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      The karyosphere capsule in Rana temporaria oocytes contains structural and DNA-binding proteins

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          ABSTRACT

          During the last stages of oogenesis, oocyte chromosomes condense and come close together, forming the so-called karyosphere. Karyosphere formation is accompanied by an essential decrease in transcriptional activity. In the grass frog Rana temporaria, the karyosphere is surrounded by an extrachromosomal capsule that separates the chromosomes from the rest of the nucleoplasm. The karyosphere capsule (KC) of R. temporaria has been investigated in detail at the ultrastructural level, but its protein composition remained largely unknown. We demonstrate here that nuclear actin, especially F-actin, as well as lamins A/C and B are the most abundant proteins of the KC. Key proteins of nuclear pore complexes, such as Nup93 and Nup35, are also detectable in the KC. New antibodies recognizing the telomere-binding protein TRF2 allowed us to localize TRF2 in nuclear speckles. We also found that the R. temporaria KC contains some proteins involved in chromatin remodeling, including topoisomerase II and ATRX. Thus, we believe that KC isolates the chromosomes from the rest of the nucleoplasm during the final period of oocyte growth (late diplotene) and represents a specialized oocyte nuclear compartment to store a variety of factors involved in nuclear metabolism that can be used in future early development.

          Abbreviations: BrUTP: 5-bromouridine 5’-triphosphate; CytD: cytochalasin D; IGCs: interchromatin granule clasters; IgG: immunoglobulin G; KC: karyosphere capsule; Mw: molecular weight; NE: nuclear envelope; PBS: phosphate buffered saline; SDS-PAGE: sodium dodecyl sulfate polyacrylamide gel electrophoresis; Topo II: topoisomerase II

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          Histone modifications for human epigenome analysis.

          Histones function both positively and negatively in the regulation of gene expression, mainly governed by post-translational modifications on specific amino acid residues. Although histone modifications are not necessarily prerequisite codes, they may still serve as good epigenetic indicators of chromatin state associated with gene activation or repression. In particular, six emerging classes of histone H3 modifications are subjected for epigenome profiling by the International Human Epigenome Consortium. In general, transcription start sites of actively transcribed genes are marked by trimethylated H3K4 (H3K4me3) and acetylated H3K27 (H3K27ac), and active enhancers can be identified by enrichments of both monomethylated H3K4 (H3K4me1) and H3K27ac. Gene bodies of actively transcribed genes are associated with trimethylated H3K36 (H3K36me3). Gene repression can be mediated through two distinct mechanisms involving trimethylated H3K9 (H3K9me3) and trimethylated H3K27 (H3K27me3). Enrichments of these histone modifications on specific loci, or in genome wide, in given cells can be analyzed by chromatin immunoprecipitation (ChIP)-based methods using an antibody directed against the site-specific modification. When performing ChIP experiments, one should be careful about the specificity of antibody, as this affects the data interpretation. If cell samples with preserved histone-DNA contacts are available, evaluation of histone modifications, in addition to DNA methylaion, at specific gene loci would be useful for deciphering the epigenome state for human genetics studies.
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            Regulating the chromatin landscape: structural and mechanistic perspectives.

            A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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              DNA Topoisomerases.

              DNA topoisomerases are enzymes that control the topology of DNA in all cells. There are two types, I and II, classified according to whether they make transient single- or double-stranded breaks in DNA. Their reactions generally involve the passage of a single- or double-strand segment of DNA through this transient break, stabilized by DNA-protein covalent bonds. All topoisomerases can relax DNA, but DNA gyrase, present in all bacteria, can also introduce supercoils into DNA. Because of their essentiality in all cells and the fact that their reactions proceed via DNA breaks, topoisomerases have become important drug targets; the bacterial enzymes are key targets for antibacterial agents. This article discusses the structure and mechanism of topoisomerases and their roles in the bacterial cell. Targeting of the bacterial topoisomerases by inhibitors, including antibiotics in clinical use, is also discussed.
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                Author and article information

                Journal
                Nucleus
                Nucleus
                KNCL
                kncl20
                Nucleus
                Taylor & Francis
                1949-1034
                1949-1042
                2018
                1 October 2018
                1 October 2018
                : 9
                : 1
                : 516-529
                Affiliations
                [a ]Laboratory of Cell Morphology, Institute of Cytology of the Russian Academy of Sciences , St. Petersburg, Russia
                [b ]Department of Cytology and Histology, Faculty of Biology, Saint Petersburg State University , St. Petersburg, Russia
                [c ]Laboratory of Biomedical Cell Technology, School of Biomedicine, Far Eastern Federal University , Vladivostok, Russia
                Author notes
                CONTACT Nadya Ilicheva nad9009@ 123456yandex.ru Institute of Cytology of the Russian Academy of Sciences , Tikhoretsky pr. 4, Saint Petersburg 194064, Russia
                Author information
                http://orcid.org/0000-0001-9594-7202
                Article
                1530935
                10.1080/19491034.2018.1530935
                6244735
                30272509
                ccaeb404-9609-4dd3-aeea-86358bfcc97f
                © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 13 August 2018
                : 21 September 2018
                : 26 September 2018
                Page count
                Figures: 8, Tables: 1, References: 64, Pages: 14
                Funding
                Funded by: Russian Academy of Sciences 10.13039/501100002674
                This work was supported by the granting program ‘Molecular and Cell Biology’ of the Russian Academy of Sciences.
                Categories
                Research Article

                Molecular biology
                karyosphere,karyosphere capsule,oogenesis,rana temporaria,transcription,nuclear actin,lamins,nucleoporins,atrx,topoisomerase ii

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