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H3K9me3

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https://www.readbyqxmd.com/read/28334823/h3-y-discriminates-between-hira-and-daxx-chaperone-complexes-and-reveals-unexpected-insights-into-human-daxx-h3-3-h4-binding-and-deposition-requirements
#1
Lisa-Maria Zink, Erwan Delbarre, H Christian Eberl, Eva C Keilhauer, Clemens Bönisch, Sebastian Pünzeler, Marek Bartkuhn, Philippe Collas, Matthias Mann, Sandra B Hake
Histone chaperones prevent promiscuous histone interactions before chromatin assembly. They guarantee faithful deposition of canonical histones and functionally specialized histone variants into chromatin in a spatial- and temporally-restricted manner. Here, we identify the binding partners of the primate-specific and H3.3-related histone variant H3.Y using several quantitative mass spectrometry approaches, and biochemical and cell biological assays. We find the HIRA, but not the DAXX/ATRX, complex to recognize H3...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28328977/jmjd3-aids-in-reprogramming-of-bone-marrow-progenitor-cells-to-hepatic-phenotype-through-epigenetic-activation-of-hepatic-transcription-factors
#2
Veena Kochat, Zaffar Equbal, Prakash Baligar, Vikash Kumar, Madhulika Srivastava, Asok Mukhopadhyay
The strictly regulated unidirectional differentiation program in some somatic stem/progenitor cells has been found to be modified in the ectopic site (tissue) undergoing regeneration. In these cases, the lineage barrier is crossed by either heterotypic cell fusion or direct differentiation. Though studies have shown the role of coordinated genetic and epigenetic mechanisms in cellular development and differentiation, how the lineage fate of adult bone marrow progenitor cells (BMPCs) is reprogrammed during liver regeneration and whether this lineage switch is stably maintained are not clearly understood...
2017: PloS One
https://www.readbyqxmd.com/read/28326190/malat1-regulates-myogenic-differentiation-and-muscle-regeneration-through-modulating-myod-transcriptional-activity
#3
Xiaona Chen, Liangqiang He, Yu Zhao, Yuying Li, Suyang Zhang, Kun Sun, Karl So, Fengyuan Chen, Liang Zhou, Leina Lu, Lijun Wang, Xihua Zhu, Xichen Bao, Miguel A Esteban, Shinichi Nakagawa, Kannanganattu V Prasanth, Zhenguo Wu, Hao Sun, Huating Wang
Malat1 is one of the most abundant long non-coding RNAs in various cell types; its exact cellular function is still a matter of intense investigation. In this study we characterized the function of Malat1 in skeletal muscle cells and muscle regeneration. Utilizing both in vitro and in vivo assays, we demonstrate that Malat1 has a role in regulating gene expression during myogenic differentiation of myoblast cells. Specifically, we found that knockdown of Malat1 accelerates the myogenic differentiation in cultured cells...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28293300/silencing-markers-are-retained-on-pericentric-heterochromatin-during-murine-primordial-germ-cell-development
#4
Aristea Magaraki, Godfried van der Heijden, Esther Sleddens-Linkels, Leonidas Magarakis, Wiggert A van Cappellen, Antoine H F M Peters, Joost Gribnau, Willy M Baarends, Maureen Eijpe
BACKGROUND: In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-binding protein 1 isoforms (HP1 isoforms). Maintenance of this specialized chromatin structure is of great importance for genome integrity and for the controlled repression of the repetitive elements within the pericentric DNA sequence. Here we have studied histone modifications at pericentric heterochromatin during primordial germ cell (PGC) development using different fixation conditions and fluorescent immunohistochemical and immunocytochemical protocols...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28292917/paternal-genome-elimination-in-liposcelis-booklice-insecta-psocodea
#5
Christina N Hodson, Phineas T Hamilton, David Dilworth, Chris J Nelson, Caitlin I Curtis, Steve J Perlman
How sex is determined in insects is diverse and dynamic, and includes male heterogamety, female heterogamety, and haplodiploidy. In many insect lineages, sex determination is either completely unknown or poorly studied. We studied sex determination in Psocodea, a species-rich order of insects that includes parasitic lice, barklice, and booklice. We focus on a recently discovered species of Liposcelis booklice (Troctomorpha: Psocodea), which are among the closest free-living relatives of parasitic lice. Using genetic, genomic, and immunohistochemical approaches, we show that this group exhibits paternal genome elimination (PGE), an unusual mode of sex determination that involves genomic imprinting...
March 14, 2017: Genetics
https://www.readbyqxmd.com/read/28283545/macroh2a-histone-variants-maintain-nuclear-organization-and-heterochromatin-architecture
#6
Julien Douet, David Corujo, Roberto Malinverni, Justine Renauld, Viola Sansoni, Melanija Posavec Marjanović, Neus Cantari'o, Vanesa Valero, Fabien Mongelard, Philippe Bouvet, Axel Imhof, Marc Thiry, Marcus Buschbeck
Genetic loss-of-function studies in development, cancer and somatic cell reprogramming have suggested that the group of macroH2A histone variants might function through stabilizing the differentiated state by a yet unknown mechanism. Here, we present results demonstrating that macroH2A variants have a major function in maintaining nuclear organization and heterochromatin architecture. Specifically, we find that a substantial amount of macroH2A is associated with heterochromatic repeat sequences. We further identify macroH2A on sites of interstitial heterochromatin decorated by H3K9me3...
March 10, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/28276635/3d-culture-increases-pluripotent-gene-expression-in-mesenchymal-stem-cells-through-relaxation-of-cytoskeleton-tension
#7
Ying Zhou, Haiyan Chen, Hong Li, Yaojiong Wu
Three-dimensional (3D) culture has been shown to improve pluripotent gene expression in mesenchymal stem cells (MSCs), but the underlining mechanisms were poorly understood. Here, we found that the relaxation of cytoskeleton tension of MSCs in 3D culture was critically associated with the expressional up-regulation of Nanog. Cultured in spheroids, MSCs showed decreased integrin-based cell-matrix adhesion but increased cadherin-based cell-cell interaction. Different from that in 2D culture, where MSCs exhibited branched and multiple-directed F-actin stress bundles at the cell edge and strengthened stress fibres transversing the cell body, MSCs cultured in spheroids showed compact cell body, relaxed cytoskeleton tension with very thin cortical actin filament outlining the cell, and increased expression of Nanog along with reduced levels of Suv39h1 (H3K9 methyltransferase) and H3K9me3...
March 9, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28273906/identifying-novel-transcriptional-and-epigenetic-features-of-nuclear-lamina-associated-genes
#8
Feinan Wu, Jie Yao
Because a large portion of the mammalian genome is associated with the nuclear lamina (NL), it is interesting to study how native genes resided there are transcribed and regulated. In this study, we report unique transcriptional and epigenetic features of nearly 3,500 NL-associated genes (NL genes). Promoter regions of active NL genes are often excluded from NL-association, suggesting that NL-promoter interactions may repress transcription. Active NL genes with higher RNA polymerase II (Pol II) recruitment levels tend to display Pol II promoter-proximal pausing, while Pol II recruitment and Pol II pausing are not correlated among non-NL genes...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28273063/krab-zinc-finger-proteins-contribute-to-the-evolution-of-gene-regulatory-networks
#9
Michaël Imbeault, Pierre-Yves Helleboid, Didier Trono
The human genome encodes some 350 Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the products of a rapidly evolving gene family that has been traced back to early tetrapods. The function of most KZFPs is unknown, but a few have been demonstrated to repress transposable elements in embryonic stem (ES) cells by recruiting the transcriptional regulator TRIM28 and associated mediators of histone H3 Lys9 trimethylation (H3K9me3)-dependent heterochromatin formation and DNA methylation...
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28271186/suv39h1-mediated-sirt1-trans-repression-contributes-to-cardiac-ischemia-reperfusion-injury
#10
Guang Yang, Xinjian Zhang, Xinyu Weng, Peng Liang, Xin Dai, Sheng Zeng, Huihui Xu, Hailin Huan, Mingming Fang, Yuehua Li, Dachun Xu, Yong Xu
Ischemic reperfusion (I/R) contributes to deleterious cardiac remodeling and heart failure. The deacetylase SIRT1 has been shown to protect the heart from I/R injury. We examined the mechanism whereby I/R injury represses SIRT1 transcription in the myocardium. There was accumulation of trimethylated histone H3K9 on the proximal SIRT1 promoter in the myocardium in mice following I/R injury and in cultured cardiomyocytes exposed to hypoxia-reoxygenation (H/R). In accordance, the H3K9 trimethyltransferase SUV39H1 bound to the SIRT1 promoter and repressed SIRT1 transcription...
May 2017: Basic Research in Cardiology
https://www.readbyqxmd.com/read/28257702/gene-resistance-to-transcriptional-reprogramming-following-nuclear-transfer-is-directly-mediated-by-multiple-chromatin-repressive-pathways
#11
Jerome Jullien, Munender Vodnala, Vincent Pasque, Mami Oikawa, Kei Miyamoto, George Allen, Sarah Anne David, Vincent Brochard, Stan Wang, Charles Bradshaw, Haruhiko Koseki, Vittorio Sartorelli, Nathalie Beaujean, John Gurdon
Understanding the mechanism of resistance of genes to reactivation will help improve the success of nuclear reprogramming. Using mouse embryonic fibroblast nuclei with normal or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2AK119ub1 from transplanted nuclei, we reveal the basis for resistance of genes to transcriptional reprogramming by oocyte factors. A majority of genes is affected by more than one type of treatment, suggesting that resistance can require repression through multiple epigenetic mechanisms...
March 2, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28250819/smyd5-regulates-h4k20me3-marked-heterochromatin-to-safeguard-es-cell-self-renewal-and-prevent-spurious-differentiation
#12
Benjamin L Kidder, Gangqing Hu, Kairong Cui, Keji Zhao
BACKGROUND: Epigenetic regulation of chromatin states is thought to control the self-renewal and differentiation of embryonic stem (ES) cells. However, the roles of repressive histone modifications such as trimethylated histone 4 lysine 20 (H4K20me3) in pluripotency and development are largely unknown. RESULTS: Here, we show that the histone lysine methyltransferase SMYD5 mediates H4K20me3 at heterochromatin regions. Depletion of SMYD5 leads to compromised self-renewal, including dysregulated expression of OCT4 targets, and perturbed differentiation...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28228846/decoupling-the-downstream-effects-of-germline-nuclear-rnai-reveals-that-h3k9me3-is-dispensable-for-heritable-rnai-and-the-maintenance-of-endogenous-sirna-mediated-transcriptional-silencing-in-caenorhabditis-elegans
#13
Natallia Kalinava, Julie Zhouli Ni, Kimberly Peterman, Esteban Chen, Sam Guoping Gu
BACKGROUND: Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous double-stranded RNA (dsRNA) or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in siRNA-mediated transcriptional silencing and inheritance of the silencing state at native target genes is unclear...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28220356/overexpression-of-line-1-retrotransposons-in-autism-brain
#14
Svitlana Shpyleva, Stepan Melnyk, Oleksandra Pavliv, Igor Pogribny, S Jill James
Long interspersed nuclear elements-1 (LINE-1 or L1) are mobile DNA sequences that are capable of duplication and insertion (retrotransposition) within the genome. Recently, retrotransposition of L1 was shown to occur within human brain leading to somatic mosaicism in hippocampus and cerebellum. Because unregulated L1 activity can promote genomic instability and mutagenesis, multiple mechanisms including epigenetic chromatin condensation have evolved to effectively repress L1 expression. Nonetheless, L1 expression has been shown to be increased in patients with Rett syndrome and schizophrenia...
February 20, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28169523/the-suv39h1-protein-lysine-methyltransferase-methylates-chromatin-proteins-involved-in-heterochromatin-formation-and-vdj-recombination
#15
Srikanth Kudithipudi, Maren Kirstin Schuhmacher, Adam Fiseha Kebede, Albert Jeltsch
SUV39H1 is an H3K9 methyltransferase involved in the formation of heterochromatin. We investigated its substrate specificity profile and show recognition of H3 residues between K4 and G12 with highly specific readout of R8. The specificity profile of SUV39H1 is distinct from its paralog SUV39H2, indicating that they can have different additional substrates. Using the specificity profile, several novel SUV39H1 candidate substrates were identified. We observed methylation of 19 novel substrates at the peptide level and for six of them at the protein level...
February 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28148216/histone-h3-lysine-27-trimethylation-leads-to-loss-of-mesendodermal-competence-during-gastrulation-in-zebrafish-ectodermal-cells
#16
Taishi Shiomi, Akihiko Muto, Shunya Hozumi, Hiroshi Kimura, Yutaka Kikuchi
Previous studies in Xenopus have shown that forced expression of Nodal signaling can change ectodermal cells to a mesodermal fate by the early gastrula stage, suggesting mesodermal competence in early ectoderm cells. This mesodermal competence in ectodermal cells has been shown to be regulated at the level of nucleocytoplasmic localization of Smad2 in Xenopus. However, the regulation of mesodermal competence through epigenetic mechanisms has not been fully elucidated. Here, we used a constitutively active form of zebrafish Smad2 (Smad2ca) to overcome the inhibition of Nodal signaling via the nuclear exclusion of Smad2...
February 2017: Zoological Science
https://www.readbyqxmd.com/read/28132817/systematic-mapping-of-rna-chromatin-interactions-in%C3%A2-vivo
#17
Bharat Sridhar, Marcelo Rivas-Astroza, Tri C Nguyen, Weizhong Chen, Zhangming Yan, Xiaoyi Cao, Lucie Hebert, Sheng Zhong
RNA molecules can attach to chromatin. It remains difficult to know what RNAs are associated with chromatin and where the genomic target loci of these RNAs are. Here, we present MARGI (mapping RNA-genome interactions), a technology to massively reveal native RNA-chromatin interactions from unperturbed cells. The gist of this technology is to ligate chromatin-associated RNAs (caRNAs) with their target genomic sequences by proximity ligation, forming RNA-DNA chimeric sequences, which are converted to a sequencing library for paired-end sequencing...
February 20, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28118853/allele-specific-analysis-of-cell-fusion-mediated-pluripotent-reprograming-reveals-distinct-and-predictive-susceptibilities-of-human-x-linked-genes-to-reactivation
#18
Irene Cantone, Gopuraja Dharmalingam, Yi-Wah Chan, Anne-Celine Kohler, Boris Lenhard, Matthias Merkenschlager, Amanda G Fisher
BACKGROUND: Inactivation of one X chromosome is established early in female mammalian development and can be reversed in vivo and in vitro when pluripotency factors are re-expressed. The extent of reactivation along the inactive X chromosome (Xi) and the determinants of locus susceptibility are, however, poorly understood. Here we use cell fusion-mediated pluripotent reprograming to study human Xi reactivation and allele-specific single nucleotide polymorphisms (SNPs) to identify reactivated loci...
January 25, 2017: Genome Biology
https://www.readbyqxmd.com/read/28100021/identifying-the-biphasic-role-of-calcineurin-nfat-signaling-enables-replacement-of-sox2-in-somatic-cell-reprogramming
#19
Sherif Khodeer, Takumi Era
Induction of pluripotency with defined factors (Oct4, Sox2, Klf4, c-Myc) raises hopes for successful clinical trials. Despite considerable efforts, the molecular mechanism of reprogramming remains poorly understood. The aim of the present study was to identify the role of calcineurin/nuclear factor of activated T cells (NFAT) in reprogramming. Our results demonstrated a biphasic role for calcineurin/NFAT signaling during reprogramming. In the early phase of reprogramming, calcineurin activity is required to maintain proper cell cycle division and for mesenchymal-epithelial transition...
January 18, 2017: Stem Cells
https://www.readbyqxmd.com/read/28091569/epigenetic-regulation-of-plasmodium-falciparum-clonally-variant-gene-expression-during-development-in-anopheles-gambiae
#20
Elena Gómez-Díaz, Rakiswendé S Yerbanga, Thierry Lefèvre, Anna Cohuet, M Jordan Rowley, Jean Bosco Ouedraogo, Victor G Corces
P. falciparum phenotypic plasticity is linked to the variant expression of clonal multigene families such as the var genes. We have examined changes in transcription and histone modifications that occur during sporogonic development of P. falciparum in the mosquito host. All var genes are silenced or transcribed at low levels in blood stages (gametocyte/ring) of the parasite in the human host. After infection of mosquitoes, a single var gene is selected for expression in the oocyst, and transcription of this gene increases dramatically in the sporozoite...
January 16, 2017: Scientific Reports
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