gene annotation - Overlapping genetic information in eukaryotes

In general, the compactnes of genomes is a characteristic of prokaryotes, but there are several eykaryotes that have overlapping genes: many parasites and endosymbionts. The best studied of these are the fungal parasites of the phylum microsporidia and the nucleomorphs (remnant nuclei of algal endosymbionts in cryptophytes and chlorarachniophytes).

cDNA library was constructed from the microsporidian Antonospora locustae and 1,146 cDNA clones were sequenced. Here is part of the expression profile (1):

Of the 871 clones found to encode recognizable genes, 97 transcripts (11%) from 70 distinct loci encoded sequence from more than one gene (Fig. 1 A ; see also Table 1, which is published as supporting information on the PNAS web site). The polyA sites of these clones do not correspond to polyA tracts in the genome, so they are unlikely to derive from DNA contamination (see also below), but instead come from polyA RNA. In prokaryotes, polycistronic mRNAs commonly code for multiple proteins (11), but with few exceptions (12) eukaryotic mRNAs encode a single gene. A. locustae multigene transcripts encode two or three genes or gene fragments in various orientations (Fig. 1 B–I ), but they cannot all be polycistronic messages because there is no bias for genes being on the same strand.

Here is part of a review paper on the nucleomorphs genome (2):

As in other reduced genomes, the G. theta nucleomorph genome possesses a very high A+T content (75%) and gene density is extremely high: 1 gene per 977 bp and 44 genes overlap by as many as 76 nucleotides. Williams et al. (84) showed that transcription of the G. theta nucleomorph genome is affected by this compaction, with nucleomorph-derived messenger RNAs often possessing coding sequence for more than one gene, albeit with no strand bias. It appears that during the process of genome compaction, transcription regulatory elements (e.g., promoters, terminators) have moved from the intergenic spacers into the coding regions themselves (84).

I also have to point out that there are a few examples of overlapping genes in yeast: CCT6 overlaps with YDR187C and CCT8 overlaps with YJL009W (3).

1. A high frequency of overlapping gene expression in compacted eukaryotic genomes


2. Nucleomorph Genomes, Annual Review of Genetics


3. The Chemical Genomic Portrait of Yeast: Uncovering a Phenotype for All Genes