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Recently, the team of Associate Professor Ouyang Xinhao published a research paper titled "Genome-Wide Prediction of Activating Regulatory Elements in Rice by Combining STARR-seq with FACS" in Plant Biotechnology Journa.
Regarding whether the traditional STARR-seq experimental method can be directly applied to plant systems, previous studies in rice and tobacco have reached the opposite conclusio.
Figure 1: Traditional STARR-seq can be directly applied to the rice protoplast system
(a) Schematic representation of the vectors used in the validation experiment.
(b) Microfluorescence observation of SPE-transformed protoplast.
(c) Flow quantification of SPE-transformed protoplast.
In order to improve the accuracy of the prediction results, the researchers improved the traditional STARR-seq experimental method: first, the positive protoplasts were isolated by FACS to reduce the background noise of the experiment; The interference of non-specific expansion of repeat sequences was eliminated, and the entire amplicon was maximally preserved for transcriptional activation element prediction (Fi.
Figure 2: The accuracy of the optimized STARR-seq experimental method has increased significantly
(a) Schematic illustration of the optimized version of the STARR-seq experimental approac.
(b) Comparison of cell populations before and after flow sortin.
(c) Microfluorescence observation of FSPE-transformed protoplast.
(d) Flow quantification of FSPE-transformed protoplast.
(e) Comparison of the positive rate of prediction results between the traditional method and the optimized metho.
This study provides a more accurate plant enhancer capture technology, enriches the plant enhancer identification technology, and provides a new method for the study of plant chromatin high-level structure and functio.
Associate Professor Ouyang Xinhao, School of Life Sciences, Xiamen University, State Key Laboratory of Cellular Stress Biology, is the corresponding author of the pape.
Original link: https://onlinelibrar.
(Photo/Wen Ouyang Xinhao's research group)
