Gene promoter evolution targets the center of the human protein interaction network

Network Centrality Analysis in Fungi Reveals Complex Regulation of Lost and Gained Genes

Gene gain and loss shape both proteomes and the networks they form. The increasing availability of closely related sequenced genomes and of genome-wide network data should enable a better understanding of the evolutionary forces driving gene gain, gene loss and evolutionary network rewiring. Using orthology mappings across 23 ascomycete fungi genomes, we identified proteins that were lost, gained or universally conserved across the tree, enabling us to compare genes across all stages of their life-cycle. Based on a collection of genome-wide network and gene expression datasets from baker's yeast, as well as a few from fission yeast, we found that gene loss is more strongly associated with network and expression features of closely related species than that of distant species, consistent with the evolutionary modulation of gene loss propensity through network rewiring. We also discovered that lost and gained genes, as compared to universally conserved "core" genes, have more regulators, more complex expression patterns and are much more likely to encode for transcription factors. Finally, we found that the relative rate of network integration of new genes into the different types of networks agrees with experimentally measured rates of network rewiring. This systems-level view of the life-cycle of eukaryotic genes suggests that the gain and loss of genes is tightly coupled to the gain and loss of network interactions, that lineage-specific adaptations drive regulatory complexity and that the relative rates of integration of new genes are consistent with network rewiring rates.

The c.-360 T>C mutation affects PGAM2 transcription activity and is linked with the water holding capacity of the longissimus lumborum muscle in pigs

The phosphoglycerate mutase 2 (PGAM2) gene encodes a key enzyme in the glycolytic process. This study examined a functional mutation in the PGAM2 gene and evaluated its relationship with water holding capacity (WHC). RT-qPCR analysis showed the PGAM2 mRNA level was significantly higher in the low-WHC group than in the high-WHC group (P<0.05). The c.-360 T>C mutation was identified through sequencing and found to have opposite allele distributions in the two groups. The allele was further genotyped in 170 Duroc×Large White×Yorkshire crossbred pigs using allele-specific PCR. The CC genotype was associated with lower WHC and higher PGAM2 mRNA levels, whereas the TT genotype corresponded to a higher WHC and lower PGAM2 mRNA levels (P<0.05). A luciferase activity assay also showed that the CC-genotype promoter had higher activity than the TT-genotype promoter (P<0.05). In conclusion, we discovered the c.-360 T>C mutation in the PGAM2 gene, which is a promising marker for improving pork WHC.

Human-specific transcriptional networks in the brain

Understanding human-specific patterns of brain gene expression and regulation can provide key insights into human brain evolution and speciation. Here, we use next-generation sequencing, and Illumina and Affymetrix microarray platforms, to compare the transcriptome of human, chimpanzee, and macaque telencephalon. Our analysis reveals a predominance of genes differentially expressed within human frontal lobe and a striking increase in transcriptional complexity specific to the human lineage in the frontal lobe. In contrast, caudate nucleus gene expression is highly conserved. We also identify gene coexpression signatures related to either neuronal processes or neuropsychiatric diseases, including a human-specific module with CLOCK as its hub gene and another module enriched for neuronal morphological processes and genes coexpressed with FOXP2, a gene important for language evolution. These data demonstrate that transcriptional networks have undergone evolutionary remodeling even within a given brain region, providing a window through which to view the foundation of uniquely human cognitive capacities.

Variation in the IGF2 gene promoter region is associated with intramuscular fat content in porcine skeletal muscle

Intramuscular fat (IMF) and subcutaneous fat (back fat-BF) are two of the major fat depots in livestock. A QTN located in the insulin-like growth factor 2 gene (IGF2) has been associated with a desirable reduction in BF depth in pigs. Given that the lipid metabolism of intramuscular adipocytes differs from that of subcutaneous fat adipocytes, this study aimed to search for genetic variation in the IGF2 gene that may be associated with IMF, as well as BF, in diverse pig breeds. Four proximal promoter regions of the IGF2 gene were characterised and the association of IGF2 genetic variation with IMF and BF was assessed. Six promoter SNPs were identified in four promoter regions (P1-P4; sequence coverage 945, 866, 784 and 864 bp, respectively) in phenotypically diverse F1 cross populations. Three promoter SNPs were subsequently genotyped in three pure breeds (Pietrain = 98, Duroc = 99 and Large White = 98). All three SNPs were >95% monomorphic in the Pietrain and Duroc breeds but minor alleles were at moderate frequencies in the Large White breed. These SNPs were linked and one was located in a putative transcription factor binding site. Five haplotypes were inferred and three combined diplotypes tested for association with IMF and BF in the Large White. As expected haplotype 1 (likely in LD with the beneficial QTN allele) was superior for BF level. In contrast, the heterozygote diplotype of the most common haplotypes (1 and 2) was associated with higher IMF and marbling scores compared to either homozygote. Gene expression analysis of divergent animals showed that IGF2 was 1.89 fold up-regulated in muscle with higher compared to lower IMF content. These findings suggest that genetic variation in the promoter region of the IGF2 gene is associated with IMF content in porcine skeletal muscle and that greater expression of the IGF2 gene is associated with higher IMF content.

Functional characterisation of the bovine neuropeptide Y gene promoter and evaluation of the transcriptional activities of promoter haplotypes

Neuropeptide Y (NPY) is a potent orexigenic agent. The molecular mechanisms underlying the regulation of bovine NPY gene expression by its promoter region is currently unknown. The objectives of this research were to: (i) identify the SNPs in the promoter region of the bovine NPY gene, (ii) investigate the effects of these SNPs by measuring promoter transcriptional activities of different bovine NPY promoter haplotypes and; (iii) identify the minimal promoter region (MPR) required for basal activity of the NPY gene in vitro. Seventeen SNPs were identified in the promoter region. Of these, 14 affected putative transcription factors binding motifs including a TATA binding protein factor at -20, GC-Box factors SP1 at -170 and GATA binding motifs at -120 and -347. The SNPs were assigned to five major haplotypes (BtNPY_H1-5), of which BtNPY_H5 had maximum transcriptional activity. The region extending to -134 nt was identified as the MPR. This MPR was confirmed by the identification of a putative TATA box (-29 nt) and two SP1/GC binding sites (-94 and -118 nt), within this region. However, promoter expression was significantly enhanced when the construct contained the -614 to -1019 nt region. In conclusion, a number of SNPs characterised in the bovine NPY promoter especially those affecting the transcription factor binding sites, enhancer and repressor regions have the potential to affect NPY gene expression. Natural variation exists in the promoter region of the bovine NPY gene, which should be further explored for selection of energetic efficiency in cattle.

Regulatory polymorphisms in the bovine Ankyrin 1 gene promoter are associated with tenderness and intramuscular fat content

Background

Recent QTL and gene expression studies have highlighted ankyrins as positional and functional candidate genes for meat quality. Our objective was to characterise the promoter region of the bovine ankyrin 1 gene and to test polymorphisms for association with sensory and technological meat quality measures.

Results

Seven novel promoter SNPs were identified in a 1.11 kb region of the ankyrin 1 promoter in Angus, Charolais and Limousin bulls (n = 15 per breed) as well as 141 crossbred beef animals for which meat quality data was available. Eighteen haplotypes were inferred with significant breed variation in haplotype frequencies. The five most frequent SNPs and the four most frequent haplotypes were subsequently tested for association with sensory and technological measures of meat quality in the crossbred population. SNP1, SNP3 and SNP4 (which were subsequently designated regulatory SNPs) and SNP5 were associated with traits that contribute to sensorial and technological measurements of tenderness and texture; Haplotype 1 and haplotype 4 were oppositely correlated with traits contributing to tenderness (P < 0.05). While no single SNP was associated with intramuscular fat (IMF), a clear association with increased IMF and juiciness was observed for haplotype 2.

Conclusion

The conclusion from this study is that alleles defining haplotypes 2 and 4 could usefully contribute to marker SNP panels used to select individuals with improved IMF/juiciness or tenderness in a genome-assisted selection framework.