Search results for "Genome"
showing 10 items of 1913 documents
Epigenetic Mechanisms as Key Regulators in Disease
2016
Epigenetics is a rapidly growing field of research which studies the changes in the gene expression that do not involve changes in the nucleotide sequence. The cellular metabolism is directly connected to epigenetic regulation through the inflow of different metabolites such as S-adenosylmethionine, acetyl-CoA, and α-ketoglutarate among others, which serve as substrates or cofactors for chromatin-modifying enzymes. These metabolites define how our lifestyle (i.e., nutrition, physical activity, and other healthy behaviors) acts on gene expression by epigenetic mechanisms. Therefore, proper coordination between components of the epigenetic machineries is essential for the correct control of t…
Histone-mediated transgenerational epigenetics
2019
Abstract Epigenetic mechanisms operate at the interface between the environment and genome, by converting the environmental stimuli to phenotypic responses through changes in the chromatin landscape, which ultimately affects gene expression in the absence of alterations in DNA sequence. In this scenario, transgenerational inheritance occurs when epigenetic variations induced by environmental stimuli are transmitted through the germ line to succeeding generations that had never experienced those stimuli. There is an ever-growing list of reports indicating that histones are fundamental players in these processes in a variety of organisms. In this chapter, we provide a perspective on histone-d…
The IStron CdISt1 of Clostridium difficile: molecular symbiosis of a group I intron and an insertion element
2003
Abstract The IStron CdISt1 was first discovered as an insertion into the tcdA gene of the clinical isolate C34. It combines structural and functional properties of a group I intron at its 5′-end with those of an insertion element at its 3′-end. Up to date four different types could be found, mainly differing in their IS-element portions. Contrasting classical group I introns, CdISt1 is always integrated in ORFs encoding bacterial protein. In case CdISt1 had only the IS-element function such insertion would inactivate the protein encoded by the host gene. It is only due to the self-splicing activity of the group I intron parts that CdISt1 integration does not abolish protein function. Both e…
CellLineNavigator: a workbench for cancer cell line analysis
2012
The CellLineNavigator database, freely available at http://www.medicalgenomics.org/celllinenavigator, is a web-based workbench for large scale comparisons of a large collection of diverse cell lines. It aims to support experimental design in the fields of genomics, systems biology and translational biomedical research. Currently, this compendium holds genome wide expression profiles of 317 different cancer cell lines, categorized into 57 different pathological states and 28 individual tissues. To enlarge the scope of CellLineNavigator, the database was furthermore closely linked to commonly used bioinformatics databases and knowledge repositories. To ensure easy data access and search abili…
De novo t(12;17)(p13.3;q21.3) translocation with a breakpoint near the 5' end of the HOXB gene cluster in a patient with developmental delay and skel…
2007
A boy with severe mental retardation, funnel chest, bell-shaped thorax, and hexadactyly of both feet was found to have a balanced de novo t(12;17)(p13.3;q21.3) translocation. FISH with BAC clones and long-range PCR products assessed in the human genome sequence localized the breakpoint on chromosome 17q21.3 to a 21-kb segment that lies <30 kb upstream of the HOXB gene cluster and immediately adjacent to the 3′ end of the TTLL6 gene. The breakpoint on chromosome 12 occurred within telomeric hexamer repeats and, therefore, is not likely to affect gene function directly. We propose that juxtaposition of the HOXB cluster to a repetitive DNA domain and/or separation from required cis-regulatory …
Development of “universal” gene-specific markers from Malus spp. cDNA sequences, their mapping and use in synteny studies within Rosaceae
2009
The Rosaceae contains many economically valuable crop genera, including Malus (apple), Fragaria (strawberry), and Prunus (stone fruit). There has been increasing interest in the development of linkage maps for these species, with a view to marker-assisted selection to assist breeding programs and, recently, in the development of transferable markers to permit syntenic comparisons of maps of different rosaceous genera. In this investigation, a set of Malus cDNA sequences were downloaded from the European Molecular Biology Laboratory database. The sequences were aligned with homologous full-length Arabidopsis genomic DNA sequences to identify putative intron–exon junctions and conserved flank…
Quantitative real-time PCR with SYBR Green detection to assess gene duplication in insects: study of gene dosage in Drosophila melanogaster (Diptera)…
2011
Abstract Background The accurate determination of the number of copies of a gene in the genome (gene dosage) is essential for a number of genetic analyses. Quantitative real time PCR (qPCR) with TaqMan detection has shown advantages over traditional Southern-blot and FISH techniques, however the high costs of the required labeled probes is an important limitation of this method. qPCR with SYBR Green I detection is a simple and inexpensive alternative, but it has never been applied to the determination of the copy number of low copy number genes in organisms with high allelic variability (as some insects), where a very small margin of error is essential. Findings We have tested the suitabili…
Murine Cytomegalovirus Major Immediate-Early Enhancer Region Operating as a Genetic Switch in Bidirectional Gene Pair Transcription
2007
ABSTRACT Enhancers are defined as DNA elements that increase transcription when placed in any orientation relative to a promoter. The major immediate-early (MIE) enhancer region of murine cytomegalovirus is flanked by transcription units ie1/3 and ie2 , which are transcribed in opposite directions. We have addressed the fundamental mechanistic question of whether the enhancer synchronizes transcription of the bidirectional gene pair (synchronizer model) or whether it operates as a genetic switch, enhancing transcription of either gene in a stochastic alternation (switch model). Clonal analysis of cytokine-triggered, transcription factor-mediated MIE gene expression from latent viral genomes…
Interactions between the yeast mitochondrial and nuclear genomes: isogenic suppressive and hypersuppressive petites differ in their resistance to the…
1990
In a previous paper we have shown that the alkaloid lycorine inhibits growth of rho+, mit- and rho-, strains of Saccharomyces cerevisiae, whereas strains devoid of mitochondrial DNA (rho degrees) are resistant to more than 200 micrograms/ml of the alkaloid. In this report we show that hypersuppressive petites are almost as resistant as rho degrees mutants, whereas isogenic rho- petites, which have retained longer segments of the genome, are sensitive to the drug.
The molecular characterization of new types of Saccharomyces cerevisiae × S. kudriavzevii hybrid yeasts unveils a high genetic diversity
2012
New double- and triple-hybrid Saccharomyces yeasts were characterized using PCR-restriction fragment length polymorphism of 35 nuclear genes, located on different chromosome arms, and the sequencing of one nuclear and one mitochondrial gene. Most of these new hybrids were originally isolated from fermentations; however, two of them correspond to clinical and dietary supplement isolates. This is the first time that the presence of double-hybrid S. cerevisiae×S. kudriavzevii in non-fermentative substrates has been reported and investigated. Phylogenetic analysis of the MET6 nuclear gene confirmed the double or triple parental origin of the new hybrids. Restriction analysis of gene regions in …