세미나/행사
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| 제목 | 2017년 4월 12일 생물정보학세미나 | ||
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| 작성자 | 관리자 | 작성일 | 2017-04-05 |
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서울대학교 생물정보연구소와 생물정보학 협동과정 공동 주최로 세미나를 아래와 같이 열고자 하오니, 많은 참여 바랍니다. 일시: 2017년 4월 12일 수요일 오전 11시 연사: 노태영 (포항공과대학교 융합생명공학부) 장소: 서울대학교 25동 411호 Title : Epigenetically encoded transcriptional potential is associated with Z-DNA-forming sites in the human genome Abstract : Epigenetic modifications are closely related with transcriptional activities. A left-handed double strand DNA, Z-DNA is structurally different from the most abundant B-DNA and has been known to play a significant role in transcription and genome stability. However, the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. Here we obtained the genome-wide map of ZFSs by ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examinedin vivo. Among histone modifications, active histone marks such as H3K4me3 and H3K9ac were positively correlated with the position of ZFSs in the genome and genes containing ZFSs were occupied by RNA polymerase II at the promoters and showed high levels of expression.Overall, our results suggest that Z-DNA formation depends on chromatin structure as well as sequence composition, and is associated with active transcription in human cells. The global information of ZFSs positioning will provide a useful resource for further understanding of DNA structure-dependent transcriptional regulation. Education 1998 – 2002 Ph.D. in Biochemistry School of Chemistry and Molecular Engineering Seoul National University, Seoul, Korea 1996 – 1998 M.S. in Biochemistry School of Chemistry and Molecular Engineering Seoul National University, Seoul, Korea 1990 – 1996 B.E. in Chemical Engineering Hanyang University, Seoul, Korea
Professional experience 2008 – present Assistant, Associate Professor, POSTECH, Korea 2007 – 2008 Research Fellow, Supervisor: Dr. Keji Zhao Laboratory of Molecular Immunology, NHLBI / NIH 2002 – 2007 Visiting Fellow, Supervisor: Dr. Keji Zhao Laboratory of Molecular Immunology, NHLBI / NIH 2002 Postdoctoral Fellow, Center for Molecular Catalysis Seoul National University 1998 – 2002 Ph.D., Supervisor: Prof. Myung-Un Choi Thesis title: Chemical Modification and Mutational Studies of Cysteine Residues in α-type Phospholipase D from Cabbage 1998 – 2001 Teaching Assistant of General Chemistry 1998 – 1999 Lab Manager 1996 – 1998 M.S., Supervisor: Prof. Myung-Un Choi Thesis title: Identification of Crucial Residues of Cabbage Phospholipase D by Site-directed Mutagenesis Selected Publications RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans Son HG, Seo M, Ham S, Hwang W, Lee D, An SW, Artan M, Seo K, Kaletsky R, Arey RN, Ryu Y, Ha CM, Kim YK, Murphy CT, Roh TY, Nam HG, Lee SV. Nat Commun. 2017 Mar 9;8:14749. doi: 10.1038/ncomms14749. Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts Park J, Kwon YW, Ham S, Hong CP, Seo S, Choe MK, Shin SI, Lee CS, Kim HS, Roh TY. PLoS ONE 2017 Feb. 2;12(2): e0171300. (corresponding) Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome Shin SI, Ham S, Park J, Seo SH, Lim CH, Jeon H, Huh J, Roh TY. (corresponding) DNA Res. 2016 Oct. 23(5):477-486 ZNF224, Kr�ppel like zinc finger protein, induces cell growth and apoptosis-resistance by downregulation of p21 and p53 via miR-663a Cho JG, Park S, Lim CH, Kim HS, Song SY, Roh TY, Sung JH, Suh W, Ham SJ, Lim KH, Park SG. Oncotarget. 2016 May 24;7(21):31177-90 CTCF-Mediated Chromatin Loop for the Posterior Hoxc Gene Expression in MEF Cells Min H, Kong KA, Lee JY, Hong CP, Seo SH, Roh TY, Bae SS, Kim MH. IUBMB Life. 2016 Jun;68(6):436-44 CD82/KAI1 Maintains the Dormancy of Long-Term Hematopoietic Stem Cells through Interaction with DARC-Expressing Macrophages Hur J, Choi JI, Lee H, Nham P, Kim TW, Chae CW, Yun JY, Kang JA, Kang J, Lee SE, Yoon CH, Boo K, Ham S, Roh TY, Jun JK, Lee H, Baek SH, Kim HS. Cell Stem Cell. 2016 Apr 7;18(4):508-21 SREBP and MDT-15 protect C. elegans from glucose-induced accelerated aging by preventing accumulation of saturated fat Lee D, Jeong DE, Son HG, Yamaoka Y, Kim H, Seo K, Khan AA, Roh TY, Moon DW, Lee Y, Lee SJ. Genes Dev. 2015 Dec 1;29(23):2490-503 miR-93/miR-106b/miR-375-CIC-CRABP1: A novel regulatory axis in prostate cancer progression Choi N, Park J, Lee JS, Yoe J, Park GY, Kim E, Jeon H, Cho YM, Roh TY, Lee Y. Oncotarget. 2015 Sep 15;6(27):23533-47 Impaired IL-2 expression in Latent HIV-1 Infection Shin Y, Yoon CH, Lim H, Park J, Roh TY, Kang C, Choi BS. Biochem Biophys Res Commun. 2015 Aug 7;463(4):1237-42 Role of Zscan4 in secondary murine iPSC derivation mediated by protein extracts of ESC or iPSC. Kwon YW, Paek JS, Cho HJ, Lee CS, Lee HJ, Park IH, Roh TY, Kang CM, Yang HM, Park YB, Kim HS Biomaterials. 2015 Aug;59:102-15 EVpedia: A Community Web Portal for Extracellular Vesicles Research Kim DK, et al. Bioinformatics 2015 Mar 15;31(6):933-9. Polycomb group protein-mediated histone modifications during cell differentiation Khan AA, Lee AJ, Roh TY. (corresponding) Epigenomics 2015 Feb;7(1):75-84 Egr-1 activation by cancer-derived extracellular vesicles promotes endothelial cell migration via ERK1/2 and JNK signaling pathways Yoon YJ, Kim DK, Yoon CM, Park J, Kim YK, Roh TY, Gho YS. (co-corresponding) PLoS One. 2014 Dec 12;9(12):e115170 A follow-up association study of genetic variants for bone mineral density in a Korean population Ham S, Roh TY. (corresponding) Genomics & Informatics 2014 Sep;12(3):114-20 NUCKS1, a novel Tat coactivator, plays a crucial role in HIV-1 replication by increasing Tat-mediated viral transcription on the HIV-1 LTR promoter Kim HY, Choi BS, Kim SS, Roh TY, Park J, Yoon CH Retrovirology 2014 Aug 13;11(1):67 Genome-wide analysis of histone modifications in latently HIV-1 infected T cells Park J, Lim CH, Ham S, Kim SS, Choi BS, Roh TY. (corresponding) AIDS 2014 Jul 31;28(12):1719-28 Transcription-related element gene expression pattern differs between microglia and macrophages during inflammation Lee HT, Kim SK, Kim SH, Kim K, Lim CH, Park J, Roh TY, Kim N, Chai YG. Inflamm Res. 2014 May;63(5):389-97 Comparative Study of Efficacy of Dopaminergic Neuron Differentiation between Embryonic Stem Cell and Protein-Based Induced Pluripotent Stem Cell Kwon YW, Chung YJ, Kim J, Lee HJ, Park J, Roh TY, Cho HJ, Yoon CH, Koo BK, Kim HS. PLoS One. 2014 Jan 22;9(1):e85736. Twist1 is essential in maintaining mesenchymal state and tumor-initiating properties in synovial sarcoma Lee KW, Lee NK, Ham S, Roh TY, Kim SH. (co-corresponding) Cancer Lett. 2014 Feb 1;343(1):62-73. Extracellular Vesicles Derived from Gut Microbiota, Especially Akkermansia muciniphila, Protect the Progression of Dextran Sulfate Sodium-Induced Colitis Kang CS, Ban M, Choi EJ, Moon HG, Jeon JS, Kim DK, Park SK, Jeon SG, Roh TY, Myung SJ, Gho YS, Kim JG, Kim YK. PLoS One. 2013 Oct 24;8(10):e76520 Bioinspired Exosome-Mimetic Nanovesicles for Targeted Delivery of Chemotherapeutics to Malignant Tumors Jang SC, Kim OY, Yoon CM, Choi DS, Roh TY, Park J, Nilsson J, L�tvall J, Kim YK, Gho YS. ACS Nano. 2013 Sep 24;7(9):7698-710. Staphylococcus aureus Extracellular Vesicles Carry Biologically Active Beta-lactamas Lee J, Lee EY, Kim SH, Kim DK, Park KS, Kim KP, Kim YK, Roh TY, Gho YS. (co-corresponding) Antimicrob Agents Chemother. 2013 Jun;57(6):2589-95 Extracellular vesicles, especially derived from Gram-negative bacteria, in indoor dust induce neutrophilic pulmonary inflammation associated with both Th1 and Th17 cell responses Kim YS, Choi EJ, Lee WH, Choi SJ, Roh TY, Park J, Jee YK, Zhu Z, Koh YY, Gho YS, Kim YK. Clin Exp Allergy. 2013 Apr;43(4):443-54. Immunization with Escherichia coli Outer Membrane Vesicles Protects Bacteria-Induced Lethality via Th1 and Th17 Cell Response Kim OY, Hong BS, Park KS, Yoon YJ, Choi SJ, Lee WH, Roh TY, L�tvall J, Kim YK, Gho YS. J Immunol. 2013 Apr 15;190(8):4092-102 Synthetic RNA devices to expedite the evolution of metabolite-producing microbes Yang J, Seo SW, Jang S, Shin SI, Lim CH, Roh TY, Jung GY Nat. Commun. 2013 Jan 29;4:1413 DNA-binding motif and target genes of the imprinted transcription factor PEG3 Thiaville MM, Huang JM, Kim H, Ekram MB, Roh TY, Kim J. Gene. 2013 Jan 10;512(2):314-20 Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells Hong CP, Choe MK, Roh TY. (corresponding) Genomics & Informatics 2012 10(3):145-152 TNF-alpha is a key mediator in the development of Th2 cell response to inhaled allergens induced by a viral PAMP double-stranded RNA Choi JP, Kim YS, Kim OY, Kim YM, Jeon SG, Roh TY, Park JS, Gho YS, Kim YK. Allergy. 2012 Sep;67(9):1138-48 A novel human polycomb binding site acts as a functional polycomb response element in Drosophila Cuddapah S, Roh TY, Cui K, Jose CC, Fuller MT, Zhao K, Chen X. PLoS ONE. 2012 May;7(5):e36365 Functional elements demarcated by histone modifications in breast cancer cells Choe MK, Hong CP, Park J, Seo SH, Roh TY. (corresponding) Biochem Biophys Res Commun. 2012 Feb 17;418(3):475-82 Airway activation of formyl peptide receptors inhibits Th1 and Th17 cell responses via inhibition of mediator release from immune and inflammatory cells and maturation of dendritic cells Tae YM, Park HT, Moon HG, Kim YS, Jeon SG, Roh TY, Bae YS, Gho YS, Ryu SH, Kwon HS, Kim YK. J Immunol. 2012 Feb 15;188(4):1799-808. Epub 2012 Jan 18. Aebp2 as an Epigenetic Regulator for Neural Crest Cells Kim H, Kang K, Ekram MB, Roh TY, Kim J. PLoS ONE 2011 Sep; 6(9) e25174 Gene Silencing in HIV-1 Latency by Polycomb Repressive Group Kim HG, Kim KC, Roh TY, Park J, Jung KM, Lee JS, Choi SY, Kim SS, Choi BS. Virol J. 2011 Apr 18;8(1):179. Epigenetic regulation in cell reprogramming revealed by genome-wide analysis Hong CP, Park J, Roh TY. (corresponding) Epigenomics 2011 Feb 1;3(1):73-81 Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions Cuddapah S, Schones DE, Cui K, Roh TY, Barski A, Wei G, Rochman M, Bustin M, Zhao K Mol Cell Biol. 2011 Feb;31(4):700-9 The Effect of CD4 Receptor Downregulation and Its Downstream Signaling Molecules on HIV-1 Latency Kim KC, Kim HG, Roh TY, Park J, Jung KM, Lee JS, Choi SY, Kim SS, Choi BS. Biochem Biophys Res Commun. 2011 Jan 14;404(2):646-51 Induction of pluripotent stem cells from adult somatic cells by protein-based reprogramming without genetic manipulation Cho HJ, Lee CS, Kwon YW, Paek JS, Lee SH, Hur J, Lee EJ, Roh TY, Chu IS, Leem SH, Kim Y, Kang HJ, Park YB, Kim HS. Blood 2010 Jul 22;116(3):386-95 Chromatin poises miRNA- and protein-coding genes for expression Barski A, Jothi R, Cuddapah S, Cui K, Roh TY, Schones DE, Zhao K. Genome Res 2009 Oct;19(10):1742-51 Genome-wide analysis of histone methylation reveals chromatin state-based regulation of gene transcription and function of memory CD8+ T cells Araki Y, Wang Z, Zang C, Wood WH 3rd, Schones D, Cui K, Roh TY, Lhotsky B, Wersto RP, Peng W, Becker KG, Zhao K, Weng NP. Immunity 2009 Jun 19;30(6):912-25 Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells Wei G, Wei L, Zhu J, Zang C, Hu-Li J, Yao Z, Cui K, Kanno Y, Roh TY, Watford WT, Schones DE, Peng W, Sun HW, Paul WE, O'Shea JJ, Zhao K. Immunity 2009 Jan;30(1):155-67 Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation Cui K, Zang C, Roh TY, Schones DE, Childs RW, Peng W, Zhao K. Cell Stem Cell 2009 Jan 9;4(1):80-93 Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K. Genome Res. 2009 Jan;19(1):24-32. Epub 2008 Dec 3 Priming for T helper type 2 differentiation by interleukin 2-mediated induction of interleukin 4 receptor alpha-chain expression Liao W, Schones DE, Oh J, Cui Y, Cui K, Roh TY, Zhao K, Leonard WJ. Nat Immunol. 2008 Nov;9(11):1288-96. Epub 2008 Sep 28 Combinatorial patterns of histone acetylations and methylations in the human genome Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S, Cui K, Roh TY, Peng W, Zhang MQ, Zhao K. Nat Genet. 2008 Jul;40(7):897-903. Epub 2008 Jun 15 Dynamic regulation of nucleosome positioning in the human genome Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Cell 2008 Mar 7;132(5):887-98 High-resolution, genome-wide mapping of chromatin modifications by GMAT Roh TY, Zhao K. Methods in molecular biology (Clifton, N.J.) Methods Mol Biol. 2008;387:95-108 High-resolution profiling of histone methylations in the human genome Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. Cell 2007 May 18;129(4):823-37 Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns Roh TY, Wei G, Farrell CM, Zhao K. Genome Res. 2007 Jan;17(1):74-81. Epub 2006 Nov 29 The genomic landscape of histone modifications in human T cells Roh TY, Cuddapah S, Cui K, Zhao K. Proc Natl Acad Sci U S A. 2006 Oct 24;103(43):15782-7. Epub 2006 Oct 16 Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping Roh TY, Cuddapah S, Zhao K. Genes Dev. 2005 Mar 1;19(5):542-52. Epub 2005 Feb 10 High-resolution genome-wide mapping of histone modifications Roh TY, Ngau WC, Cui K, Landsman D, Zhao K. Nat Biotechnol. 2004 Aug;22(8):1013-6. Epub 2004 Jul 4 Investigation of sulfhydryl groups in cabbage phospholipase D by combination of derivatization methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry Hwang IS, Park SJ, Roh T, Choi M, Kim HJ. Rapid Commun Mass Spectrom. 2001;15(2):110-5 Molecular cloning and functional expression of a phospholipase D from cabbage (Brassica oleracea var. capitata) Kim DU, Roh TY, Lee J, Noh JY, Jang YJ, Hoe KL, Yoo HS, Choi MU. Biochim Biophys Acta. 1999 Mar 25;1437(3):409-14 서울대학교 생물정보연구소 생물정보학 협동과정 공동주최 |
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