Computational Analysis of Neighboring Genes on Arabidopsis thaliana Chromosomes 4 and 5: Their Genomic Association as Functional Subunits

The genes related to specific events or pathways in bacteria are frequently localized proximate to the genome of their neighbors, as with the structures known as operon, but eukaryotic genes seem to be independent of their neighbors, and are dispersed randomly throughout genomes. Although cases are rare, the findings from structures similar to prokaryotic operons in the nematode genome, and the clustering of housekeeping genes on human genome, lead us to assess the genomic association of genes as functional subunits. We evaluated the genomic association of neighboring genes on chromosomes 4 and 5 of Arabidopsis thaliana with and without respectively consideration of the scaffold/matrix-attached regions (S/MAR) loci. The observed number of functionally identical bigrams and trig rams were significantly higher than expected, and these results were verified statistically by calculating rho-values for weighted random distributions. The observed frequency of functionally identical big rams and trig rams were much higher in chromosome 4 than in chromosome 5, but the frequencies with, and without, consideration of the S/MAR in each chromosome were similar. In this study, a genomic association among functionally related neighboring genes in Arabidopsis thaliana was suggested.

Role of Polymorphism in HLA DQ-alpha and -beta Chain Loci in the Pathophysiology of Autoimmune Thyroid Disease in Children with and without Turner Syndrome

PURPOSE: About 10% of girls with Turner syndrome may have autoimmune thyroid disease(AIT), but the disease's pathophysiology has not yet been elucidated. Accordingly, this study was performed to observe whether the pathogenesis of AIT in children with Turner syndrome and without Turner syndrome correlate with special loci of DQ and chain in HLA. METHODS: Blood samples were drawn from children with and without Turner syndrome. Thyroid antibodies(anti-thyroglobulin and anti-microsomal antibody) were measured from the samples to determine AIT. DNAs were extracted with the DNA extraction kit and processed in PCR reaction for amplification of exon 2 region of HLA-DQA1 and -DQB1, and then eluted again. The eluted PCR products were sequenced directly with an automatic sequencer. The sequences were compared with those of normal control. RESULTS: There was a signficant increase in frequencies of HLA DQA1*0301(P<0.05) and HLA DQB1*0601 but without statistical significance(P=0.06) in normal children with AIT, compared with those in control group. There was signficantly but slightly increased frequency of HLA DQA1*0104, 0105 and DQB1*0202 in the group of children with Turner syndrome who had AIT than in control group. The frequency of the marker chromosome(45,X/46,XX+mar) increased in children with Turner syndrome who had AIT, compared with these in children with Turner syndrome who did not have AIT. Children with Turner syndrome who had spontaneous puberty had higher a incidence rate of AIT than those who did not have spontaneous puberty(P<0.01). CONCLUSION: The results suggest that HLA DQA1*0301 and HLA DQB1*0601 play a role in the pathogenesis of AIT in children without Turner syndrome, but not in children with Turner syndrome. Additionally, there seem to be other factors participating in the pathogenesis of AIT in children with Turner syndrome, such as chromosomal karyotype and spontaneous puberty. Therefore, the factors participitating in the pathogenesis of AIT in children with Turner syndrome remain to be elucidated with further study.