Literature DB >> 25753672

Dissecting the behavior and function of MBD3 in DNA methylation homeostasis by single-molecule spectroscopy and microscopy.

Yi Cui1, Joseph Irudayaraj2.   

Abstract

The detailed mechanism for DNA methylation homeostasis relies on an intricate regulatory network with a possible contribution from methyl-CpG-binding domain protein 3 (MBD3). In this study we examine the single-molecule behavior of MBD3 and its functional implication in balancing the activity of DNA methyltransferases (DNMTs). Besides a localization tendency to DNA demethylating sites, MBD3 experiences a concurrent transcription with DNMTs in cell cycle. Fluorescence lifetime correlation spectroscopy (FLCS) and photon counting histogram (PCH) were applied to characterize the chromatin binding kinetics and stoichiometry of MBD3 in different cell phases. In the G1-phase, MBD3, in the context of the Mi-2/NuRD (nucleosome remodeling deacetylase) complex, could adopt a salt-dependent homodimeric association with its target epigenomic loci. Along with cell cycle progression, utilizing fluorescence lifetime imaging microscopy-based Förster resonance energy transfer (FLIM-FRET) we revealed that a proportion of MBD3 and MBD2 would co-localize with DNMT1 during DNA maintenance methylation, providing a proofreading and protective mechanism against a possible excessive methylation by DNMT1. In accordance with our hypothesis, insufficient MBD3 induced by small interfering RNA (siRNA) was found to result in a global DNA hypermethylation as well as increased methylation in the promoter CpG islands (CGIs) of a number of cell cycle related genes.
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Year:  2015        PMID: 25753672      PMCID: PMC4381056          DOI: 10.1093/nar/gkv098

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  62 in total

1.  Maintenance of DNA methylation: Dnmt3b joins the dance.

Authors:  Emma L Walton; Claire Francastel; Guillaume Velasco
Journal:  Epigenetics       Date:  2011-11-01       Impact factor: 4.528

2.  p66Alpha-MBD2 coiled-coil interaction and recruitment of Mi-2 are critical for globin gene silencing by the MBD2-NuRD complex.

Authors:  Merlin Nithya Gnanapragasam; J Neel Scarsdale; Maria L Amaya; Heather D Webb; Megha A Desai; Ninad M Walavalkar; Shou Zhen Wang; Sheng Zu Zhu; Gordon D Ginder; David C Williams
Journal:  Proc Natl Acad Sci U S A       Date:  2011-04-13       Impact factor: 11.205

3.  Proliferating cell nuclear antigen (PCNA) is required for cell cycle-regulated silent chromatin on replicated and nonreplicated genes.

Authors:  Andrew Miller; Jiji Chen; Taichi E Takasuka; Jennifer L Jacobi; Paul D Kaufman; Joseph M K Irudayaraj; Ann L Kirchmaier
Journal:  J Biol Chem       Date:  2010-09-02       Impact factor: 5.157

4.  Genome-wide DNA methylation profiling using Infinium® assay.

Authors:  Marina Bibikova; Jennie Le; Bret Barnes; Shadi Saedinia-Melnyk; Lixin Zhou; Richard Shen; Kevin L Gunderson
Journal:  Epigenomics       Date:  2009-10       Impact factor: 4.778

5.  Mbd3/NURD complex regulates expression of 5-hydroxymethylcytosine marked genes in embryonic stem cells.

Authors:  Ozlem Yildirim; Ruowang Li; Jui-Hung Hung; Poshen B Chen; Xianjun Dong; Ly-Sha Ee; Zhiping Weng; Oliver J Rando; Thomas G Fazzio
Journal:  Cell       Date:  2011-12-23       Impact factor: 41.582

6.  Single molecule in vivo analysis of toll-like receptor 9 and CpG DNA interaction.

Authors:  Jiji Chen; Suman Nag; Pierre-Alexandre Vidi; Joseph Irudayaraj
Journal:  PLoS One       Date:  2011-04-04       Impact factor: 3.240

7.  NuRD-mediated deacetylation of H3K27 facilitates recruitment of Polycomb Repressive Complex 2 to direct gene repression.

Authors:  Nicola Reynolds; Mali Salmon-Divon; Heidi Dvinge; Antony Hynes-Allen; Gayan Balasooriya; Donna Leaford; Axel Behrens; Paul Bertone; Brian Hendrich
Journal:  EMBO J       Date:  2011-12-02       Impact factor: 11.598

8.  Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation.

Authors:  Hideharu Hashimoto; Yiwei Liu; Anup K Upadhyay; Yanqi Chang; Shelley B Howerton; Paula M Vertino; Xing Zhang; Xiaodong Cheng
Journal:  Nucleic Acids Res       Date:  2012-02-22       Impact factor: 16.971

9.  Recognition of methylated DNA through methyl-CpG binding domain proteins.

Authors:  Xueqing Zou; Wen Ma; Ilia A Solov'yov; Christophe Chipot; Klaus Schulten
Journal:  Nucleic Acids Res       Date:  2011-11-22       Impact factor: 16.971

10.  NuRD suppresses pluripotency gene expression to promote transcriptional heterogeneity and lineage commitment.

Authors:  Nicola Reynolds; Paulina Latos; Antony Hynes-Allen; Remco Loos; Donna Leaford; Aoife O'Shaughnessy; Olukunbi Mosaku; Jason Signolet; Philip Brennecke; Tüzer Kalkan; Ita Costello; Peter Humphreys; William Mansfield; Kentaro Nakagawa; John Strouboulis; Axel Behrens; Paul Bertone; Brian Hendrich
Journal:  Cell Stem Cell       Date:  2012-05-04       Impact factor: 24.633

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  18 in total

1.  Chromosome loading of cohesin depends on conserved residues in Scc3.

Authors:  Anjali Pathania; Wenjie Liu; Avi Matityahu; Joseph Irudayaraj; Itay Onn
Journal:  Curr Genet       Date:  2021-01-06       Impact factor: 3.886

2.  Epigenetic Toxicity of Trichloroethylene: A Single-Molecule Perspective.

Authors:  Yi Cui; Samrat Roy Choudhury; Joseph Irudayaraj
Journal:  Toxicol Res (Camb)       Date:  2016-01-27       Impact factor: 3.524

3.  Optical Clearing Delivers Ultrasensitive Hyperspectral Dark-Field Imaging for Single-Cell Evaluation.

Authors:  Yi Cui; Xiaolei Wang; Wen Ren; Jing Liu; Joseph Irudayaraj
Journal:  ACS Nano       Date:  2016-02-24       Impact factor: 15.881

4.  MBD3 mediates epigenetic regulation on EPAS1 promoter in cancer.

Authors:  Jie Cui; Biao Duan; Xuyang Zhao; Yan Chen; Shixun Sun; Wenjie Deng; Yujie Zhang; Jun Du; Yongchang Chen; Luo Gu
Journal:  Tumour Biol       Date:  2016-07-27

5.  Single-Cell Quantification of Cytosine Modifications by Hyperspectral Dark-Field Imaging.

Authors:  Xiaolei Wang; Yi Cui; Joseph Irudayaraj
Journal:  ACS Nano       Date:  2015-11-02       Impact factor: 15.881

6.  Monomeric cohesin state revealed by live-cell single-molecule spectroscopy.

Authors:  Wenjie Liu; Elisheva Biton; Anjali Pathania; Avi Matityahu; Joseph Irudayaraj; Itay Onn
Journal:  EMBO Rep       Date:  2019-12-29       Impact factor: 8.807

7.  The hypomethylating agent Decitabine causes a paradoxical increase in 5-hydroxymethylcytosine in human leukemia cells.

Authors:  Basudev Chowdhury; Andrew McGovern; Yi Cui; Samrat Roy Choudhury; Il-Hoon Cho; Bruce Cooper; Timothy Chevassut; Amy C Lossie; Joseph Irudayaraj
Journal:  Sci Rep       Date:  2015-04-22       Impact factor: 4.379

8.  DNA methylation directs genomic localization of Mbd2 and Mbd3 in embryonic stem cells.

Authors:  Sarah J Hainer; Kurtis N McCannell; Jun Yu; Ly-Sha Ee; Lihua J Zhu; Oliver J Rando; Thomas G Fazzio
Journal:  Elife       Date:  2016-11-16       Impact factor: 8.140

9.  Optogenetic regulation of site-specific subtelomeric DNA methylation.

Authors:  Samrat Roy Choudhury; Yi Cui; Anoop Narayanan; David P Gilley; Nazmul Huda; Chiao-Ling Lo; Feng C Zhou; Dinesh Yernool; Joseph Irudayaraj
Journal:  Oncotarget       Date:  2016-08-02

10.  Oxygen nanobubbles revert hypoxia by methylation programming.

Authors:  Pushpak N Bhandari; Yi Cui; Bennett D Elzey; Craig J Goergen; Christopher M Long; Joseph Irudayaraj
Journal:  Sci Rep       Date:  2017-08-24       Impact factor: 4.379

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