- MeSH
- Cell Nucleus ultrastructure MeSH
- Embryo, Mammalian MeSH
- Mice MeSH
- RNA, Nuclear biosynthesis MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
We analysed the size, relative age and chromosomal localization of nuclear sequences of plastid and mitochondrial origin (NUPTs-nuclear plastid DNA and NUMTs-nuclear mitochondrial DNA) in six completely sequenced plant species. We found that the largest insertions showed lower divergence from organelle DNA than shorter insertions in all species, indicating their recent origin. The largest NUPT and NUMT insertions were localized in the vicinity of the centromeres in the small genomes of Arabidopsis and rice. They were also present in other chromosomal regions in the large genomes of soybean and maize. Localization of NUPTs and NUMTs correlated positively with distribution of transposable elements (TEs) in Arabidopsis and sorghum, negatively in grapevine and soybean, and did not correlate in rice or maize. We propose a model where new plastid and mitochondrial DNA sequences are inserted close to centromeres and are later fragmented by TE insertions and reshuffled away from the centromere or removed by ectopic recombination. The mode and tempo of TE dynamism determines the turnover of NUPTs and NUMTs resulting in their species-specific chromosomal distributions.
- MeSH
- Cell Nucleus MeSH
- Chromosomes, Plant genetics MeSH
- Species Specificity MeSH
- Genome, Plant MeSH
- DNA, Mitochondrial genetics MeSH
- Mitochondria genetics MeSH
- INDEL Mutation genetics MeSH
- Plastids genetics MeSH
- Plants genetics MeSH
- Sequence Analysis, DNA MeSH
- DNA Transposable Elements genetics MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Interruption of chromosomal integrity by DNA double-strand breaks (DSBs) causes a major threat to genomic stability. Despite tremendous progress in understanding the genetic and biochemical aspects of DSB-induced genome surveillance and repair mechanisms, little is known about organization of these molecular pathways in space and time. Here, we outline the key spatio-temporal problems associated with DSBs and focus on the imaging approaches to visualize the dynamics of DSB-induced responses in mammalian cells. We delineate benefits and limitations of these assays and highlight the key recent discoveries where live microscopy provided unprecedented insights into how cells defend themselves against genome-destabilizing effects of DNA damage.
- MeSH
- Cell Nucleus physiology radiation effects MeSH
- Diagnostic Imaging MeSH
- DNA MeSH
- Endonucleases metabolism MeSH
- Radiation, Ionizing MeSH
- Microscopy, Confocal MeSH
- Humans MeSH
- DNA Repair physiology MeSH
- Proteins * physiology MeSH
- Saccharomyces cerevisiae genetics MeSH
- Chromosome Breakage * MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
polo and CDC5 are two genes required for passage through mitosis in Drosophila melanogaster and Saccharomyces cerevisiae, respectively. Both genes encode structurally related protein kinases that have been implicated in regulating the function of the mitotic spindle. Here, we report the characterization of a human protein kinase that displays extensive sequence similarity to Drosophila polo and S. cerevisiae Cdc5; we refer to this kinase as Plk1 (for polo-like kinase 1). The largest open reading frame of the Plk1 cDNA encodes a protein of 68,254 daltons, and a protein of this size is detected by immunoblotting of HeLa cell extracts with monoclonal antibodies raised against the C-terminal part of Plk1 expressed in Escherichia coli. Northern blot analysis of RNA isolated from human cells and mouse tissues shows that a single Plk1 mRNA of 2.3 kb is highly expressed in tissues with a high mitotic index, consistent with a possible function of Plk1 in cell proliferation. The Plk1 gene maps to position p12 on chromosome 16, a locus for which no associations with neoplastic malignancies are known. The Plk1 protein levels and its distribution change during the cell cycle, in a manner consistent with a role of Plk1 in mitosis. Thus, like Drosophila polo and S. cerevisiae Cdc5, human Plk1 is likely to function in cell cycle progression.
- MeSH
- Cell Cycle MeSH
- DNA-Binding Proteins genetics MeSH
- Drosophila melanogaster genetics MeSH
- Fungal Proteins genetics MeSH
- Gene Library MeSH
- Genes MeSH
- HeLa Cells MeSH
- Carcinoma genetics MeSH
- Cloning, Molecular MeSH
- Humans MeSH
- Chromosomes, Human, Pair 16 * MeSH
- Chromosome Mapping MeSH
- Mitosis * MeSH
- Molecular Sequence Data MeSH
- Antibodies, Monoclonal immunology MeSH
- Nasopharyngeal Neoplasms genetics MeSH
- Open Reading Frames MeSH
- Protein Serine-Threonine Kinases genetics MeSH
- Protein Kinases genetics immunology isolation & purification physiology MeSH
- Cell Cycle Proteins * MeSH
- Drosophila Proteins * MeSH
- RNA-Binding Proteins MeSH
- Proto-Oncogene Proteins MeSH
- Gene Expression Regulation, Neoplastic MeSH
- Saccharomyces cerevisiae Proteins MeSH
- Saccharomyces cerevisiae genetics MeSH
- Amino Acid Sequence MeSH
- Base Sequence MeSH
- Sequence Homology, Amino Acid MeSH
- Sequence Alignment MeSH
- Subcellular Fractions MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Comparative Study MeSH
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple loci genomewide. In LD networks, vertices represent loci, and connections between vertices represent the LD between them. We analysed such networks in two test cases: a new restriction-site-associated DNA sequence (RAD-seq) data set for Anopheles baimaii, a Southeast Asian malaria vector; and a well-characterized single nucleotide polymorphism (SNP) data set from 21 three-spined stickleback individuals. In each case, we readily identified five distinct LD network clusters (single-outlier clusters, SOCs), each comprising many loci connected by high LD. In A. baimaii, further population-genetic analyses supported the inference that each SOC corresponds to a large inversion, consistent with previous cytological studies. For sticklebacks, we inferred that each SOC was associated with a distinct evolutionary phenomenon: two chromosomal inversions, local adaptation, population-demographic history and geographic structure. LDna is thus a useful exploratory tool, able to give a global overview of LD associated with diverse evolutionary phenomena and identify loci potentially involved. LDna does not require a linkage map or reference genome, so it is applicable to any population-genomic data set, making it especially valuable for nonmodel species.
- MeSH
- Anopheles classification genetics MeSH
- Chromosome Inversion * MeSH
- Polymorphism, Single Nucleotide MeSH
- Evolution, Molecular MeSH
- Genetics, Population methods MeSH
- Sequence Analysis, DNA MeSH
- Cluster Analysis MeSH
- Smegmamorpha classification genetics MeSH
- Linkage Disequilibrium * MeSH
- Computational Biology methods MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
- Research Support, Non-U.S. Gov't MeSH
The genus Xenopus represents important model organisms in the field of developmental biology and chromosomal evolution. Developmental processes are tightly coupled with the analysis of gene function via genetic linkage and mapping. Cytogenetic techniques such as chromosome banding or FISH are essential tools for the determination of gene position and subsequently for the construction of linkage and physical maps. Here, we present a summary of key achievements in X. tropicalis and X. laevis cytogenetics with emphasis on the gene localization to chromosomes. The second part of this review is focused on the chromosomal evolution regarding both above-mentioned species. With respect to methodology, hybridization techniques such as FISH and chromosome-specific painting FISH are highlighted.
- MeSH
- Chromosomes genetics ultrastructure MeSH
- Diploidy MeSH
- Species Specificity MeSH
- Genetic Markers MeSH
- Genome MeSH
- Chromosome Painting MeSH
- Chromosome Mapping MeSH
- Evolution, Molecular * MeSH
- Oocytes ultrastructure MeSH
- Polymorphism, Genetic MeSH
- Synteny genetics MeSH
- Tandem Repeat Sequences MeSH
- Tetraploidy MeSH
- Genetic Speciation * MeSH
- Xenopus laevis genetics MeSH
- Xenopus classification genetics MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Comparative Study MeSH
Nucleosome movement is, at least in part, facilitated by ISWI ATPase Smarca5 (Snf2h). Smarca5 gene inactivation in mouse demonstrated its requirement at blastocyst stage; however its role at later stages is not completely understood. We herein determined nuclear distribution of Smarca5 and histone marks associated with actively transcribed and repressed chromatin structure in embryonic and adult murine tissues and in tumor cells. Confocal microscopy images demonstrate that Smarca5 is localized mainly in euchromatin and to lesser extent also in heterochromatin and nucleoli. Smarca5 heterozygous mice for a null allele display decreased levels of histone H3 modifications and defects in heterochromatin foci supporting role of Smarca5 as a key regulator of global chromatin structure.
- MeSH
- Adenosine Triphosphatases genetics metabolism MeSH
- Blastocyst metabolism MeSH
- Cell Nucleolus metabolism MeSH
- Chromosomal Proteins, Non-Histone genetics metabolism MeSH
- Euchromatin metabolism MeSH
- Heterochromatin metabolism MeSH
- Microscopy, Confocal MeSH
- Mice, Inbred C57BL MeSH
- Mice MeSH
- Cell Line, Tumor MeSH
- Gene Silencing MeSH
- Animals MeSH
- Check Tag
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Research Support, N.I.H., Extramural MeSH
- Keywords
- NaBt, sodium butyrate,
- MeSH
- Adenocarcinoma MeSH
- Cell Differentiation MeSH
- HT29 Cells * MeSH
- Butyrates * MeSH
- Chromosome Aberrations MeSH
- Cytophotometry instrumentation MeSH
- In Situ Hybridization, Fluorescence * MeSH
- Cells, Cultured MeSH
- Chromosomes, Human, Pair 8 MeSH
- Image Processing, Computer-Assisted MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
