The topology of early- and late-replicating chromatin in differentially decondensed chromosomes

Kobliakova, Ioulia; Зацепина, О. В.; Stefanova, V. N.; Polyakov, V. B.; Kireev, Igor I.

doi:10.1007/s10577-005-0308-y

Cited by 6 publications

(5 citation statements)

References 44 publications

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“…At the chromosomal level TR can be of profound structural as well as evolutionary importance, since genomic regions with a high density of TR, e.g., telomeric, centromeric, and heterochromatic regions, often have specific properties such as alternative DNA structure and packaging [47-49]. At the nuclear level of organization, constitutive heterochromatin may help maintain the proper spatial relationships necessary for the efficient operation of the cell through the stages of mitosis and meiosis.…”

Section: Discussionmentioning

confidence: 99%

Tandemly repeated DNA families in the mouse genome

et al. 2011

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BackgroundFunctional and morphological studies of tandem DNA repeats, that combine high portion of most genomes, are mostly limited due to the incomplete characterization of these genome elements. We report here a genome wide analysis of the large tandem repeats (TR) found in the mouse genome assemblies.ResultsUsing a bioinformatics approach, we identified large TR with array size more than 3 kb in two mouse whole genome shotgun (WGS) assemblies. Large TR were classified based on sequence similarity, chromosome position, monomer length, array variability, and GC content; we identified four superfamilies, eight families, and 62 subfamilies - including 60 not previously described. 1) The superfamily of centromeric minor satellite is only found in the unassembled part of the reference genome. 2) The pericentromeric major satellite is the most abundant superfamily and reveals high order repeat structure. 3) Transposable elements related superfamily contains two families. 4) The superfamily of heterogeneous tandem repeats includes four families. One family is found only in the WGS, while two families represent tandem repeats with either single or multi locus location. Despite multi locus location, TRPC-21A-MM is placed into a separated family due to its abundance, strictly pericentromeric location, and resemblance to big human satellites.To confirm our data, we next performed in situ hybridization with three repeats from distinct families. TRPC-21A-MM probe hybridized to chromosomes 3 and 17, multi locus TR-22A-MM probe hybridized to ten chromosomes, and single locus TR-54B-MM probe hybridized with the long loops that emerge from chromosome ends. In addition to in silico predicted several extra-chromosomes were positive for TR by in situ analysis, potentially indicating inaccurate genome assembly of the heterochromatic genome regions.ConclusionsChromosome-specific TR had been predicted for mouse but no reliable cytogenetic probes were available before. We report new analysis that identified in silico and confirmed in situ 3/17 chromosome-specific probe TRPC-21-MM. Thus, the new classification had proven to be useful tool for continuation of genome study, while annotated TR can be the valuable source of cytogenetic probes for chromosome recognition.

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Section: Discussionmentioning

confidence: 99%

Tandemly repeated DNA families in the mouse genome

et al. 2011

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“…Standard fixation uses methanol-acetic acid or formaldhyde. The former operates by dehydration and is particularly damaging to 3D architecture, causing a flattened nucleus and damaged chromosome morphology [2], [3]. Whilst formaldehyde is thought to be more satisfactory, the tendency of this fixative to trigger retraction of cells' cytoskeletal protrusions urges for caution [4].…”

Section: Introductionmentioning

confidence: 99%

Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells

et al. 2010

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Despite the distinctive structure of mitotic chromosomes, it has not been possible to visualise individual chromosomes in living interphase cells, where chromosomes spend over 90% of their time. Studies of interphase chromosome structure and dynamics use fluorescence in-situ hybridisation (FISH) on fixed cells, which potentially damages structure and loses dynamic information. We have developed a new methodology, involving photoactivation of labelled histone H3 at mitosis, to visualise individual and specific human chromosomes in living interphase cells. Our data revealed bulk chromosome volume and morphology are established rapidly after mitosis, changing only incrementally after the first hour of G1. This contrasted with the behaviour of specific loci on labelled chromosomes, which showed more progressive reorganisation, and revealed that “looping out” of chromatin from chromosome territories is a dynamic state. We measured considerable heterogeneity in chromosome decondensation, even between sister chromatids, which may reflect local structural impediments to decondensation and could potentially amplify transcriptional noise. Chromosome structure showed tremendous resistance to inhibitors of transcription, histone deacetylation and chromatin remodelling. Together, these data indicate steric constraints determine structure, rather than innate chromosome architecture or function-driven anchoring, with interphase chromatin organisation governed primarily by opposition between needs for decondensation and the space available for this to happen.

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“…Interphase nuclei in such preparations are flattened and have an increased diameter (Kozubek et al 2000 and present study). Hypotonic treatment (Kobliakova et al 2005) and other changes in ion concentration (Belmont et al 1989) have been shown to disturb chromosome morphology. Distributions of core histones and of the splicing factor SC-35 were observed to change substantially under these conditions (Hendzel and Bazett-Jones 1997), suggesting a redistribution of chromatin components.…”

Section: Introductionmentioning

confidence: 99%

Preservation of large-scale chromatin structure in FISH experiments

et al. 2006

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The nuclear organization of specific endogenous chromatin regions can be investigated only by fluorescence in situ hybridization (FISH). One of the two fixation procedures is typically applied: (1) buffered formaldehyde or (2) hypotonic shock with methanol acetic acid fixation followed by dropping of nuclei on glass slides and air drying. In this study, we compared the effects of these two procedures and some variations on nuclear morphology and on FISH signals. We analyzed mouse erythroleukemia and mouse embryonic stem cells because their clusters of subcentromeric heterochromatin provide an easy means to assess preservation of chromatin. Qualitative and quantitative analyses revealed that formaldehyde fixation provided good preservation of large-scale chromatin structures, while classical methanol acetic acid fixation after hypotonic treatment severely impaired nuclear shape and led to disruption of chromosome territories, heterochromatin structures, and large transgene arrays. Our data show that such preparations do not faithfully reflect in vivo nuclear architecture.

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The topology of early- and late-replicating chromatin in differentially decondensed chromosomes

Cited by 6 publications

References 44 publications

Tandemly repeated DNA families in the mouse genome

Tandemly repeated DNA families in the mouse genome

Stable Morphology, but Dynamic Internal Reorganisation, of Interphase Human Chromosomes in Living Cells

Preservation of large-scale chromatin structure in FISH experiments

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