A gene is called essential when an organism cannot survive if it is lost or damaged. Finding these genes is important because they reveal the core machinery that keeps cells and tissues alive. Traditionally, scientists have used tools like CRISPR to turn genes on or off in cell cultures to see which ones are essential. While powerful, these methods usually focus on a single cell type and do not capture the bigger picture of how genes behave across different tissues.
Researchers from the University of Queensland have taken a new approach by combining large single-cell RNA sequencing datasets with known lists of essential genes. They developed a method called scEssentials to evaluate how consistently these genes are expressed in more than 60 different human and mouse cell types.
Overall workflow to determine essential genes for single-cell data (scEssentials)
Experimental-derived essential genes were queried from the DEG 15 database for mouse and human, respectively. To ensure the detectability of scEssentials genes, we select the essential genes which have at least three nonzero reads in every sequencing method that was sequenced only with cell line samples and also at least three cells in each cell type in TM/TS and retain the intersection of genes for downstream analysis.
The team found that essential genes tend to be highly active across many tissues and that they form tightly connected networks, working together to perform key biological functions. They also created a scoring system to measure how critical each gene is, linking these scores with mutation rates and chromatin accessibility, which affect how genes are turned on or off.
When applying scEssentials to ageing research, the scientists discovered that most essential genes remained stable across age groups, highlighting their importance in maintaining fundamental cellular processes. Only about one-fifth showed age-related changes.
By providing a reliable way to analyze essential genes across tissues, scEssentials offers scientists a valuable reference for interpreting RNA sequencing data and exploring complex topics like development, ageing, and disease.
Availability – Human and mouse scEssentials gene and the code to generate the plots and processing scheme can be found at the GitHub repository https://github.com/huiwenzh/scEssentials
Zheng H, Taherian Fard A, Mar J. (2025) Assessing tissue-specific gene expression of essential genes from human and mouse. Briefings in Bioinformatics 26(5): bbaf487. [article]
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A gene is called essential when an organism cannot survive if it is lost or damaged. Finding these genes is important because they reveal the core machinery that keeps cells and tissues alive. Traditionally, scientists have used tools like CRISPR to turn genes on or off in cell cultures to see which ones are essential. While powerful, these methods usually focus on a single cell type and do not capture the bigger picture of how genes behave across different tissues.
Researchers from the University of Queensland have taken a new approach by combining large single-cell RNA sequencing datasets with known lists of essential genes. They developed a method called scEssentials to evaluate how consistently these genes are expressed in more than 60 different human and mouse cell types.
Overall workflow to determine essential genes for single-cell data (scEssentials)
Experimental-derived essential genes were queried from the DEG 15 database for mouse and human, respectively. To ensure the detectability of scEssentials genes, we select the essential genes which have at least three nonzero reads in every sequencing method that was sequenced only with cell line samples and also at least three cells in each cell type in TM/TS and retain the intersection of genes for downstream analysis.
The team found that essential genes tend to be highly active across many tissues and that they form tightly connected networks, working together to perform key biological functions. They also created a scoring system to measure how critical each gene is, linking these scores with mutation rates and chromatin accessibility, which affect how genes are turned on or off.
When applying scEssentials to ageing research, the scientists discovered that most essential genes remained stable across age groups, highlighting their importance in maintaining fundamental cellular processes. Only about one-fifth showed age-related changes.
By providing a reliable way to analyze essential genes across tissues, scEssentials offers scientists a valuable reference for interpreting RNA sequencing data and exploring complex topics like development, ageing, and disease.
Availability – Human and mouse scEssentials gene and the code to generate the plots and processing scheme can be found at the GitHub repository https://github.com/huiwenzh/scEssentials
Zheng H, Taherian Fard A, Mar J. (2025) Assessing tissue-specific gene expression of essential genes from human and mouse. Briefings in Bioinformatics 26(5): bbaf487. [article]
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