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Silin
Zhong Lab | Plant Functional Genomics CUHK
Research (list of publications) 在果实成 熟研究方向，我们实验室发现DNA甲基化是除了转录因子 和乙烯之外控制番茄成熟的重要因子。通过比较基因组学对比11种果实的超过300个基因表达(RNA-seq)，染色质开合(DNase-seq)， 核小体修饰(Histone ChIP-seq)，DNA甲基化 (BS-seq)，转录因子结合位点(TF ChIP-seq)数据，发现开花 植物用了三种方式进化出呼吸跃变果实，其关键基因都受到保守的H3K27me3控 制，并且可以追溯到 拟南芥水稻等干果以及草莓黄瓜等非跃变果实里面。这说明在进化过程中，番茄等水果不仅继承并改进了其祖先被子植物 (angiosperm)的基因，还沿用了它们的表观遗传标记来控制成熟。该研究首次从分子水平解释了果实 成熟的调 控是如何趋 同进化的。在比较完各个物种后，现在实验室的果实方向研究已经从新聚焦回模式植物番茄，用大规模的转录 因子ChIP-seq构建一个精细的番茄成熟转录调控网路。 我们实验 室的另一个主要研究方向是玉米等单子叶植物的碳4光合通路，它恰好也是趋同进化 的产物。我们实验室通过开发新的高通量原生质体转化方法，更有效的epitope tag和新的Tn5转座子，成功使 用ChIP-seq定位了104个玉米叶片转录因 子的结合位点。有了这些数据，我们实验室和Corenll大学 Ed Buckler的生信团队合作重构并且利用机器学习对比不同物种的叶片转录调控网路。 我们现在正通过功能基因组学和生物信息学等多层面更深入的研究玉米C4基因的调控机制，并利用比较基因组学研究C4进化。也正 在开发新的单细胞测序的方法，研究叶片内不同细胞族群的分工。 Fruit ripening Lv P, Yu S, Zhu N, Chen Y, Zhou B, Pan Y, Tzeng D, Fabi J, Argyris J, Garcia-Mas J, Ye N, Zhang J, Grierson D,Xiang J, Fei Z, Giovannoni J, and Zhong S. (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nature Plants. 4:784-791. Zhong S., Fei Z., Chen Y.C., Zheng Y., Huang M., Vrebalov J., Gapper N., McQuinn R. Liu B., Xiang J., Shao, Y. and Giovannoni J. (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nature Biotechnology. 31:154-159. Zhong S., Lin Z. and Grierson D. (2008) Tomato ethylene receptor interaction: visualization of NEVER-RIPE interaction with multiple CTRs at the endoplasmic reticulum. Journal of Experimental Botany. 59:965-972. C3 C4 Photosynthesis Tu, X., S. Ren, W. Shen, J. Li, Y. Li, C. Li, Y. Li, Z. Zong, W. Xie, D. Grierson, Z. Fei, J. Giovannoni, P. Li and S. Zhong (2022). Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence. Nature Communications 13(1): 7632. Dai, X., Tu, X., Du, B., Dong, P., Sun, S., Wang, X., Sun, J., Li, G., Lu, T., Zhong, S., & Li, P. (2022). Chromatin and regulatory differentiation between bundle sheath and mesophyll cells in maize. The Plant Journal, 109(3), 675–692. Tu X., Mejía-Guerra M.K., Franco J.V., Tzeng D., Chu P.Y., Shen W., Wei Y., Dai X., Li P., Buckler E. and Zhong S (2020) Reconstructing the maize leaf regulatory network using ChIP-seq data of 104 transcription factors. Nature Communications. 11, 5089. Epigenome and 3D chromatin architecture Dong P, Tu X, Liang Z, Kang B-H. & Zhong S. (2020) Plant
and animal chromatin three-dimensional organization:
similar structures but different functions. Journal
of Experimental Botany. doi.org/10.1093/jxb/eraa220 Dong P, Tu X, Li H, Zhang J, Grierson D, Li P & Zhong
S (2019) Tissue‐specific
Hi‐C analyses of rice, foxtail millet and maize suggest
non‐canonical function of plant chromatin domains.
JIPB. 10.1111/jipb.12809. Dong P, Tu X, Chu PY, Lv P, Zhu N, Grierson D, Du B, Li P
and Zhong S. (2017). 3D chromatin architecture of
large plant genomes determined by local A/B compartments.
Molecular Plant. 10, 1497-1509.
Tu X, Marand AP, Schmitz R, Zhong S (2022) A
combinatorial indexing strategy for low-cost epigenomic
profiling of plant single cells. Plant
Communications, 100308.
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