title: Stably Expressed Genes Involved in Basic Cellular Functions.
abstract: Stably Expressed Genes (SEGs) whose expression varies within a narrow range may be involved in core cellular processes necessary for basic functions. To identify such genes, we re-analyzed existing RNA-Seq gene expression profiles across 11 organs at 4 developmental stages (from immature to old age) in both sexes of F344 rats (n = 4/group; 320 samples). Expression changes (calculated as the maximum expression / minimum expression for each gene) of >19000 genes across organs, ages, and sexes ranged from 2.35 to >109-fold, with a median of 165-fold. The expression of 278 SEGs was found to vary ≤4-fold and these genes were significantly involved in protein catabolism (proteasome and ubiquitination), RNA transport, protein processing, and the spliceosome. Such stability of expression was further validated in human samples where the expression variability of the homologous human SEGs was significantly lower than that of other genes in the human genome. It was also found that the homologous human SEGs were generally less subject to non-synonymous mutation than other genes, as would be expected of stably expressed genes. We also found that knockout of SEG homologs in mouse models was more likely to cause complete preweaning lethality than non-SEG homologs, corroborating the fundamental roles played by SEGs in biological development. Such stably expressed genes and pathways across life-stages suggest that tight control of these processes is important in basic cellular functions and that perturbation by endogenous (e.g., genetics) or exogenous agents (e.g., drugs, environmental factors) may cause serious adverse effects.
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America.
authors.forename: Kejian
authors.initials: K
authors.lastname: Wang
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America.
authors.forename: Vikrant
authors.identifier: http://orcid.org/0000-0001-8425-1285
authors.initials: V
authors.lastname: Vijay
authors.affiliation: Division of Systems Biology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas, United States of America.
authors.forename: James C
authors.initials: JC
authors.lastname: Fuscoe
mesh_terms: D000375:Aging / Q000235:genetics*; D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D006801:Humans; D008297:Male; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D046988:Proteasome Endopeptidase Complex / Q000235:genetics; D011499:Protein Processing, Post-Translational; D034443:RNA Transport / Q000235:genetics; D051381:Rats; D011916:Rats, Inbred F344; D017381:Spliceosomes / Q000235:genetics; D054875:Ubiquitination
chemical_list: D046988:Proteasome Endopeptidase Complex