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1 to 10 of 10 Results
NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons
Mar 4, 2024 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Dossmann, Leonie; Emperle, Max, 2024, "NGS data related to Dossmann et al.: Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons", https://doi.org/10.18419/darus-3386, DaRUS, V1
Cloning and site-directed mutagenesis The gene of the catalytic, C-terminal domain of murine DNMT3C (amino acid residues 439-740 of P0DOY1) was obtained in E. coli codon optimized form from IDT Integrated DNA Technologies. The gene fragment was cloned with the StrataClone PCR Clo...
NGS data related to Adam et al.: On the accuracy of the epigenetic copy machine - comprehensive specificity analysis of the DNMT1 DNA methyltransferase
NGS data related to Adam et al.: On the accuracy of the epigenetic copy machine - comprehensive specificity analysis of the DNMT1 DNA methyltransferase
Apr 27, 2023 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2023, "NGS data related to Adam et al.: On the accuracy of the epigenetic copy machine - comprehensive specificity analysis of the DNMT1 DNA methyltransferase", https://doi.org/10.18419/darus-3334, DaRUS, V2, UNF:6:ERMvcNuV8nq+mI9Q5Xu53A== [fileUNF]
Expression and purification of DNMT1 for biochemical work Full length murine DNMT1 (UniProtKB P13864) was overexpressed and purified as described (Adam, et al. 2020) using the Bac-to-Bac baculovirus expression system (Invitrogen). The expression construct of the DNMT1 with mutate...
NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation
NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation
Sep 27, 2022 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2022, "NGS data related to Dukatz et al.: DNA methyltransferase DNMT3A forms interaction networks with the CpG site and flanking sequence elements for efficient methylation", https://doi.org/10.18419/darus-2993, DaRUS, V1
The naming of the files is described in the Supplemental Tables 1 of the accompanying manuscript.
NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3
Nov 25, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Bröhm, Alexander; Dukatz, Michael; Adam, Sabrina, 2021, "NGS data related to Bröhm et al.: Methylation of recombinant mononucleosomes by DNMT3A demonstrates efficient linker DNA methylation and a role of H3K36me3", https://doi.org/10.18419/darus-1252, DaRUS, V2
Methylation experiments: For the competitive nucleosome methylation experiments, 0.6 pmol of each nucleosome variant were digested with MluI (NEB) for 60 min at 37°C in 10 µL NEB Cutsmart buffer (50 mM KOAc/20 mM Tris-acetate pH 7.9, 10 mM Magnesium Acetate, 100 µg/mL BSA) to rem...
Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"
Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"
Nov 11, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Mack, Alexandra; Emperle, Max, 2021, "Data related to "Preferential interaction of DNMT3A subunits containing the R882H cancer mutation leads to dominant changes of flanking sequence effects"", https://doi.org/10.18419/darus-2231, DaRUS, V1
Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with a distance of 12 base pairs between CpG sites were obtained from IDT. Second strand synthesis was conducted by a primer extension reaction using one univ...
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"
Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"
Apr 12, 2021 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina; Kunert, Stefan, 2021, "Data related to "Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by DNMT3A"", https://doi.org/10.18419/darus-1781, DaRUS, V1
Methylation of substrate libraries Single-stranded DNA oligonucleotides used for generation of double stranded substrates with different distance between CpG sites were obtained from IDT. Sixteen single-stranded oligonucleotides were pooled in equimolar amounts and the second str...
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.
Sep 1, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Dukatz, Michael; Adam, Sabrina, 2020, "Deep enzymology data related to Dukatz et al.: Complex DNA sequence readout mechanisms of the DNMT3B DNA methyltransferase.", https://doi.org/10.18419/darus-815, DaRUS, V3
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards, the DNA w...
Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Emperle, Max; Adam, Sabrina; Dukatz, Michael, 2020, "Deep enzymology data related to Gao et al.: Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms", https://doi.org/10.18419/darus-627, DaRUS, V1
Experimental procedures: Libraries of double stranded DNA substrates with CpG, CpH or CpN sites in randomized sequence context were methlyated by DNMT3A or DNMT3B. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K for 2 hours. Afterwards,...
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2020, "Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation", https://doi.org/10.18419/darus-629, DaRUS, V1
Methylation of long hemimethylated DNA substrates: Methylation of the 349 bp long hemimethylated substrate with DNMT1 was carried out in 1X methylation buffer (100 mM HEPES, 1 mM EDTA, 0.5 mM DTT, 0.1 mg/mL BSA, pH 7.2 with KOH) in the presence of 1 mM AdoMet. For the methylation...
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation
Jan 30, 2020 - Amplicon based bisulfite NGS data
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2020, "Deep enzymology data related to Adam et al.: DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation", https://doi.org/10.18419/darus-628, DaRUS, V1
Methylation of random flank substrates: Libraries of double stranded DNA substrates with unmethylated or hemimethylated CpG sites in randomized sequence context were methlyated by DNMT1. Reactions were stopped by shock freezing in liquid nitrogen, then treated with proteinase K f...
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