Polymorphism in regulatory gene sequences

Genetic polymorphism in core promoter sequence of ACTRIIB gene and association analysis with growth traits in chicken

Molecular breeding exploiting candidate genes is burgeoning reproductive approach to improve growth traits in poultry. The activin type IIB receptor (ACTRIIB) is a negative growth regulator, modulating action of many muscle growth regulators. PCR-single-strand conformation polymorphism was employed to unravel polymorphism in promoter region of the ACTRIIB gene and delineate its association with growth traits in Aseel and control broiler (CB). Analysis of 5' promoter region (1122bp) of ACTRIIB gene identified five SNPs, that is g. [56 G > C (SNP1), 352A > C (SNP2), 580G > A (SNP3), 625C > T (SNP4) and 962C > T (SNP5)] at SMAD, paired box 7 homeodomain binding motif, GC box and bHLH-PAS type transcription factors in CB and Aseel. CB had significantly higher body weight (BW) and average daily gain (ADG) at all SNP sites, except at SNP 1. The haplotype construction resulted 8 haplotypes in CB and Aseel population. The BW and ADG differed significantly (p < .05) at all ages in CB and Aseel. The diplotypes H1H8 and H1H4 manifested higher BW and ADG, while diplotypes H3H8 and H3H7 displayed BW and ADG at each age in both lines (p < .05). Aseel exhibited higher expression of ACTRIIB gene than CB by 70.17, 4.83, 1.41, 2.38, 5.13, 1.20, 2.90, 6.53 and 11.75 times for h1h2, h1h3, h1h4, h1h6, h1h7, h1h8 h3h4, h3h7 and h3h8, respectively. The H3H8 and H3H7 diplotypes exhibited higher level of mRNA and protein than H1H8 and H1H4. The regulatory upstream region of ACTRIIB gene demonstrates high degree of genetic diversity and can be harnessed as potential marker in genetic selection programmes for increasing meat production.

Effect of Cytokines and Chemokines (TGF-β, TNF-α, IL-6, IL-10, MCP-1, RANTES) Gene Polymorphisms in Kidney Recipients on Posttransplantation Outcome: Influence of Donor-Recipient Match

Posttransplantation alloantigen-dependent and alloantigen-independent processes are both mediated by cytokines and chemokines. Recently cytokines and chemokines, as well as their receptors, have been shown to be highly polymorphic. The cytokine and chemokine gene polymorphisms are associated with variable production, activity, expression, or ligand-receptor affinity. The aim of our study was to analyze the relation between selected cytokine and chemokine gene polymorphisms in kidney donors and recipients as a function of donor-recipient match and posttransplantation outcome. Polymorphisms transforming growth factor-beta (TGF-beta); tumor necrosis factor-alpha (TNF-alpha); interleukin (IL)-6, and IL-10; monocyte chemoattractant protein-1 (MCP-1); and RANTES (regulated upon activation, normal T-cell expressed and secreted) genes were determined using DNA polymerase chain reaction technology in 268 healthy volunteers, 345 kidney transplant recipients (1997 to 1999), and 298 cadaveric donors. Patients were followed up for 4 to 6 years. The distribution of alleles of selected genes was identical in control subjects, cadaveric donors, and recipients. Low TGF-beta production in both the donor and recipient genotypes was associated with risk for early rejection (6 months) and worse graft function at 4 years. The only tendency for worse graft outcome was observed among donor-recipient combinations mismatched for TGF-beta genotype. Genetic determination of TNF-alpha and IL-10 production was associated with delayed graft function and rejection. IL-6 gene polymorphisms had no effect on the incidence of early acute rejections, but was associated with worse 5-year outcomes. Determinations of MCP-1 overproduction and RANTES-109 TT allele were associated with significant deterioration of graft function. Our data support the hypothesis that the strength of the alloimmune response after transplantation is in part genetically determined. Donor-recipient matching of cytokine gene polymorphisms has a marginal effect.

Polymorphisms in the trace amine receptor 4 (TRAR4) gene on chromosome 6q23.2 are associated with susceptibility to schizophrenia

Several linkage studies across multiple population groups provide convergent support for a susceptibility locus for schizophrenia--and, more recently, for bipolar disorder--on chromosome 6q13-q26. We genotyped 192 European-ancestry and African American (AA) pedigrees with schizophrenia from samples that previously showed linkage evidence to 6q13-q26, focusing on the MOXD1-STX7-TRARs gene cluster at 6q23.2, which contains a number of prime candidate genes for schizophrenia. Thirty-one screening single-nucleotide polymorphisms (SNPs) were selected, providing a minimum coverage of at least 1 SNP/20 kb. The association observed with rs4305745 (P=.0014) within the TRAR4 (trace amine receptor 4) gene remained significant after correction for multiple testing. Evidence for association was proportionally stronger in the smaller AA sample. We performed database searches and sequenced genomic DNA in a 30-proband subsample to obtain a high-density map of 23 SNPs spanning 21.6 kb of this gene. Single-SNP analyses and also haplotype analyses revealed that rs4305745 and/or two other polymorphisms in perfect linkage disequilibrium (LD) with rs4305745 appear to be the most likely variants underlying the association of the TRAR4 region with schizophrenia. Comparative genomic analyses further revealed that rs4305745 and/or the associated polymorphisms in complete LD with rs4305745 could potentially affect gene expression. Moreover, RT-PCR studies of various human tissues, including brain, confirm that TRAR4 is preferentially expressed in those brain regions that have been implicated in the pathophysiology of schizophrenia. These data provide strong preliminary evidence that TRAR4 is a candidate gene for schizophrenia; replication is currently being attempted in additional clinical samples.

Patterned variation in murine MHC promoters

To compare variation in regulatory and coding DNA, promoter sequences have been obtained from wild-derived mice and laboratory rats. The sequences are from the proximal promoter of the H2Aa, H2Ab, H2Eb, and H2K genes of 24 wild-derived inbred strains and a sample of the corresponding exon 2 sequences and of the RT1.Ba gene of six strains of laboratory rat. They reveal a high level of variation in the mouse MHC class II promoters (H2A and H2E), a low level in MHC class I (H2K), and none in the rat. The variation is pronounced in and around the cAMP response element, a major binding site for modulating promoter activity in response to external stimulation. This finding, together with the different levels of variation in MHC classes I and II, is suggestive of natural selection. However, selection operating via the MHC coding sequences must also contribute, as indicated by the minimal variation in both the MHC class II promoter and coding sequences of the rat. Furthermore CIITA (trans-activator of class II) of the mouse has been reported to have minimal variation in its promoter and none in its coding sequence. Taken together these data suggest that the regulatory and coding sequences undergo coselection. Each of the mouse class II promoters has a pattern of variation that appears to be basically dimorphic, with further variation added by recombination/mutation. The dimorphic allelic lineages are in marginally detectable linkage disequilibrium with the exon 2 sequences, particularly in H2Aa, thus lending further support to the coevolution hypothesis.

The immunological synapse

The immunological synapse plays a central role in organising the immune system. Through their synaptic activity both T and B cells usually, but not always, acquire the information that critically determines the level and nature of the responses that they make. For T cells much of that information comes from epicrine and paracrine cell-cell interactions in the cluster that forms around a dendritic cell. These interactions are being dissected by experiments in which two populations of TCR-transgenic T cells are combined in vivo. Another important aspect of synaptic activity is the way in which different levels of expression of MHC class II molecules influence Th1/Th2 balance. In exploring this form of control we are learning something of general importance about cis-regulation.