Silin Zhong Lab CUHK

Silin Zhong Lab | Plant Functional Genomics CUHK

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

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** Each year, we have PhD studentships for those who are interested in plant functional genomics and bioinfomatics, as well as JRA position for those who need to take IELTS/TOFEL. We are also looking for highly motivated wet lab postdocs with solid molecular biology skills to work on fruit ripening and C4 photosynthesis projects.


2018 | The fruitENCODE paper published

Fleshy fruits using ethylene to regulate ripening have developed multiple times in the history of angiosperms, presenting a clear case of convergent evolution whose molecular basis remains largely unknown. Analysis of the fruitENCODE data consisting of 361 transcriptome, 71 accessible chromatin, 147 histone and 45 DNA methylation profiles 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.

C4 ENCODE project

2017 |
The C3C4 ENCODE project data is online

Maize is the most important crop grown worldwide. It operates a highly efficient C4 photosynthesis system that separates CO2 harvest and fixation in two different cell types to minimize energy lost in photorespiration. As genes involved in C4 photosynthesis are already present in C3 plants, understanding their regulation is the key to unlock the secrect of C4. We used ChIP-Seq to identify the direct targets of hundreds of maize transcription factors that are expressed in the leaf tissue to reconstruct its gene regulatory network. We are comparing the mesophyll and bundle sheath specific Hi-C, DNA methylation, open chromatin, histone modification and gene expression data from different C3 C4 plants to investigate their evolutionary path.
maize Hi-C

2017 | 5 crop genome Hi-C data is online

The spatial organization of the genome plays an important role in the regulation of gene expression. We have used Hi-C to examined the 3D chromatin architecture of maize, tomato, sorghum, foxtail millet and rice with genome sizes ranging from 0.4 Gb to 2.4 Gb. We also profiled their DNA methylation, histone modifications, accessible chromatin and gene expression. The processed Hi-C data is now available for download and viewed locally using Juicer (

2017 | The fruitENCODE project data is online

The fruitENCODE: an encyclopedia of DNA elements for fruit ripening. Fleshy fruit ripening is an irreversible developmental process that the physiological and biochemical properties of the seed-bearing organ are altered to aid seed dispersal. 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. It could play an important role in coordinating embryo/seed development and seed dispersal.
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.