Publications

Brooks J F, Heath-Heckman E and Kuang Z. Editorial: Environmental rhythms at the host-microbe interface. Front. Genet. Sep 2021; 14:1290552. doi: 10.3389/fgene.2023.1290552

Wang Y, Wang M, Chen J, Li Y, Kuang Z, Dende C, Raj P, Quinn G, Hu Z, Srinivasan T, Hassell B, Ruhn KA, Behrendt CL, Liang T, Dou X, Song Z, Hooper LV. The gut microbiota reprograms intestinal lipid metabolism through long noncoding RNA Snhg9. Science. 2023 Aug 25;381(6660):851-857. doi: 10.1126/science.ade0522.

Ma J, Zhang J and Kuang Z. A microbiota-epigenetic circuit controls systematic circadian programs in the gut epithelium. Front. Syst. Biol. Aug 2023; 3:1175306. doi: 10.3389/fsysb.2023.1175306

Publications from ZK postdoctoral work, UT Southwestern Medical Center and New York University (2014-2020)

Kuang Z, Wang Y, Li Y, Ye C, Ruhn KA, Behrendt CL, Olson EN, Hooper LV. The intestinal microbiota programs diurnal rhythms in host metabolism through histone deacetylase 3. Science. 2019 Sep 27;365(6460):1428-1434. doi: 10.1126/science.aaw3134. PubMed PMID: 31604271; PubMed Central PMCID: PMC7158748.

De Ioannes P, Leon VA, Kuang Z, Wang M, Boeke JD, Hochwagen A, Armache KJ. Structure and function of the Orc1 BAH-nucleosome complex. Nat Commun. 2019 Jul 1;10(1):2894. doi: 10.1038/s41467-019-10609-y. PubMed PMID: 31263106; PubMed Central PMCID: PMC6602975.

Harris TA, Gattu S, Propheter DC, Kuang Z, Bel S, Ruhn KA, Chara AL, Edwards M, Zhang C, Jo JH, Raj P, Zouboulis CC, Kong HH, Segre JA, Hooper LV. Resistin-like Molecule α Provides Vitamin-A-Dependent Antimicrobial Protection in the Skin. Cell Host Microbe. 2019 Jun 12;25(6):777-788.e8. doi: 10.1016/j.chom.2019.04.004. Epub 2019 May 14. PubMed PMID: 31101494; PubMed Central PMCID: PMC6628910.

Gattu S, Bang YJ, Pendse M, Dende C, Chara AL, Harris TA, Wang Y, Ruhn KA, Kuang Z, Sockanathan S, Hooper LV. Epithelial retinoic acid receptor β regulates serum amyloid A expression and vitamin A-dependent intestinal immunity. Proc Natl Acad Sci U S A. 2019 May 28;116(22):10911-10916. doi: 10.1073/pnas.1812069116. Epub 2019 May 16. PubMed PMID: 31097581; PubMed Central PMCID: PMC6561173.

Ye C, Sutter BM, Wang Y, Kuang Z, Zhao X, Yu Y, Tu BP. Demethylation of the Protein Phosphatase PP2A Promotes Demethylation of Histones to Enable Their Function as a Methyl Group Sink. Mol Cell. 2019 Mar 21;73(6):1115-1126.e6. doi: 10.1016/j.molcel.2019.01.012. Epub 2019 Feb 13. PubMed PMID: 30772176; PubMed Central PMCID: PMC6628921.

Sánchez-Gaya V, Casaní-Galdón S, Ugidos M, Kuang Z, Mellor J, Conesa A, Tarazona S. Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach. Front Genet. 2018;9:578. doi: 10.3389/fgene.2018.00578. eCollection 2018. PubMed PMID: 30555512; PubMed Central PMCID: PMC6284056.

Kuang Z, Ji H, Boeke JD. Stress response factors drive regrowth of quiescent cells. Curr Genet. 2018 Aug;64(4):807-810. doi: 10.1007/s00294-018-0813-0. Epub 2018 Feb 17. Review. PubMed PMID: 29455333; NIHMSID:NIHMS944262.

Venkataraman A, Yang K, Irizarry J, Mackiewicz M, Mita P, Kuang Z, Xue L, Ghosh D, Liu S, Ramos P, Hu S, Bayron Kain D, Keegan S, Saul R, Colantonio S, Zhang H, Behn FP, Song G, Albino E, Asencio L, Ramos L, Lugo L, Morell G, Rivera J, Ruiz K, Almodovar R, Nazario L, Murphy K, Vargas I, Rivera-Pacheco ZA, Rosa C, Vargas M, McDade J, Clark BS, Yoo S, Khambadkone SG, de Melo J, Stevanovic M, Jiang L, Li Y, Yap WY, Jones B, Tandon A, Campbell E, Montelione GT, Anderson S, Myers RM, Boeke JD, Fenyö D, Whiteley G, Bader JS, Pino I, Eichinger DJ, Zhu H, Blackshaw S. A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. Nat Methods. 2018 May;15(5):330-338. doi: 10.1038/nmeth.4632. Epub 2018 Mar 19. PubMed PMID: 29638227; PubMed Central PMCID: PMC6063793.

Kuang Z, Ji Z, Boeke JD, Ji H. Dynamic motif occupancy (DynaMO) analysis identifies transcription factors and their binding sites driving dynamic biological processes. Nucleic Acids Res. 2018 Jan 9;46(1):e2. doi: 10.1093/nar/gkx905. PubMed PMID: 29325176; PubMed Central PMCID: PMC5758894.

Kuang Z, Canzar S. Tracking Alternatively Spliced Isoforms from Long Reads by SpliceHunter. Methods Mol Biol. 2018;1751:73-88. doi: 10.1007/978-1-4939-7710-9_5. PubMed PMID: 29508290.

Kuang Z, Pinglay S, Ji H, Boeke JD. Msn2/4 regulate expression of glycolytic enzymes and control transition from quiescence to growth. Elife. 2017 Sep 26;6. doi: 10.7554/eLife.29938. PubMed PMID: 28949295; PubMed Central PMCID: PMC5634782.

Wang Y, Kuang Z, Yu X, Ruhn KA, Kubo M, Hooper LV. The intestinal microbiota regulates body composition through NFIL3 and the circadian clock. Science. 2017 Sep 1;357(6354):912-916. doi: 10.1126/science.aan0677. PubMed PMID: 28860383; PubMed Central PMCID: PMC5702268.

Ye C, Sutter BM, Wang Y, Kuang Z, Tu BP. A Metabolic Function for Phospholipid and Histone Methylation. Mol Cell. 2017 Apr 20;66(2):180-193.e8. doi: 10.1016/j.molcel.2017.02.026. Epub 2017 Mar 30. PubMed PMID: 28366644; PubMed Central PMCID: PMC5482412.

Zhang W, Zhao G, Luo Z, Lin Y, Wang L, Guo Y, Wang A, Jiang S, Jiang Q, Gong J, Wang Y, Hou S, Huang J, Li T, Qin Y, Dong J, Qin Q, Zhang J, Zou X, He X, Zhao L, Xiao Y, Xu M, Cheng E, Huang N, Zhou T, Shen Y, Walker R, Luo Y, Kuang Z, Mitchell LA, Yang K, Richardson SM, Wu Y, Li BZ, Yuan YJ, Yang H, Lin J, Chen GQ, Wu Q, Bader JS, Cai Y, Boeke JD, Dai J. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf3981. PubMed PMID: 28280149.

Mitchell LA, Wang A, Stracquadanio G, Kuang Z, Wang X, Yang K, Richardson S, Martin JA, Zhao Y, Walker R, Luo Y, Dai H, Dong K, Tang Z, Yang Y, Cai Y, Heguy A, Ueberheide B, Fenyö D, Dai J, Bader JS, Boeke JD. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4831. PubMed PMID: 28280154.

Wu Y, Li BZ, Zhao M, Mitchell LA, Xie ZX, Lin QH, Wang X, Xiao WH, Wang Y, Zhou X, Liu H, Li X, Ding MZ, Liu D, Zhang L, Liu BL, Wu XL, Li FF, Dong XT, Jia B, Zhang WZ, Jiang GZ, Liu Y, Bai X, Song TQ, Chen Y, Zhou SJ, Zhu RY, Gao F, Kuang Z, Wang X, Shen M, Yang K, Stracquadanio G, Richardson SM, Lin Y, Wang L, Walker R, Luo Y, Ma PS, Yang H, Cai Y, Dai J, Bader JS, Boeke JD, Yuan YJ. Bug mapping and fitness testing of chemically synthesized chromosome X. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4706. PubMed PMID: 28280152; PubMed Central PMCID: PMC5679077.

Xie ZX, Li BZ, Mitchell LA, Wu Y, Qi X, Jin Z, Jia B, Wang X, Zeng BX, Liu HM, Wu XL, Feng Q, Zhang WZ, Liu W, Ding MZ, Li X, Zhao GR, Qiao JJ, Cheng JS, Zhao M, Kuang Z, Wang X, Martin JA, Stracquadanio G, Yang K, Bai X, Zhao J, Hu ML, Lin QH, Zhang WQ, Shen MH, Chen S, Su W, Wang EX, Guo R, Zhai F, Guo XJ, Du HX, Zhu JQ, Song TQ, Dai JJ, Li FF, Jiang GZ, Han SL, Liu SY, Yu ZC, Yang XN, Chen K, Hu C, Li DS, Jia N, Liu Y, Wang LT, Wang S, Wei XT, Fu MQ, Qu LM, Xin SY, Liu T, Tian KR, Li XN, Zhang JH, Song LX, Liu JG, Lv JF, Xu H, Tao R, Wang Y, Zhang TT, Deng YX, Wang YR, Li T, Ye GX, Xu XR, Xia ZB, Zhang W, Yang SL, Liu YL, Ding WQ, Liu ZN, Zhu JQ, Liu NZ, Walker R, Luo Y, Wang Y, Shen Y, Yang H, Cai Y, Ma PS, Zhang CT, Bader JS, Boeke JD, Yuan YJ. “Perfect” designer chromosome V and behavior of a ring derivative. Science. 2017 Mar 10;355(6329). doi: 10.1126/science.aaf4704. PubMed PMID: 28280151.

Kuang Z, Boeke JD, Canzar S. The dynamic landscape of fission yeast meiosis alternative-splice isoforms. Genome Res. 2017 Jan;27(1):145-156. doi: 10.1101/gr.208041.116. Epub 2016 Nov 17. PubMed PMID: 27856494; PubMed Central PMCID: PMC5204338.

Publications from ZK predoctoral work, Johns Hopkins University (2008-2014)

Sliva A, Kuang Z, Meluh PB, Boeke JD. Barcode Sequencing Screen Identifies SUB1 as a Regulator of Yeast Pheromone Inducible Genes. G3 (Bethesda). 2016 Apr 7;6(4):881-92. doi: 10.1534/g3.115.026757. PubMed PMID: 26837954; PubMed Central PMCID: PMC4825658.

Kuang Z, Cai L, Zhang X, Ji H, Tu BP, Boeke JD. High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast. Nat Struct Mol Biol. 2014 Oct;21(10):854-63. doi: 10.1038/nsmb.2881. Epub 2014 Aug 31. PubMed PMID: 25173176; PubMed Central PMCID: PMC4190017.

Annaluru N, Muller H, Mitchell LA, Ramalingam S, Stracquadanio G, Richardson SM, Dymond JS, Kuang Z, Scheifele LZ, Cooper EM, Cai Y, Zeller K, Agmon N, Han JS, Hadjithomas M, Tullman J, Caravelli K, Cirelli K, Guo Z, London V, Yeluru A, Murugan S, Kandavelou K, Agier N, Fischer G, Yang K, Martin JA, Bilgel M, Bohutski P, Boulier KM, Capaldo BJ, Chang J, Charoen K, Choi WJ, Deng P, DiCarlo JE, Doong J, Dunn J, Feinberg JI, Fernandez C, Floria CE, Gladowski D, Hadidi P, Ishizuka I, Jabbari J, Lau CY, Lee PA, Li S, Lin D, Linder ME, Ling J, Liu J, Liu J, London M, Ma H, Mao J, McDade JE, McMillan A, Moore AM, Oh WC, Ouyang Y, Patel R, Paul M, Paulsen LC, Qiu J, Rhee A, Rubashkin MG, Soh IY, Sotuyo NE, Srinivas V, Suarez A, Wong A, Wong R, Xie WR, Xu Y, Yu AT, Koszul R, Bader JS, Boeke JD, Chandrasegaran S. Total synthesis of a functional designer eukaryotic chromosome. Science. 2014 Apr 4;344(6179):55-8. doi: 10.1126/science.1249252. Epub 2014 Mar 27. PubMed PMID: 24674868; PubMed Central PMCID: PMC4033833.

Zhao L, Zhao X, Tian T, Lu Q, Skrbo-Larssen N, Wu D, Kuang Z, Zheng X, Han Y, Yang S, Zhang C, Meng A. Heart-specific isoform of tropomyosin4 is essential for heartbeat in zebrafish embryos. Cardiovasc Res. 2008 Nov 1;80(2):200-8. doi: 10.1093/cvr/cvn177. Epub 2008 Jun 25. PubMed PMID: 18583338.

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