Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.

BACKGROUND: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. RESULTS: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon. CONCLUSIONS: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.

A systematic survey of loss-of-function variants in human protein-coding genes.

Genome-sequencing studies indicate that all humans carry many genetic variants predicted to cause loss of function (LoF) of protein-coding genes, suggesting unexpected redundancy in the human genome. Here we apply stringent filters to 2951 putative LoF variants obtained from 185 human genomes to determine their true prevalence and properties. We estimate that human genomes typically contain ~100 genuine LoF variants with ~20 genes completely inactivated. We identify rare and likely deleterious LoF alleles, including 26 known and 21 predicted severe disease-causing variants, as well as common LoF variants in nonessential genes. We describe functional and evolutionary differences between LoF-tolerant and recessive disease genes and a method for using these differences to prioritize candidate genes found in clinical sequencing studies.

A novel hepatitis B virus subgenotype, D7, in Tunisian blood donors.

Tunisia is a medium-level epidemic country for hepatitis B virus (HBV). This study characterizes, for the first time, full genome HBV strains from Tunisia. Viral load quantification and phylogenetic analyses of full genome or pre-S/S sequences were performed on 196 hepatitis B surface antigen (HBsAg)-positive plasma samples from Tunisian blood donors. The median viral load was 64.65 IU ml(-1) (range<5-7.7x10(8) IU ml(-1)) and 89% of samples had viral loads below 10,000 IU ml(-1). Fifty-nine strains formed a novel subgenotype D7, 41 strains clustered in subgenotype D1, seven strains in subgenotype A2 and one strain in genotype C. The novel subgenotype D7 was defined by maximum Bayesian posterior probability, a genetic divergence from other HBV/D subgenotypes by >4% and a stronger HBV/E signal in the X to core genes than subgenotype D1. In conclusion, HBV/D is dominant in asymptomatic Tunisian HBsAg carriers and a novel subgenotype, D7, was the most common subgenotype found in this population.

Role of the Campylobacter jejuni Cj1461 DNA methyltransferase in regulating virulence characteristics.

Mutation of the cj1461 predicted methyltransferase gene reduced the motility of Campylobacter jejuni 81-176. Electron microscopy revealed that the mutant strain had flagella but with aberrant structure. The Deltacj1461 mutant was sevenfold more adherent to but 50-fold less invasive of INT-407 human epithelial cells than the wild type.

Gamma-glutamyl transpeptidase has a role in the persistent colonization of the avian gut by Campylobacter jejuni.

The contribution of gamma-glutamyl transpeptidase (GGT) to Campylobacter jejuni virulence and colonization of the avian gut has been investigated. The presence of the ggt gene in C. jejuni strains directly correlated with the expression of GGT activity as measured by cleavage and transfer of the gamma-glutamyl moiety. Inactivation of the monocistronic ggt gene in C. jejuni strain 81116 resulted in isogenic mutants with undetectable GGT activity; nevertheless, these mutants grew normally in vitro. However, the mutants had increased motility, a 5.4-fold higher invasion efficiency into INT407 cells in vitro and increased resistance to hydrogen peroxide stress. Moreover, the apoptosis-inducing activity of the ggt mutant was significantly lower than that of the parental strain. In vivo studies showed that, although GGT activity was not required for initial colonization of 1-day-old chicks, the enzyme was required for persistent colonization of the avian gut.