HIC1 (hypermethylated in cancer 1) is a tumor suppressor gene located on chromosome 17p13.3, a region frequently hypermethylated or deleted in human neoplasias. In mouse, Hic1 is essential for embryonic development and exerts an antitumor role in adult animals. Since Hic1-deficient mice die perinatally, we generated a conditional Hic1 null allele by flanking the Hic1-coding region by loxP sites. When crossed to animals expressing Cre recombinase in a cell-specific manner, the Hic1 conditional mice will provide new insights into the function of Hic1 in developing and mature tissues. Additionally, we used gene targeting to replace sequence-encoding amino acids 186-893 of Hic1 by citrine fluorescent protein cDNA. We demonstrate that the distribution of Hic1-citrine fusion polypeptide corresponds to the expression pattern of wild-type Hic1. Consequently, Hic1-citrine "reporter" mice can be used to monitor the activity of the Hic1 locus using citrine fluorescence.

• MeSH
• alely * MeSH
• delece genu MeSH
• DNA vazebné proteiny genetika   MeSH
• embryo savčí metabolismus   MeSH
• genový targeting MeSH
• integrasy genetika   metabolismus   MeSH
• myši transgenní MeSH
• myši MeSH
• reportérové geny MeSH
• transkripční faktory Krüppel-like genetika   MeSH
• transkripční faktory genetika   MeSH
• tumor supresorové geny * MeSH
• vývojová regulace genové exprese * MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Cre recombinase MeSH Prohlížeč
• DNA vazebné proteiny MeSH
• Hic1 protein, mouse MeSH Prohlížeč
• integrasy MeSH
• transkripční faktory Krüppel-like MeSH
• transkripční faktory MeSH

OBJECTIVES: Extensive polymorphism of HLA class II genes is not restricted to the coding region of the gene. It extends also to the linked promoter region, where it forms the basis for different levels of individual allele's expression. Differential expression of HLA class II alleles can shape an immune response and influence the risk of developing autoimmune disease. In addition to genetic variability, variation in epigenetic modifications, including DNA methylation, can be another cause of the uneven expression of individual alleles. We aimed to analyze the DNA methylation of promoter sequences and the levels of expression of individual DQA1 gene alleles, interallelic variation of these two characteristics and the relationship between them. METHODS: The 60 healthy donors included into study were HLA-DRB1, HLA-DQB1 and HLA-DQA1 genotyped using PCR-SSP. Genomic DNA was treated by sodium bisulfite and the target segment in the HLA-DQA1 gene promoter was PCR amplified. PCR product was cloned into Escherichia coli and individual clones were sequenced. Transcripts of individual DQA1 alleles in peripheral blood leukocytes were quantified by Real-Time PCR. RESULTS: In this study, we have described detailed DNA methylation profile of promoter area of DQA1 gene alleles. The overall promoter methylation is increased for DQA1*02:01 and DQA1*04:01 alleles, on the other side, DQA1*05:01 allele shows decreased methylation level. Our results suggest that there are only minor interindividual differences in DRA-normalized expression level of specific allele. Furthermore, expression levels of individual alleles followed DQA1*03>*01:03 (in DRB1*13-DQA1*01:03-DQB1*06:03 haplotype)>*01:01,*05:05, and DQA1*03>*02:01>*05:05 hierarchy. The statistically significantly most expressed allele, DQA1*03, comprises part of DQ8 molecule, which is commonly linked to autoimmune diseases. A clear relationship between promoter DNA methylation and mRNA expression level of the DQA1 gene could not be identified.

• Klíčová slova
• DNA methylation, DQA1, HLA class II, Polymorphism, mRNA expression,
• MeSH
• alely * MeSH
• CpG ostrůvky MeSH
• dospělí MeSH
• haplotypy MeSH
• HLA-DQ alfa řetězec genetika   MeSH
• HLA-DQ beta řetězec genetika   MeSH
• HLA-DRB1 řetězec genetika   MeSH
• lidé MeSH
• messenger RNA genetika   MeSH
• metylace DNA * MeSH
• mladý dospělý MeSH
• promotorové oblasti (genetika) * MeSH
• regulace genové exprese * MeSH
• zdraví dobrovolníci pro lékařské studie MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mladý dospělý MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• HLA-DQ alfa řetězec MeSH
• HLA-DQ beta řetězec MeSH
• HLA-DQA1 antigen MeSH Prohlížeč
• HLA-DQB1 antigen MeSH Prohlížeč
• HLA-DRB1 řetězec MeSH
• messenger RNA MeSH

A catalog of common, intermediate and well-documented (CIWD) HLA-A, -B, -C, -DRB1, -DRB3, -DRB4, -DRB5, -DQB1 and -DPB1 alleles has been compiled from over 8 million individuals using data from 20 unrelated hematopoietic stem cell volunteer donor registries. Individuals are divided into seven geographic/ancestral/ethnic groups and data are summarized for each group and for the total population. P (two-field) and G group assignments are divided into one of four frequency categories: common (≥1 in 10 000), intermediate (≥1 in 100 000), well-documented (≥5 occurrences) or not-CIWD. Overall 26% of alleles in IPD-IMGT/HLA version 3.31.0 at P group resolution fall into the three CIWD categories. The two-field catalog includes 18% (n = 545) common, 17% (n = 513) intermediate, and 65% (n = 1997) well-documented alleles. Full-field allele frequency data are provided but are limited in value by the variations in resolution used by the registries. A recommended CIWD list is based on the most frequent category in the total or any of the seven geographic/ancestral/ethnic groups. Data are also provided so users can compile a catalog specific to the population groups that they serve. Comparisons are made to three previous CWD reports representing more limited population groups. This catalog, CIWD version 3.0.0, is a step closer to the collection of global HLA frequencies and to a clearer view of HLA diversity in the human population as a whole.

• Klíčová slova
• HLA, alleles, ethnic groups, gene frequency,
• MeSH
• alely * MeSH
• frekvence genu MeSH
• haplotypy MeSH
• lidé MeSH
• MHC antigeny I. třídy genetika   MeSH
• MHC antigeny II. třídy genetika   MeSH
• populační genetika * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• MHC antigeny I. třídy MeSH
• MHC antigeny II. třídy MeSH

Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.

• Klíčová slova
• GWAS, alleles, breeding, causal gene, causative mutation, genetic variation, soybean,
• Publikační typ
• časopisecké články MeSH

New adenosine deaminase variants ADA C and ADA D were found by means of agarose gel electrophoresis in pig erythrocytes. Family data supported the hypothesis that these are controlled by codominant alleles ADAC and ADAD. The ADAC allele was present in Large White (q = 0.076), Landrace (q = 0.037) and their crosses with other breeds. The ADAD allele was present in Duroc (q = 0.067) and its crosses. Allele frequencies for six pig breeds are given.

• MeSH
• adenosindeaminasa genetika   MeSH
• alely MeSH
• druhová specificita MeSH
• elektroforéza v agarovém gelu veterinární   MeSH
• erytrocyty enzymologie   MeSH
• frekvence genu MeSH
• křížení genetické MeSH
• polymorfismus genetický MeSH
• prasata genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• adenosindeaminasa MeSH

BACKGROUND: Ribosomal RNA (rRNA) accounts for the majority of the RNA in eukaryotic cells, and is encoded by hundreds to thousands of nearly identical gene copies, only a subset of which are active at any given time. In Arabidopsis thaliana, 45S rRNA genes are found in two large ribosomal DNA (rDNA) clusters and little is known about the contribution of each to the overall transcription pattern in the species. RESULTS: By taking advantage of genome sequencing data from the 1001 Genomes Consortium, we characterize rRNA gene sequence variation within and among accessions. Notably, variation is not restricted to the pre-rRNA sequences removed during processing, but it is also present within the highly conserved ribosomal subunits. Through linkage mapping we assign these variants to a particular rDNA cluster unambiguously and use them as reporters of rDNA cluster-specific expression. We demonstrate that rDNA cluster-usage varies greatly among accessions and that rDNA cluster-specific expression and silencing is controlled via genetic interactions between entire rDNA cluster haplotypes (alleles). CONCLUSIONS: We show that rRNA gene cluster expression is controlled via complex epistatic and allelic interactions between rDNA haplotypes that apparently regulate the entire rRNA gene cluster. Furthermore, the sequence polymorphism we discovered implies that the pool of rRNA in a cell may be heterogeneous, which could have functional consequences.

• Klíčová slova
• Dominance, Epistasis, Ribosomes, Transcription, rRNA genes,
• MeSH
• alely MeSH
• Arabidopsis genetika   MeSH
• genetická epistáze * MeSH
• haplotypy MeSH
• multigenová rodina * MeSH
• regulace genové exprese u rostlin * MeSH
• RNA ribozomální genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• RNA ribozomální MeSH
• RNA, ribosomal, 45S MeSH Prohlížeč

A comprehensive knowledge of human leukocyte antigen (HLA) molecular variation worldwide is essential in human population genetics research and disease association studies and is also indispensable for clinical applications such as allogeneic hematopoietic cell transplantation, where ensuring HLA compatibility between donors and recipients is paramount. Enormous progress has been made in this field thanks to several decades of HLA population studies allowing the development of helpful databases and bioinformatics tools. However, it is still difficult to appraise the global HLA population diversity in a synthetic way. We thus introduce here a novel approach, based on approximately 2000 data sets, to assess this complexity by providing a fundamental synopsis of the most frequent HLA alleles observed in different regions of the world. This new knowledge will be useful not only as a fundamental reference for basic research, but also as an efficient guide for clinicians working in the field of transplantation.

• Klíčová slova
• CWD catalogues, HLA allele frequencies, HLA biostatistical tools, HLA databases, HLA population genetics, HLA workshops,
• MeSH
• alely * MeSH
• frekvence genu MeSH
• HLA antigeny * genetika   imunologie   MeSH
• lidé MeSH
• transplantace hematopoetických kmenových buněk * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• HLA antigeny * MeSH

The frequencies of phenotypes, alleles and allelic subtypes of DRB1 and DQB1 HLA loci in 420 unrelated individuals from the Czech population were determined. The frequencies of DPB1 alleles of the HLA locus were determined in 92 individuals. The assays were performed using the polymerase chain reaction (PCR) method or the restriction fragment length polymorphism (RFLP) analysis. The most frequent DRB1 allele was *07, the most frequent DQB1 allele was *03 and the most frequent DPB1 allele detected was *04. These assays define the extent of polymorphism of the HLA system and are useful for determining the selection strategy of HLA-identical donor-recipient pair suitable for bone marrow transplantation.

• MeSH
• alely MeSH
• frekvence genu * MeSH
• genotyp MeSH
• geny MHC třídy II * MeSH
• HLA-DP antigeny genetika   MeSH
• HLA-DP beta řetězec MeSH
• HLA-DQ antigeny genetika   MeSH
• HLA-DQ beta řetězec MeSH
• HLA-DR antigeny genetika   MeSH
• HLA-DRB1 řetězec MeSH
• lidé MeSH
• transplantace kostní dřeně MeSH
• získávání tkání a orgánů MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• HLA-DP antigeny MeSH
• HLA-DP beta řetězec MeSH
• HLA-DPB1 antigen MeSH Prohlížeč
• HLA-DQ antigeny MeSH
• HLA-DQ beta řetězec MeSH
• HLA-DQB1 antigen MeSH Prohlížeč
• HLA-DR antigeny MeSH
• HLA-DRB1 řetězec MeSH

Congenital adrenal hyperplasia (CAH) is comprised of a group of autosomal recessive disorders caused by an enzymatic deficiency which impairs the biosynthesis of cortisol and, in most of the severe cases, also the biosynthesis of aldosterone. Approximately 90-95% of all the CAH cases are due to mutations in the steroid 21-hydroxylase gene (CYP21A2). In this study, the molecular genetic analysis of CYP21A2 was performed in 267 Czech probands suspected of 21-hydroxylase deficiency (21OHD). 21OHD was confirmed in 241 probands (2 mutations were detected). In 26 probands, a mutation was found only in 1 CYP21A2 allele. A set of 30 different mutant alleles was determined. We describe i) mutated CYP21A2 alleles carrying novel point mutations (p.Thr168Asn, p.Ser169X and p.Pro386Arg), ii) mutated CYP21A2 alleles carrying the novel chimeric gene designated as CH-7, which was detected in 21.4% of the mutant alleles, iii) an unusual genotype with a combination of the CYP21A2 duplication, 2 point mutations and the CYP21A2 large-scale gene conversion on the second allele, and (iv) a detailed analysis of the chimeric CYP21A1P/CYP21A2 genes. In conclusion, our genotyping approach allowed for the accurate identification of the CYP21A2 gene mutations in 21OHD patients and their families and provided some useful information on diagnosis and genetic counselling.

• MeSH
• alely * MeSH
• bodová mutace MeSH
• delece genu MeSH
• duplikace genu MeSH
• fenotyp MeSH
• genotyp MeSH
• kongenitální adrenální hyperplazie diagnóza   genetika   MeSH
• lidé MeSH
• mutace * MeSH
• steroid-21-hydroxylasa genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH
• Názvy látek
• CYP21A2 protein, human MeSH Prohlížeč
• steroid-21-hydroxylasa MeSH

The aim of this study was to characterize the spectrum of 13-glucocerebrosidase gene mutations in Czech and Slovak Gaucher patients and to study genotype/phenotype associations. We have analyzed fifty-eight chromosomes from twenty-six type I, two type 2, and one type 3 13-glucocerebrosidase deficient subjects by direct sequencing of PCR products. Fifty-eight mutant alleles were identified. Seventy-eight percent of mutant alleles carried common mutations (N370S 28/58, L444P 11/58, recNciI 5/58, and IVS2(+1)A 1/58), the remaining twenty-two percent carried rare and private mutations (1263del55, l326insT, S196P, rec(g4889-6506), 2O3delC, G202E, F216Y, R257X, R12OW, R359Q, S1O7L, L444P + V460V, and D409H + T369M). Six of these alleles have not been previously described (rec(g4889-6506), 1326insT, SI96P. G202E, D409H + T369M, and L444P + V460V). The most common genotypes were N370S/L444P (8/29). N370S/recNciI (5/29), and N370S/N370S (2/29). The spectrum of the mutations is characteristic for a Caucasian (non-Jewish) population, with N370S, L444P and recNciI being the most prevalent mutations. The absence of the mutation 84insG that is frequently associated with severe bone disease may have contributed to the low incidence of severe bone disease in Czech and Slovak Gaucher subjects.

• MeSH
• alely MeSH
• běloši genetika   MeSH
• dítě MeSH
• dospělí MeSH
• fenotyp MeSH
• frekvence genu MeSH
• Gaucherova nemoc epidemiologie   etnologie   genetika   MeSH
• genetická variace MeSH
• genotyp MeSH
• glukosylceramidasa nedostatek   genetika   MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mutace genetika   MeSH
• mutační analýza DNA MeSH
• předškolní dítě MeSH
• senioři MeSH
• Southernův blotting MeSH
• Židé genetika   MeSH
• Check Tag
• dítě MeSH
• dospělí MeSH
• kojenec MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• předškolní dítě MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Česká republika epidemiologie   MeSH
• Slovenská republika epidemiologie   MeSH
• Názvy látek
• glukosylceramidasa MeSH