The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform

Li Shen - One of the best experts on this subject based on the ideXlab platform.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Kun Zhang, Dinh Diep, Ana C Dalessio, Holim Fung, Yi Zhang
    Abstract:

    TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg-deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Hao Wu, Dinh Diep, Ana C Dalessio, Holim Fung, Kun Zhang
    Abstract:

    Summary TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg -deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

Ana C Dalessio - One of the best experts on this subject based on the ideXlab platform.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Kun Zhang, Dinh Diep, Ana C Dalessio, Holim Fung, Yi Zhang
    Abstract:

    TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg-deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Hao Wu, Dinh Diep, Ana C Dalessio, Holim Fung, Kun Zhang
    Abstract:

    Summary TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg -deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

Shinpei Yamaguchi - One of the best experts on this subject based on the ideXlab platform.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Kun Zhang, Dinh Diep, Ana C Dalessio, Holim Fung, Yi Zhang
    Abstract:

    TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg-deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Hao Wu, Dinh Diep, Ana C Dalessio, Holim Fung, Kun Zhang
    Abstract:

    Summary TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg -deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

Paul J Campagnola - One of the best experts on this subject based on the ideXlab platform.

  • optical properties of mutant versus Wild Type Mouse skin measured by reflectance mode confocal scanning laser microscopy rcslm
    Journal of Biomedical Optics, 2008
    Co-Authors: Ravikant Samatham, Steven L Jacques, Paul J Campagnola
    Abstract:

    Separation of the two optical scattering properties, the scat- tering coefficient s and the anisotropy of scattering g, has been experimentally difficult in tissues. A new method for measuring these properties in tissues uses reflectance-mode confocal scanning laser microscopy rCSLM. Experimentally, the focus at depth z is scanned down into the tissue. The measured data is the exponential decay of the confocal reflectance signal as a function of the depth of the focal volume, Rz= expz, summarized as a local reflectivity and an exponential decay constant . The and map uniquely into the s and g of the tissue. The method was applied to three Mouse skin tissues: one Wild-Type wt/wt, one heterozygous mutant oim/ wt, and one homozygous mutant oim/oim, where oim indicates the mutation for osteogenesis imperfecta, a bone disease that affects Type I collagen structure. The mutation affects the collagen fibrils of the skin and the assembly of collagen fiber bundles. The anisotropy of scattering g at 488 nm wavelength decreased from 0.81 to 0.46 with the added mutant allele. There was a slight increase in the scattering coefficient s with the mutation from 74 to 94 cm 1 . The decrease in g toward more isotropic scattering is likely due to the failure of the mutant fibrils to assemble into the larger collagen fiber bundles that yield forward scattering. © 2008 Society of Photo-Optical Instrumentation Engineers. DOI: 10.1117/1.2953195

  • optical properties of mutant versus Wild Type Mouse skin measured by reflectance mode confocal scanning laser microscopy rcslm
    Journal of Biomedical Optics, 2008
    Co-Authors: Ravikant Samatham, Steven L Jacques, Paul J Campagnola
    Abstract:

    Separation of the two optical scattering properties, the scattering coefficient (mu(s)) and the anisotropy of scattering (g), has been experimentally difficult in tissues. A new method for measuring these properties in tissues uses reflectance-mode confocal scanning laser microscopy (rCSLM). Experimentally, the focus at depth z is scanned down into the tissue. The measured data is the exponential decay of the confocal reflectance signal as a function of the depth of the focal volume, R(z)=rho exp(-muz), summarized as a local reflectivity (rho) and an exponential decay constant (mu). The rho and mu map uniquely into the mu(s) and g of the tissue. The method was applied to three Mouse skin tissues: one Wild-Type (wt/wt), one heterozygous mutant (oim/wt), and one homozygous mutant (oim/oim), where oim indicates the mutation for osteogenesis imperfecta, a bone disease that affects Type I collagen structure. The mutation affects the collagen fibrils of the skin and the assembly of collagen fiber bundles. The anisotropy of scattering (g) at 488 nm wavelength decreased from 0.81 to 0.46 with the added mutant allele. There was a slight increase in the scattering coefficient (mu(s)) with the mutation from 74 to 94 cm(-1). The decrease in g (toward more isotropic scattering) is likely due to the failure of the mutant fibrils to assemble into the larger collagen fiber bundles that yield forward scattering.

Kun Zhang - One of the best experts on this subject based on the ideXlab platform.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Kun Zhang, Dinh Diep, Ana C Dalessio, Holim Fung, Yi Zhang
    Abstract:

    TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg-deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.

  • genome wide analysis reveals tet and tdg dependent 5 methylcytosine oxidation dynamics
    Cell, 2013
    Co-Authors: Li Shen, Shinpei Yamaguchi, Hao Wu, Dinh Diep, Ana C Dalessio, Holim Fung, Kun Zhang
    Abstract:

    Summary TET dioxygenases successively oxidize 5-methylcytosine (5mC) in mammalian genomes to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC/5caC can be excised and repaired to regenerate unmodified cytosines by thymine-DNA glycosylase (TDG) and base excision repair (BER) pathway, but it is unclear to what extent and at which part of the genome this active demethylation process takes place. Here, we have generated genome-wide distribution maps of 5hmC/5fC/5caC using modification-specific antibodies in Wild-Type and Tdg -deficient Mouse embryonic stem cells (ESCs). In Wild-Type Mouse ESCs, 5fC/5caC accumulates to detectable levels at major satellite repeats but not at nonrepetitive loci. In contrast, Tdg depletion in Mouse ESCs causes marked accumulation of 5fC and 5caC at a large number of proximal and distal gene regulatory elements. Thus, these results reveal the genome-wide view of iterative 5mC oxidation dynamics and indicate that TET/TDG-dependent active DNA demethylation process occurs extensively in the mammalian genome.