DNA damage and Repair Modify DNA methylation and Chromatin Domain of the Targeted Locus: Mechanism of allele methylation polymorphism.

Abstract:

:We characterize the changes in chromatin structure, DNA methylation and transcription during and after homologous DNA repair (HR). We find that HR modifies the DNA methylation pattern of the repaired segment. HR also alters local histone H3 methylation as well chromatin structure by inducing DNA-chromatin loops connecting the 5' and 3' ends of the repaired gene. During a two-week period after repair, transcription-associated demethylation promoted by Base Excision Repair enzymes further modifies methylation of the repaired DNA. Subsequently, the repaired genes display stable but diverse methylation profiles. These profiles govern the levels of expression in each clone. Our data argue that DNA methylation and chromatin remodelling induced by HR may be a source of permanent variation of gene expression in somatic cells.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Russo G,Landi R,Pezone A,Morano A,Zuchegna C,Romano A,Muller MT,Gottesman ME,Porcellini A,Avvedimento EV

doi

10.1038/srep33222

subject

Has Abstract

pub_date

2016-09-15 00:00:00

pages

33222

issn

2045-2322

pii

srep33222

journal_volume

6

pub_type

杂志文章
  • Regulatory Crosstalk of Doxorubicin, Estradiol and TNFα Combined Treatment in Breast Cancer-derived Cell Lines.

    abstract::We present a new model of ESR1 network regulation based on analysis of Doxorubicin, Estradiol, and TNFα combination treatment in MCF-7. We used Doxorubicin as a therapeutic agent, TNFα as marker and mediator of an inflammatory microenvironment and 17β-Estradiol (E2) as an agonist of Estrogen Receptors, known predispos...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-51349-9

    authors: Nassiri I,Inga A,Meškytė EM,Alessandrini F,Ciribilli Y,Priami C

    更新日期:2019-10-23 00:00:00

  • Quantum-enhanced absorption refrigerators.

    abstract::Thermodynamics is a branch of science blessed by an unparalleled combination of generality of scope and formal simplicity. Based on few natural assumptions together with the four laws, it sets the boundaries between possible and impossible in macroscopic aggregates of matter. This triggered groundbreaking achievements...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep03949

    authors: Correa LA,Palao JP,Alonso D,Adesso G

    更新日期:2014-02-04 00:00:00

  • Quantifying the Pathway and Predicting Spontaneous Emulsification during Material Exchange in a Two Phase Liquid System.

    abstract::Kinetic restriction of a thermodynamically favourable equilibrium is a common theme in materials processing. The interfacial instability in systems where rate of material exchange is far greater than the mass transfer through respective bulk phases is of specific interest when tracking the transient interfacial area, ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-14638-9

    authors: Spooner S,Rahnama A,Warnett JM,Williams MA,Li Z,Sridhar S

    更新日期:2017-10-30 00:00:00

  • Replica Symmetry Breaking in a Weakly Scattering Optofluidic Random Laser.

    abstract::We report the observation of replica symmetry breaking (RSB) in a weakly scattering optofluidic random laser (ORL). Coherent random lasing is indicated by the presence of narrow peaks rising out of the spectral background. This coherence helps to identify a random laser threshold, which is expected to be gradual with ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-59575-2

    authors: Sarkar A,Bhaktha BNS,Andreasen J

    更新日期:2020-02-14 00:00:00

  • Down-regulation of nuclear HMGB1 reduces ischemia-induced HMGB1 translocation and release and protects against liver ischemia-reperfusion injury.

    abstract::Hepatocyte-specific HMGB1 deletion has been found to worsen the injury and inflammation in liver ischemia-reperfusion injury (IRI), highlighting a role for intracellular HMGB1 in cellular protection. Down-regulation of nuclear HMGB1 by small interfering RNA (siRNA) might not only decrease its injurious extracellular r...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep46272

    authors: Zhao G,Fu C,Wang L,Zhu L,Yan Y,Xiang Y,Zheng F,Gong F,Chen S,Chen G

    更新日期:2017-04-06 00:00:00

  • Cost-effectiveness Analysis of Fluorouracil, Leucovorin, and Irinotecan versus Epirubicin, Cisplatin, and Capecitabine in Patients with Advanced Gastric Adenocarcinoma.

    abstract::No standard treatment has been accepted widely for the first-/second-line therapy for advanced gastric cancer (AGC). The current study aimed to determine a preferred strategy between FOLFIRI (fluorouracil, leucovorin, and irinotecan) and ECX (epirubicin, cisplatin,and capecitabine) for AGC from the cost-effectiveness ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep36060

    authors: Wen F,Zheng H,Wu Y,Wheeler J,Zeng X,Fu P,Li Q

    更新日期:2016-11-08 00:00:00

  • Stem cells from the dental apical papilla in extracellular matrix hydrogels mitigate inflammation of microglial cells.

    abstract::After spinal cord injury (SCI) chronic inflammation hampers regeneration. Influencing the local microenvironment after SCI may provide a strategy to modulate inflammation and the immune response. The objectives of this work were to determine whether bone or spinal cord derived ECM hydrogels can deliver human mesenchym...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-50367-x

    authors: Tatic N,Rose FRAJ,des Rieux A,White LJ

    更新日期:2019-09-30 00:00:00

  • The formation of chromatin domains involves a primary step based on the 3-D structure of DNA.

    abstract::The general model presented here for the formation of chromatin domains, LADs and TADs, is primarily based on the 3-D structures of the corresponding DNA sequences, the GC-poor and GC-rich isochores. Indeed, the low-heterogeneity GC-poor isochores locally are intrinsically stiff and curved because of the presence of i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-35851-0

    authors: Bernardi G

    更新日期:2018-12-13 00:00:00

  • The Arabidopsis defensin gene, AtPDF1.1, mediates defence against Pectobacterium carotovorum subsp. carotovorum via an iron-withholding defence system.

    abstract::Plant defensins (PDFs) are cysteine-rich peptides that have a range of biological functions, including defence against fungal pathogens. However, little is known about their role in defence against bacteria. In this study, we showed that the protein encoded by ARABIDOPSIS THALIANA PLANT DEFENSIN TYPE 1.1 (AtPDF1.1) is...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08497-7

    authors: Hsiao PY,Cheng CP,Koh KW,Chan MT

    更新日期:2017-08-23 00:00:00

  • Submicron-scale broadband polarization beam splitter using CMOS-compatible materials.

    abstract::We propose a polarization beam splitter (PBS) with a footprint of only 600 × 790 nm2 operating at a wavelength of λ = 1550 nm, which is the smallest PBS ever demonstrated. This device uses CMOS-compatible materials, namely, silicon and silica. The present PBS comprises two Si waveguides with different geometrical aspe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-05019-3

    authors: Lai MS,Huang CC

    更新日期:2017-07-03 00:00:00

  • A Fluorescent Tile DNA Diagnocode System for In Situ Rapid and Selective Diagnosis of Cytosolic RNA Cancer Markers.

    abstract::Accurate cancer diagnosis often requires extraction and purification of genetic materials from cells, and sophisticated instrumentations that follow. Otherwise in order to directly treat the diagnostic materials to cells, multiple steps to optimize dose concentration and treatment time are necessary due to diversity i...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep18497

    authors: Park KS,Shin SW,Jang MS,Shin W,Yang K,Min J,Cho SW,Oh BK,Bae JW,Jung S,Choi JW,Um SH

    更新日期:2015-12-18 00:00:00

  • Comparative antibacterial activities of neutral electrolyzed oxidizing water and other chlorine-based sanitizers.

    abstract::There is increasing demand for safe and effective sanitizers for irrigation water disinfection to prevent transmission of foodborne pathogens to fresh produce. Here we compared the efficacy of pH-neutral electrolyzed oxidizing water (EOW), sodium hypochlorite (NaClO) and chlorine dioxide (ClO2) against single and mixe...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-56248-7

    authors: Ogunniyi AD,Dandie CE,Ferro S,Hall B,Drigo B,Brunetti G,Venter H,Myers B,Deo P,Donner E,Lombi E

    更新日期:2019-12-27 00:00:00

  • Lipid-II Independent Antimicrobial Mechanism of Nisin Depends On Its Crowding And Degree Of Oligomerization.

    abstract::Nisin inhibits bacterial growth by generating pores in cell membrane and interrupting cell-wall biosynthesis through specific lipid II interaction. However, the role of the hinge region and C-terminus residues of the peptide in antibacterial action of nisin is largely unknown. Here, using molecular dynamics simulation...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep37908

    authors: Prince A,Sandhu P,Ror P,Dash E,Sharma S,Arakha M,Jha S,Akhter Y,Saleem M

    更新日期:2016-11-29 00:00:00

  • Possible Involvement of F1F0-ATP synthase and Intracellular ATP in Keratinocyte Differentiation in normal skin and skin lesions.

    abstract::The F1F0-ATP synthase, an enzyme complex, is mainly located on the mitochondrial inner membrane or sometimes cytomembrane to generate or hydrolyze ATP, play a role in cell proliferation. This study focused on the role of F1F0-ATP synthase in keratinocyte differentiation, and its relationship with intracellular and ext...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep42672

    authors: Xiaoyun X,Chaofei H,Weiqi Z,Chen C,Lixia L,Queping L,Cong P,Shuang Z,Juan S,Xiang C

    更新日期:2017-02-17 00:00:00

  • High-throughput physical vapour deposition flexible thermoelectric generators.

    abstract::Flexible thermoelectric generators (TEGs) can provide uninterrupted, green energy from body-heat, overcoming bulky battery configurations that limit the wearable-technologies market today. High-throughput production of flexible TEGs is currently dominated by printing techniques, limiting material choices and performan...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-019-41000-y

    authors: Morgan KA,Tang T,Zeimpekis I,Ravagli A,Craig C,Yao J,Feng Z,Yarmolich D,Barker C,Assender H,Hewak DW

    更新日期:2019-03-13 00:00:00

  • Isolation and no-entry marine reserves mitigate anthropogenic impacts on grey reef shark behavior.

    abstract::Reef sharks are vulnerable predators experiencing severe population declines mainly due to overexploitation. However, beyond direct exploitation, human activities can produce indirect or sub-lethal effects such as behavioral alterations. Such alterations are well known for terrestrial fauna but poorly documented for m...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-37145-x

    authors: Juhel JB,Vigliola L,Wantiez L,Letessier TB,Meeuwig JJ,Mouillot D

    更新日期:2019-02-27 00:00:00

  • Strong anisotropy of Dirac cones in SrMnBi2 and CaMnBi2 revealed by angle-resolved photoemission spectroscopy.

    abstract::The Dirac materials, such as graphene and three-dimensional topological insulators, have attracted much attention because they exhibit novel quantum phenomena with their low energy electrons governed by the relativistic Dirac equations. One particular interest is to generate Dirac cone anisotropy so that the electrons...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep05385

    authors: Feng Y,Wang Z,Chen C,Shi Y,Xie Z,Yi H,Liang A,He S,He J,Peng Y,Liu X,Liu Y,Zhao L,Liu G,Dong X,Zhang J,Chen C,Xu Z,Dai X,Fang Z,Zhou XJ

    更新日期:2014-06-20 00:00:00

  • Interference experiment with asymmetric double slit by using 1.2-MV field emission transmission electron microscope.

    abstract::Advanced electron microscopy technologies have made it possible to perform precise double-slit interference experiments. We used a 1.2-MV field emission electron microscope providing coherent electron waves and a direct detection camera system enabling single-electron detections at a sub-second exposure time. We devel...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-19380-4

    authors: Harada K,Akashi T,Niitsu K,Shimada K,Ono YA,Shindo D,Shinada H,Mori S

    更新日期:2018-01-17 00:00:00

  • Chemoprevention of Colonic Aberrant Crypt Foci by Novel Schiff Based Dichlorido(4-Methoxy-2-{[2-(Piperazin-4-Ium-1-Yl)Ethyl]Iminomethyl}Phenolate)Cd Complex in Azoxymethane-Induced Colorectal Cancer in Rats.

    abstract::Schiff-based complexes as a source of cancer chemotherapeutic compounds have been subjected to the variety of anticancer studies. The in-vitro analysis confirmed the CdCl2(C14H21N3O2) complex possess cytotoxicity and apoptosis induction properties in colon cancer cells, so lead to investigate the inhibitory efficiency...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep12379

    authors: Hajrezaie M,Shams K,Moghadamtousi SZ,Karimian H,Hassandarvish P,Emtyazjoo M,Zahedifard M,Majid NA,Mohd Ali H,Abdulla MA

    更新日期:2015-07-23 00:00:00

  • Spectroscopic observation of oxygen dissociation on nitrogen-doped graphene.

    abstract::Carbon nanomaterials' reactivity towards oxygen is very poor, limiting their potential applications. However, nitrogen doping is an established way to introduce active sites that facilitate interaction with gases. This boosts the materials' reactivity for bio-/gas sensing and enhances their catalytic performance for t...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-08651-1

    authors: Scardamaglia M,Susi T,Struzzi C,Snyders R,Di Santo G,Petaccia L,Bittencourt C

    更新日期:2017-08-11 00:00:00

  • Atmospheric Pressure Non-Equilibrium Plasma as a Green Tool to Crosslink Gelatin Nanofibers.

    abstract::Electrospun gelatin nanofibers attract great interest as a natural biomaterial for cartilage and tendon repair despite their high solubility in aqueous solution, which makes them also difficult to crosslink by means of chemical agents. In this work, we explore the efficiency of non-equilibrium atmospheric pressure pla...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep38542

    authors: Liguori A,Bigi A,Colombo V,Focarete ML,Gherardi M,Gualandi C,Oleari MC,Panzavolta S

    更新日期:2016-12-07 00:00:00

  • Hospital-acquired Clostridium difficile infection in Mainland China: A seven-year (2009-2016) retrospective study in a large university hospital.

    abstract::Clostridium difficile infection (CDI) is associated with risk for severe disease and high mortality. Little is known about the extent of hospital-acquired CDI in Mainland China. In this study, we aimed to investigate the annual CDI incidence, bacterial genotypes, risk factors for severe CDI and survival over a 7-year ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-09961-0

    authors: Xu Q,Chen Y,Gu S,Lv T,Zheng B,Shen P,Quan J,Fang Y,Li L

    更新日期:2017-08-29 00:00:00

  • Tailoring Plasmonic Enhanced Upconversion in Single NaYF4:Yb(3+)/Er(3+) Nanocrystals.

    abstract::By using silver nanoplatelets with a widely tunable localized surface plasmon resonance (LSPR), and their corresponding local field enhancement, here we show large manipulation of plasmonic enhanced upconversion in NaYF4:Yb(3+)/Er(3+) nanocrystals at the single particle level. In particular, we show that when the plas...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep10196

    authors: Wang YL,Mohammadi Estakhri N,Johnson A,Li HY,Xu LX,Zhang Z,Alù A,Wang QQ,Shih CK

    更新日期:2015-05-15 00:00:00

  • Cholesterol 25-hydroxylase protects against experimental colitis in mice by modulating epithelial gut barrier function.

    abstract::Cholesterol 25-hydroxylase (CH25H) encodes the enzyme that converts cholesterol to 25-hydroxycholesterol (25-HC). 25-HC has been demonstrated to be involved in the pathogenesis of inflammatory bowel disease. However, the role of CH25H in experimental colitis remains unknown. Dextran sulfate sodium (DSS)-induced coliti...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-71198-1

    authors: Sheng N,Ma Z,Zhou Y,Xu J,Gao Y,Fu XY

    更新日期:2020-08-28 00:00:00

  • Nintedanib inhibits growth of human prostate carcinoma cells by modulating both cell cycle and angiogenesis regulators.

    abstract::Prostate cancer (PCa) is the most common malignancy and second leading cause of cancer-related deaths in American men. Proliferating cells have higher need for nutrients and oxygen, triggering angiogenesis that plays a critical role in tumor growth, progression and metastasis. Consequently, immense focus has converged...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-018-27831-1

    authors: da Silva RF,Dhar D,Raina K,Kumar D,Kant R,Cagnon VHA,Agarwal C,Agarwal R

    更新日期:2018-06-22 00:00:00

  • Post-glacial biogeography of trembling aspen inferred from habitat models and genetic variance in quantitative traits.

    abstract::Using species distribution models and information on genetic structure and within-population variance observed in a series of common garden trials, we reconstructed a historical biogeography of trembling aspen in North America. We used an ensemble classifier modelling approach (RandomForest) to reconstruct palaeoclima...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-04871-7

    authors: Ding C,Schreiber SG,Roberts DR,Hamann A,Brouard JS

    更新日期:2017-07-05 00:00:00

  • Identification and comparative analysis of the epidermal differentiation complex in snakes.

    abstract::The epidermis of snakes efficiently protects against dehydration and mechanical stress. However, only few proteins of the epidermal barrier to the environment have so far been identified in snakes. Here, we determined the organization of the Epidermal Differentiation Complex (EDC), a cluster of genes encoding protein ...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep45338

    authors: Holthaus KB,Mlitz V,Strasser B,Tschachler E,Alibardi L,Eckhart L

    更新日期:2017-03-27 00:00:00

  • Pore Structure Changes Occur During CO2 Injection into Carbonate Reservoirs.

    abstract::Observations and modeling studies have shown that during CO2 injection into underground carbonate reservoirs, the dissolution of CO2 into formation water forms acidic brine, leading to fluid-rock interactions that can significantly impact the hydraulic properties of the host formation. However, the impacts of these in...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-020-60247-4

    authors: Seyyedi M,Mahmud HKB,Verrall M,Giwelli A,Esteban L,Ghasemiziarani M,Clennell B

    更新日期:2020-02-27 00:00:00

  • New recombinant cyclohexylamine oxidase variants for deracemization of secondary amines by orthogonally assaying designed mutants with structurally diverse substrates.

    abstract::To further expand the substrate range of the cyclohexylamine oxidase (CHAO) from Brevibacterium oxydans, a library of diverse mutants was created and assayed toward a group of structurally diverse substrates. Among them, mutants T198A and M226A exhibited enhanced activity relative to wt CHAO for most (S)-enantiomers o...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/srep24973

    authors: Li G,Yao P,Cong P,Ren J,Wang L,Feng J,Lau PC,Wu Q,Zhu D

    更新日期:2016-05-03 00:00:00

  • A nucleotide-controlled conformational switch modulates the activity of eukaryotic IMP dehydrogenases.

    abstract::Inosine-5'-monophosphate dehydrogenase (IMPDH) is an essential enzyme for nucleotide metabolism and cell proliferation. Despite IMPDH is the target of drugs with antiviral, immunosuppressive and antitumor activities, its physiological mechanisms of regulation remain largely unknown. Using the enzyme from the industria...

    journal_title:Scientific reports

    pub_type: 杂志文章

    doi:10.1038/s41598-017-02805-x

    authors: Buey RM,Fernández-Justel D,Marcos-Alcalde Í,Winter G,Gómez-Puertas P,de Pereda JM,Luis Revuelta J

    更新日期:2017-06-01 00:00:00