SUSTech And NIH Scientists Developed Novel Method For Simultaneously Investigating Chromatin Interaction And Chromatin Accessibility
2018-09-25 Research News
Recently, a highly innovative approach for investigation gene regulation, called Trac-looping, was published in "Nature Methods". The work were mainly completely by Dr. Keji ZHAO’s lab in National Institutes of Health (NIH) and Dr. JIN Wenfei’s lab in Southern University of Science and Technology (SUSTech). This method is a new technique for simultaneously detection of chromatin accessibility and chromatin interactions, which will greatly enhance our understanding of the regulation of gene expression by long-term chromatin interaction.
Dr. JIN Wenfei was selected to the “National young exports” and joined in Department of Biology in SUSTech in 2017. Jin Wenfei is a forefront of genomics and computational biology, developing and utilizing high-throughput experiments and computational methods to study the genetic and epigenetic mechanisms underling human health and disease. A number of his papers have been published in top journals such as Nature, Nature Methods, AJHG, Genome Research, Molecular Cell, and Genome Biology.
The eukaryotic genomic DNA exists in the form of chromatin, among which both chromatin accessibility and chromatin interaction played important role in precise regulation of gene expression. In this study, researchers have developed transposon-mediated Transposase-mediated analysis of chromatin looping (Trac-looping; shown above), which simultaneously detected chromatin accessibility and chromatin interaction. Unlike traditional three-dimensional structural research methods, Trac-looping uses transposase to directly insert a bivalent oligonucleotide linker on the interacting DNA to detect chromatin interactions. The transposase is mainly inserted into the naked DNA, Thus could detect chromatin accessible simultaneously. Based on this feature, Trac-looping can efficiently detect the interaction between promoter and enhancer, which is of great significance for understanding of long-distance regulation of gene expression.
Currently, Dr. JIN Wenfei lab in SUSTech is using this technology for further biological research.
Full-text download: https://www.nature.com/articles/s41592-018-0107-y
Q: What is the significance of this study on chromatin accessibility and chromatin interaction for promoting the development of relevant theories in biology?
A: In general, we detect either chromatin accessibility or chromatin interaction using one approach. Trac-looping could simultaneously detect chromatin openness and chromatin interaction, which provides a lot biological insight on gene regulation. Especially, Trac-looping can efficiently detect the interaction between promoter and enhancer, which is of great significance for understanding long-distance regulation of gene expression.
Q: As a junior faculty, what is your plan for your future? What is the goal of the next stage?
A: As a junior faculty, I feel that the most important thing to do is focus on my own research and teaching work. My goal is simple: making a real contribution to our understanding of genetic and epigenetic mechanism underlying human health by taking advantage of single cell technologies; helping each student or researcher in my lab have a bright future.
Q: This research was done together with your previous advisor, NIH scientist Keji ZHAO. How does this cooperation feel?
A: I always have very enjoyable collaborations with him and I appreciate him very much.
I am very happy to learn the rigorous scientific thinking and diligent attitude from him. I also inspired by the enthusiasm and commitment to science.
Q: What projects are the team ready to do next?
A: Most of our projects have been on the way. We have several projects that use single-cell sequencing technology to study cancer and biological development, which have produced a lot of nice figures.
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Photo: Student News Agency Xiao Linting