Molecular Biology and Evolution | The team led by Chen Xiaoshu from the Zhongshan School of Medicine has put forward additional evidence supporting the hypothesis of X chromosome insensitivity.

A well-known controversy in evolutionary genetics is whether dosage compensation is required to address the gene dosage (X:AA) imbalance between the X chromosome and autosomes. ScRNA-seq data can provide in-depth insights into this issue at the single-cell level. However, before conducting the analysis, it is essential to carefully evaluate whether the inherent characteristics of scRNA-seq, such as sparsity, can bias the X:AA expression ratio in mammals.

 Recently, the team led by Professor Chen Xiaoshu from Sun Yat-sen University published an online research paper titled "Human single-cell RNA-sequencing data supports the hypothesis of X chromosome insensitivity but is ineffective in testing the dosage compensation model" in *Molecular Biology and Evolution*. This paper comprehensively studied the inherent characteristics of scRNA-seq to reveal whether it can correctly test the dosage compensation model. 

  The researchers first used simulated scRNA-seq and bulk RNA-seq datasets to evaluate two common X:AA gene selection strategies, namely filtering by gene expression level and filtering by gene expression proportion. They found that both strategies would generate exaggerated X:AA expression ratios, thus artificially supporting the dosage compensation model. 

  In addition, although there were biases in the average expression levels, the researchers discovered that scRNA-seq data could be used to detect differences in expression noise between the X chromosome and autosomes as small as 10%, enabling the study of the distribution of genes that are more insensitive to changes in gene dosage. The analysis of Smart-seq2 data showed that compared with autosomes, the expression noise of the X chromosome increased by 10-15%, and the number of dosage-sensitive genes on the X chromosome significantly decreased. 

  Overall, these results emphasize the need for great caution when interpreting scRNA-seq data, especially when comparing the expression levels of different genes, and provide additional evidence for the hypothesis of X chromosome insensitivity. 

  This article has two authors. Professor Chen Xiaoshu from Sun Yat-sen University is the sole corresponding author of this article, and Dr. Chen Jiabi, a doctoral student enrolled in 2022 and a member of the team, is the sole first author of this article. 

Original link: https://doi.org/10.1093/molbev/msaf004