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Swedlow, Jason R.; Lamond, Angus I.

doi:10.1186/gb-2001-2-3-reviews0002

Cited by 16 publications

(3 citation statements)

References 57 publications

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“…Located in pericentric, telomeric, and some internal chromosomal regions, heterochromatin plays an important role in cell division [ 1 ], meiotic pairing [ 2 ], regulation of DNA replication, and gene expression [ 3 ]. Among insect species, the most detailed analysis of heterochromatin has been performed in Drosophila [ 4 - 7 ].…”

Section: Introductionmentioning

confidence: 99%

Genome mapping and characterization of the Anopheles gambiae heterochromatin

et al. 2010

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BackgroundHeterochromatin plays an important role in chromosome function and gene regulation. Despite the availability of polytene chromosomes and genome sequence, the heterochromatin of the major malaria vector Anopheles gambiae has not been mapped and characterized.ResultsTo determine the extent of heterochromatin within the An. gambiae genome, genes were physically mapped to the euchromatin-heterochromatin transition zone of polytene chromosomes. The study found that a minimum of 232 genes reside in 16.6 Mb of mapped heterochromatin. Gene ontology analysis revealed that heterochromatin is enriched in genes with DNA-binding and regulatory activities. Immunostaining of the An. gambiae chromosomes with antibodies against Drosophila melanogaster heterochromatin protein 1 (HP1) and the nuclear envelope protein lamin Dm0 identified the major invariable sites of the proteins' localization in all regions of pericentric heterochromatin, diffuse intercalary heterochromatin, and euchromatic region 9C of the 2R arm, but not in the compact intercalary heterochromatin. To better understand the molecular differences among chromatin types, novel Bayesian statistical models were developed to analyze genome features. The study found that heterochromatin and euchromatin differ in gene density and the coverage of retroelements and segmental duplications. The pericentric heterochromatin had the highest coverage of retroelements and tandem repeats, while intercalary heterochromatin was enriched with segmental duplications. We also provide evidence that the diffuse intercalary heterochromatin has a higher coverage of DNA transposable elements, minisatellites, and satellites than does the compact intercalary heterochromatin. The investigation of 42-Mb assembly of unmapped genomic scaffolds showed that it has molecular characteristics similar to cytologically mapped heterochromatin.ConclusionsOur results demonstrate that Anopheles polytene chromosomes and whole-genome shotgun assembly render the mapping and characterization of a significant part of heterochromatic scaffolds a possibility. These results reveal the strong association between characteristics of the genome features and morphological types of chromatin. Initial analysis of the An. gambiae heterochromatin provides a framework for its functional characterization and comparative genomic analyses with other organisms.

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Section: Introductionmentioning

confidence: 99%

Genome mapping and characterization of the Anopheles gambiae heterochromatin

et al. 2010

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“…Nevertheless, we observed varying degrees of negative staining in the nucleus that presumably highlight the nucleoli, Cajal bodies, and other nuclear components 25 . We hypothesize that such negative contrasts are generated because highly condensed structures such as these prevent GFP from freely diffusing into the core.…”

Section: Resultsmentioning

confidence: 79%

A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging

Tanaka

Takakuwa

2016

Sci Rep

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Secretory granules (SGs) in mast cells contain various molecules that elicit allergy symptoms and are generally considered therapeutic targets. However, the biogenesis, maintenance, regulation, and recycling of these granules remain controversial, mainly due to the lack of suitable live-cell imaging methods. In this study, we applied negative contrast imaging with soluble green fluorescent protein (GFP) expressed in the cytoplasm as a method to validate structural information of mast cell SGs. We evaluated the accuracy of the method in detail, and we demonstrated that it can be used for quantitative analysis. Using this technique, secretory granules, the nucleus, mitochondria, and the cell body were visualized in individual RBL-2H3 mast cells without any influence. When combined with conventional multicolor fluorescence imaging, visualization of SG-associated proteins and SG–SG fusion was achieved. Moreover, 3D images were constructed based on this method, and detailed information on the number, size, and shape of individual SGs was obtained. We found that cell volume was correlated with SG number. In summary, the technique provides valuable and unique data, and will therefore advance SG research.

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“…14) [8, 63, 84]. Study of movement of specific genes within the nucleus has been proposed and recently performed with 4D nucelome methods, human colon crypts could be used as the film recording the life from stem cells to differentiated cells [63, 85]. Correlating morphogenesis with oscillatory gene expression, oscillatory gene movement, super-resolution periodic patterns of chromatin and structural perspective of cooperative transcription factor binding (HES1 & NR3C1 for example) which biophysically shape DNA double helix in poloidal and toroidal directions will be required to generate convincing proof of gene morphogen hypothesis following Alan Turing’s “NON-LINEAR THEORY.…”

Section: Data Notesmentioning

confidence: 99%

Rotational 3D mechanogenomic Turing patterns of human colon Caco-2 cells during differentiation

Zheng

Kalinin

Dinov

et al. 2018

Preprint

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Recent reports suggest that actomyosin meshwork act in a mechanobiological manner alter cell/nucleus/tissue morphology, including human colon epithelial Caco-2 cancer cells that form polarized 2D epithelium or 3D sphere/tube when placed in different culture conditions. We observed the rotational motion of the nucleus in Caco-2 cells in vitro that appears to be driven by actomyosin network prior to the formation of a differentiated confluent epithelium. Caco-2 cell monolayer preparations demonstrated 2D patterns consistent with Allan Turing’s “gene morphogen” hypothesis based on live cell imaging analysis of apical tight junctions indicating the actomyosin meshwork. Caco-2 cells in 3D culture are frequently used as a model to study 3D epithelial morphogenesis involving symmetric and asymmetric cell divisions. Differentiation of Caco-2 cells in vitro demonstrated similarity to intestinal enterocyte differentiation along the human colon crypt axis. We observed rotational 3D patterns consistent with gene morphogens during Caco-2 cell differentiation. Single- to multi-cell ring/torus-shaped genomes were observed that were similar to complex fractal Turing patterns extending from a rotating torus centre in a spiral pattern consistent with gene morphogen motif. Rotational features of the epithelial cells may contribute to well-described differentiation from stem cells to the luminal colon epithelium along the crypt axis. This dataset may be useful to study the role of mechanobiological processes and the underlying molecular mechanisms as determinants of cellular and tissue architecture in space and time, which is the focal point of the 4D nucleome initiative.

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Untitled

Cited by 16 publications

References 57 publications

Genome mapping and characterization of the Anopheles gambiae heterochromatin

Genome mapping and characterization of the Anopheles gambiae heterochromatin

A method for detailed analysis of the structure of mast cell secretory granules by negative contrast imaging

Rotational 3D mechanogenomic Turing patterns of human colon Caco-2 cells during differentiation

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