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

Home Research Jobs ENCODE data browser

2022 | Plant cistome evolution

We compared the GLK binding sites in 5 plant species using ChIP-seq. It turns out that despite the biological function of GLK is conserved, their binding sites have diverged during evolution. Only 10-20% of the binding are conserved.

https://www.nature.com/articles/s41467-022-35438-4

2022 | Single-cell ATAC-seq

We developed a low cost single-cell ATAC-seq protocol for plant tissue using combinatorial index Tn5 without the need of 10X genomics machines.

https://pubmed.ncbi.nlm.nih.gov/35605196/

2020 | C3C4 ENCODE: the 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.

https://www.nature.com/articles/s41467-020-18832-8

2018 | The FruitENCODE project

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

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 plant chromatin 3D organizations are different from the mammalian one, and they lack clear regulatory function.

2017 MP cross-species comparison
2019 JIPB Tissue-specific Hi-C
2020 JXB Review

2013 | DNA methylation regulate fruit ripening

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.

https://www.nature.com/articles/nbt.2462

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 Home Research Jobs ENCODE data browser
	2022 \| Plant cistome evolution We compared the GLK binding sites in 5 plant species using ChIP-seq. It turns out that despite the biological function of GLK is conserved, their binding sites have diverged during evolution. Only 10-20% of the binding are conserved. https://www.nature.com/articles/s41467-022-35438-4
	2022 \| Single-cell ATAC-seq We developed a low cost single-cell ATAC-seq protocol for plant tissue using combinatorial index Tn5 without the need of 10X genomics machines. https://pubmed.ncbi.nlm.nih.gov/35605196/
	2020 \| C3C4 ENCODE: the 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. https://www.nature.com/articles/s41467-020-18832-8
	2018 \| The FruitENCODE project 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
	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 plant chromatin 3D organizations are different from the mammalian one, and they lack clear regulatory function. 2017 MP cross-species comparison 2019 JIPB Tissue-specific Hi-C 2020 JXB Review
	2013 \| DNA methylation regulate fruit ripening 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. https://www.nature.com/articles/nbt.2462