Abstract
Essential genes are those that are critical for life. In the specific case of the mouse, they are the set of genes whose deletion means that a mouse is unable to survive after birth. As such, they are the key minimal set of genes needed for all the steps of development to produce an organism capable of life ex utero. We explored a wide range of sequence and functional features to characterise essential (lethal) and non-essential (viable) genes in mice. Experimental data curated manually identified 1301 essential genes and 3451 viable genes. Very many sequence features show highly significant differences between essential and viable mouse genes. Essential genes generally encode complex proteins, with multiple domains and many introns. These genes tend to be: long, highly expressed, old and evolutionarily conserved. These genes tend to encode ligases, transferases, phosphorylated proteins, intracellular proteins, nuclear proteins, and hubs in protein-protein interaction networks. They are involved with regulating protein-protein interactions, gene expression and metabolic processes, cell morphogenesis, cell division, cell proliferation, DNA replication, cell differentiation, DNA repair and transcription, cell differentiation and embryonic development. Viable genes tend to encode: membrane proteins or secreted proteins, and are associated with functions such as cellular communication, apoptosis, behaviour and immune response, as well as housekeeping and tissue specific functions. Viable genes are linked to transport, ion channels, signal transduction, calcium binding and lipid binding, consistent with their location in membranes and involvement with cell-cell communication. From the analysis of the composite features of essential and viable genes, we conclude that essential genes tend to be required for intracellular functions, and viable genes tend to be involved with extracellular functions and cell-cell communication. Knowledge of the features that are over-represented in essential genes allows for a deeper understanding of the functions and processes implemented during mammalian development.
Highlights
Essential genes are those whose presence is imperative for the survival of an organism
Mutant phenotypes generated from other experimental methods were not included in our dataset, since we could not exclude the possibility that essential genes might have hypomorphic alleles with viable phenotypes in gene trap, knockdown, or chemical mutagenesis experiments
Our non-culled dataset contained a total of 1,301 essential and 3,451 viable mouse genes, which were obtained from the Mouse Genome Informatics (MGI)
Summary
Essential genes are those whose presence is imperative for the survival of an organism. Mammalian essential genes can be identified using experimental techniques [2], which include single gene knockouts [3,4,5], conditional knockouts [6, 7], forward genetic screens [8], RNA interference [9, 10], and transposon mutagenesis [11]. Though these experimental methods are the gold standard, they are time consuming and expensive. An initial set of essential genes has been identified through these experimental approaches [13, 14]
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