Lower rate of genomic variation identified in the trans-membrane domain of monoamine sub-class of Human G-Protein Coupled Receptors: The Human GPCR-DB Database
BMC GENOMICS
Authors: Wahlestedt, C; Brookes, AJ; Mottagui-Tabar, S
Abstract
Background: We have surveyed, compiled and annotated nucleotide variations in 338 human 7-transmembrane receptors (G-protein coupled receptors). In a sample of 32 chromosomes from a Nordic population, we attempted to determine the allele frequencies of 80 non- synonymous SNPs, and found 20 novel polymorphic markers. GPCR receptors of physiological and clinical importance were prioritized for statistical analysis. Natural variation and rare mutation information were merged and presented online in the Human GPCR- DB database http://cyrix.cgb.ki.se. Results: The average number of SNPs per 1000 bases of exonic sequence was found to be twice the average number of SNPs per Kilobase of intronic regions (2.2 versus 1.0). Of the 338 genes, 111 were single exon genes, that is, were intronless. The average number of exonic-SNPs per single-exon gene was 3.5 ( n = 395) while that for multi-exon genes was 0.8 ( n = 1176). The average number of variations within the different protein domain (N-terminus, internal- and external-loops, trans-membrane region, C-terminus) indicates a lower rate of variation in the trans-membrane region of Monoamine GPCRs, as compared to Chemokine-and Peptide-receptor sub-classes of GPCRs. Conclusions: Single-exon GPCRs on average have approximately three times the number of SNPs as compared to GPCRs with introns. Among various functional classes of GPCRs, Monoamine GPRCs have lower number of natural variations within the trans-membrane domain indicating evolutionary selection against non- synonymous changes within the membrane-localizing domain of this sub-class of GPCRs.
Methylation status of human chorionic gonadotropin beta subunit promoter and TFAP2A expression as factors regulating CGB gene expression in placenta
FERTILITY AND STERILITY
Authors: Glodek, Aleksandra; Kubiczak, Marta J.; Walkowiak, Grzegorz P.; Nowak-Markwitz, Ewa; Jankowska, Anna
Abstract
Objective: To evaluate mechanisms regulating the expression of CGB genes in placental tissues from uncomplicated pregnancies and chorionic samples from spontaneous miscarriages. Design: Molecular analyses in human samples. Setting: Laboratory of molecular biology. Patient(s): Nine placental samples from term deliveries and 21 chorionic samples from miscarriages at 7-13 weeks of gestation. Intervention(s): None. Main Outcome Measure(s): The expression level of CGBs and genes encoding SP1, SP3, and AP2 transcription factors was analyzed using quantitative polymerase chain reaction (qPCR). The methylation status of the CGBs' promoter regions was determined using methylation-specific PCR. Result(s): The experiments showed significant differences in CGBs' expression and their regulation between placental and chorionic tissues. In placental tissues and chorionic tissues from 7 to 9 weeks of gestation, the expression level of CGBs was shown to be associated with the amount of TFAP2A transcripts. It was also demonstrated that variation in the expression level of CGB genes relies on changes in methylation of CGB3-9 and CGB1-2 promoter sequences. Conclusion(s): During pregnancy, regulation of hCG beta subunit genes expression correlates with both methylation of their promoters and TFAP2A expression level. The results suggest that these factors may be very influential in the early stages of pregnancy and may be associated with pregnancy outcome. (C) 2014 by American Society for Reproductive Medicine.