Intronic RS-abundance and RS-specificity define characteristic gene functions in different mammalian lineages
We first classified genes in a similar way to what we did for introns: (1) TS, genes have both transposons and satellites in their introns; (2) T, genes have only transposons in their introns; (3) S, genes have only satellites in their introns; (4) N, genes have neither transposons nor satellites in their introns. In general, we observed an order of TS > N > T > S in chicken and anole, but a different order of TS > T > N > S in the rest vertebrates. When compared the same RS classes from different species, the most abundant four classes for TS, T, S, and N are 83.1% in mouse, 33% in horse, 8.32% in chicken, and 28.4% in chicken, respectively (Fig. 7). Furthermore, we considered functional categorization of the four gene classes in the four mammalian lineages: mammals, primates, large mammals, and rodents. We found diverse development- and transcription-related functions in S and/or N genes, including “embryonic skeletal system development” and “transcription regulator activity” in mammals (Table 2), “negative regulation of neuron differentiation” and “gene expression” in primates (Table 3), “midbrain development” and “regulation of transcription” in large mammals (Table 4), and “inner ear morphogenesis” and “regulation of gene expression” in the rodents (Table 5). There are also lineage-specific and tissue-specific profiles for the expression of these genes. For instance, “hormone activity” of N genes is shared by all the major groups of mammals and “pheromone binding” of S genes is unique to the rodents. There are also genes with immunological functions identified in the primate S (eg, “positive regulation of chronic inflammatory response to antigenic stimulus”) and N genes (eg, “MHC class I receptor activity”), in S genes of the large mammals (eg, “antigen processing and presentation”), and in N genes of the rodents (eg, “inflammatory response”). In addition, some TS genes are related to fundamental structures and metabolic functions, including “cytoskeleton” and “protein homodimerization activity” in the mammals, “extracellular matrix structural constituent” and “regulation of cell shape” in the primates, “ATP biosynthetic process” in the large mammals, and “acyltransferase activity”, “protein ubiquitination”, and “phosphoinositide binding” in the rodents. There are also rodent TS genes involved in the nervous system and being response to external stimulus or environment. As to T genes, mitochondrial structure related functions are found in both the primates and the large mammals.