Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease.

BACKGROUND: Autoimmune disease is one of the leading causes of morbidity and mortality worldwide. In Addison's disease, the adrenal glands are targeted by destructive autoimmunity. Despite being the most common cause of primary adrenal failure, little is known about its aetiology. METHODS: To understand the genetic background of Addison's disease, we utilized the extensively characterized patients of the Swedish Addison Registry. We developed an extended exome capture array comprising a selected set of 1853 genes and their potential regulatory elements, for the purpose of sequencing 479 patients with Addison's disease and 1394 controls. RESULTS: We identified BACH2 (rs62408233-A, OR = 2.01 (1.71-2.37), P = 1.66 × 10-15 , MAF 0.46/0.29 in cases/controls) as a novel gene associated with Addison's disease development. We also confirmed the previously known associations with the HLA complex. CONCLUSION: Whilst BACH2 has been previously reported to associate with organ-specific autoimmune diseases co-inherited with Addison's disease, we have identified BACH2 as a major risk locus in Addison's disease, independent of concomitant autoimmune diseases. Our results may enable future research towards preventive disease treatment.

Conservation of gene structure and activity in the regulation of reproductive organ development of conifers and angiosperms.

The Norway spruce (Picea abies) gene DAL2 shows distinct structural similarities to angiosperm MADS-box genes which act in the control of the development of the sexual organs of the flower. Transcription of DAL2 is restricted to the reproductive organs, the unisexual cones, of Norway spruce. In this paper we show that DAL2 in the compound female cone is exclusively expressed in the developing ovule-bearing organ, the ovuliferous scale. When expressed constitutively in transgenic Arabidopsis the gene causes developmental alterations very similar to those observed in plants ectopically expressing the Arabidopsis gene AGAMOUS and the closely related Brassica napus gene BAG1. These alterations include homeotic transformations of floral organs. On the basis of these data and analysis of the phylogeny of the plant MADS-box gene family, we propose that DAL2 acts to control reproductive organ development in spruce. We also propose that DAL2 shares a common origin with AGAMOUS and related genes from other angiosperms, in an ancestral MADS-box gene that was active in the control of ontogeny of ovule-bearing organs in the unknown last common ancestor of conifers and angiosperms.

A cdc2 homologue and closely related processed retropseudogenes from Norway spruce.

The p34cdc2 protein kinase is a key component in the regulation of the eukaryotic cell cycle and has been conserved during evolution. We have isolated cDNA clones corresponding to a cdc2 gene (cdc2Pa) from the conifer Norway spruce, Picea abies (L.) Karst. The deduced amino acid sequence is 85-90% identical to p34cdc2 homologues from other plants, contains eleven subdomains characteristic for the protein kinase family, and three sequence motifs specific for the cdc2 protein kinases. A partial genomic clone of cdc2Pa reveals two introns at positions identical to intron positions in Arabidopsis thaliana cdc2a. A Southern blot analysis shows that cdc2Pa is a single-copy gene belonging to a family of about 10 related genes. Partial genomic sequences of six of the genes in this family (86-92% identical to cdc2Pa) show distinct features of processed retropseudogenes. These lack introns and contain deletions, insertions and/or non-silent point mutations. This result is consistent with the hypothesis that processed retropseudogenes in plants may be common among genes expressed in the apical meristem, that is, in cells which have the potential to take part in the formation of reproductive organs. Although cdc2Pa transcripts were abundant in the epicotyl and thus likely in the apical meristem, we observed no strict coupling of expression to cell division in embryos and seedlings.

Conifer homologues to genes that control floral development in angiosperms.

A set of MADS-box genes in flowering plants encode transcription factors that control both flower meristem formation and organ identity in the developing flower. In this report we present the first documentation of the presence of MADS-box genes in a non-flowering seed plant, and indeed from a plant bearing truly unisexual reproductive axes. A MADS-box-specific screening of a cDNA library from immature female strobili of the conifer Norway spruce, Picea abies (L.) Karst, resulted in cDNA clones that correspond to three different deficiens-agamous-like (dal) genes, dal1, dal2 and dal3. In addition to the MADS box, the spruce genes contain a second sequence element conserved among angiosperm genes, the K box, which is located downstream to the MADS box. A phylogenetic analysis of the nucleotide sequences confirms common ancestry of the gene superfamily. dal1 is related to agl2, agl4 and agl6 from Arabidopsis thaliana, all genes with unknown functions, and is expressed in vegetative as well as reproductive shoots on the adult spruce tree. dal2 is sister to angiosperm genes that control the identity of sexual organs, and is expressed only in the developing male and female strobili. dal3 is related to the vegetatively expressed tomato gene tm3 and is transcribed in both vegetative and reproductive shoots. These results strongly suggest that the functional and structural complexity within the MADS-box superfamily of reproduction-control genes is an ancestral property of seed plants and not a novelty in the angiosperm lineage.

cDNA sequence and expression of an intron-containing histone H2A gene from Norway spruce, Picea abies.

We have isolated a cDNA clone corresponding to a histone H2A gene from Norway spruce, Picea abies (L.) Karst. The clone was isolated on the basis of the preferential expression of the corresponding gene during germination. The identification of the clone was based on the high degree of nucleotide sequence identity (60-65%) to a range of eukaryotic histone H2A genes and the presence of a 9 amino acids long sequence identical to the conserved 'H2A box' in the deduced amino acid sequence. Like other plant histone genes, the spruce histone H2A gene encodes a polyadenylated transcript. Further, the spruce gene contains an intervening sequence of 891 bp in the coding region. The presence of introns is typical of a distinct class of replication-independent histone genes in other eukaryotes. However, the sequence of the spruce gene and its high expression in mitotically active tissues such as the apical meristem, strongly suggests that it belongs to the class of replication-dependent histone genes. This is the first documentation of an intervening sequence in this class of histone genes and the finding implies that introns were present in the ancestral histone H2A gene before the divergence of the two classes of histone genes.

Differential gene expression during germination and after the induction of adventitious bud formation in Norway spruce embryos.

A pulse treatment of embryos of Norway spruce with cytokinin suppresses germinative development and induces the coordinate formation of adventitious buds from subepidermal cell layers. To analyse the patterns of gene expression associated with germination and the alterations induced by the bud induction treatment, we have isolated cDNA clones corresponding to genes that are differentially expressed in cytokinin-treated and untreated in vitro germinating embryos. One category of 14 clones hybridized to transcripts that were abundant specifically during germination. The expression of 8 of these genes was reduced by the bud induction treatment. Four clones, including one identified as a histone H2A gene, recognized transcripts that showed an increased abundance in bud-induced versus in vitro germinating embryos. A second category of 13 clones hybridized to transcripts that increased in abundance during post-germinative development of the seedling. Among these a subset of 8 clones, including an alpha-tubulin clone, corresponds to genes suppressed by the bud induction treatment, whereas 5 clones, including a gene with sequence similarity to polyubiquitin, were unaffected by the treatment. One clone hybridized to a message abundant in the seed, during early germination as well as in the vegetative bud, and showed 60% partial sequence identity to a barley (1----3)-beta-glucanase gene. Genes expressed exclusively in bud-induced or in vitro germinating embryos were not found. The results show that a major difference in gene expression between treated and untreated embryos is related to the shift from extensive cell proliferation to elongation and differentiation that occurs at the transition from germination to post-germinative development, and which is suppressed in the bud-induced embryos.