Charles Zhijie Chen

All Publications

• Two-way magnetic resonance tuning and enhanced subtraction imaging for non-invasive and quantitative biological imaging Nature Nanotechnology Wang et al, Z. 2020; 15 (5)

  View details for DOI 10.1038/s41565-020-0678-5

• A screen for deeply conserved non-coding GWAS SNPs uncovers a MIR-9-2 functional mutation associated to retinal vasculature defects in human Nucleic Acids Research Madelaine, R., Notwell, J. H., Skariah, G., Halluin, C., Chen, C. C., Bejerano, G., Mourrain, P. 2018; 1

  Abstract

  Thousands of human disease-associated single nucleotide polymorphisms (SNPs) lie in the non-coding genome, but only a handful have been demonstrated to affect gene expression and human biology. We computationally identified risk-associated SNPs in deeply conserved non-exonic elements (CNEs) potentially contributing to 45 human diseases. We further demonstrated that human CNE1/rs17421627 associated with retinal vasculature defects showed transcriptional activity in the zebrafish retina, while introducing the risk-associated allele completely abolished CNE1 enhancer activity. Furthermore, deletion of CNE1 led to retinal vasculature defects and to a specific downregulation of microRNA-9, rather than MEF2C as predicted by the original genome-wide association studies. Consistent with these results, miR-9 depletion affects retinal vasculature formation, demonstrating MIR-9-2 as a critical gene underpinning the associated trait. Importantly, we validated that other CNEs act as transcriptional enhancers that can be disrupted by conserved non-coding SNPs. This study uncovers disease-associated non-coding mutations that are deeply conserved, providing a path for in vivo testing to reveal their cis-regulated genes and biological roles.

  View details for DOI 10.1093/nar/gky166

  View details for PubMedCentralID PMC5909433