Auwerx, J., Mun, J.Y., Rhee, H.W., Kim, W.K.**, Bae, K.H.**, and Suh, J.M.** (2023). Mitochondrial matrix protein LETMD1 maintains thermogenic capacity of brown adipose tissue in male mice. Nat. Commun. 14, 3746.

Li, Z., Kim, H., Kim, J., and Park, J.H. (2023). EP400NL is involved in PD-L1 gene activation by forming a transcriptional coactivator complex. Biochim. Biophys. Acta Gene Regul. Mech. 1866, 194889.

Min, K.W., Kim, N., Lee, J.H., Sung, Y., Kim, M., Lee, E.J., Kim, J.M., Kim, J.H., Lee, J., Cho, W., Yang, J.M., Kim, N., Kim, J., Lee, C.J., Park, Y.G., Lee, S.H., Lee, H.W., and Kim, J.W. (2023). Visuomotor anomalies in achiasmatic mice expressing a transfer-defective Vax1 mutant. Exp. Mol. Med. 55, 385-400. 

Shin, S.*, Hyun, K.*, Lee, J., Joo, D., Kulikowicz, T., Bohr, V.A., Kim, J., and Hohng, S. (2023). Werner syndrome protein works as a dimer for unwinding and replication fork regression. Nucleic Acids Res. 51, 337-348.

Park, M., Moon, B., Kim, J.H., Park, S.J., Kim, S.K., Park, K., Kim, J., Kim, S.Y., Kim, J.H.**, and Kim, J.A.** (2022). Downregulation of SETD5 suppresses the tumorigenicity of hepatocellular carcinoma cells. Mol. Cells 45, 550-563.

Beon, J.*, Han, S.*, Yang, H., Park, S.E., Hyun, K., Lee, S.Y., Rhee, H.W., Seo, J.K., Kim, J., Kim, S.**, and Lee, D.** (2022). Inositol polyphosphate multikinase physically binds to the SWI/SNF complex and modulates BRG1 occupancy in mouse embryonic stem cells. eLife 11, e73523.

Park, K., Zhong, J., Jang, J.S., Kim, J., Kim, H.J., Lee, J.H.**, and Kim, J.** (2022). ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters. Nucleic Acids Res. 50, 3835-3851.

Lee, S.*, Park, B.B.*, Kwon, H., Kim, V., Jeon, J.S., Lee, R., Subedi, M., Lim, T., Ha, H., An, D., Kim, J., Kim, D., Kim, S.K.**, Kim, S.**, and Byun Y.** (2022). TNP and its analogs: Modulation of IP6K and CYP3A4 inhibition. J. Enzyme Inhib. Med. Chem. 37, 269-279.

Moon, H.M.*, Park, J.S.*, Lee, I.B., Kang, Y.I., Jung, H.J., An, D., Shin, Y., Kim, M.J., Kim, H.I., Song, J.J., Kim. J., Lee. N.K., and Hong. S.C. (2021). Cisplatin fastens chromatin irreversibly even at a high chloride concentration. Nucleic Acids Res. 49, 12035-12047.

Seo, L.*, Kim, Y.I.*, Kim, H., Hyun, K., Kim, J.**, and Lee, J.E.** (2021). Discovery of Klf2 interactors in mouse embryonic stem cells by immunoprecipitation-mass spectrometry utilizing exogenously expressed bait. Biochim. Biophys. Acta Proteins Proteom. 1869, 140672.

Kim, S.*, Park, D.*, Kim, J.*, Kim, D., Kim, H., Mori, T., Jung, H., Lee, D., Hong, S., Jeon, J., Tabuchi, K., Cheong, E., Kim, J., Um, J.W.**, and Ko, J.** (2021). Npas4 regulates IQSEC3 expression in hippocampal somatostatin interneurons to mediate anxiety-like behavior. Cell Rep. 36, 109417.

Park, T.J.*, Park, A.*, Kim, J., Kim, J.Y., Han, B.S., Oh, K.J., Lee, E.W., Lee, S.C., Bae, K.H.**, and Kim, W.K.** (2021). Myonectin inhibits adipogenesis in 3T3-L1 preadipocytes by regulating the p38 MAPK pathway. BMB Rep. 54, 124-129.

Fu, J.**, Liao, L., Balaji, K.S., Wei, C., Kim, J.**, and Peng, J.** (2021). Epigenetic modification and a role for the E3 ligase RNF40 in cancer development and metastasis. Oncogene 40, 465-474. (Review)

Lee, J.Y.*, Nam, M.*, Son, H.Y.*, Hyun, K., Jang, S.Y., Kim, J.W., Kim, M.W., Jung, Y., Jang, E., Yoon, S.J., Kim, J., Kim, J., Seo, J., Min, J.K., Oh, K.J., Han, B.S., Kim, W.K., Bae, K.H., Song, J., Kim, J., Huh, Y.M.**, Hwang, G.S.**, Lee, E.W.**, and Lee, S.C.** (2020). Polyunsaturated fatty acid biosynthesis pathway determines ferroptosis sensitivity in gastric cancer. Proc. Natl. Acad. Sci. USA 117, 32433-32442.

Park, K., Kim, J.A.**, and Kim J.** (2020). Transcriptional regulation by the KMT2 histone H3K4 methyltransferases. Biochim. Biophys. Acta Gene Regul. Mech. 1863, 194545. (Invited Review)

Kwon, M.*, Park, K.*, Hyun, K., Lee, J.H., Zhou, L., Cho, Y.W., Ge, K., Skalnik, D.G., Muir, T.W., and Kim, J. (2020). H2B ubiquitylation enhances H3K4 methylation activities of human KMT2 family complexes. Nucleic Acids Res. 48, 5442-5456.

Bae, H.J.*, Dubarry, M.*, Jeon, J., Soares, L.M., Dargemont, C., Kim. J., Geli, V.**, and Buratowski, S.** (2020). The Set1 N-terminal domain and Swd2 interact with RNA polymerase II CTD to recruit COMPASS. Nat. Commun. 11, 2181.

Jang, H., Park, S., Kim, J., Kim, J.H., Kim, S.Y., Cho, S., Park, S.G., Park, B.C.**, Kim, S.**, and Kim, J.H.** (2020). The tumor suppressor, p53, negatively regulates non-canonical NF-κB signaling through miRNA-induced silencing of NF-κB-inducing kinase. Mol. Cells 43, 23-33.

In, S., Kim, Y.I., Lee, J.E., and Kim, J. (2019). RNF20/40-mediated eEF1BdL monoubiquitylation stimulates transcription of heat shock-responsive genes. Nucleic Acids Res. 47, 2840-2855.

Kim, J.A.**, Kwon, M., and Kim, J.** (2019). Allosteric regulation of chromatin-modifying enzymes. Biochemistry 58, 15-23. (Invited Review)

Jeon, J., McGinty, R.K., Muir, T.W., Kim, J.A.**, and Kim, J.** (2018). Crosstalk among Set1 complex subunits involved in H2B ubiquitylation-dependent H3K4 methylation. Nucleic Acids Res. 46, 11129-11143. (Selected as a 'Breakthrough Article')

Ahn, J.*, Lee, J.G.*, Chin, C., In, S., Yang, A., Park, H.S., Kim, J.**, and Park, J.H.** (2018). MSK1 functions as a transcriptional coactivator of p53 in the regulation of p21 gene expression. Exp. Mol. Med. 50, 132.

Deng, P.*, Zhou, Y.*, Jiang, J., Li, H., Tian, W., Cao, Y., Qin, Y., Kim, J., Roeder, R.G., Patel, D.J**, and Wang, Z.** (2018). Transcriptional elongation factor Paf1 core complex adopts a spirally-wrapped solenoidal topology. Proc. Natl. Acad. Sci. USA 115, 9998-10003.

Lee, M.*, Shin, S.*, Uhm, H.*, Hong, H., Kirk, J., Hyun, K., Kulikowicz, T., Kim, J., Ahn, B.**, Bohr, V.A.**, and Hohng, S.** (2018). Multiple RPAs make WRN syndrome protein a superhelicase. Nucleic Acids Res. 46, 4689-4698.

Shin, S.*, Hyun, K.*, Kim, J.**, and Hohng, S.** (2018). ATP binding to Rad5 initiates the replication fork reversal by inducing the unwinding of the leading arm and the formation of the Holliday junction. Cell Rep. 23, 1831-1839.

Luciano, P.*, Jeon, J.*, El-kaoutari, A.*, Challal, D.*, Bonnet, A., Barucco A., Candelli, T., Jourquin, F., Lesage, P., Kim, J.**, Libri, D.**, Géli, V.** (2017). Binding to RNA regulates Set1 function. Cell Discov. 3, 17040.

Hyun, K., Jeon, J., Park, K., and Kim, J. (2017). Writing, erasing and reading histone lysine methylations. Exp. Mol. Med. 49, e324. (Invited Review)

Van Oss, S.B.*, Shirra, M.K.*, Bataille, A.R.*, Wier, A.D., Yen, K., Vinayachandran, V., Byeon, I.L., Cucinotta, C.E., Héroux, A., Jeon, J., Kim, J., VanDemark, A.P., Pugh, B.F., and Arndt, K.M. (2016). The histone modification domain of Paf1 complex subunit Rtf1 directly stimulates H2B ubiquitylation through an interaction with Rad6. Mol. Cell 64, 815-825.

Yang, A., Ha, S., Ahn, J., Kim, R., Kim, S., Lee, Y., Kim, J., Söll, D.**, Lee, H.Y.**, and Park, H.S.** (2016). A chemical biology route to site-specific authentic protein modifications. Science 354, 623-626.

Yang, J.H.*, Song, T.Y.*, Jo, C.*, Park, J., Lee, H.Y., Song, I., Hong, S., Jung, K.Y., Kim, J., Han, J.W., Youn, H.D., and Cho, E.J. (2016). Differential regulation of the histone chaperone HIRA during muscle cell differentiation by a phosphorylation switch. Exp. Mol. Med. 48, e252.

Holt, M.T., David, Y., Pollock, S., Tang, Z., Jeon, J., Kim, J., Roeder, R.G., and Muir, T.W. (2015). Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin. Proc. Natl. Acad. Sci. USA 112, 10365-10370. 

Kim, K., Lee, B., Kim, J., Choi, J., Kim, J.M., Xiong, Y., Roeder, R.G., and An, W. (2013). Linker histone H1.2 cooperates with Cul4A and PAF1 to drive H3K41 ubiquitylation-mediated transactivation. Cell Rep. 5, 1690-1703.

Tang, Z., Chen, W.Y., Shimada, M., Nguyen, U.T., Kim, J., Sun X.J., Sengoku, T., McGinty, R.K., Fernandez, J.P., Muir, T.W., and Roeder, R.G. (2013). SET1 and p300 act synergistically, through coupled histone modifications, in transcriptional activation by p53. Cell 154, 297-310.

Kim, J.*, Kim, J.A.*, McGinty, R.K., Nguyen, U.T., Muir T.W., Allis, C.D.**, and Roeder, R.G.** (2013). The n-SET domain of Set1 regulates H2B ubiquitylation-dependent H3K4 methylation. Mol. Cell 49, 1121-1133. (Featured in a 'Preview' in the same issue of Molecular Cell, 49, 1019-1020)

Marazzi, I., Ho, J., Kim, J., Manicassamy, B., Dewell, S., Albrecht, R.A., Seibert, C., Schaefer, U., Jeffrey, K.L., Prinjha, R.K., Lee, K., García-Sastre, A., Roeder, R.G., and Tarakhovsky, A. (2012). Suppression of the antiviral response by an influenza histone mimic. Nature 483, 428-433.

Jaaskelainen, T., Harri Makkonen, H., Visakorpi, T., Kim J., Roeder, R.G., and Palvimo, J.J. (2012). Histone H2B ubiquitin ligases RNF20 and RNF40 in androgen signaling and prostate cancer cell growth. Mol. Cell. Endocrinol. 350, 87-98.

Fujiki, R., Hashiba, W., Sekine, H., Yokoyama, A., Chikanishi, T., Ito, S., Imai, Y., Kim, J., He, H.H., Igarashi, K., Kanno, J., Ohtake, F., Kitagawa, H., Roeder, R.G., Brown, M., Kato, S. (2011). GlcNAcylation of histone H2B facilitates its monoubiquitination. Nature 480, 557-560.

Biswas, D., Milne, T.A., Basrur, V., Kim, J., Elenitoba-Johnson, K.S.J., Allis, C.D., and Roeder, R.G. (2011). Function of leukemogenic MLL fusion proteins through distinct partner protein complexes. Proc. Natl. Acad. Sci. USA 108, 15751-15756.

Kim, J., and Roeder, R.G. (2011). Nucleosomal H2B ubiquitylation with purified factors. Methods 54, 331-338.

Shema, E., Kim, J., Roeder, R.G., and Oren, M. (2011). RNF20 inhibits TFIIS-facilitated transcriptional elongation to suppress pro-oncogenic gene expression. Mol. Cell 42, 477-488.

Milne, T.A., Kim, J., Wang, G.G., Stadler, S.C., Basrur, V., Whitcomb, S.J., Wang, Z., Ruthenburg, A.J., Elenitoba-Johnson, K.S., Roeder, R.G., and Allis, C.D. (2010). Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Mol. Cell 38, 853-863.

Kim, J.*, Guermah, M.*, and Roeder, R.G. (2010). The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140, 491-503.

Guermah, M., Kim, J., and Roeder, R.G. (2009).Transcription of in vitro assembled chromatin templates in a highly purified RNA polymerase II system. Methods 48, 353-360.

Kim, J., and Roeder, R.G. (2009). Direct Bre1-Paf1 complex interactions and RING finger-independent Bre1-Rad6 interactions mediate H2B ubiquitylation in yeast. J. Biol. Chem. 284, 20582-20592.

Kim, J., Guermah, M., McGinty, R.K., Lee, J.S., Tang, Z., Milne, T.A., Shilatifard, A., Muir, T.W., and Roeder, R.G. (2009). RAD6-mediated transcription-coupled H2B ubiquitylation directly stimulates H3K4 methylation in human cells. Cell 137, 459-471.

Gamper, A.M., Kim, J., and Roeder, R.G. (2009). The STAGA subunit ADA2b is an important regulator of human GCN5 catalysis. Mol. Cell. Biol. 29, 266-280.

McGinty, R.K., Kim, J., Chatterjee, C., Roeder, R.G., and Muir, T.W. (2008). Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation. Nature 453, 812-816.

Vermeulen, M., Walter, W., Le Guezennec, X., Kim, J., Edayathumangalam, R.S., Lasonder, E., Luger, K., Roeder, R.G., Logie, C., Berger, S.L., and Stunnenberg, H.G. (2006). A feed-forward repression mechanism anchors the Sin3/histone deacetylase and N-CoR/SMRT corepressors on chromatin. Mol. Cell. Biol. 26, 5226-5236.

Kim, J., Hake, S.B., and Roeder R.G.  (2005). The human homolog of yeast BRE1 functions as a transcriptional coactivator through direct activator interactions. Mol. Cell 20, 759-770.

An, W., Kim, J., and Roeder R.G. (2004). Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53. Cell 117, 735-748.

Kim, J.H., Kim, J., Kim, D.H., Ryu, G.H., Bae, S.H., and Seo, Y.S. (2004). SCFhFBH1 can act as helicase and E3 ubiquitin ligase. Nucleic Acids Res. 32, 2287-2297.

Kim, J., Kim, J.H., Lee, S.H., Kim, D.H., Kang, H.Y., Bae, S.H., Pan, Z.Q., and Seo, Y.S. (2002). The novel human DNA helicase hFBH1 is an F-box protein. J. Biol. Chem. 277, 24530-24537.

Bae, S.H., Kim, J.A., Choi, E., Lee, K.H., Kang, H.Y., Kim, H.D., Kim, J.H., Bae, K.H., Cho, Y., Park, C., and Seo, Y.S. (2001). Tripartite structure of Saccharomyces cerevisiae Dna2 helicase/endonuclease. Nucleic Acids Res. 15, 3069-3079.

Park, K., Kim, J., Kim, H.S., and Shin, H.S. (1998). Isolated human germinal center centroblasts have an intact mismatch repair system. J. Immunol. 161, 6128-6132.

Lee, G.M., Kim, J.H., and Lee, H.G. (1996). Flow cytometric analysis of antibody producing cells using double immunofluorescent staining. Biotechnol. Tech. 10, 615-620.

Kim, J.H., Bae, S.W., Hong, H.J., and Lee, G.M.  (1996). Decreased specific chimeric antibody productivity of KR12H-1 transfectoma during a long-term culture results from decreased antibody gene copy number. Biotechnol. Bioeng. 51, 479-487.