On January 9, the internationally renowned journal Nature Communications(Q1, Chinese Academy of Sciences, 2022 Impact Factor (IF) 16.6) published A Full-body Transcription Factor Expression Atlas with Completely Resolved Cell Identities in C. Elegans online, research results of Functional Genomics Lab by Professor Liu Xiao, the College of Life Sciences.

Liu Xiao's team has developed an automatic recognition algorithm RAPCAT (i.e., Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool). This technology is specially designed to automatically annotate the cell identities in a three-dimensional image stack of C. Elegans L1 larvae. Therefore, it is possible to analyze the fluorescent transgenic lines of large-scale nematodes. Via the technology, the team managed to analyze the report expression of 620 TFs covering two-thirds of the total number of TFs encoded by the nematode genome. The team quantified the fluorescence of each cell in the TF reporter nematode image to generate a single-cell resolution TF expression atlas covering all cells. Based on cluster analysis of TF gene expression atlas, the team compared the relationship between TF-based classification and nematode cell phenotypic classification, and identified phenotypic patterns and regulatory genes associated with these classifications. First, the team found extensive down-regulation of resting transcription factors in Hermaphrodite Specific Neuron (HSN). Second, the team found that transcription factor expression was more closely related to cell morphological patterns at different development stages before and after cell differentiation. Finally, the team found that the embryonic cell atlas influences specific transcription factor expression patterns and functions, persisting into adulthood.

Professor Liu Xiao from the College of Life Sciences, Capital Normal University (CNU) is the corresponding author of this paper. Li Yongbin, a lecturer from the College of Life Sciences, CNU, Chen Siyu, a doctoral student at Tsinghua University, Liu Weihong, an executive of Hanvon, Zhao Di, a lecturer at Tianjin University of Sport, and Gao Yimeng, a doctoral student at CNU are the co-first authors of this paper. Hu Shipeng and Liu Hanyu, postgraduate students enrolled in 2020 at CNU, as well as lecturer Li Yuanyuan and Professor Qu Lei from Anhui University, made key contributions to this paper. This research was strongly supported by the National Natural Science Foundation of China (NSFC).

Full text link: <span style="Times New Roman","serif";color:windowtext;text-decoration: none;text-underline:none">https://doi.org/10.1038/s41467-023-42677-6