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Jonghwan Kim

Associate Professor
Molecular Biosciences

Transcriptional and epigenetic regulations in Pluripotent stem cells and trophoblast lineage development


Phone: 512-232-8045

Office Location
NMS 4.314

Postal Address
AUSTIN, TX 78712

Associate Professor (2017-present).
Assistant Professor, CPRIT Scholar (2011-2017).
     Department of Molecular Biosciences
     Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology
     The University of Texas at Austin
Instructor (2010-2011). Pediatrics, Children’s Hospital Boston, Harvard Medical School
Research Fellow (2009-2010). Children’s Hospital Boston, Harvard Medical School
Research Associate (2006-2009). Laboratory of Dr. Stuart H. Orkin
     Howard Hughes Medical Institute, Division of Hematology/Oncology, Harvard Medical School
Doctoral Research (2000-2005). Laboratory of Dr. Vishwanath R. Iyer, The University of Texas at Austin
Research Assistant (1999-2000). Laboratory of Dr. Chul Geun Kim, Department of Biology
     Hanyang University, Seoul, Korea
Mandatory Military Service (1994-1996). ROKA/EUSA, Yongsan, Seoul, Korea

NIH Bibliography: https://www.ncbi.nlm.nih.gov/sites/myncbi/jonghwan.kim.1/bibliography/40768405/public/?sort=date&direction=descending

49. Beck S#, Rhee C, Song J, Lee BK, Leblanc L, Cannon L, Kim J# (2018) CpG islands-mediated linear and spatial gene partitioning accounts for the divergence in global transcriptional regulatory mechanisms. Nucleic Acids Res. (Accepted)

48. Lee BK*, Uprety N*, Jang YJ, Tucker S, Rhee R, LeBlanc L, Beck S, Kim J# (2018) Fosl1 overexpression directly activates trophoblast-specific gene expression programs in embryonic stem cells. Stem Cell Research. 26(1): 95–102.

47. Skamagki M, Dogan Y, Yeung P, Ross C, Baslan T, Dang L, Wang J, Beck S, Giunta S, Liu Z, Bohndorf M, Adjaye J, Funabiki H, Kim J, Lowe S, Collins J, Li H, Lu CW, Zhao R, Kim K (2017) Recovery of Genomic Stability by ZSCAN10 in Induced Pluripotent Stem Cells from Aged Donors. Nature Cell Biology. 19(9):1037-1048.

46. Rhee C, Lee BK, Beck S, LeBlanc L, Tucker HO, Kim J# (2017) Mechanisms of transcription factor-mediated direct reprogramming of mouse embryonic stem cells to trophoblast stem-like cells. Nucleic Acids Res. 45(17):10103-10114.

45. Wang L, Zhang F, Rode S, Ko K, Kim J, Iyer VR, Chen J, Qiao H (2017) Ethylene induces combinatorial effects of histone H3 acetylation in gene expression in Arabidopsis. BMC Genomics. 18(1):538.

44. Lee BK, Lee J, Shen W, Rhee C, Chung H, Kim J# (2017) Fbxl19 Recruits Rnf20 to CpG Islands and Regulates H2B Mono-Ubiquitination. Nucleic Acids Res. 45 (12):7151-7166.

43. Rhee C, Edwards M, Dang C, Harris J, Kim J, Tucker HO (2017) Arid3a is required for mammalian placenta development. Developmental Biology. 422(2):83-91.

42. Sanchez A, De Vivo A, Uprety N, Kim J, Stevens SM Jr., Kee Y (2016) The BMI1-UBR5 Axis Regulates Transcriptional Repression at Damaged Chromatin. Proc Natl Acad Sci U S A.  113(40): 11243-11248.

41. Bordiya Y, Zheng Y, Nam J, Choi HW, Lee BK, Kim J, Klessig DF, Fei Z, Kang HG (2016) Arabidopsis MORC1 is Associated with a Subset of Transposable Elements that are Proximal to Defense Genes. Mol Plant Microbe Interact. 2016 Aug 2. [Epub ahead of print]

40. Chung H, Lee BK, Uprety N, Kim J (2016) Yap1 is Dispensable for Self-Renewal but Required for Proper Differentiation of Mouse Embryonic Stem (ES) Cells. EMBO Reports. 17(4):519-29.

39. Li Q, Lex RK, Chung H, Giovanetti SM, Ji Z, Ji H, Person MD, Kim J, Vokes SA (2016) Nanog Binds to Gli Proteins and Represses Hedgehog-Mediated Transcription. JBC. 291(13):7171-82.

38. Kim S, Ezhilarasan R, Phillips M, Gallego-Perez D, Sparks A, Taylor D,  Ladner K, Furuta T, Sabit H, Chhipa R, Cho JH, Beck S, Kurozumi K, Kuroiwa T, Iwata R, Asai A, Kim J, Sulman EP, Cheng S, Lee LJ, Nakada M, Guttridge D, DasGupta B, Goidts V, Bhat KP, Nakano I (2016), Serine/Threonine kinase MLK4 determines Mesenchymal Identity in Glioma Stem Cells in an NF-κB-dependent manner. Cancer Cell. 29(2):201-13.

37. Hoshino K, Chung H, Wu CH, Rajendran K, Huang YY, Chen P, Sokolov KV, Kim J, Zhang X (2015) Immunofluorescence-Assisted Microfluidic Single-Cell Quantitative Reverse Transcription Polymerase Chain Reaction Analysis for Tumour Cells Separated from Blood. Journal of Circulating Biomarkers. 4:11. doi: 10.5772/61822

36. Lee BK, Shen W, Lee J, Rhee C, Chung H, Kim K, Park IH, Kim J (2015) Tgif1 Counterbalances the Activity of Core Pluripotency Factors in Mouse Embryonic Stem Cells. Cell Reports. 13(1):52-60.

35. Das PP, Hendrix DA, Apostolou E, Buchner AH, Canver MC, Beyaz S, Ljuboja D, Kuintzle R, Kim W, Karnik R, Shao Z, Xie H, Xu J, De Los Angeles A, Zhang Y, Choe J, Jun DL, Shen X, Gregory RI, Daley GQ, Meissner A, Kellis M, Hochedlinger K, Kim J, Orkin SH (2015) PRC2 Is Required to Maintain Expression of the Maternal Gtl2-Rian-Mirg Locus by Preventing De Novo DNA Methylation in Mouse Embryonic Stem Cells. Cell Reports. 12;1-12.

34. Beck S*, Lee BK*, Kim J (2015) Multi-Layered Global Gene Regulation in Mouse Embryonic Stem Cells. Cell Mol Life Sci. 72(2):199-216.

33. Beck S, Lee BK, Rhee C, Song J, Woo AJ, Kim J (2014) CpG Island-Mediated Global Gene Regulatory Modes in Mouse Embryonic Stem Cells. Nature Communications. 18;5:5490.

32. Rhee C, Lee BK, Beck S, Cook KR, Anjum A, Tucker HO*, Kim J* (2014) Arid3a is Essential to Execution of the First Cell Fate Decision via Direct Embryonic and Extraembryonic Transcriptional Regulation. Genes and Development. 28(20):2219-32.

31. Ki S*, Park D*, Selden HJ, Seita J, Chung H, Kim J, Iyer VR, Ehrlich L (2014) Global Transcriptional Profiling Reveals Distinct Functions of Thymic Stromal Subsets and Age-Related Changes During Thymic Involution. Cell Reports. 9:402-415.

30. Kim MY, Park J, Lee JJ, Ha DH, Kim J, Kim CG, Hwang J, Kim CG (2014) Staufen1-Mediated mRNA Decay Induces Requiem mRNA Decay through Binding of Staufen1 to the Requiem 3’UTR. Nucleic Acid Research. 2014 May 5. [Epub ahead of print]

29. Pratim PD, Shao Z, Beyaz S, Apostolou E, Pinello L, De Los Angeles A, O’Brien K, Atsma JM, Fujiwara Y, Nguyen M, Ljuboja D, Guo G, Woo AJ, Yuan GC, Onder T, Daley GQ, Hochedlinger K, Kim J, Orkin SH (2014) Distinct and Combinatorial Functions of Jmjd2b/Kdm4b and Jmjd2c/Kdm4c in Mouse Embryonic Stem Cells Identity. Mol Cell. 53(1), 1–17

28. Kim J, Chen JK, Kim J, Jeong S, Ohn T (2013) Splicing Factor SRSF3 Represses the Translation of Programmed Cell Death 4 mRNA by Associating with the 5’UTR Region. Cell Death Differ. 21(3):481-90

27. Woo AJ, Wieland K, Huang H, Akie TE, Piers T, Fleming MD, Boyd T, Kim J, Cantor AB (2013) Developmental Differences in IFN Signaling Affect GATA1s-Induced Megakaryocyte Hyperproliferation. J Clin Invest. 123(8):3292–3304

26. Baena E, Shao Z, Linn DE, Glass K, Hamblen MJ, Fujiwara Y, Kim J, Nguyen M, Zhang X, Godinho FJ, Bronson RT, Mucci LA, Loda M, Yuan GC, Orkin SH, Li Z (2013) ETV1 Directs Androgen Metabolism and Confers Aggressive Prostate Cancer in Targeted Mice and Patients. Genes and Development. 5;27(6):683-98

25. Park KS, Cha Y, Kim CH, Ahn HJ, Kim D, Ko S, Kim KH, Chang MY, Ko JH, Noh YS, Han YM, Kim J, Song J, Kim JY, Tesar PJ, Lanza R, Lee KA, Kim KS. (2013) Transcription Elongation Factor Tcea3 Regulates the Pluripotent Differentiation Potential of Mouse Embryonic Stem Cells, via the Lefty1-Nodal-Smad2 Pathway. Stem Cells. 31(2):282-92

24. Lee JH, Kim J, Gludish D, Roach RR, Saunders AH, Chen H, Conner DA, Fujiwara Y, Stripp BR, Kim CF (2013) Surfactant Protein-C Chromatin-Bound Green Fluorescence Protein Reporter Mice Reveal Heterogeneity of Surfactant Protein C-Expressing Lung Cells. Am J Respir Cell Mol Biol. 48(3):288-98

23. Kim J, Di Vizio D, Kim TK, Kim J, Kim M, Pelton K, Clinton SK, Hai T, Hwang D, Solomon KR, Freeman MR (2012) The Response of the Prostate to Circulating Cholesterol: Activating Transcription Factor 3 (ATF3) as a Prominent Node in a Cholesterol-Sensing Network. PLoS One. 7(7):e39448

22. Kim J, Orkin SH (2011) Embryonic Stem Cell-Specific Signatures in Cancer: Insights into Genomic Regulatory Networks and Implications for Medicine. Genome Medicine. 3(11):75




Burroughs Wellcome Fund (BWF), Preterm Birth Initiative Award, 2017
Cancer Prevention Research Institute of Texas (CPRIT). Award for Recruitment of First-Time,
Tenure-Track Faculty Members, 2011-2016.
Institute for Cellular and Molecular Biology Fellow, University of Texas, 2011-2017
The 22nd Annual Meeting of the Korean Society for Molecular and Cellular Biology (KSMCB), Travel Award, 2010.
NIH Pathway to Independence (PI) Award, 2009-2014.
International Society for Stem Cell Research (ISSCR), Travel Award, 2008.
William S. Livingston Outstanding Employee Award Honorable Mention, UT-Austin, 2005.
The A. P. Bradie Endowed Fellowship, UT-Austin, 2002.



BIO344, Molecular Biology. Spring, 2013 - 2017.
BIO383K, Current Literature in Cell and Developmental Biology. Spring, 2012.
BIO397H, Dean’s Scholar’s Honors Thesis Program, Supervising Professor. Spring, 2012-present.

Positions Available (2017-2018)

1 Graduate Student
1 Postdoctoral Fellow