朱方捷，教授，博士生导师
一、个人简介：
菌草生态产业协同创新中心副主任、“闽江学者”特聘教授、“雏鹰计划”青年拔尖人才、省引进高层次人才、人社部高层次留学回国人才
《Molecular Cell》、《Genome Biology》、《Plant Physiology》杂志审稿人
二、联系方式：
福建农林大学海峡联合研究院 350002
Email: fjzhu@fafu.edu.cn
三、实验室介绍：
转录系统生物学实验室（Transysbio Lab）：http://hbmcsysbio.team
欢迎对AI/顺式元件组/表观组感兴趣的老师、同学加入
四、学习及工作经历：
2003–2010 清华大学 学士，硕士
2010–2013 东京大学 博士
2014–2018 卡罗林斯卡医学院 博士后
2018–2020 剑桥大学 Research Associate
2020– 福建农林大学海峡联合研究院 教授
五、主持项目：
2021-2023 福建省“闽江学者奖励计划”特聘教授
2021-2024 福建省重大专项（2021NZ029009，课题负责人）
2022-2025 福建省自然科学基金杰出青年项目（2022J06017）
2022-2025 国家自然科学基金面上项目（32170554）
2024-2027 国家自然科学基金面上项目（32370582）
2024-2027 人社部高层次留学回国人才资助
2025-2029 福建省“雏鹰计划”青年拔尖人才
2025-2027 国家重点研发计划（2024YFC3407200，课题负责人）
2026-2029 国家自然科学基金面上项目（3257040305）
六、研究方向：
植物顺式元件组（Cistrome）的
1）鉴定（高通量技术开发）
2）功能（转录调控机制解析）
3）应用（菌草种质创新）
研究内容：
转录系统生物学实验室（Transysbio Lab）的研究目标是——系统鉴定植物顺式元件组，解析其调控转录的机制，为育种提供定时、定点、定量调控关键基因表达的功能位点。并解析顺式元件组与其他表观组的互作机制。
目前为止已有超1000种植物基因组公开发表，除编码蛋白质的基因外，基因组中还存在大量”暗物质”——非编码调控元件，其功能有待系统解读。非编码基因组中的所有转录因子结合位点组成顺式元件组，是决定各基因时空特异性表达的关键。本课题组围绕植物中的顺式元件组及其互作因子（核小体、转录因子、lncRNA等）开展高通量研究，力求解析转录调控的普遍性规律。
起源于福建农林大学，由林占禧研究员开发的菌草技术，为国际贫困地区的生态治理与经济发展提供了中国方案。为进一步提升菌草的加工性能、产量、抗逆性等农艺性状，本实验室针对菌草关键生理过程，绘制表观基因组图谱，解析功能基因及其顺式元件，构建转录调控网络，为菌草种质创新中精确调节目的基因表达提供理论依据与育种靶标。
七、发表文章
主要成果：
· N. Ma, D. Jiang, T. Li, L. Luo, H. Chen, X. Zhang, Z. Mu, S. Chen, P. Chen, Q. Liu, J. Lin, Q. Wang, Y. Yin, J. Taipale, J. Huang*, H. Guo*, F. Zhu*, The Specificity Landscape of AtWRKYs Reveals the Bidirectional Influence of non-CG Methylation. Nucleic Acids Res. (IF = 13.1), 2025, (Accepted)
· (Review) T. Li, W. Zeng, F. Zhu*, P. Lü*, Cis-regulatory elements: systematic identification and horticultural applications. aBIOTECH (IF = 5.0), 2025, 6, 510-527.
· T. Li, H. Chen, N. Ma, D. Jiang, J. Wu, X. Zhang, H. Li, J. Su, P. Chen, Q. Liu, Y. Guan, X. Zhu, J. Lin, J. Zhang, Q. Wang*, H. Guo*, F. Zhu*, Specificity landscapes of 40 R2R3‐MYBs reveal how paralogs target different cis‐elements by homodimeric binding. iMeta (IF = 33.2), 2025, 4, e70009.
· L. Luo, D. Lin, J. Li, H. Chen, Q. Qi, L. Zhang, Y. Luo, J. Chen, D. Jiang, P. Lü, W. Zhu, H, Lin, E. Shao, H. Yan, Y. Jin, G. Lu, Z. Lin, L. Xun, F. Zhu*, L. Huang*, J. Xiao*, EGDB: a comprehensive multi-omics database for energy grasses and the epigenomic atlas of pearl millet. iMeta (IF = 23.7), 2024, 3, e263.
· C. Wen, Z. Yuan, X. Zhang, H. Chen, L. Luo, W. Li, T. Li, N. Ma, F. Mao, D. Lin, Z. Lin, C. Lin, T. Xu, P. Lü*, J. Lin*, F. Zhu*, Sea-ATI Unravels Novel Vocabularies of Plant Active Cistrome. Nucleic Acids Res. (IF = 14.9), 2023, 51, p11568.
· M. Sun, H. Yan, A. Zhang, Y. Jin ... X. Zhang, F. Zhu*, L. Huang*, Milletdb: A Multi-Omics Database to Accelerate the Research of Functional Genomics and Molecular Breeding of Millets. Plant Biotechnol. J. (IF = 13.8), 2023, 21, p2348.
· S.O. Dodonova, F. Zhu, C. Dienemann, J. Taipale, P. Cramer, Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function. Nature (IF = 49.9) 2020, 580, p669.
· F. Zhu, L. Farnung, E. Kaasinen, B. Sahu, Y. Yin, B. Wei, S.O. Dodonova, K.R. Nitta, E. Morgunova, M. Taipale, P. Cramer, J. Taipale, The interaction landscape between transcription factors and the nucleosome. Nature (IF = 41.577), 2018, 562, p76.
其他成果：
· L. Luo, Q. Qu, M. Cao, Y. Zhang, Y. Sun, F. Mao, J. Chen, Y. Zhu, Y. Yang, H. Liu, C. Li, D. Lin, G. Lu, Z. Lin, F. Zhu*, J. Xiao*, Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression. aBIOTECH (IF = 5.0), 2025, 6, 394-410.
· D. Jiang, X. Zhang, L. Luo, T. Li, H. Chen, N. Ma, L. Fu, P. Tian, F. Mao, P. Lü, H. Guo*, F. Zhu*, Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14. Int. J. Mol. Sci. (IF = 4.9), 2025, 26, 763.
· F. Zhu, T. Nishimura and T. Kato, Organic/inorganic fusion materials: cyclodextrin-based polymer/CaCO3 hybrids incorporating dye molecules through host-guest interactions. Polym. J. (IF = 2.8), 2015, 47, p122.
· F. Zhu, T. Nishimura, H. Eimura, and T. Kato, Supramolecular effects on formation of CaCO3 thin films on a polymer matrix. CrystEngComm (IF = 3.756), 2014, 16, p1496.
· F. Zhu, T. Nishimura, T. Sakamoto, H. Tomono, H. Nada, Y. Okumura, H. Kikuchi, and T. Kato, Tuning the stability of CaCO3 crystals with magnesium ions for formation of aragonite thin films on organic polymer templates. Chem. Asian J. (IF = 4.839), 2013, 8, p3232.
· F. Zhu, Y. Kong, J. Liang, C. Li, Y. Hu, Y. Zhou, X. Liu, L. Xie, and R. Zhang, Tuning calcite magnesium content by soluble shell matrices: Insights into biomineral impurity control. Mater. Sci. Eng. C (IF = 8.457), 2010, 30, p963.
· W. Xue, ... N. Ma, F. Zhu, C. Chen*, Y. Yin*, Y. Zhang*, K. Xu*, Structural basis of nucleosome binding and destabilization by the extended DNA binding domain of RFX5. Nucleic Acids Res., 2025, 53, gkaf734.
· M. Fei, L. Luo, N. Ma, Q. Qi, H. Chen, Y. Chao, M. Cao, E. Shao, H. Lin, Z. Lin, F. Zhu, G, Lu*, D. Lin*, A Spatiotemporal Transcriptome Reveals Stalk Development in Pearl Millet. Int. J. Mol. Sci., 2024, 25, 9798.
· Z. Li, ... F. Zhu, C. Shao, G. Wang, T. Sun, N. Wang, G. Liu, J. Ni, Y. Liu, A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity. Nucleic Acids Res., 2024, 52.
· E. Morgunova, G. Nagy, Y. Yin, F. Zhu, S. Nayak, T. Xiao, I. Sokolov, A. Popov, C. Laughton, H. Grubmuller, J. Taipale, Interfacial water confers transcription factors with dinucleotide specificity. Nat. Struct. Mol. Biol., 2025, 32, 650-661.
· B. Zhang, X. Dang, H. Chen, T. Li, F. Zhu, S. Nagawa. Ectopic Expression of FvVND4c Promotes Secondary Cell Wall Thickening and Flavonoid Accumulation in Fragaria Vesca. Int. J. Mol. Sci. 2023, 24, p8110.
· B. Sahu, T. Hartonen, P. Pihlajamaa, B. Wei, K. Dave, F. Zhu, E. Kaasinen, K. Lidschreiber, M. Lidschreiber, C.O. Daub, P. Cramer, T. Kivioja, J. Taipale. Sequence determinants of human gene regulatory elements. Nat. Genet. 2022, 54, p283.
· A. Jolma, J. Zhang, E. Mondragon, E. Morgunova, T. Kivioja, K.U. Laverty, Y. Yin, F. Zhu, G. Bourenkov, Q. Morris, T.R. Hughes, L.J.III Maher, J. Taipale, Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences. Genome Res. 2020, 30, p962.
· B. Wei, A. Jolma, B. Sahu, L.M. Orre, F. Zhong, F. Zhu, T. Kivioja, I. Sur, J. Lehtio, M. Taipale, J. Taipale, A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility. Nat. Biotechnol. 2018, 36, p521.
· E. Morgunova, Y. Yin, P.K. Das, A. Jolma, F. Zhu, A. Popov, Y. Xu, L. Nilsson, J. Taipale, Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima. Elife 2018, 7.
· J. Su, F. Zhu, G. Zhang, H. Wang, L. Xie and R. Zhang, Transformation of amorphous calcium carbonate nanoparticles into aragonite controlled by ACCBP. CrystEngComm, 2016, 18, p2125.
· T. Nishimura, F. Zhu, H. Tomono, H. Nada, T. Kato, バイオミネラリゼーションに学ぶ有機／無機複合体の設計と合成：高分子およびマグネシウムイオンによる炭酸カルシウムのモルホロジー制御, オレオサイエンス, 2014, 14, p417.
· H. Tomono, H. Nada, F. Zhu, T. Sakamoto, T. Nishimura, and T. Kato, Effects of magnesium ions and water molecules on the structure of amorphous calcium carbonate: a molecular dynamics study. J. Phys. Chem. B, 2013, 117, p14849.
· Y. Lin, W. Zhang, F. Zhu, J. Su, D. Fang, Y. Yang, G. Zhang, L. Xie, R. Zhang, and H. Wang, Subcellular localization of N-deoxyribosyltransferase in Lactobacillus fermentum: cell surface association of an intracellular nucleotide metabolic enzyme. FEMS Microbiol. Lett., 2011, 323, p132.
· L. Xie, F. Zhu, Y. Zhou, C. Yang, and R. Zhang, Molecular approaches to understand biomineralization of shell nacreous layer. Prog. Mol. Subcell. Biol., 2011, 52, p331.
· Y. Zhou, Z. He, C. Li, L. Xiang, F. Zhu, G. Zhang, L. Xie, and R. Zhang, Correlations among mRNA expression levels of Engrailed, BMP2 and Smad3 in mantle cells of pearl oyster Pinctada fucata. Prog. Biochem. Biophys., 2010, 37, p737.
· C. Li, J. Huang, S. Li, W. Fan, Y. Hu, Q. Wang, F. Zhu, L. Xie, and R. Zhang, Cloning, characterization and immunolocalization of two subunits of calcineurin from pearl oyster (Pinctada fucata). Comp. Biochem. Physiol. B: Biochem. Mol. Biol., 2009, 153, p43.
· Y. Kong, G. Jing, Z. Yan, C. Li, N. Gong, F. Zhu, D. Li, Y. Zhang, G. Zheng, H. Wang, L. Xie, and R. Zhang, Cloning and characterization of Prisilkin-39, a novel matrix protein serving a dual role in the prismatic layer formation from the oyster pinctada fucata. J. Biol. Chem., 2009, 284, p10841.
八、招生专业
生物育种、生物技术与工程等