Zvýšené hladiny lipoproteinu(a) jsou považovány za nezávislý rizikový faktor v procesu aterogeneze. Strukturní i funkční charakteristika částice lipoproteinu(a) je určena přítomností apolipoproteinu(a). Přestože jsou plazmatické hladiny tohoto lipoproteinu téměř zcela pod genetickou kontrolou genu pro apolipoprotein(a), vykazují značnou populační variabilitu. Velká část této variability je způsobena délkovým polymorfizmem genu pro apolipoprotein(a). Zbývající variabilita může být dána jak přítomností sekvenčních polymorfizmů v kódující sekvenci zmíněného genu, tak v jeho regulačních elementech. V kódující oblasti genu pro apolipoprotein(a) bylo zatím odhaleno jen málo polymorfních variant s funkčním významem. Rovněž analýza tří oblastí schopných regulovat expresi genu (promotor, zesilovače DHII a DHIII) prokázala nižší variabilitu, než se očekávalo. I přes dominantní úlohu jediného genu je genetická determinace hladin Lp(a) velice komplexní. Hlavní úlohu zde hraje délkový polymorfizmus genu pro apolipoprotein(a) a celá řada sekvenčních variant ovlivňujících jeho expresi a efektivitu tvorby lipoproteinové částice. Svou roli mají pravděpodobně i další genetické lokusy s minoritním účinkem a modulace negenetickými faktory.
Increased levels of lipoprotein(a) are supposed to be an independent risk factor for atherosclerosis. Apolipoprotein(a) determines structural and functional characteristics of the lipoprotein particle. The lipoprotein(a) concentration is almost entirely genetically determined at the apolipoprotein(a) gene locus, nevertheless it varies widely between individuals in all populations studied so far. Large part of the variance is correlated to the apolipoprotein(a) gene length polymorphism. Some of the variance could be additionally related to polymorphic sites either in the coding sequence or in the transcription regulatory regions. Only a few functional variants were discovered in the coding sequence of apolipoprotein(a) gene so far. Moreover, analyses of relevant regulatory regions (promoter, DHII and DHIII enhancers) have revealed less variability than was expected. Despite the lipoprotein(a) levels are under dominant control of a single locus its genetic determination is quite complex. The basic role belongs to the apolipoprotein(a) gene length polymorphism and to a panel of sequence variants affecting apolipoprotein(a) gene expression and lipoprotein(a) particle production rate. Besides, minor impact of other locuses and modulation by non–genetic factors should be considered.
Staphylococcus aureus is a serious human and veterinary pathogen in which new strains with increasing virulence and antimicrobial resistance occur due to acquiring new genes by horizontal transfer. It is generally accepted that temperate bacteriophages play a major role in gene transfer. In this study, we proved the presence of various bacterial genes of the S. aureus COL strain directly within the phage particles via qPCR and quantified their packaging frequency. Non-parametric statistical analysis showed that transducing bacteriophages φ11, φ80 and φ80α of serogroup B, in contrast to serogroup A bacteriophage φ81, efficiently package selected chromosomal genes localized in 4 various loci of the chromosome and 8 genes carried on variable elements, such as staphylococcal cassette chromosome SCCmec, staphylococcal pathogenicity island SaPI1, genomic islands vSaα and vSaβ, and plasmids with various frequency. Bacterial gene copy number per ng of DNA isolated from phage particles ranged between 1.05 × 10(2) for the tetK plasmid gene and 3.86 × 10(5) for the SaPI1 integrase gene. The new and crucial finding that serogroup B bacteriophages can package concurrently ccrA1 (1.16 × 10(4)) and mecA (1.26 × 10(4)) located at SCCmec type I into their capsids indicates that generalized transduction plays an important role in the evolution and emergence of new methicillin-resistant clones.
- MeSH
- Chromosomes, Bacterial genetics MeSH
- Genes, Bacterial * MeSH
- Bacterial Proteins genetics MeSH
- Bacteriophages genetics metabolism MeSH
- DNA, Bacterial genetics MeSH
- Gene Frequency MeSH
- Genetic Loci MeSH
- Cloning, Molecular MeSH
- Penicillinase genetics MeSH
- Plasmids genetics MeSH
- Polymerase Chain Reaction MeSH
- Gene Transfer, Horizontal MeSH
- Methicillin Resistance genetics MeSH
- Interspersed Repetitive Sequences * MeSH
- Sequence Analysis, DNA MeSH
- Virus Assembly MeSH
- Staphylococcus aureus genetics physiology virology MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
A promoter can be regulated by various cis-acting elements so that delineation of the regulatory modes among them may help understand developmental, environmental and genetic mechanisms in gene activity. Here we report that the human dopamine transporter gene SLC6A3 carries a 5' distal 5-kb super enhancer (5KSE) which upregulated the promoter by 5-fold. Interestingly, 5KSE is able to prevent 3' downstream variable number tandem repeats (3'VNTRs) from silencing the promoter. This new enhancer consists of a 5'VNTR and three repetitive sub-elements that are conserved in primates. Two of 5KSE's sub-elements, E-9.7 and E-8.7, upregulate the promoter, but only the later could continue doing so in the presence of 3'VNTRs. Finally, E-8.7 is activated by novel dopaminergic transcription factors including SRP54 and Nfe2l1. Together, these results reveal a multimodal regulatory mechanism in SLC6A3.
- MeSH
- Models, Biological MeSH
- Adult MeSH
- Transcription, Genetic * MeSH
- Haplotypes genetics MeSH
- Humans MeSH
- Minisatellite Repeats genetics MeSH
- Mice, Inbred C57BL MeSH
- Cell Line, Tumor MeSH
- Promoter Regions, Genetic * MeSH
- Dopamine Plasma Membrane Transport Proteins genetics MeSH
- Transcription Factors metabolism MeSH
- Enhancer Elements, Genetic MeSH
- Animals MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Male MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- MeSH
- DNA, Bacterial analysis MeSH
- Escherichia coli genetics MeSH
- Research Support as Topic MeSH
- Humans MeSH
- Polymerase Chain Reaction methods MeSH
- Polymorphism, Restriction Fragment Length MeSH
- Interspersed Repetitive Sequences genetics MeSH
- Bacterial Typing Techniques methods MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
Most common genetic risk variants associated with neuropsychiatric disease are noncoding and are thought to exert their effects by disrupting the function of cis regulatory elements (CREs), including promoters and enhancers. Within each cell, chromatin is arranged in specific patterns to expose the repertoire of CREs required for optimal spatiotemporal regulation of gene expression. To further understand the complex mechanisms that modulate transcription in the brain, we used frozen postmortem samples to generate the largest human brain and cell-type-specific open chromatin data set to date. Using the Assay for Transposase Accessible Chromatin followed by sequencing (ATAC-seq), we created maps of chromatin accessibility in two cell types (neurons and non-neurons) across 14 distinct brain regions of five individuals. Chromatin structure varies markedly by cell type, with neuronal chromatin displaying higher regional variability than that of non-neurons. Among our findings is an open chromatin region (OCR) specific to neurons of the striatum. When placed in the mouse, a human sequence derived from this OCR recapitulates the cell type and regional expression pattern predicted by our ATAC-seq experiments. Furthermore, differentially accessible chromatin overlaps with the genetic architecture of neuropsychiatric traits and identifies differences in molecular pathways and biological functions. By leveraging transcription factor binding analysis, we identify protein-coding and long noncoding RNAs (lncRNAs) with cell-type and brain region specificity. Our data provide a valuable resource to the research community and we provide this human brain chromatin accessibility atlas as an online database "Brain Open Chromatin Atlas (BOCA)" to facilitate interpretation.
- MeSH
- Chromatin genetics MeSH
- Humans MeSH
- Brain metabolism MeSH
- Mice MeSH
- Promoter Regions, Genetic MeSH
- Gene Expression Regulation genetics MeSH
- Regulatory Elements, Transcriptional genetics MeSH
- Sequence Analysis, DNA MeSH
- Transposases MeSH
- Protein Binding MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
Cystathionine beta-synthase [CBS; l-serine hydro-lyase (adding homocysteine), EC 4.2.1.22] catalyzes the first committed step of transsulfuration and is the enzyme deficient in classical homocystinuria. In this report, we describe the molecular cloning and the complete nucleotide sequence of the human CBS gene. We report a total of 28,046 nucleotides of sequence, which, in addition to the CBS gene, contains approximately 5 kb of the 5' flanking region. The human CBS gene contains 23 exons ranging from 42 to 209 bp. The 5' UTR is formed by 1 of 5 alternatively used exons and 1 invariably present exon, while the 3' UTR is encoded by exons 16 and 17. We also describe the identification of two alternatively used promoter regions that are GC rich (approximately 80%) and contain numerous putative binding sites for Sp1, Ap1, Ap2, and c-myb, but lack the classical TATA box. The CBS locus contains an unusually high number of Alu repeats, which may predispose this gene to deleterious rearrangements. Additionally, we report on a number of DNA sequence repeats that are polymorphic in North American and European Caucasians. Copyright 1998 Academic Press.
- MeSH
- Alternative Splicing * genetics MeSH
- White People MeSH
- Cystathionine beta-Synthase * genetics MeSH
- Alu Elements genetics MeSH
- Exons genetics MeSH
- Cloning, Molecular MeSH
- Humans MeSH
- Minisatellite Repeats genetics MeSH
- Molecular Sequence Data MeSH
- Polymorphism, Genetic genetics MeSH
- Promoter Regions, Genetic genetics MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA MeSH
- Sequence Homology, Nucleic Acid MeSH
- Transcription Factors genetics MeSH
- Binding Sites genetics MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Research Support, U.S. Gov't, P.H.S. MeSH
The abundance and chromosomal organization of two repetitive sequences named 12-13P and 18-24J were analyzed in 24 diploid and nine polyploid species of Chenopodium s.l., with special attention to Chenopodium s.s. Both sequences were predominantly present in species of Chenopodium s.s.; however, differences in the amplification levels were observed among the species. The 12-13P repeat was highly amplified in all of the analyzed Eurasian species, whereas the American diploids showed a marked variation in the amplification levels. The 12-13P repeat contains a tandemly arranged 40 bp minisatellite element forming a large proportion of the genome of Chenopodium (up to 3.5%). FISH revealed its localization to the pericentromeric regions of the chromosomes. The chromosomal distribution of 12-13P delivered additional chromosomal marker for B-genome diploids. The 18-24J repeat showed a dispersed organization in all of the chromosomes of the analyzed diploid species and the Eurasian tetraploids. In the American allotetraploids (C. quinoa, C. berlandieri) and Eurasian allohexaploids (e.g., C. album) very intense hybridization signals of 18-24J were observed only on 18 chromosomes that belong to the B subgenome of these polyploids. Combined cytogenetic and molecular analyses suggests that reorganization of these two repeats accompanied the diversification and speciation of diploid (especially A genome) and polyploid species of Chenopodium s.s.
The appearance of somaclonal variability induced by in vitro cultivation is relatively frequent and can, in some cases, provide a valuable source of new genetic variation for crop improvement. The cause of this phenomenon remains unknown; however, there are a number of reports suggesting that epigenetics, including DNA methylations, are an important factor. In addition to the non-heritable DNA methylation changes caused by transient and reversible stress-responsive gene regulation, recent evidence supports the existence of mitotically and meiotically inherited changes. The induction of phenotypes via stable DNA methylation changes has occasionally great economical value; however, very little is known about the genetic or molecular basis of these phenotypes. We used a novel approach consisting of a standard MSAP analysis followed by deep amplicon sequencing to better understand this phenomenon. Our models included two wheat genotypes, and their somaclones induced using in vitro cultivation with a changed heritable phenotype (shortened stem height and silenced high molecular weight glutenin). Using this novel procedure, we obtained information on the dissimilarity of DNA methylation landscapes between the standard cultivar and its respective somaclones, and we extracted the sequences and genome regions that were differentially methylated between subjects. Transposable elements were identified as the most likely factor for producing changes in somaclone properties. In summary, the novel approach of combining MSAP and NGS is relatively easy and widely applicable, which is a rather unique feature compared with the currently available techniques in the epigenetics field.
... ENVIRONMENTAL HEALTH CRITERIA FOR PRINCIPLES AND METHODS FOR THE ASSESSMENT OF RISK FROM ESSENTIAL TRACE ELEMENTS ... ... INTRODUCTION 3 -- 2.1 Scope and purpose 3 -- 2.2 Criteria for essentiality of trace elements 5 -- 2.2.1 ... ... THE ACCEPTABLE RANGE OF ORAL INTAKE -- FOR AN ESSENTIAL TRACE ELEMENT 16 -- 3.1 Definition of an AROI ... ... 16 hi -- EHC 228: Assessment of Risk from Essential Trace Elements -- 3.2 Boundaries of an AROI 17 - ... ... 24 -- 4.2.1 Bioavailability and utilization 25 -- 4.3 Age-related variables 25 -- 4.3.1 In utero 25 ...
Environmental health criteria, ISSN 0250-863X 228
xviii, 60 s. : grafy ; 22 cm
- MeSH
- Safety MeSH
- Nutritional Physiological Phenomena MeSH
- Risk Assessment MeSH
- Homeostasis MeSH
- Nutritional Requirements MeSH
- Trace Elements MeSH
- Conspectus
- Veřejné zdraví a hygiena
- NML Fields
- veřejné zdravotnictví
- chemie, klinická chemie
- nutriční terapie, dietoterapie a výživa
- environmentální vědy
- biochemie
- NML Publication type
- publikace WHO
Population surveys of Blumeria graminis f. sp. hordei (Bgh), a causal agent of more than 50% of barley fungal infections in the Czech Republic, have been traditionally based on virulence tests, at times supplemented with non-specific Restriction fragment length polymorphism or Random amplified polymorphic DNA markers. A genomic sequence of Bgh, which has become available recently, enables identification of potential markers suitable for population genetics studies. Two major strategies relying on transposable elements and microsatellites were employed in this work to develop a set of Repeat junction markers, Single sequence repeat and Single nucleotide polymorphism markers. A resolution power of the new panel of markers comprising 33 polymorphisms was demonstrated by a phylogenetic analysis of 158 Bgh isolates. A core set of 97 Czech isolates was compared to a set 50 Australian isolates on the background of 11 diverse isolates collected throughout the world. 73.2% of Czech isolates were found to be genetically unique. An extreme diversity of this collection was in strong contrast with the uniformity of the Australian one. This work paves the way for studies of population structure and dynamics based on genetic variability among different Bgh isolates originating from geographically limited regions.
