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Heterochromatin

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https://www.readbyqxmd.com/read/28449087/methyl-cpg-binding-domain-protein-1-regulates-localization-and-activity-of-tet1-in-a-cxxc3-domain-dependent-manner
#1
Peng Zhang, Cathia Rausch, Florian D Hastert, Boyana Boneva, Alina Filatova, Sujit J Patil, Ulrike A Nuber, Yu Gao, Xinyu Zhao, M Cristina Cardoso
Cytosine modifications diversify and structure the genome thereby controlling proper development and differentiation. Here, we focus on the interplay of the 5-methylcytosine reader Mbd1 and modifier Tet1 by analyzing their dynamic subcellular localization and the formation of the Tet oxidation product 5-hydroxymethylcytosine in mammalian cells. Our results demonstrate that Mbd1 enhances Tet1-mediated 5-methylcytosine oxidation. We show that this is due to enhancing the localization of Tet1, but not of Tet2 and Tet3 at heterochromatic DNA...
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449085/guanine-quadruplex-monoclonal-antibody-1h6-cross-reacts-with-restrained-thymidine-rich-single-stranded-dna
#2
Hinke G Kazemier, Katrin Paeschke, Peter M Lansdorp
Previously we reported the production and characterization of monoclonal antibody 1H6 raised against (T4G4)2 intermolecular guanine quadruplex (G4) DNA structures (Henderson A. et al. (2014) Nucleic Acids Res., 42, 860-869; Hoffmann R.F. et al. (2016) Nucleic Acids Res., 44, 152-163). It was shown that 1H6 strongly stains nuclei and has exquisite specificity for heterochromatin by immuno-electron microscopy. Here we extend our studies of 1H6 reactivity using enzyme-linked immunosorbent assay (ELISA) and microscale thermophoresis (MST)...
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28449026/guanine-quadruplex-structures-localize-to-heterochromatin
#3
Roland F Hoffmann, Yuri M Moshkin, Stijn Mouton, Nicola A Grzeschik, Ruby D Kalicharan, Jeroen Kuipers, Anouk H G Wolters, Kazuki Nishida, Aleksander V Romashchenko, Jan Postberg, Hans Lipps, Eugene Berezikov, Ody C M Sibon, Ben N G Giepmans, Peter M Lansdorp
No abstract text is available yet for this article.
April 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28448516/natural-variation-of-pirna-expression-affects-immunity-to-transposable-elements
#4
Sergei Ryazansky, Elizaveta Radion, Anastasia Mironova, Natalia Akulenko, Yuri Abramov, Valeriya Morgunova, Maria Y Kordyukova, Ivan Olovnikov, Alla Kalmykova
In the Drosophila germline, transposable elements (TEs) are silenced by PIWI-interacting RNA (piRNA) that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains. The I-element is a retrotransposon involved in the phenomenon of I-R hybrid dysgenesis in Drosophila melanogaster. Genomes of R strains do not contain active I-elements, but harbour remnants of ancestral I-related elements...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28445143/the-igh-locus-relocalizes-to-a-recombination-compartment-in-the-perinucleolar-region-of-differentiating-b-lymphocytes
#5
Andrey Pichugin, Olga V Iarovaia, Alexey Gavrilov, Ilya Sklyar, Natalja Barinova, Aleksandr Barinov, Evgeny Ivashkin, Gersende Caron, Said Aoufouchi, Sergey V Razin, Thierry Fest, Marc Lipinski, Yegor S Vassetzky
The immunoglobulin heavy chain (IGH) gene loci are subject to specific recombination events during B-cell differentiation including somatic hypermutation and class switch recombination which mark the end of immunoglobulin gene maturation in germinal centers of secondary lymph nodes. These two events rely on the activity of activation-induced cytidine deaminase (AID) which requires DNA double strand breaks be created, a potential danger to the cell. Applying 3D-fluorescence in situ hybridization coupled with immunofluorescence staining to a previously described experimental system recapitulating normal B-cell differentiation ex vivo, we have kinetically analyzed the radial positioning of the two IGH gene loci as well as their proximity with the nucleolus, heterochromatin and γH2AX foci...
April 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/28440422/variable-terra-abundance-and-stability-in-cervical-cancer-cells
#6
Bong-Kyeong Oh, Ponnarath Keo, Jaeman Bae, Jung Hwa Ko, Joong Sub Choi
Telomeres are transcribed into long non-coding RNA, referred to as telomeric repeat-containing RNA (TERRA), which plays important roles in maintaining telomere integrity and heterochromatin formation. TERRA has been well characterized in HeLa cells, a type of cervical cancer cell. However, TERRA abundance and stability have not been examined in other cervical cancer cells, at least to the best of our knowledge. Thus, in this study, we measured TERRA levels and stability, as well as telomere length in 6 cervical cancer cell lines, HeLa, SiHa, CaSki, HeLa S3, C-33A and SNU-17...
April 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28437173/the-karyotype-of-microsternarchus-aff-bilineatus-a-first-case-of-y-chromosome-degeneration-in-gymnotiformes
#7
Jéssica Almeida Batista, Adauto Lima Cardoso, Susana Suely Rodrigues Milhomem Paixão, Jonathan Stuart Ready, Julio Cesar Pieczarka, Cleusa Yoshiko Nagamachi
Various species and lineages that until recently were identified as Microsternarchus bilineatus (Hypopomidae, Gymnotiformes) have a widespread distribution in the Amazon and Orinoco river basins and across the Guiana shield. Recent molecular studies show five distinct lineages for Microsternarchus from different localities. These results suggest that this previously monotypic genus actually consists of more than one species. Here, we describe the karyotype of M. aff. bilineatus from the Cururutuia River (Bragança, Pará, Brazil)...
March 6, 2017: Zebrafish
https://www.readbyqxmd.com/read/28428341/ctf4-related-protein-recruits-lhp1-prc2-to-maintain-h3k27me3-levels-in-dividing-cells-in-arabidopsis-thaliana
#8
Yue Zhou, Emmanuel Tergemina, Haitao Cui, Alexander Förderer, Benjamin Hartwig, Geo Velikkakam James, Korbinian Schneeberger, Franziska Turck
Polycomb Repressive Complex (PRC) 2 catalyzes the H3K27me3 modification that warrants inheritance of a repressive chromatin structure during cell division, thereby assuring stable target gene repression in differentiated cells. It is still under investigation how H3K27me3 is passed on from maternal to filial strands during DNA replication; however, cell division can reinforce H3K27me3 coverage at target regions. To identify novel factors involved in the Polycomb pathway in plants, we performed a forward genetic screen for enhancers of the like heterochromatin protein 1 (lhp1) mutant, which shows relatively mild phenotypic alterations compared with other plant PRC mutants...
April 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28427179/comprehensive-mapping-of-the-effects-of-azacitidine-on-dna-methylation-repressive-permissive-histone-marks-and-gene-expression-in-primary-cells-from-patients-with-mds-and-mds-related-disease
#9
Magnus Tobiasson, Hani Abdulkadir, Andreas Lennartsson, Shintaro Katayama, Francesco Marabita, Ayla De Paepe, Mohsen Karimi, Kaarel Krjutskov, Elisabet Einarsdottir, Michael Grövdal, Monika Jansson, Asmaa Ben Azenkoud, Lina Corddedu, Sören Lehmann, Karl Ekwall, Juha Kere, Eva Hellström-Lindberg, Johanna Ungerstedt
Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the histone modifications H3K18ac and H3K9me3 (ChIP seq). Aza induced a general increase in gene expression with 924 significantly upregulated genes but this increase showed no correlation with changes in DNA methylation or H3K18ac, and only a weak association with changes in H3K9me3...
February 28, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423373/distribution-of-interstitial-telomeric-sequences-in-primates-and-the-pygmy-tree-shrew-scandentia
#10
Sofia Mazzoleni, Odessa Schillaci, Luca Sineo, Francesca Dumas
It has been hypothesized that interstitial telomeric sequences (ITSs), i.e., repeated telomeric DNA sequences found at intrachromosomal sites in many vertebrates, could be correlated to chromosomal rearrangements and plasticity. To test this hypothesis, we hybridized a telomeric PNA probe through FISH on representative species of 2 primate infraorders, Strepsirrhini (Lemur catta, Otolemur garnettii, Nycticebus coucang) and Catarrhini (Erythrocebus patas, Cercopithecus petaurista, Chlorocebus aethiops, Colobus guereza), as well as on 1 species of the order Scandentia, Tupaia minor, used as an outgroup for primates in phylogenetic reconstructions...
April 20, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28420800/setdb1-plays-an-essential-role-in-maintenance-of-gonocyte-survival-in-pigs
#11
Tian Tian Liu, Pengfei Zhang, Tian Jiao Li, Xiao Xu Chen, Zhen Shuo Zhu, Ying Hua Lyu, Xue Liang Li, Xiue Tian, Wen Xian Zeng
Histone methyltransferase SETDB1 suppresses gene expression and modulates heterochromatin formation through H3K9me2/3. Previous studies have revealed that SETDB1 catalyzes lysine 9 of histone H3 tri-methylation and plays essential roles in maintaining the survival of embryonic stem cells and spermatogonial stem cells in mice. However, the function of SETDB1 in porcine male germ cells remains unclear. The aim of the present study was to reveal the expression profile and function of SETDB1 in porcine germ cells...
April 18, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28413449/links-between-dna-methylation-and-nucleosome-occupancy-in-the-human-genome
#12
Clayton K Collings, John N Anderson
BACKGROUND: DNA methylation is an epigenetic modification that is enriched in heterochromatin but depleted at active promoters and enhancers. However, the debate on whether or not DNA methylation is a reliable indicator of high nucleosome occupancy has not been settled. For example, the methylation levels of DNA flanking CTCF sites are higher in linker DNA than in nucleosomal DNA, while other studies have shown that the nucleosome core is the preferred site of methylation. In this study, we make progress toward understanding these conflicting phenomena by implementing a bioinformatics approach that combines MNase-seq and NOMe-seq data and by comprehensively profiling DNA methylation and nucleosome occupancy throughout the human genome...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28411854/the-molecular-revolution-in-cutaneous-biology-chromosomal-territories-higher-order-chromatin-remodeling-and-the-control-of%C3%A2-gene-expression-in-keratinocytes
#13
REVIEW
Vladimir A Botchkarev
Three-dimensional organization of transcription in the nucleus and mechanisms controlling the global chromatin folding, including spatial interactions between the genes, noncoding genome elements, and epigenetic and transcription machinery, are essential for establishing lineage-specific gene expression programs during cell differentiation. Spatial chromatin interactions in the nucleus involving gene promoters and distal regulatory elements are currently considered major forces that drive cell differentiation and genome evolution in general, and such interactions are substantially reorganized during many pathological conditions...
May 2017: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/28407782/triatoma-vitticeps-subcomplex-hemiptera-reduviidae-triatominae-a-new-grouping-of-chagas-disease-vectors-from-south-america
#14
Kaio Cesar Chaboli Alevi, Jader de Oliveira, Maria Tercília Vilela de Azeredo-Oliveira, João Aristeu da Rosa
BACKGROUND: Triatomines have been grouped into complexes and subcomplexes based largely on morphological and geographical distribution. Although these groupings are not formally recognised as taxonomic ranks, they are likely monophyletic. However, recent studies have demonstrated that some subcomplexes from South America did not form monophyletic groups, and reorganisations have been suggested. One suggested reorganisation is to exclude Triatoma vitticeps, T. melanocephala, and T. tibiamaculata from the T...
April 13, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28406749/nucleosome-repositioning-during-differentiation-of-a-human-myeloid-leukemia-cell-line
#15
Vladimir B Teif, Jan-Philipp Mallm, Tanvi Sharma, David B Mark Welch, Karsten Rippe, Roland Eils, Jörg Langowski, Ada L Olins, Donald E Olins
Cell differentiation is associated with changes in chromatin organization and gene expression. In this study, we examine chromatin structure following differentiation of the human myeloid leukemia cell line (HL-60/S4) into granulocytes with retinoic acid (RA) or into macrophage with phorbol ester (TPA). We performed ChIP-seq of histone H3 and its modifications, analyzing changes in nucleosome occupancy, nucleosome repeat length, eu-/heterochromatin redistribution and properties of epichromatin (surface chromatin adjacent to the nuclear envelope)...
March 4, 2017: Nucleus
https://www.readbyqxmd.com/read/28404620/accumulation-of-rna-on-chromatin-disrupts-heterochromatic-silencing
#16
Cornelia Brönner, Luca Salvi, Manuel Zocco, Ilaria Ugolini, Mario Halic
Long non-coding RNAs (lncRNAs) play a conserved role in regulating gene expression, chromatin dynamics and cell differentiation. They serve as a platform for RNA interference (RNAi)-mediated heterochromatin formation or DNA methylation in many eukaryotic organisms. We found in Schizosaccharomyces pombe, that heterochromatin is lost at transcribed regions in absence of RNA degradation. We show that heterochromatic RNAs are retained on chromatin, form DNA:RNA hybrids and need to be degraded by the Ccr4-Not complex or RNAi to maintain heterochromatic silencing...
April 12, 2017: Genome Research
https://www.readbyqxmd.com/read/28400559/knockdown-of-broad-complex-gene-expression-of-bombyx-mori-by-oligopyrrole-carboxamides-enhances-silk-production
#17
Asfa Ali, Venugopal Reddy Bovilla, Danti Kumari Mysarla, Prasanthi Siripurapu, Rashmi U Pathak, Bhakti Basu, Anitha Mamillapalli, Santanu Bhattacharya
Bombyx mori (B. mori) is important due to its major role in the silk production. Though DNA binding ligands often influence gene expression, no attempt has been made to exploit their use in sericulture. The telomeric heterochromatin of B. mori is enriched with 5'-TTAGG-3' sequences. These sequences were also found to be present in several genes in the euchromatic regions. We examined three synthetic oligopyrrole carboxamides that target 5'-TTAGG-3' sequences in controlling the gene expression in B. mori. The ligands did not show any defect or feeding difference in the larval stage, crucial for silk production...
April 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28394248/highest-diploid-number-among-gymnotiformes-first-cytogenetic-insights-into-rhabdolichops-sternopygidae
#18
Pablo Suárez, Inaê Cristina Guerreiro Pinto Barroso, Danillo Dos Santos Silva, Susana S R Milhomem, Diogo Cavalcanti Cabral-de-Mello, Cesar Martins, Julio Cesar Pieczarka, Cleusa Yoshiko Nagamachi
We report the first comparative cytogenetic analysis of two species from electrogenic fish of genus Rhabdolichops (Sternopygidae, Gymnotiformes): Rhabdolichops troscheli and Rhabdolichops cf eastwardi. R. troscheli has 2n = 54 (fundamental number [FN] = 66), whereas R. cf. eastwardi has 2n = 74 (FN = 78). C-banding revealed centromeric constitutive heterochromatin in both species. Ag-NORs mapped on pair 6 in R. troscheli and pair 30 in R. cf eastwardi. Fluorescense in situ hybridization with 18S rDNA probes confirmed the Ag-NOR staining results and revealed additional (presumably silent) ribosomal genes on pairs 12, 13, 21, 23, 26, and 27 in R...
April 10, 2017: Zebrafish
https://www.readbyqxmd.com/read/28392109/compartmentalization-of-dna-damage-response-between-heterochromatin-and-euchromatin-is-mediated-by-distinct-h2a-histone-variants
#19
Zdravko J Lorković, Chulmin Park, Malgorzata Goiser, Danhua Jiang, Marie-Therese Kurzbauer, Peter Schlögelhofer, Frédéric Berger
DNA double-strand break (DSB) repair depends on the ataxia telangiectasia mutated (ATM) kinase that phosphorylates the conserved C-terminal SQ motif present in the histone variant H2A.X [1-7]. In constitutive heterochromatin of mammals, DSB repair is delayed and relies on phosphorylation of the proteins HP1 and KAP1 by ATM [2, 8-14]. However, KAP1 is not conserved in plants and the HP1-related protein Like-HP1 (LHP1) is not localized at constitutive heterochromatin [15], suggesting that in plants, alternative mechanisms could be responsible for repair of DSBs in heterochromatin...
April 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28389691/deletion-of-adseverin-in-osteoclasts-affects-cell-structure-but-not-bone-metabolism
#20
Yixuan Cao, Yongqiang Wang, Sara Sprangers, Daisy I Picavet, Michael Glogauer, Christopher A McCulloch, Vincent Everts
Adseverin is an actin-severing/capping protein that may contribute to osteoclast differentiation in vitro but its role in bone remodeling of healthy animals is not defined. We analyzed bone and osteoclast structure in adseverin conditional null mice at alveolar and long bone sites. In wild-type and adseverin null mice, as measured by dual-energy X-ray absorptiometry, there were no differences of bone mineral content or bone mineral density, indicating no change of bone metabolism. In tibiae, TRAcP(+) osteoclasts were formed in comparable numbers in adseverin null and wild-type mice...
April 7, 2017: Calcified Tissue International
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