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Noncoding Regions (noncoding + regions)
Selected AbstractsElectrophoretic variants of cardiac myosin heavy chain-, in Sprague Dawley ratsELECTROPHORESIS, Issue 3 2004Peter J. Reiser Abstract Analysis of cardiac myosin revealed differences in gel electrophoretic migration patterns of the ,-isoform of myosin heavy chain, but not the ,-isoform, in Sprague Dawley rats. No differences in the migration patterns of the ,-or ,-isoforms were observed in other rat strains. Three electrophoretic migration patterns of the ,-isoforms were observed in individual rats: a slower migrating isoform alone (4% of all rats tested), a faster migrating isoform alone (55%), and both isoforms (41%). The isoform expression pattern was identical in all myocardial regions in each rat. Frequency of expression patterns suggests multiple gene sequences for ,-cardiac myosin heavy chain in Sprague Dawley rats. Sequence analysis of amplified regions of the Sprague Dawley and Brown Norway rat ,-myosin genes, specifically the 5'-untranslated region, exons 1,3, and associated introns, showed numerous single nucleotide polymorphisms in coding and noncoding regions, including putative regulatory sites in Sprague Dawley rats, but not in Brown Norway rats. All Sprague Dawley rats varied from Brown Norway rats and no heterogeneity was observed in Brown Norway rats. Several deletions and dimorphic positions were also observed. Dimorphic positions were evident on automated sequencing comparisons. The data indicate that at least two ,-myosin heavy chain isoforms exist in Sprague Dawley rats and these rats exhibit sequence diversity within that portion of the ,-myosin heavy chain gene reported in this study. [source] RAPID ADAPTIVE DIVERGENCE IN NEW WORLD ACHILLEA, AN AUTOPOLYPLOID COMPLEX OF ECOLOGICAL RACESEVOLUTION, Issue 3 2008Justin Ramsey Adaptive evolution is often associated with speciation. In plants, however, ecotypic differentiation is common within widespread species, suggesting that climatic and edaphic specialization can outpace cladogenesis and the evolution of postzygotic reproductive isolation. We used cpDNA sequence (5 noncoding regions, 3.5 kb) and amplified fragment length polymorphisms (AFLPs: 4 primer pairs, 1013 loci) to evaluate the history of ecological differentiation in the North American Achillea millefolium, an autopolyploid complex of "ecological races" exhibiting morphological, physiological, and life-history adaptations to diverse environments. Phylogenetic analyses reveal North American A. millefolium to be a monophyletic group distinct from its European and Asian relatives. Based on patterns of sequence divergence, as well as fossil and paleoecological data, colonization of North America appears to have occurred via the Bering Land Bridge during the Pleistocene (1.8 MYA to 11,500 years ago). Population genetic analyses indicate negligible structure within North American A. millefolium associated with varietal identity, geographic distribution, or ploidy level. North American populations, moreover, exhibit the signature of demographic expansion. These results affirm the "ecotype" concept of the North American Achillea advocated by classical research and demonstrate the rapid rate of ecological differentiation that sometimes occurs in plants. [source] The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterpartsFEMS YEAST RESEARCH, Issue 1 2006Paraskevi V. Pramateftaki Abstract The complete sequence of the apiculate wine yeast Hanseniaspora uvarum mtDNA has been determined and analysed. It is an extremely compact linear molecule containing the shortest functional region ever found in fungi (11 094 bp long), flanked by Type 2 telomeric inverted repeats. The latter contained a 2704-bp-long subterminal region and tandem repeats of 839-bp units. In consequence, a population of mtDNA molecules that differed at the number of their telomeric reiterations was detected. The functional region of the mitochondrial genome coded for 32 genes, which included seven subunits of respiratory complexes and ATP synthase (the genes encoding for NADH oxidoreductase subunits were absent), two rRNAs and 23 tRNA genes which recognized codons for all amino acids. A single intron interrupted the cytochrome oxidase subunit 1 gene. A number of reasons contributed towards its strikingly small size, namely: (1) the remarkable size reduction (by >40%) of the rns and rnl genes; (2) that most tRNA genes and five of the seven protein-coding genes were the shortest among known yeast homologs; and (3) that the noncoding regions were restricted to 5.1% of the genome. In addition, the genome showed multiple changes in the orientation of transcription and the gene order differed drastically from other yeasts. When all protein coding gene sequences were considered as one unit and were compared with the corresponding molecules from all other complete mtDNAs of yeasts, the phylogenetic trees constructed robustly supported its placement basal to the yeast species of the ,Saccharomyces complex', demonstrating the advantage of this approach over single-gene or multigene approaches of unlinked genes. [source] Microsatellites: genomic distribution, putative functions and mutational mechanisms: a reviewMOLECULAR ECOLOGY, Issue 12 2002You-Chun Li Abstract Microsatellites, or tandem simple sequence repeats (SSR), are abundant across genomes and show high levels of polymorphism. SSR genetic and evolutionary mechanisms remain controversial. Here we attempt to summarize the available data related to SSR distribution in coding and noncoding regions of genomes and SSR functional importance. Numerous lines of evidence demonstrate that SSR genomic distribution is nonrandom. Random expansions or contractions appear to be selected against for at least part of SSR loci, presumably because of their effect on chromatin organization, regulation of gene activity, recombination, DNA replication, cell cycle, mismatch repair system, etc. This review also discusses the role of two putative mutational mechanisms, replication slippage and recombination, and their interaction in SSR variation. [source] Genetic variants in the noncoding region of RPS19 gene in Diamond-Blackfan anemia: Potential implications for phenotypic heterogeneity,AMERICAN JOURNAL OF HEMATOLOGY, Issue 2 2010Aurore Crétien Mutations in the RPS19 gene have been identified in 25% of individuals affected by Diamond-Blackfan anemia (DBA), a congenital erythroblastopenia characterized by an aregenerative anemia and a variety of malformations. More than 60 mutations in the five coding exons of RPS19 have been described to date. We previously reported a mutation (c.-1 + 26G>T) and an insertion at ,631 upstream of ATG (c.-147_-146insGCCA) in the noncoding region. Because DBA phenotype is extremely heterogeneous from silent to severe and because haploinsufficiency seems to play a role in this process, it is likely that genetic variations in the noncoding regions affecting translation of RPS19 can modulate the phenotypic expression of DBA. However, to date, very few studies have addressed this question comprehensively. In this study, we performed detailed sequence analysis of the RPS19 gene in 239 patients with DBA and 110 of their relatives. We found that 6.2% of the patients with DBA carried allelic variations upstream of ATG: 3.3% with c.-1 + 26G>T; 2.5% with c.-147_-146insGCCA; and 0.4% with c.-174G>A. Interestingly, the c.-147_-146insGCCA, which has been found in a black American and French Caribbean control population, was not found in 500 Caucasian control chromosomes we studied. However, it was found in association with the same haplotype distribution of four intronic polymorphisms in our patients with DBA. Although a polymorphism, the frequency of this variant in the patients with DBA and its association with the same haplotype raises the possibility that this polymorphism and the other genetic variations in the noncoding region could play a role in DBA pathogenesis. Am. J. Hematol., 2010. © 2009 Wiley-Liss, Inc. [source] Gene expression profiling differentiates autism case,controls and phenotypic variants of autism spectrum disorders: evidence for circadian rhythm dysfunction in severe autismAUTISM RESEARCH, Issue 2 2009Valerie W. Hu Abstract Autism spectrum disorders (ASD) are neurodevelopmental disorders characterized by delayed/abnormal language development, deficits in social interaction, repetitive behaviors and restricted interests. The heterogeneity in clinical presentation of ASD, likely due to different etiologies, complicates genetic/biological analyses of these disorders. DNA microarray analyses were conducted on 116 lymphoblastoid cell lines (LCL) from individuals with idiopathic autism who are divided into three phenotypic subgroups according to severity scores from the commonly used Autism Diagnostic Interview-Revised questionnaire and age-matched, nonautistic controls. Statistical analyses of gene expression data from control LCL against that of LCL from ASD probands identify genes for which expression levels are either quantitatively or qualitatively associated with phenotypic severity. Comparison of the significant differentially expressed genes from each subgroup relative to the control group reveals differentially expressed genes unique to each subgroup as well as genes in common across subgroups. Among the findings unique to the most severely affected ASD group are 15 genes that regulate circadian rhythm, which has been shown to have multiple effects on neurological as well as metabolic functions commonly dysregulated in autism. Among the genes common to all three subgroups of ASD are 20 novel genes mostly in putative noncoding regions, which appear to associate with androgen sensitivity and which may underlie the strong 4:1 bias toward affected males. [source] Trans -splicing in DrosophilaBIOESSAYS, Issue 11 2002Vincenzo Pirrotta Splicing is an efficient and precise mechanism that removes noncoding regions from a single primary RNA transcript. Cutting and rejoining of the segments occurs on nascent RNA. Trans -splicing between small specialized RNAs and a primary transcript has been known in some organisms but recent papers show that trans -splicing between two RNA molecules containing different coding regions is the normal mode in a Drosophila gene.1,3 The mod(mdg4) gene produces 26 different mRNAs encoding as many protein isoforms. The differences lie in alternative 3, exons encoded by different transcriptional units and spliced to the 5, common region by a surprising trans -splicing mechanism. BioEssays 24:988,991, 2002. © 2002 Wiley-Periodicals, Inc. [source] | |||||||||||||