Silin Zhong Lab CUHK

Silin Zhong Lab | Plant Functional Genomics CUHK
钟思林 实验室 | 植物功能基因组学 香港中文大学

EG12 Science Centre East
School of Life Sciences
The Chinese University of Hong Kong
Tel: 3943 6280

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实验室主要使用大数据来研究植物转录调控的机制。主要使用的模式植物是番茄果实和水稻玉米等作物。实验室现有多个博后位置:生物信息学博后, 利用 ChIP-seq, Hi-C, ChIA-PET, single-cell RNA/ATAC 数据,研究水稻玉米和小麦等单子叶植物的转录调控机制,要求有好的数学统计背景。我们也招一个 wet lab 博后研究新的测序方法。我们在广州中科院的合作实验室也招博后和助理/副研究员。对功能基因组学感兴趣的同 学可以联系钟老师。

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 室的另一个主要方向玉米的碳4光合通路恰好也是趋同进化 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。
 

The Zhong lab focuses on functional genomics, and is not interested in genome sequencing or re-sequencing. We like highly motivated individual who can work/collaborate closely with the team. He/she must process good molecular biology skill, good team working spirit and ideally have experience with monocot or fruits. He/she must be highly motivated to do challenging experiments in this very competitive field. Experience in NGS and bioinformatics is not required. We will provide training to perform sequencing experiments such as RNA-Seq, ChIP-Seq, ChIP-exo, ATAC-Seq, Hi-C, ChIA-PET etc.

 


maize leaf
                TF network

2020 | The C4 maize leaf transcription regulatory network.

The transcription regulatory network underlying essential and complex functionalities inside a eukaryotic cell is defined by the combinatorial actions of transcription factors (TFs). However, TF binding studies in plants are too few in number to produce a general picture of this complex regulatory netowrk. We used ChIP-seq to determine the binding profiles of 104 TF expressed in the maize leaf. With this large dataset, we could reconstruct a transcription regulatory network that covers over 77% of the expressed genes, and reveal its scale-free topology and functional modularity like a real-world network. We found that TF binding occurs in clusters covering ∼2% of the genome, and shows enrichment for sequence variations associated with eQTLs and GWAS hits of complex agronomic traits. Machine-learning analyses were used to identify TF sequence preferences, and showed that co-binding is key for TF specificity. The trained models were used to predict and compare the regulatory networks in other species and showed that the core network is evolutionarily conserved.

https://www.nature.com/articles/s41467-020-18832-8
fruitENCODE
2018 | The fruitENCODE paper published in Nature Plant

Analysis of the fruitENCODE data reveals three types of transcriptional feedback circuits controlling ethylene-dependent fruit ripening. These circuits are evolved from senescence or floral organ identity pathways in the ancestral angiosperms either by neofunctionalisation or repurposing pre-existing genes. The epigenome, H3K27me3 in particular, has played a conserved role in restricting ripening genes and their orthologues in dry and ethylene-independent fleshy fruits.

https://www.nature.com/articles/s41477-018-0249-z


C4 ENCODE project



2017 |
The 104 maize TF ChIP-Seq data is online

C4 plants separates CO2 harvest and fixation in two different cell types to minimize energy lost in photorespiration. As these C4 genes are already present in C3 plants, understanding their regulation is the key to generate C4 crops. The 104 maize TF ChIP-Seq data can be accessed from our C3C4 ENCODE project Jbrowser.


maize Hi-C



2017 | Large crop genome chromatin 3D organization revealed by Hi-C analysis


We have used Hi-C to examined the 3D chromatin architecture of maize, tomato, sorghum, foxtail millet and rice. The processed Hi-C data is now available for download and viewed locally using Juicer. It seems the plant chromatin 3D organization is very different from the mammalian one in term of function.
2017 MP cross-species comparison
2019 JIPB Tissue-specific HiC
2020 JXB Review

fruit
                encode

2017 | The fruitENCODE project data is online


The goal of the fruitENCODE project is to provide a comprehensive annotation of functional elements in not just the tomato genome, but a wide-range of fleshy fruit species.

tomato methylome
2013 | Tomato epigenome on the front page

Our study revealed that the plant epigenome (DNA methylation) is not always static. Its very dynamic during tomato fruit growth and actually served as a developmental switch that controls the timing of fruit ripening.
tomato genome 2012 | The genome of tomato has finally ripened 

The genome of the tomato, Solanum lycopersicum, has been decoded. The starting point of our journey into functional genomics.