Dzip3 regulates developmental genes in mouse embryonic stem cells by reorganizing 3D chromatin conformation.

Abstract:

:In mouse embryonic stem (mES) cells, ubiquitylation of histone H2A lysine 119 represses a large number of developmental genes and maintains mES cell pluripotency. It has been suggested that a number of H2A ubiquitin ligases as well as deubiquitylases and related peptide fragments contribute to a delicate balance between self-renewal and multi-lineage differentiation in mES cells. Here, we tested whether known H2A ubiquitin ligases and deubiquitylases are involved in mES cell regulation and discovered that Dzip3, the E3 ligase of H2AK119, represses differentiation-inducible genes, as does Ring1B. The two sets of target genes partially overlapped but had different spectra. We found that Dzip3 represses gene expression by orchestrating changes in 3D organization, in addition to regulating ubiquitylation of H2A. Our results shed light on the epigenetic mechanism of transcriptional regulation, which depends on 3D chromatin reorganization to regulate mES cell differentiation.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Inoue D,Aihara H,Sato T,Mizusaki H,Doiguchi M,Higashi M,Imamura Y,Yoneda M,Miyanishi T,Fujii S,Okuda A,Nakagawa T,Ito T

doi

10.1038/srep16567

subject

Has Abstract

pub_date

2015-11-16 00:00:00

pages

16567

issn

2045-2322

pii

srep16567

journal_volume

5

pub_type

杂志文章
  • Histological and transcriptome analyses of testes from Duroc and Meishan boars.

    abstract::Meishan boars are known for their early sexual maturity. However, they exhibit a significantly smaller testicular size and a reduced proportion of Sertoli cells and daily sperm production compared with Duroc boars. The testes of Duroc and Meishan boars at 20, 75 and 270 days of age were used for histological and trans...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20758

    authors: Ding H,Luo Y,Liu M,Huang J,Xu D

    更新日期:2016-02-11 00:00:00

  • Role of Early PET/CT Imaging with 68Ga-PSMA in Staging and Restaging of Prostate Cancer.

    abstract::Ga-68 Prostate-Specific Membrane Antigen PET/CT is a new tool for the assessment of prostate cancer. Standard imaging time is 60 minutes post injection of radiotracer. At 60 minutes, there is physiologic accumulation of radiotracer in the urinary bladder which may cause some lesions in its vicinity to be obscured. Our...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59296-6

    authors: Barakat A,Yacoub B,Homsi ME,Saad Aldine A,El Hajj A,Haidar MB

    更新日期:2020-02-17 00:00:00

  • High corrosion resistance and weak corrosion anisotropy of an as-rolled Mg-3Al-1Zn (in wt.%) alloy with strong crystallographic texture.

    abstract::Combining with electrochemical corrosion measurements, immersion and hydrogen evolution testing performed in 0.9 wt.% NaCl solution at 37 °C, the corrosion resistance of an as-rolled Mg-3%Al-1%Zn alloy before and after a 3% compressive strain along the rolling direction was investigated. Results revealed that the corr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-16351-z

    authors: Wang BJ,Xu DK,Xin YC,Sheng LY,Han EH

    更新日期:2017-11-22 00:00:00

  • Magnetic-charge ordering and phase transitions in monopole-conserved square spin ice.

    abstract::Magnetic-charge ordering and corresponding magnetic/monopole phase transitions in spin ices are the emergent topics of condensed matter physics. In this work, we investigate a series of magnetic-charge (monopole) phase transitions in artificial square spin ice model using the conserved monopole density algorithm. It i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep15875

    authors: Xie YL,Du ZZ,Yan ZB,Liu JM

    更新日期:2015-10-29 00:00:00

  • Fermi level tuning of Ag-doped Bi2Se3 topological insulator.

    abstract::The temperature dependence of the resistivity (ρ) of Ag-doped Bi2Se3 (AgxBi2-xSe3) shows insulating behavior above 35 K, but below 35 K, ρ suddenly decreases with decreasing temperature, in contrast to the metallic behavior for non-doped Bi2Se3 at 1.5-300 K. This significant change in transport properties from metalli...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-41906-7

    authors: Uesugi E,Uchiyama T,Goto H,Ota H,Ueno T,Fujiwara H,Terashima K,Yokoya T,Matsui F,Akimitsu J,Kobayashi K,Kubozono Y

    更新日期:2019-03-29 00:00:00

  • Attentional Control in Adolescent Mice Assessed with a Modified Five Choice Serial Reaction Time Task.

    abstract::Adolescence is a critical period for the development of higher-order cognitive functions. Unlike in humans, very limited tools are available to assess such cognitive abilities in adolescent rodents. We implemented a modified 5-Choice Serial Reaction Time Task (5CSRTT) to selectively measure attentiveness, impulsivity,...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-10112-8

    authors: Ciampoli M,Contarini G,Mereu M,Papaleo F

    更新日期:2017-08-30 00:00:00

  • Broadband Optical Cavity Mode Measurements at Hz-Level Precision With a Comb-Based VIPA Spectrometer.

    abstract::Optical frequency comb spectrometers open up new avenues of investigation into molecular structure and dynamics thanks to their accuracy, sensitivity and broadband, high-speed operation. We combine broadband direct frequency comb spectroscopy with a dispersive spectrometer providing single-spectrum acquisition time of...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44711-4

    authors: Kowzan G,Charczun D,Cygan A,Trawiński RS,Lisak D,Masłowski P

    更新日期:2019-06-03 00:00:00

  • A novel allele of L-galactono-1,4-lactone dehydrogenase is associated with enhanced drought tolerance through affecting stomatal aperture in common wheat.

    abstract::In higher plants, L-galactono-1,4-lactone dehydrogenase (GLDH) plays important roles in ascorbic acid (AsA) biosynthesis and assembly of respiration complex I. Here we report three homoeologous genes (TaGLDH-A1, -B1 and -D1) encoding common wheat GLDH isozymes and a unique allelic variant (TaGLDH-A1b) associated with ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep30177

    authors: Zhang J,Li B,Yang Y,Mu P,Qian W,Dong L,Zhang K,Liu X,Qin H,Ling H,Wang D

    更新日期:2016-07-22 00:00:00

  • Identification of Key Signaling Pathways Orchestrating Substrate Topography Directed Osteogenic Differentiation Through High-Throughput siRNA Screening.

    abstract::Fibrous scaffolds are used for bone tissue engineering purposes with great success across a variety of polymers with different physical and chemical properties. It is now evident that the correct degree of curvature promotes increased cytoskeletal tension on osteoprogenitors leading to osteogenic differentiation. Howe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37554-y

    authors: Ozdemir T,Bowers DT,Zhan X,Ghosh D,Brown JL

    更新日期:2019-01-30 00:00:00

  • Comb-rooted multi-channel synthesis of ultra-narrow optical frequencies of few Hz linewidth.

    abstract::We report a multi-channel optical frequency synthesizer developed to generate extremely stable continuous-wave lasers directly out of the optical comb of an Er-doped fiber oscillator. Being stabilized to a high-finesse cavity with a fractional frequency stability of 3.8 × 10-15 at 0.1 s, the comb-rooted synthesizer pr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-44122-5

    authors: Jang H,Kim BS,Chun BJ,Kang HJ,Jang YS,Kim YW,Kim YJ,Kim SW

    更新日期:2019-05-21 00:00:00

  • Publisher Correction: Molecular mechanisms of Charcot-Marie-Tooth neuropathy linked to mutations in human myelin protein P2.

    abstract::A correction to this article has been published and is linked from the HTML version of this paper. The error has been fixed in the paper. ...

    journal_title:Scientific reports

    pub_type: 杂志文章,已发布勘误

    doi:10.1038/s41598-017-18751-7

    authors: Ruskamo S,Nieminen T,Kristiansen CK,Vatne GH,Baumann A,Hallin EI,Raasakka A,Joensuu P,Bergmann U,Vattulainen I,Kursula P

    更新日期:2018-01-08 00:00:00

  • Abnormal Growth and Feeding Behavior Persist After Removal of Upper Airway Obstruction in Juvenile Rats.

    abstract::Pediatric obstructive sleep-disordered breathing is associated with growth retardation, but also with obesity that has a tendency to persist following treatment. We investigated the effect of upper airways obstruction (AO) and of obstruction removal (OR) in juvenile rats on gut-derived ghrelin and related hypothalamic...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02843-5

    authors: Assadi MH,Shknevsky E,Segev Y,Tarasiuk A

    更新日期:2017-06-02 00:00:00

  • Levosimendan displays anti-inflammatory effects and decreases MPO bioavailability in patients with severe heart failure.

    abstract::Treatment of decompensated heart failure often includes administration of levosimendan. Myeloperoxidase (MPO) is released during polymorphonuclear neutrophil (PMN) degranulation, and mediates dysregulation of vascular tone in heart failure. We evaluated the effects of levosimendan-treatment on MPO in patients with acu...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep09704

    authors: Adam M,Meyer S,Knors H,Klinke A,Radunski UK,Rudolph TK,Rudolph V,Spin JM,Tsao PS,Costard-Jäckle A,Baldus S

    更新日期:2015-04-13 00:00:00

  • Suit-type Wearable Robot Powered by Shape-memory-alloy-based Fabric Muscle.

    abstract::A suit-type wearable robot (STWR) is a new type of soft wearable robot (SWR) that can be worn easily anywhere and anytime to assist the muscular strength of wearers because it can be worn like normal clothes and is comfortable to wear even with no power supply. This paper proposes an STWR, in which a shape-memory-allo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-45722-x

    authors: Park SJ,Park CH

    更新日期:2019-06-24 00:00:00

  • Association of plasma free amino acids with hyperuricemia in relation to diabetes mellitus, dyslipidemia, hypertension and metabolic syndrome.

    abstract::Previous studies demonstrated independent contributions of plasma free amino acids (PFAAs) and high uric acid (UA) concentrations to increased risks of lifestyle-related diseases (LSRDs), but the important associations between these factors and LSRDs remain unknown. We quantified PFAAs and UA amongst Japanese subjects...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-17710-6

    authors: Mahbub MH,Yamaguchi N,Takahashi H,Hase R,Ishimaru Y,Sunagawa H,Amano H,Kobayashi-Miura M,Kanda H,Fujita Y,Yamamoto H,Yamamoto M,Kikuchi S,Ikeda A,Kageyama N,Nakamura M,Tanabe T

    更新日期:2017-12-15 00:00:00

  • Ocular Manifestations of Leukemia and Results of Treatment with Intravitreal Methotrexate.

    abstract::Ocular involvement in leukemia is considered rare. Ocular symptoms can be the presenting signs of leukemia, they can appear after diagnosis has been established, or they can be the first manifestation of a relapse after remission. We report, to the best of our knowledge for the first time, the ocular manifestation of ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-58654-8

    authors: Vishnevskia-Dai V,Sella King S,Lekach R,Fabian ID,Zloto O

    更新日期:2020-02-06 00:00:00

  • Loss of Parkinson's susceptibility gene LRRK2 promotes carcinogen-induced lung tumorigenesis.

    abstract::Pathological links between neurodegenerative disease and cancer are emerging. LRRK2 overactivity contributes to Parkinson's disease, whereas our previous analyses of public cancer patient data revealed that decreased LRRK2 expression is associated with lung adenocarcinoma (LUAD). The clinical and functional relevance ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-81639-0

    authors: Lebovitz C,Wretham N,Osooly M,Milne K,Dash T,Thornton S,Tessier-Cloutier B,Sathiyaseelan P,Bortnik S,Go NE,Halvorsen E,Cederberg RA,Chow N,Dos Santos N,Bennewith KL,Nelson BH,Bally MB,Lam WL,Gorski SM

    更新日期:2021-01-22 00:00:00

  • An inhibitor of the Keap1-Nrf2 protein-protein interaction protects NCM460 colonic cells and alleviates experimental colitis.

    abstract::Ulcerative colitis (UC) is a chronic relapsing-remitting form of inflammatory bowel disease (IBD) that increases the risk of colorectal cancer, the third most common malignancy in humans. Oxidative stress is a risk factor for the development of UC. The Keap1-Nrf2-ARE pathway is one of the most important defensive mech...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep26585

    authors: Lu MC,Ji JA,Jiang YL,Chen ZY,Yuan ZW,You QD,Jiang ZY

    更新日期:2016-05-24 00:00:00

  • Extensive vegetation browning and drying in forests of India's Tiger Reserves.

    abstract::Forest conservation includes stemming deforestation as well as preserving its vegetation condition. Traditional Protected Area (PA) effectiveness evaluations have assessed changes in forest extent but have mostly ignored vegetation condition. Tiger Reserves (TRs) are India's PAs with highest protection and management ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-51118-8

    authors: Koulgi PS,Clinton N,Karanth KK

    更新日期:2019-10-18 00:00:00

  • Carrier-Mediated and Energy-Dependent Uptake and Efflux of Deoxynivalenol in Mammalian Cells.

    abstract::Deoxynivalenol (DON) is one of the most abundant mycotoxins and exerts many adverse effects on humans and animals. To date, the transporting mechanism of DON in mammalian cells remains unclear. In this study, the parallel artificial membrane permeability assay (PAMPA), Transwell models and metabolic inhibitors were us...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-06199-8

    authors: Li X,Mu P,Wen J,Deng Y

    更新日期:2017-07-19 00:00:00

  • Impact of different cell penetrating peptides on the efficacy of antisense therapeutics for targeting intracellular pathogens.

    abstract::There is a pressing need for novel and innovative therapeutic strategies to address infections caused by intracellular pathogens. Peptide nucleic acids (PNAs) present a novel method to target intracellular pathogens due to their unique mechanism of action and their ability to be conjugated to cell penetrating peptides...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep20832

    authors: Abushahba MF,Mohammad H,Thangamani S,Hussein AA,Seleem MN

    更新日期:2016-02-10 00:00:00

  • Efficient second-harmonic imaging of collagen in histological slides using Bessel beam excitation.

    abstract::Second-harmonic generation (SHG) is the most specific label-free indicator of collagen accumulation in widespread pathologies such as fibrosis, and SHG-based measurements hold important potential for biomedical analyses. However, efficient collagen SHG scoring in histological slides is hampered by the limited depth-of...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29863

    authors: Vuillemin N,Mahou P,Débarre D,Gacoin T,Tharaux PL,Schanne-Klein MC,Supatto W,Beaurepaire E

    更新日期:2016-07-20 00:00:00

  • Droplet digital PCR-based EGFR mutation detection with an internal quality control index to determine the quality of DNA.

    abstract::In clinical translational research and molecular in vitro diagnostics, a major challenge in the detection of genetic mutations is overcoming artefactual results caused by the low-quality of formalin-fixed paraffin-embedded tissue (FFPET)-derived DNA (FFPET-DNA). Here, we propose the use of an 'internal quality control...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-18642-x

    authors: Kim SS,Choi HJ,Kim JJ,Kim MS,Lee IS,Byun B,Jia L,Oh MR,Moon Y,Park S,Choi JS,Chae SW,Nam BH,Kim JS,Kim J,Min BS,Lee JS,Won JK,Cho SY,Choi YL,Shin YK

    更新日期:2018-01-11 00:00:00

  • Tyrosine Hydroxylase is crucial for maintaining pupal tanning and immunity in Anopheles sinensis.

    abstract::Tyrosine hydroxylase (TH), the initial enzyme in the melanin pathway, catalyzes tyrosine conversion into Dopa. Although expression and regulation of TH have been shown to affect cuticle pigmentation in insects, no direct functional studies to date have focused on the specific physiological processes involving the enzy...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29835

    authors: Qiao L,Du M,Liang X,Hao Y,He X,Si F,Mei T,Chen B

    更新日期:2016-07-15 00:00:00

  • Few basepairing-independent motifs in the apical half of the avian HBV ε RNA stem-loop determine site-specific initiation of protein-priming.

    abstract::Hepadnaviruses, including human hepatitis B virus (HBV), replicate their tiny DNA genomes by protein-primed reverse transcription of a pregenomic (pg) RNA. Replication initiation as well as pgRNA encapsidation depend on the interaction of the viral polymerase, P protein, with the ε RNA element, featuring a lower and a...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-07657-z

    authors: Gajer M,Dörnbrack K,Rösler C,Schmid B,Beck J,Nassal M

    更新日期:2017-08-02 00:00:00

  • Initiation of programmed cell death in the suspensor is predominantly regulated maternally in a tobacco hybrid.

    abstract::Maternal gene products deposited in the egg regulate early embryogenesis before activation of the embryonic genome in animals. While in higher plants, it is believed that genes of parental origin contribute to early embryogenesis. However, little is known regarding the particular processes in which genes of parental o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29467

    authors: Luo A,Zhao P,Zhang LY,Sun MX

    更新日期:2016-07-19 00:00:00

  • Exotic superfluidity and pairing phenomena in atomic Fermi gases in mixed dimensions.

    abstract::Atomic Fermi gases have been an ideal platform for simulating conventional and engineering exotic physical systems owing to their multiple tunable control parameters. Here we investigate the effects of mixed dimensionality on the superfluid and pairing phenomena of a two-component ultracold atomic Fermi gas with a sho...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-13321-3

    authors: Zhang L,Che Y,Wang J,Chen Q

    更新日期:2017-10-11 00:00:00

  • Electrophysiology of the rhythmic defecation program in nematode Heterorhabditis megidis.

    abstract::The nervous system controls most rhythmic behaviors, with a remarkable exception. In Caenorhabditis elegans periodic defecation rhythm does not appear to involve the nervous system. Such oscillations are studied in detail with genetic and molecular biology tools. The small size of C. elegans cells impairs the use of s...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-18118-y

    authors: Kuznetsov VP,Slivko-Koltchik GA,Voronov DA,Panchin YV

    更新日期:2017-12-19 00:00:00

  • Minicollagen cysteine-rich domains encode distinct modes of polymerization to form stable nematocyst capsules.

    abstract::The stinging capsules of cnidarians, nematocysts, function as harpoon-like organelles with unusual biomechanical properties. The nanosecond discharge of the nematocyst requires a dense protein network of the capsule structure withstanding an internal pressure of up to 150 bar. Main components of the capsule are short ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep25709

    authors: Tursch A,Mercadante D,Tennigkeit J,Gräter F,Özbek S

    更新日期:2016-05-11 00:00:00

  • Manipulating size of Li3V2(PO4)3 with reduced graphene oxide: towards high-performance composite cathode for lithium ion batteries.

    abstract::Lithium vanadium phosphate (Li3V2(PO4)3, LVP)/reduced graphene oxide (rGO) composite is prepared with a rheological method followed by heat treatment. The size and interface of LVP particles, two important merits for a cathode material, can be effectively tuned by the rGO in the composite, which plays as surfactant to...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05768

    authors: Zhu X,Yan Z,Wu W,Zeng W,Du Y,Zhong Y,Zhai H,Ji H,Zhu Y

    更新日期:2014-08-29 00:00:00