Differential landscape of non-CpG methylation in embryonic stem cells and neurons caused by DNMT3s.

Abstract:

:Methylated non-CpGs (mCpH; H means A, C, and T) have emerged as key epigenetic marks in mammalian embryonic stem cells (ESCs) and neurons, regulating cell type-specific functions. In these two cell types, mCpHs show distinct motifs and correlations to transcription that could be a key in understanding the cell type-specific regulations. Thus, we attempted to uncover the underlying mechanism of the differences in ESCs and neurons by conducting a comprehensive analysis of public whole genome bisulfite sequencing data. Remarkably, there were cell type-specific mCpH patterns around methylated CpGs (mCpGs), resulted from preferential methylation at different contexts by DNA methyltransferase (DNMT) 3a and 3b. These DNMTs are differentially expressed in ESCs and brain tissues, resulting in distinct mCpH motifs in these two cell types. Furthermore, in ESCs, DNMT3b interacts with histone H3 tri-methylated at lysine 36 (H3K36me3), resulting in hyper-methylation at CpHs upon actively transcribed genes, including those involved in embryo development. Based on the results, we propose a model to explain the differential establishment of mCpHs in ESCs and neurons, providing insights into the mechanism underlying cell type-specific formation and function of mCpHs.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Lee JH,Park SJ,Nakai K

doi

10.1038/s41598-017-11800-1

subject

Has Abstract

pub_date

2017-09-12 00:00:00

pages

11295

issue

1

issn

2045-2322

pii

10.1038/s41598-017-11800-1

journal_volume

7

pub_type

杂志文章
  • Non-linear optical flow cytometry using a scanned, Bessel beam light-sheet.

    abstract::Modern flow cytometry instruments have become vital tools for high-throughput analysis of single cells. However, as issues with the cellular labeling techniques often used in flow cytometry have become more of a concern, the development of label-free modalities for cellular analysis is increasingly desired. Non-linear...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10751

    authors: Collier BB,Awasthi S,Lieu DK,Chan JW

    更新日期:2015-05-29 00:00:00

  • The Us2 Gene Product of Herpes Simplex Virus 2 modulates NF-κB activation by targeting TAK1.

    abstract::HSV-2 is one of the most common sexually transmitted pathogens worldwide and HSV-2 infection triggers cytokine and chemokine production. However, little is known about which HSV-2 genes engage in the regulation of NF-κB signaling and what mechanisms are involved. In a screen of the unique short (Us) regions of HSV-2, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08856-4

    authors: Lu X,Huang C,Zhang Y,Lin Y,Wang X,Li Q,Liu S,Tang J,Zhou L

    更新日期:2017-08-21 00:00:00

  • Structural and mechanistic divergence of the small (p)ppGpp synthetases RelP and RelQ.

    abstract::The nutritional alarmones ppGpp and pppGpp (collectively: (p)ppGpp) are nucleotide-based second messengers enabling bacteria to respond to environmental and stress conditions. Several bacterial species contain two highly homologous (p)ppGpp synthetases named RelP (SAS2, YwaC) and RelQ (SAS1, YjbM). It is established t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20634-4

    authors: Steinchen W,Vogt MS,Altegoer F,Giammarinaro PI,Horvatek P,Wolz C,Bange G

    更新日期:2018-02-01 00:00:00

  • Modality-specific improvements in sensory processing among baseball players.

    abstract::Long-term skills training is known to induce neuroplastic alterations, but it is still debated whether these changes are always modality-specific or can be supramodal components. To address this issue, we compared finger-targeted somatosensory-evoked and auditory-evoked potentials under both Go (response) and Nogo (re...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-021-81852-x

    authors: Yamashiro K,Yamazaki Y,Siiya K,Ikarashi K,Baba Y,Otsuru N,Onishi H,Sato D

    更新日期:2021-01-26 00:00:00

  • Influence of electric current pulses on the solidification of Cu-Bi-Sn immiscible alloys.

    abstract::Continuous solidification experiments were carried out with Cu-Bi-Sn alloys under the effects of Electric Current Pulses (ECPs). A model describing the microstructure evolution was developed. The formation of the microstructure in the continuously solidified alloys was calculated. The calculations demonstrated that EC...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep12680

    authors: Hongxiang J,Jie H,Jiuzhou Z

    更新日期:2015-07-31 00:00:00

  • Nanoscopic X-ray tomography for correlative microscopy of a small meiofaunal sea-cucumber.

    abstract::In the field of correlative microscopy, light and electron microscopy form a powerful combination for morphological analyses in zoology. Due to sample thickness limitations, these imaging techniques often require sectioning to investigate small animals and thereby suffer from various artefacts. A recently introduced n...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60977-5

    authors: Ferstl S,Schwaha T,Ruthensteiner B,Hehn L,Allner S,Müller M,Dierolf M,Achterhold K,Pfeiffer F

    更新日期:2020-03-03 00:00:00

  • Reversal of aberrant cancer methylome and transcriptome upon direct reprogramming of lung cancer cells.

    abstract::Recent reports on direct reprogramming of cancer cells (iPCs) which results in reduced tumorigenic potential has attributed the importance of epigenetics in tumorigenesis, but lacked genome-wide analysis. Here we describe successful generation of iPCs from non-small cell lung cancer (NSCLC) cell lines. Following repro...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep00592

    authors: Mahalingam D,Kong CM,Lai J,Tay LL,Yang H,Wang X

    更新日期:2012-01-01 00:00:00

  • Sodium-hydrogen exchanger 6 (NHE6) deficiency leads to hearing loss, via reduced endosomal signalling through the BDNF/Trk pathway.

    abstract::Acid-base homeostasis is critical for normal growth, development, and hearing function. The sodium-hydrogen exchanger 6 (NHE6), a protein mainly expressed in early and recycling endosomes, plays an important role in regulating organellar pH. Mutations in NHE6 cause complex, slowly progressive neurodegeneration. Little...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60262-5

    authors: Kucharava K,Brand Y,Albano G,Sekulic-Jablanovic M,Glutz A,Xian X,Herz J,Bodmer D,Fuster DG,Petkovic V

    更新日期:2020-02-27 00:00:00

  • Neurodevelopment and asymmetry of auditory-related responses to repetitive syllabic stimuli in preterm neonates based on frequency-domain analysis.

    abstract::Sensory development of the human brain begins prenatally, allowing cortical auditory responses to be recorded at an early age in preterm infants. Despite several studies focusing on the temporal characteristics of preterm infants' cortical responses, few have been conducted on frequency analysis of these responses. In...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-47064-0

    authors: Daneshvarfard F,Abrishami Moghaddam H,Dehaene-Lambertz G,Kongolo G,Wallois F,Mahmoudzadeh M

    更新日期:2019-07-23 00:00:00

  • High-energy spin fluctuation in low-Tc iron-based superconductor LaFePO0.9.

    abstract::Spin fluctuations are widely believed to play an important role in the superconducting mechanisms of unconventional high temperature superconductors. Spin fluctuations have been observed in iron-based superconductors as well. However, in some iron-based superconductors such as LaFePO0.9, they have not been observed by...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-33878-x

    authors: Ishikado M,Shamoto SI,Kodama K,Kajimoto R,Nakamura M,Hong T,Mutka H

    更新日期:2018-11-05 00:00:00

  • Association of circulating miR-20a, miR-27a, and miR-126 with non-alcoholic fatty liver disease in general population.

    abstract::Non-alcoholic fatty liver disease (NAFLD) is closely associated with obesity, metabolic syndrome, and type II diabetes mellitus. Recently, circulating microRNAs (miRNAs) have been proposed as useful disease biomarkers. We examined whether circulating miRNAs, such as miR-20a, miR-27a, and miR-126, were useful biomarker...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55076-z

    authors: Ando Y,Yamazaki M,Yamada H,Munetsuna E,Fujii R,Mizuno G,Ichino N,Osakabe K,Sugimoto K,Ishikawa H,Ohashi K,Teradaira R,Ohta Y,Hamajima N,Hashimoto S,Suzuki K

    更新日期:2019-12-11 00:00:00

  • Tmc2 expression partially restores auditory function in a mouse model of DFNB7/B11 deafness caused by loss of Tmc1 function.

    abstract::Mouse Tmc1 and Tmc2 are required for sensory transduction in cochlear and vestibular hair cells. Homozygous Tmc1∆/∆ mice are deaf, Tmc2∆/∆ mice have normal hearing, and double homozygous Tmc1∆/∆; Tmc2∆/∆ mice have deafness and profound vestibular dysfunction. These phenotypes are consistent with their different spatio...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-29709-8

    authors: Nakanishi H,Kurima K,Pan B,Wangemann P,Fitzgerald TS,Géléoc GS,Holt JR,Griffith AJ

    更新日期:2018-08-14 00:00:00

  • Understanding non-linear effects from Hill-type dynamics with application to decoding of p53 signaling.

    abstract::Analytical equations are derived depicting four possible scenarios resulting from pulsed signaling of a system subject to Hill-type dynamics. Pulsed Hill-type dynamics involves the binding of multiple signal molecules to a receptor and occurs e.g., when transcription factor p53 orchestrates cancer prevention, during c...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-20466-2

    authors: Shi X,Reimers JR

    更新日期:2018-02-01 00:00:00

  • Cell-permeable capsids as universal antigen carrier for the induction of an antigen-specific CD8+ T-cell response.

    abstract::Vaccine platforms that can be flexibly loaded with antigens can contribute to decrease response time to emerging infections. For many pathogens and chronic infections, induction of a robust cytotoxic T lymphocytes-mediated response is desirable to control infection. Antigen delivery into the cytoplasm of antigen prese...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08787-0

    authors: Akhras S,Toda M,Boller K,Himmelsbach K,Elgner F,Biehl M,Scheurer S,Gratz M,Vieths S,Hildt E

    更新日期:2017-08-29 00:00:00

  • An extract from Taxodium distichum targets hemagglutinin- and neuraminidase-related activities of influenza virus in vitro.

    abstract::Influenza virus remains an emerging virus and causes pandemics with high levels of fatality. After screening different plant extracts with potential anti-influenza activity, a water extract of Taxodium distichum stems (TDSWex) showed excellent activity against influenza viruses. The EC50 of TDSWex was 0.051 ± 0.024 mg...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36015

    authors: Hsieh CF,Chen YL,Lin CF,Ho JY,Huang CH,Chiu CH,Hsieh PW,Horng JT

    更新日期:2016-10-31 00:00:00

  • De Novo Transcriptome Assembly and Functional Annotation in Five Species of Bats.

    abstract::High-throughput RNA sequencing is a powerful tool that allows us to perform gene prediction and analyze tissue-specific overexpression of genes, but also at species level comparisons can be performed, although in a more restricted manner. In the present study complete liver transcriptomes of five tropical bat species ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-42560-9

    authors: Moreno-Santillán DD,Machain-Williams C,Hernández-Montes G,Ortega J

    更新日期:2019-04-17 00:00:00

  • Membrane directed expression in Escherichia coli of BBA57 and other virulence factors from the Lyme disease agent Borrelia burgdorferi.

    abstract::Membrane-embedded proteins are critical to the establishment, survival and persistence in the host of the Lyme disease bacterium Borrelia burgdorferi (Bb), but to date, there are no solved structures of transmembrane proteins representing these attractive therapeutic targets. All available structures from the genus Bo...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-53830-x

    authors: Robertson KE,Truong CD,Craciunescu FM,Yang JH,Chiu PL,Fromme P,Hansen DT

    更新日期:2019-11-26 00:00:00

  • Differences in the diagnosis and management of pyriform sinus fistula between newborns and children.

    abstract::Pyriform sinus fistula (PSF) is a rare congenital entity. We hypothesized that clinical features, diagnosis and treatment may differ between newborns and children. 190 patients diagnosed with PSF were divided into two groups: neonatal (n = 15) and childhood (n = 175). The medical records including demographic and clin...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-55050-9

    authors: Sheng Q,Lv Z,Xu W,Liu J

    更新日期:2019-12-06 00:00:00

  • Electron cyclotron motion excited surface plasmon and radiation with orbital angular momentum on a semiconductor thin film.

    abstract::In this work, surface plasmons (SPs) on a germanium (Ge) thin film in terahertz (THz) region that are excited by electron cyclotron motion (ECM) and the subsequent SP emission (SPE) by adding Ge gratings on the film are explored by finite-difference time-domain (FDTD) and particle-in-cell FDTD (PIC-FDTD) simulations. ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-73725-6

    authors: Lan YC,Shen CH,Chen CM

    更新日期:2020-10-07 00:00:00

  • Generation of Non-aliased Two-dimensional Acoustic Vortex with Enclosed Metasurface.

    abstract::Two-dimensional (2D) acoustic vortex allows new physics and applications different from three-dimensional counterparts, yet existing mechanisms usually have to rely on active array composed of transducers which may result in complexity, high cost and, in particular, undesired spatial aliasing effect. We propose to gen...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60836-3

    authors: Liu JJ,Liang B,Yang J,Yang J,Cheng JC

    更新日期:2020-03-02 00:00:00

  • Author Correction: Nitric oxide mediated inhibition of antigen presentation from DCs to CD4+ T cells in cancer and measurement of STAT1 nitration.

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

    journal_title:Scientific reports

    pub_type: 已发布勘误

    doi:10.1038/s41598-018-21306-z

    authors: Markowitz J,Wang J,Vangundy Z,You J,Yildiz V,Yu L,Foote IP,Branson OE,Stiff AR,Brooks TR,Biesiadecki B,Olencki T,Tridandapani S,Freitas MA,Papenfuss T,Phelps MA,Carson WE

    更新日期:2018-03-06 00:00:00

  • Prevalent metabolic derangement and severe thrombocytopenia in ABO-incompatible liver recipients with pre-transplant plasma exchange.

    abstract::Desensitisation with therapeutic plasma exchange (TPE) is essential for ABO-incompatible (ABO-I) liver transplants (LTs). However, excessive citrate load and coagulation disturbances after TPE have been poorly studied, in particular in cirrhotic patients with hypocapnic alkalosis, metabolic compensation and electrolyt...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-24887-x

    authors: Kwon HM,Jun IG,Lee J,Moon YJ,Jung KW,Jeong HW,Park YS,Song JG,Hwang GS

    更新日期:2018-04-27 00:00:00

  • Internal epitope tagging informed by relative lack of sequence conservation.

    abstract::Many experimental techniques rely on specific recognition and stringent binding of proteins by antibodies. This can readily be achieved by introducing an epitope tag. We employed an approach that uses a relative lack of evolutionary conservation to inform epitope tag site selection, followed by integration of the tag-...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36986

    authors: Burg L,Zhang K,Bonawitz T,Grajevskaja V,Bellipanni G,Waring R,Balciunas D

    更新日期:2016-11-28 00:00:00

  • Analogue Orientation Control of a Carbon Fibre in a Nematic Liquid Crystal.

    abstract::A carbon fibre is a rod-like microstructure, the longitudinal axis of which is aligned with the orientation of the director in a nematic liquid crystal. A nematic liquid crystal with negative dielectric anisotropy is mixed with carbon fibres. By applying an electric field perpendicular to the director, the carbon fibr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-56594-6

    authors: Lee JY,Lev B,Kim JH

    更新日期:2019-12-27 00:00:00

  • Single-Crystal X-ray Structures of conductive π-Stacking Dimers of Tetrakis(alkylthio)benzene Radical Cations.

    abstract::Salts containing radical cations of 1,2,4,5-tetrakis(isopropylthio)benzene (TPB) and 1,2,4,5-tetrakis(ethylthio) benzene (TEB) have been successfully synthesized with . These newly synthesized salts have been characterized by UV-Vis absorption, EPR spectroscopy, conductivity measurement, single crystal X-ray diffracti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep29314

    authors: Chen X,Gao F,Yang W

    更新日期:2016-07-11 00:00:00

  • Extended Bose-Hubbard Model with Cavity-Mediated Infinite-Range Interactions at Finite Temperatures.

    abstract::We consider the finite-temperature properties of the extended Bose-Hubbard model realized recently in an ETH experiment [Nature 532, 476 (2016)]. Competing short- and global-range interactions accommodate fascinating collective phenomena. We formulate a self-consistent mean-field theory to describe the behaviors of th...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-66054-1

    authors: Chen HJ,Yu YQ,Zheng DC,Liao R

    更新日期:2020-06-03 00:00:00

  • Discovery and genetic characterization of diverse smacoviruses in Zambian non-human primates.

    abstract::The Smacoviridae has recently been classified as a family of small circular single-stranded DNA viruses. An increasing number of smacovirus genomes have been identified exclusively in faecal matter of various vertebrate species and from insect body parts. However, the genetic diversity and host range of smacoviruses r...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-41358-z

    authors: Anindita PD,Sasaki M,Gonzalez G,Phongphaew W,Carr M,Hang'ombe BM,Mweene AS,Ito K,Orba Y,Sawa H

    更新日期:2019-04-08 00:00:00

  • Rotating edge-field driven processing of chiral spin textures in racetrack devices.

    abstract::Topologically distinct magnetic structures like skyrmions, domain walls, and the uniformly magnetized state have multiple applications in logic devices, sensors, and as bits of information. One of the most promising concepts for applying these bits is the racetrack architecture controlled by electric currents or magne...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-77337-y

    authors: Schäffer AF,Siegl P,Stier M,Posske T,Berakdar J,Thorwart M,Wiesendanger R,Vedmedenko EY

    更新日期:2020-11-23 00:00:00

  • Transient increase of interleukin-1β after prolonged febrile seizures promotes adult epileptogenesis through long-lasting upregulating endocannabinoid signaling.

    abstract::It remains unclear how infantile febrile seizures (FS) enhance adult seizure susceptibility. Here we showed that the transient increase of interleukin-1β (IL-1β) after prolonged FS promoted adult seizure susceptibility, which was blocked by interleukin-1 receptor antagonist (IL-1Ra) within a critical time window. Post...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep21931

    authors: Feng B,Tang Y,Chen B,Xu C,Wang Y,Dai Y,Wu D,Zhu J,Wang S,Zhou Y,Shi L,Hu W,Zhang X,Chen Z

    更新日期:2016-02-23 00:00:00

  • Decreased temperature variance associated with biotic composition enhances coastal shrub encroachment.

    abstract::Regime shift from grasslands to shrub-dominated landscapes occur worldwide driven by altered land-use and climate change, affecting landscape function, biodiversity, and productivity. Warming winter temperatures are a main driver of expansion of the native, evergreen shrub, Morella cerifera, in coastal landscapes. Shr...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-65161-3

    authors: Wood LK,Hays S,Zinnert JC

    更新日期:2020-05-19 00:00:00