Genomics and genetics of gonadotropin beta-subunit genes: Unique FSHB and duplicated LHB/CGB loci

Abstract

The follicle stimulating hormone (FSH), luteinizing hormone (LH) and chorionic gonadotropin (HCG) play a critical role in human reproduction. Despite the common evolutionary ancestry and functional relatedness of the gonadotropin hormone beta (GtHB) genes, the single-copy FSHB (at 11p13) and the multi-copy LHB/CGB genes (at 19q13.32) exhibit locus-specific differences regarding their genomic context, evolution, genetic variation and expressional profile. FSHB represents a conservative vertebrate gene with a unique function and it is located in a structurally stable gene-poor region. In contrast, the primate-specific LHB/CGB gene cluster is located in a gene-rich genomic context and demonstrates an example of evolutionary young and unstable genomic region. The gene cluster is shaped by a constant balance between selection that acts on specific functions of the loci and frequent gene conversion events among duplicons. As the transcription of the GtHB genes is rate-limiting in the assembly of respective hormones, the genomic and genetic context of the FSHB and the LHB/CGB genes largely affects the profile of the hormone production.

Fig. 1

Schematic representation of the genomic context of the FSHB and the LHB/CGB genes (±100 kb). The figure was drawn based on Ensembl database (http://www.ensembl.org/; Release 54). Boxes denote the genes and triangles above or below them point to the direction of transcription. The black boxes and arrowheads indicate CGB, white LHB and grey neighbouring genes. The CGB genes of rhesus macaque (Macaca mulatta) and common marmoset (Callithrix jacchus) are indicated as CGB A–C, since their ancestral status relative to the human CGB genes is unknown (reviewed in Henke and Gromoll, 2008; Hallast and Laan, 2009).

Fig. 2

Density of polymorphisms in the human FSHB and LHB/CGB genes. The graph was drawn based on the resequencing data obtained from Hallast et al. (2005) and Grigorova et al. (2007). Bars represent the number of DNA variants calculated per 1000 bp of the re-sequenced region. The length of the analysed region for LHB, CGB, CGB2 and CGB1 genes is 1.5 kb, CGB5 and CGB8 1.6 kb, CGB7 2.2 kb and for FSHB 2.9 kb. The density fraction of common variants (minor allele frequency, MAF >10%) and rare variants (MAF <10%) is shown by the height of black and grey bars, respectively. Each gene, except for CGB8, was analysed in three populations: Est – Estonians (n = 47), Han – Chinese Han (n = 25), Man – African Mandenkalu (n = 23). CGB8 has been studied only in Estonian samples (n = 95; Rull et al., 2008a,b).

Fig. 3

Distribution of known DNA variants across the human FSHB and LHB/CGB genes. The intron/exon structure of full genic regions is drawn to scale; for FSHB only the re-sequenced region is shown. Black, white and grey boxes represent exons, introns and untranslated regions, respectively. Vertical lines mark the positions of detected polymorphisms (Grigorova et al., 2007; Rull et al., 2008a,b; Hallast et al., 2005; Tables 2–4). Non-synonymous mutations causing clinical consequences (from Table 2) are indicated with underlined font and polymorphisms associated with a distinct phenotype (from Table 3) are marked with a star above the positions. S - singleton polymorphism detected for only one individual.

Fig. 4

Schematic description of gene conversion and definition of haplotype variants. (A) During gene conversion the genetic material is transferred between highly identical gene copies or alleles. One locus acts as a donor of a gene conversion tract and the other as an acceptor. In case the two gene copies differ in some sequence positions within the converted tract, the variant specific to the acceptor is replaced by copying the donor-specific variant. The donor DNA sequence remains unchanged. In the figure, the donor locus is displayed as a black line with circles indicating the gene-specific positions. The acceptor locus is drawn as a grey dashed line and the gene-specific positions as triangles. (B) Definition of gene haplotypes using the two major FSHB gene variants as an example (Grigorova et al., 2007). Haplotypes are drawn schematically and the average frequency across European Estonians, Chinese Han and African Mandenkalu is given in brackets. The allelic composition of the two FSHB gene variants differs in every polymorphic position shown as black circles. The alternative alleles of the FSHB common polymorphisms are shown for haplotype 1 and haplotype 2. The locations of the polymorphisms within the FSHB gene are indicated. Rs-numbers correspond to NCBI human genome build 36 (http://www.ncbi.nlm.nih.gov/).

Fig. 5

Haplotype networks for the human CGB5, LHB and FSHB genes. The networks were derived based on resequencing data (Hallast et al., 2005; Grigorova et al., 2007) and using the Median-Joining network algorithm implemented in NETWORK 4.201 software (http://www.fluxus-technology.com). Singleton polymorphisms were excluded from the analysis. Each node represents a single combination of SNP alleles within a gene. The size of a node is proportional to the haplotype frequency in the total dataset and the length of a line connecting two nodes correlates with the number of sequence differences between two haplotypes. The frequency of prevalent haplotypes across studied populations is given next to the major nodes.

Fig. 6

Normal ranges of (A) serum FSH and LH concentrations in men and women; (B) serum HCG dynamics during pregnancy and (C) levels of HCG beta mRNA transcripts in placental tissue. The graphs (A) and (B) are drawn based on reference values of United Laboratory of University of Tartu Clinics, Estonia. The graph C was drawn based on the data from Rull et al. (2008a,b). The boxes represent the 25th and 75th percentile and median is denoted as the line that bisects the boxes.