Jonghwan Kim

Assistant Professor
Molecular Biosciences

Transcriptional and epigenetic regulation in Pluripotent stem cells and Cancer cells

Phone: 512-232-8046

Office Location
NMS 4.314

Postal Address
The University of Texas at Austin
Molecular Biosciences, College of Natural Sciences
2506 Speedway
Austin, TX 78712

Assistant Professor, CPRIT Scholar (2011-present).
     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



Research Summary

Defining the molecular mechanisms maintaining stemness - self-renewal and pluripotency - of Embryonic stem (ES) cells, as well as induced pluripotent stem (iPS) cells is of great interest for understanding early development and for their potential therapeutic applications in regenerative medicine. Systematic understanding of the mechanisms controlling the stemness of pluripotent stem cells relies on high-throughput tools to define gene expression and regulatory networks at the genome level. Systems biology approaches have revealed highly interconnected ES cell specific regulatory networks in which multiple cis and trans regulatory elements are involved. Our laboratory studies transcriptional and epigenetic regulation of pluripotent stem cells using a broad panel of techniques including molecular biology and high-throughput genomics approaches in combination with computational analysis. Particularly, our research interests focus on understanding 1) regulatory networks controlling stemness of ES cells and iPS cells, and early lineage specification 2) regulatory networks generating common gene expression signatures between pluripotent stem cells and cancer.


Publications while in rank of Assistant Professor:

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. (In press, Cell Reports)

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


Publications as Postdoctoral Fellow:

21. Woo AJ, Kim J, Xu J, Huang H, Cantor AB (2011) Role of ZBP-89 in Human Globin Gene Regulation and Erythroid Differentiation. Blood. 29;118(13):3684-93

20. Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG, Cantor AB, Orkin SH (2010) A Myc Network Accounts for Similarities between Embryonic Stem and Cancer Cell Transcription Programs. Cell. 143(2): 313-324

19. Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Ji H, Ehrlich L, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, Mckinney-Freeman S, Naveiras O, Yoon T, Hanna J, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg A, and Daley GQ (2010) Epigenetic Memory in Induced Pluripotent Stem Cells. Nature. 467(7313):285-90

18. Bai X, Kim J, Yang Z, Jurynec MJ, Akie TE, Lee J, LeBlanc J, Sessa A, Jiang H, DiBiase A, Zhou Y, Grunwald DJ, Lin S, Cantor AB, Orkin SH, Zon LI (2010) TIF1gamma Controls Erythroid Cell Fate by Regulating Transcriptional Elongation. Cell. 142(1):133-143

17. Snow JW, Kim J, Currie CR, Xu J, Orkin SH (2010) Sumoylation Regulates Interaction of FOG1 with CTBP. J Biol Chem. 3;285(36):28064-75

16. Kim J, Orkin SH (2010) Systematic Tracking of Cell Fate Changes. Nature Biotechnology. 28(2) 146-147

15. Trowbridge JJ, Snow JW, Kim J, Orkin SH (2009) DNA Methyltransferase 1 is Essential for and Uniquely Regulates Hematopoietic Stem and Progenitor Cells. Cell Stem Cell. 5(4) 442-449

14. Hu G, Kim J, Xu Q, Leng Y, Orkin SH, Elledge SJ (2009) A Genome-Wide RNAi Screen Identifies a New Transcriptional Module Required for Self-Renewal. Genes and Development. 23(7): 837-848

13. Kim J, Cantor AB, Orkin SH, Wang J (2009) Use of In Vivo Biotinylation to Study Protein–Protein and Protein–DNA Interactions in Mouse Embryonic Stem Cells. Nature Protocols. 4(4) : 506-517

12. Orkin SH, Wang J, Kim J, Chu J, Rao S, Theunissen TW, Shen X, Levasseur DN (2008) The Transcriptional Network Controlling Pluripotency in ES Cells. Cold Spring Harb Symp Quant Biol. 73:195-202

11. Shen X, Liu Y, Hsu YJ, Fujiwara Y, Kim J, Mao X, Yuan GC, Orkin SH (2008) EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency. Mol Cell. 32(4): 491-502

10. Kim J, Chu J, Shen X, Wang J, Orkin SH (2008) An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells. Cell. 132: 1049-1061

9. Kim J, Lee JH, Iyer VR (2008) Global Identification of Myc Target Genes Reveals Its Direct Role in Mitochondrial Biogenesis and Its E-Box Usage In Vivo. PLoS ONE. 3(3):e1798

8. Saleque S, Kim J, Rooke HM, Orkin SH (2007) Epigenetic Regulation of Hematopoietic Differentiation by Gfi-1 and Gfi-1b Is Mediated by the Cofactors CoREST and LSD1. Mol Cell. 27(4):562-72


Publications as Graduate Student: 

7. Bhinge AA*, Kim J*, Euskirchen G, Snyder M, Iyer VR (2007) Mapping the Chromosomal Targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE). Genome Research. 17: 910-916 (*equally contributed)

6. The ENCODE Project Consortium (2007). Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project. Nature. 447, 799–816

5. Giresi PG, Kim J, McDaniell R, Iyer VR, Lieb JD. (2007) FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements) Isolates Nucleosome-Depleted DNA from Human Chromatin. Genome Research. 17: 877-885

4. Kim J, Iyer VR (2005) Identifying Chromosomal Targets of DNA-Binding Proteins by Sequence Tag Analysis of Genomic Enrichment (STAGE). Curr Protoc Mol Biol. Chapter 21:Unit 21.10

3. Kim J, Bhinge AA, Morgan XC, Iyer VR (2005) Mapping DNA-Protein Interactions in Large Genomes by Sequence Tag Analysis of Genomic Enrichment. Nature Methods. 2(1): 47-53 (Epub 2004 Dec 21)

2. Kim J, Iyer VR (2004) Global Role of TATA Box-Binding Protein Recruitment to Promoters in Mediating Gene Expression Profiles. Mol Cell Biol. 24(18):8104-12

1. Kim SJ, Shin JH, Kim J, Kim SH, Chae JH, Park EJ, Seong RH, Hong SH, Park SD, Jeong S, Kim CG (1999) Isolation of Developmentally Regulated Novel Genes Based on Sequence Identity and Gene Expression Pattern. Mol Cells. 9(2):207-18

Cancer Prevention Research Institute of Texas (CPRIT). Award for Recruitment of First-Time, Tenure-Track Faculty Members, 2011.
The 22nd Annual Meeting of the Korean Society for Molecular and Cellular Biology (KSMCB), Travel Award, 2010.
NIH Pathway to Independence (PI) K99/R00 Award, 2009.
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, 2015.
BIO344, Molecular Biology. Spring, 2014.
BIO344, Molecular Biology. Spring, 2013.
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 (2015-2016)

1 Graduate Student