Chenlab:Publications

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     (*) First authorship; (^) Senior authorship

           2021

  1. Yang Yi*, Yanqiang Li*, Qingshu Meng*, Qiaqia Li, Fuxi Li, Bing Lu, Jiangchuan Shen, Ladan Fazli, Dongyu Zhao, Chao Li, Weihua Jiang, Rui Wang, Qipeng Liu, Aileen Szczepanski, Qianru Li, Wei Qin, Adam B. Weiner, Tamara L. Lotan, Zhe Ji, Sundeep Kalantry, Lu Wang, Edward M. Schaeffer, Hengyao Niu, Xuesen Dong, Wei Zhao, Kaifu Chen^, Qi Cao^.
    A PRC2-independent function for EZH2 in regulating rRNA 2′-O methylation and IRES-dependent translation.
    Nature Cell Biology. (2021)

  2. Guangyu Wang*, Bo Xia*, Jie Lv, Dongyu Zhao, Yanqiang Li, Yiwen Bu, Xin Wang, John P. Cooke, Qi Cao, Min Gyu Lee, Lili Zhang, Kaifu Chen^. MACMIC Reveals Dual Role of CTCF in Epigenetic Regulation of Cell Identity Genes.
    Genomics, Proteomics, and Bioinformatics. (2021)

  3. Christopher J Terranova, Ming Tang, Mayinuer Maitituoheti, Ayush T Raman, Archit K Ghosh, Jonathan Schulz, Samir B Amin, Elias Orouji, Katarzyna Tomczak, Sharmistha Sarkar, Junna Oba, Caitlin Creasy, Chang-Jiun Wu, Samia Khan, Rossana Lazcano, Khalida Wani, Anand Singh, Praveen Barrodia, Dongyu Zhao, Kaifu Chen, Lauren E Haydu, Wei-Lien Wang, Alexander J Lazar, Scott E Woodman, Chantale Bernatchez, Kunal Rai. Reprogramming of bivalent chromatin states in NRAS mutant melanoma suggests PRC2 inhibition as a therapeutic strategy. Cell Report. (2021)

  4. Gianfranco Matrone, Bo Xia, Kaifu Chen, Martin A. Denvir, Andrew H. Baker, and John P. Cooke. Fli1+ cells transcriptional analysis reveals an Lmo2–Prdm16 axis in angiogenesis. PNAS. (2021)

  5. Guangyu Wang*, Ana Sofia Cruz*, Keith Youker, Hernan G. Marcos-Abdala, Rajarajan A. Thandavarayan, John P. Cooke, Guillermo Torre-Amione, Kaifu Chen^, Arvind Bhimaraj^. Role of Endothelial and Mesenchymal Cell Transitions in Heart Failure and Recovery Thereafter.
    Frontiers in Genetics. (2021).

    2020

  6. Shu Meng*^, Jie Lv*, Palas K. Chanda, Iris Owusu, Kaifu Chen^, John P. Cooke^. Reservoir of Fibroblasts Promotes Recovery from Limb Ischemia.
    Circulation. (2020)

  7. Dongyu Zhao*, Lili Zhang*, Min Zhang, Bo Xia, Jie Lv, Guangyu Wang, Qingshu Meng, Yang Yi, Sen Zhu, Alin S. Tomoiaga, Min Gyu Lee, John P. Cooke, Qi Cao^, Kaifu Chen^. Broad Genic Repression Domains Signify Enhanced Silencing of Oncogenes.
    Nature Communications. (2020b)

  8. Bo Xia*, Dongyu Zhao*, Guangyu Wang*, Min Zhang, Jie Lv, Alin S. Tomoiaga, Yanqiang Li, Xin Wang, Shu Meng, John P. Cooke, Qi Cao^, Lili Zhang^, Kaifu Chen^. Machine learning reveals cell identity regulator by histone codes.
    Nature Communications. (2020a)

  9. Guangyu Wang, Qingshu Meng, Bo Xia, Jie Lu, Dongyu Zhao, Yanqiang Li, Xin Wang, Lili Zhang, John P. Cooke, Qi Cao^, Kaifu Chen^. TADsplimer reveals splits and mergers of topologically associating domains for epigenetic regulation of transcription.
    Genome Biology. (2020)

  10. Qiang Wang, Dongyu Zhao, Miao Xian, Zhuo Wang, Enguang Bi, Pan Su, Jianfei Qian, Xingzhe Ma, Maojie Yang, Lintao Liu, Youli Zu, Sai Ravi Pingali, Kaifu Chen, and Zhen Cai, Qing Yi. MIF as a biomarker and therapeutic target for overcoming resistance to proteasome inhibitors in human myeloma.
    Blood. (2020)

  11. Sen Zhu*, Dongyu Zhao*, Chao Li*, Qiaqia Li, Weihua Jiang, Qipeng Liu, Rui Wang, Ladan Fazli, Yinan Li, Lili Zhang, Yang Yi, Qingshu Meng, Wanyi Wang, Guangyu Wang, Min Zhang, Xiongbing Zu, Wei Zhao, Tuo Deng, Jindan Yu, Xuesen Dong, KaiFu Chen^, Qi Cao^. BMI1 is directly regulated by androgen receptor to promote castration-resistance in prostate cancer.
    Oncogene. (2020)

  12. Motao Zhu, Guangtong Deng, Peng Tan, Changsheng Xing, Cuiping Guan, Chongming Jiang, Yinlong Zhang, Bo Ning, Chaoran Li, Bingnan Yin, Kaifu Chen, Yuliang Zhao, Helen Y Wang, Beth Levine, Guangjun Nie, Rong-Fu Wang. Beclin 2 negatively regulates innate immune signaling and tumor development.
    The Journal of clinical investigation. (2020)

  13. Qiaqia Li*, Kilia Y. Liu*, Qipeng Liu*, Guangyu Wang*, Weihua Jiang, Dongyu Zhao,Qingshu Meng, Yang Yi, Yongyong Yang, Rui Wang, Sen Zhu, Chao Li, Lin Yan, Lili Zhang, Jung-Sun Kim, Xiongbing Zu, Anthony Kozielski, Wei Qian, Jenny Chang, Akash Patnaik, Kaifu Chen^ and Qi Cao.
    Antihistamine Drug Ebastine inhibits cancer growth by targeting Polycomb Group Protein EZH2.
    Molecular Cancer Therapeutics.

    2019

  14. Qilin Gu, Xiaojie Yang, Jie Lv, Jiaxiong Zhang, Bo Xia, Jun-dae Kim, Ruoyu Wang, Feng Xiong, Shu Meng, Thomas P. Clements, Bhavna Tandon, Daniel S. Wagner, Miguel F. Diaz, Pamela L. Wenzel, Yury I. Miller, David Traver, John P. Cooke, Wenbo Li, Leonard I. Zon, Kaifu Chen^, Yongping Bai^, Longhou Fang^. AIBP-mediated Cholesterol Efflux Instructs Hematopoietic Stem and Progenitor Cell Fate.
    Science. (2019)

  15. Qipeng Liu*, Guangyu Wang*, Qiaqia Li*, Weihua Jiang, Jung‐Sun Kim, Rui Wang, Sen Zhu, Xiaoju Wang, Lin Yan, Yang Yi, Lili Zhang, Qingshu Meng, Chao Li, Dongyu Zhao, Yuanyuan Qiao, Yong Li, Demirkan B. Gursel, Arul M. Chinnaiyan, Kaifu Chen^, Qi Cao^. Polycomb Group Proteins EZH2 and EED Directly Regulate Androgen Receptor in Advanced Prostate Cancer.
    International Journal of Cancer. (2019)

  16. Palas K. Chanda, Shu Meng, Jieun Lee, Honchiu E. Leung, Kaifu Chen, John P. Cooke. Nuclear S-nitrosylation defines an optimal zone for inducing pluripotency.
    Circulation. (2019)

  17. Zhi Long, Yinan Li, Yu Gan, Dongyu Zhao, Guangyu Wang, Ning Xie, Jessica M Lovnicki, Ladan Fazli, Qi Cao, Kaifu Chen, Xuesen Dong. Roles of the HOXA10 Gene during Castrate Resistant Prostate Cancer Progression.
    Endocrine-Related Cancer (2019)

    2018

  18. Yang Yu*, Nhung Pham*, Bo Xia*, Alma Papusha, Guangyu Wang, Zhenxin Yan, Guang Peng, Kaifu Chen^, Grzegorz Ira1^. Dna2 nuclease deficiency results in large and complex DNA insertions at chromosomal breaks.
    Nature. (2018)

  19. Sen Zhu*, Dongyu Zhao*, Lin Yan*, Weihua Jiang, Jungsun Kim, Bingnan Gu, Qipeng Liu, Rui Wang, Bo Xia, Jonathan Zhao, Gang Song, Xiaobing Shi, HungMing Lam, Xuesen Dong, Jindan Yu, Kaifu Chen^, Qi Cao^. BMI1 Regulates Androgen Receptor in Prostate Cancer Independently of the Polycomb Repressive Complex I.
    Nature Communications. (2018)
    Featured in Editors' Highlights Webpage

  20. Shilpa S. Dhar*, Dongyu Zhao*, Tao Lin, Bingnan Gu, Khusboo Pal, Hunain Alam, Jie Lv, Vidya Gopalakrishnan, Wei Li, Ali Shilatifard, Roy V. Sillitoe, Kaifu Chen^, Min Gyu Lee^. MLL4 is required to maintain broad H3K4me3 peaks and super-enhancers at tumor suppressor genes.
    Molecular Cell. (2018)

  21. Zheng Hu*, Bo Xia*, Spike Postnikoff, Troy A Harkness, JaHwan Seol, Alin S Tomoiaga, Wei Li, Kaifu Chen^, and Jessica K. Tyler^. Ssd1 and Gcn2 suppress global translational efficiency in replicatively aged yeast.
    Elife. (2018)

  22. Hyun Jung Park, Ping Ji, Soyeon Kim, Zheng Xia, Benjamin Rodriguez, Lei Li, Jianzhong Su, Kaifu Chen, Chioniso Masamha, David Baillat, Ms. Camilla Fontes, Ann-Bin Shyu, Joel Neilson, Eric Wagner, Wei Li. 3ʹ-UTR Shortening Represses Tumor Suppressor Genes in trans by Disrupting ceRNA Crosstalk.
    Nature Genetics. (2018)

  23. Shu Meng*, Qilin Gu*, Xiaojie Yang, Jie Lv, Iris B Owusu, Gianfranco Matrone, Kaifu Chen, John Cooke^, and Longhou Fang^. TBX20 Regulates Angiogenesis through the PROK2-PROKR1 Pathway.
    Circulation. (2018)

  24. Su J, Huang YH, Cui X, Zhang X, Lei Y, Wang X, Lin X, Chen K, Lv J, Goodell MA, Li W*. Homeobox Oncogene Activation by Pan-Cancer DNA Hypermethylation.
    Genome Biology (2018)

  25. Hunain Alam, Na Li, Shilpa S. Dhar, Ms. Sarah J. Wu, Jie Lv, Kaifu Chen, Elsa R. Flores, Laura Baseler, Min Gyu Lee. HP1γ promotes lung adenocarcinoma by downregulating the transcription-repressive regulators NCOR2 and ZBTB7A.
    Cancer Research. (2018)

  26. Xiaolong Zhang, Xiang Xiao, Peixiang Lan, Junhui Li, Yaling Dou, Wenhao Chen, Naoto Ishii, Shuqiu Chen, Bo Xia, Kaifu Chen, Elizabeth Taparowsky, and Xian C. Li. OX40 Costimulation Inhibits Foxp3 Expression and Treg Induction via BATF3-Dependent and Independent Mechanisms.
    Cell Reports. (2018)

  27. Moon Jong Kim, Bo Xia, Han Na Suh, Sung Ho Lee, Sohee Jun, Esther M. Lien, Jie Zhang, Kaifu Chen, and Jae-Il Park. PAF-Myc-Controlled Cell Stemness Is Required for Intestinal Regeneration and Tumorigenesis.
    Developmental Cell. (2018)

    2017

  28. Shaofeng Liu*, Zhiyun Xu*, He Leng*, Pu Zheng, Jiayi Yang, Kaifu Chen, Jianxun Feng, Qing Li. RPA binds histone H3-H4 and functions in DNA replication–coupled nucleosome assembly.
    Science. (2017)

  29. Narkhyun Bae*, Monica Viviano*, Xiaonan Su*, Jie LV, Donghang Cheng, Cari Sagum, Sabrina Castellano, Xue Bai, Claire Johnson, Mahmoud Ibrahim Khalil, Kaifu Chen, Haitao Li^, Gianluca Sbardella^ and Mark T. Bedford^. Evolving Spindlin1 Small Molecule Inhibitors Using Protein Microarrays.
    Nature Chemical Biology. (2017)

  30. Xueqiu Lin, Jianzhong Su, Kaifu Chen, Benjamin Rodrigues, Wei Li^: Sparse conserved under-methylated CpGs are associated with high-order chromatin structure.
    Genome Biology (2017)

  31. Wing Tak Wong, Gianfranco Matrone, Xiaoyu Tian, Simion Alin Tomoiaga, Kin Fai Au, Shu Meng, Sayumi Yamazoe, Kaifu Chen, Helen M. Blau, John P. Cooke. Discovery of Novel Determinants of Endothelial Lineage using Chimeric Heterokaryons.
    Elife. (2017)

  32. Gianfranco Matrone, Shu Meng, Qilin Gu, Jie Lv, Longhou Fang, Kaifu Chen, John P. Cooke. Lmo2 (LIM-Domain-Only 2) Modulates Sphk1 (Sphingosine Kinase) and Promotes Endothelial Cell Migration
    Arteriosclerosis, Thrombosis, and Vascular Biology. (2017)

  33. Rebecca Jean Watters, Ryan Hartmaier, Hatice Ulku Osmanbeyoglu, Ryan Gillihan, James Rae, Lan Liao, Kaifu Chen, Wei Li, Xinghua Lu, steffi oesterreich. Steroid receptor coactivator-1 can regulate osteoblastogenesis independently of estrogen.
    Molecular and Cellular Endocrinology. (2017)

    2016

  34. Li N*, Li Y*, Lv J*, Zheng X, Wen H, Shen H, Zhu G, Chen TY, Dhar SS, Kan PY, Wang Z, Shiekhattar R, Shi X, Lan F, Chen K, Li W, Li H, Lee MG. ZMYND8 reads the dual histone mark H3K4me1-H3K14ac to antagonize the expression of metastasis-linked genes.
    Molecular Cell (2016)

  35. Jie Lv, Chen K. Broad H3K4me3 as a Novel Epigenetic Signature for Normal Development and Disease.
    Genomics, proteomics & bioinformatics (2016)

  36. Lee S, Chen T, Dhar S, Gu B, Chen K, Kim Y, Li W, Lee M. A feedback loop comprising PRMT7 and miR-24-2 interplays with Oct4, Nanog, Klf4, c-Myc to regulate stemness.
    Nucleic Acids Research. (2016)

  37. Meng S, Matrone G, Lv J, Chen K, Wong W, Cooke J. LMO2 Regulates Endothelial Proliferation, Angiogenesis and Tissue Regeneration.
    Journal of the American Heart Association. (2016)

    2015

  38. Chen K*, Chen Z*, Wu D, Zhang L, Lin X, Su J, Rodriguez B, Xi Y, Xia Z, Chen X, Shi X, Wang Q, Li W. Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes.
    Nature Genetics. (2015) highlighted by the Cancer Discovery journal

  39. Dhar Shilpa*, Lee Sung-Hun*, Chen Kaifu*, Zhu Guangjing, Oh WonKyung, Allton Kendra, Gafni Ohad, Alin S. Tomoiga, Kim Young Zoon, Barton Michelle, Hanna Jacob H, Wang Zhibin, Li Wei, Lee Min Gyu. An essential role for UTX in resolution and activation of bivalent promoters.
    Nucleic Acids Research. (2015)

  40. Chen Kaifu*, Zheng Hu*, Zheng Xia, Dongyu Zhao, Wei Li, Jessica K. Tyler. The overlooked fact: fundamental need of spike-in controls for virtually all genome-wide analyses.
    Molecular and Cellular Biology. (2015)

  41. Chen L*, Chen K*, Baker S A, Shaw C, Li W, Zoghbi H Y. MeCP2 binds to mCH as neurons mature, influencing transcription and onset of Rett syndrome.
    PNAS. (2015) (Highlighted by the Science journal)

    2014

  42. Hu Z*, Chen K*, Xia Z, Chavez M, Pal S, Seol J, Chen C, Li W, Tyler J K. Nucleosome loss leads to global transcriptional upregulation and genomic instability during yeast aging.
    Genes & Development. (2014). (Highlighted by the Science journal), (Recommended by Faculty of 1000)

  43. Wang L, Chen J, Wang C, Zimmermann M T, Yan H, Sun Z, Zhang Y, Chen K, Huang H, Kocher J A, Li W. MACE: Model based Analysis of ChIP-exo.
    Nucleic Acids Research. (2014).

  44. Hu Z, Chen K, Li W, Tyler J. A matter of access: Nucleosome disassembly from gene promoters is the central goal of transcriptional activators.
    Transcription. (2014)

  45. Hu Z, Chen K, Li W, Tyler JK. Transcriptional and genomic mayhem due to aging-induced nucleosome loss in budding yeast.
    Microbial Cell. (2014)

    2013

  46. Chen K*, Xi Y, Pan X, Li Z, Kaestner K, Tyler J, Dent S YR, He X, Li W. DANPOS: Dynamic Analysis of Nucleosome Position and Occupancy by Sequencing.
    Genome Research (2013). (Highlighted in headlines by Epigenie).

  47. Chen K*, Wilson M A*, Hirsch C, Watson A, Liang S, Lu Y, Li W, Dent S YR: Stabilization of the Promoter Nucleosomes in Nucleosome Free Region by the Yeast Ssn6-Tup1 Corepressor.
    Genome Research. (2013).

  48. Huang Z*, Chen K*, Zhang J*, Li Y*, Wang H, Cui D, Tang J, Liu Y, Shi X, Li W, Chen R, Sucgang R S, Pan X: A functional variomics tool for discovering resistance genes and targets of small molecule compounds.
    Cell Reports. (2013).

  49. Al-Mssallem I S, Hu S, Zhang X, Tan J, Lin Q, Liu W, Yu X, … Chen K, Alkhaldi S R, Liu G, Zhang M, Guo H, Yu J. Genome Sequences and Genetic Variations of Date Palm.
    Nature Communications. (2013).

    2012

  50. Li Z, Gadue P, Chen K, Tuteja G, Schug J, Li W, Kaestner K H. Foxa2 and H2A.Z Mediate Nucleosome Depletion during Embryonic Stem Cell Differentiation.
    Cell. (2012).

  51. Chen X, Cui D, Papusha A, Zhang X, Chu C, Tang J, Chen K, Pan X, Ira G, The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends.
    Nature. (2012)

  52. Barber M F, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen R I, Chen K, et al. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation.
    Nature. (2012)

  53. Huang Z, Srinivasan S, Zhang J, Chen K, Li Y, Li W, Quiocho F A, Pan X. Discovering thiamine transporters as targets of chloroquine using a novel functional genomics strategy.
    PLOS Genetics. (2012)

  54. Badeaux A I, Yang Y, Cardenas K, Vemulapalli V, Chen K, Kusewitt D, Richie E, et al. Loss of the methyl lysine effector protein PHF20 impacts the expression of genes regulated by the lysine acetyltransferase MOF.
    The Journal of biological chemistry. (2012)

    2011

  55. Kuo A J*, Cheung P*, Chen K*, Zee B M, Kioi M, Lauring J, Xi Y, et al. NSD2 Links Dimethylation of Histone H3 at Lysine 36 to Oncogenic Programming.
    Molecular cell. (2011)

  56. Huang Z, Chen K, Xu T, Zhang J, Li Y, Li W, Agarwal A K, et al. Sampangine inhibits heme biosynthesis in both yeast and human.
    Eukaryotic cell, (2011)

  57. Ma L, Chen K, Meng Q, Liu Q, Tang P, Hu S, Yu J. An evolutionary analysis of trypanosomatid GP63 proteases.
    Parasitology research. (2011)

  58. Meng Q, Chen K, Ma L, Hu S, Yu J. A systematic identification of Kolobok superfamily transposons in Trichomonas vaginalis and sequence analysis on related transposases.
    Journal of genetics and genomics. (2011)

    2010 and before

  59. Chen K*, Wang L, Yang M, Liu J, Xin C, Hu S, Yu J. Sequence signatures of nucleosome positioning in Caenorhabditis elegans. Genomics, proteomics & bioinformatics. (2010)

  60. Yang M, Zhang X, Liu G, Yin Y, Chen K, Yun Q, Zhao D, et al. The complete chloroplast genome sequence of date palm.
    PlOS ONE. (2010)

  61. Yang M, Song S, Liu G, Chen K, Tian X, Zhao Z J, et al. A comprehensive analysis of protein phosphatases in rice and Arabidopsis.
    Plant Systematics and Evolution. (2010)

  62. Chen K*, Meng Q, Ma L, Liu Q, Tang P, Chiu C, Hu S, et al. A novel DNA sequence periodicity decodes nucleosome positioning.
    Nucleic acids research. (2008)


    Abstract

  63. A Mojiri, B Walter, C Jiang, G Matrone, R Holgate, Q Qiu, K Chen, J Cooke. TELOMERASE THERAPY REVERSES VASCULAR SENESCENCE IN HGPS. Canadian Journal of Cardiology. 2020.

  64. Shilpa S. Dhar, Dongyu Zhao, Tao Lin, Roy V. Sillitoe, Kaifu Chen and Min Gyu Lee. Heterozygous knockout of the histone modifier MLL4 promotes Ptch+/−-driven medulloblastoma. Cancer Research. 2020.

  65. Shu Meng , Jie Lv , Palas K Chanda , Iris Owusu , Kaifu Chen , John P Cooke. A Reservoir of Fibroblasts Promotes Recovery From Limb Ischemia. Circulation, 2019.

  66. Raquel A Araujo-Gutierrez, Guangyu Wang, Areeba Ali, Hernan G Marcos-Abdala, Cesar Uribe, Hilda M Gonzalez-Bonilla, Alpana Senapati, Keith A Youker, Guillermo Torre-Amione, Kaifu Chen, Arvind Bhimaraj. Genetic Determinants of Allograft Hypertrophy-A Human Myocardial Biopsy Study. Journal of Cardiac Failure. 2019.

  67. Sen Zhu, Dongyu Zhang, Lin Yan, Weihua Jiang, Qipeng Liu, Rui Wang, Bo Xia, Jonathan C Zhao, Rong-Fu Wang, Xiaobing Shi, Hung-ming Lam, Xuesen Dong, Jindan Yu, Kaifu Chen, Qi Cao. A novel role for polycomb group protein BMI1 in prostate cancer. Cancer Research. 2018

  68. Shu Meng , Qilin Gu , Xiaojie Yang , Jie Lv , Iris Owusu , Gianfranco Matrone , Kaifu Chen , Longhou Fang , and John Cooke. Discovery of a Novel Angiogenic Factor TBX20. Circulation. 2017






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