Expression level of housekeeping genes such as gyrase A could be used to normalize expression counts of genes in RNA-seq transcriptome

RNA-seq transcriptome analysis opens a window to differential gene expression in cells, and its commercialization has made it accessible to many labs. With just RNA extraction and sample preparation, the technique is facile in terms of experiment, but difficult in terms of data processing. Notwithstanding the need for high performance computing for complete analysis of RNA-seq dataset, the obtained tabulation of expression counts of all genes in the genome of the species of interest is also difficult to comprehend. Specifically, the latter point revolves around the need for normalization to answer the question of what is the relative magnitude of gene expression: high, moderate or low? Furthermore, what is the gene that can be used for normalizing gene expression count? Ideally, the gene should be conserved amongst many species and constitutively expressed in the genome and is essential for cellular function with moderate expression level. One gene that fits the criteria is gyrase A, which is the alpha subunit of DNA gyrase that serves as a topoisomerase that unwound the double stranded DNA molecule in preparation for transcription by RNA polymerase, or replication by DNA polymerase. With a moderate expression level and constitutive expression, expression count of gyrase A can be used to normalize expression count of other genes to provide ballpark estimates of high, low or moderate gene expression level. Collectively, RNA-seq processed data needs normalization by expression count of an appropriate gene to lend clarity to relative expression level with respect to cellular maintenance needs. Gyrase A provides such a candidate given its constitutive expression profile for a moderate expression level housekeeping protein subunit involved in unwounding DNA for DNA replication and transcription.