Nested genes and increasing organizational complexity of metazoan genomes

Abstract

The most common form of protein-coding gene overlap in eukaryotes is a simple nested structure, whereby one gene is embedded in an intron of another. Analysis of nested protein-coding genes in vertebrates, fruit flies and nematodes revealed substantially higher rates of evolutionary gains than losses. The accumulation of nested gene structures could not be attributed to any obvious functional relationships between the genes involved and represents an increase of the organizational complexity of animal genomes via a neutral process.

Hitting two birds with one stone: The unforeseen consequences of nested gene knockouts inCaenorhabditis elegans

“…6,7 An especially intriguing and common gene arrangement is when a "nested" gene is located within another "host" gene. 8 Interestingly, in these gene structures, nested and host genes often display weak or negative expression correlation, perhaps because of selection against transcriptional interference. [9][10][11] Most nested genes are small non-coding RNAs (ncRNAs) 12,13 for which persistence inside host genes appears to be inversely proportional to the ncRNA family size.…”

An Overview of Nested Genes in Eukaryotic Genomes

“…Finally, the expression patterns of Pcp and ade3 differ: Pcp expression is restricted to the epidermis during the prepupal stage, while the ade3 gene is expressed throughout development (25). Typically, nested intronic genes are not coexpressed with their external host genes, although, again, this is not an absolute rule (2,72).…”

“…Recent studies indicate that nested intronic genes are widespread in metazoan genomes (Table 1). Assis et al (2) analyzed NCBI annotation records to identify 792 nested genes in D. melanogaster, 429 nested genes in Caenorhabditis elegans, and 233 nested genes in Caenorhabditis briggsae. In D. melanogaster, nested intronic genes constitute approximately 6% of the organism's total gene complement, and 85% of these nested genes are predicted to encode protein.…”

“…For loci where the resulting expression patterns of nested and host genes are inversely related, Gibson and colleagues (21) posit that the transcriptional machinery traversing the host gene intron may be subject to steric hindrance from regulatory proteins in- a Nested gene counts were determined by Assis et al (2). b Identification of nested protein-coding genes and pseudogenes in the human genome was performed by Yu et al (70).…”

“…In these cases, the inserted gene arose through either gene duplication or retrotransposition; Assis and colleagues distinguished between these possibilities by searching for the presence or absence of introns in orthologs of the nested and host genes in sister species. Assis et al also report a smaller number of cases wherein the nested gene evolved de novo from an intronic sequence of a preexisting gene (2). Analysis of the 12 recently sequenced Drosophila genomes indicates that the majority of de novo genes do originate in introns.…”