1 to 10 of 16 Results
Jan 14, 2026
Jeltsch, Albert, 2026, "Sequencing data related to Gutekunst et al. "Nucleosome linker DNA methylation by DNMT3A/DNMT3B3 is controlled by nucleosome binding and multimerization of DNMT3 complexes on DNA"", https://doi.org/10.18419/DARUS-5490, DaRUS, V1
Methods DNA libraries for Illumina NGS were prepared with a two-step PCR approach. For this, the Nucleosome 1 - Linker - Nucleosome 2 sequence was split into two amplicons, one comprising the Nucleosome 1 - Linker and the second comprising Linker - Nucleosome 2. For library preparation, 1 μL of bisulfite-converted DNA was amplified in a first PCR r... |
Jeltsch, Albert; Bashtrykov, Pavel, 2025, "NGS data related to Sogl et al. "Systematic analysis of specificities and flanking sequence preferences of bacterial DNA-(cytosine C5)-methyltransferases reveals mechanisms of enzyme- and sequence-specific DNA readout"", https://doi.org/10.18419/DARUS-4515, DaRUS, V1, UNF:6:bSvQoJxvb+T/iyQGPOvTBA== [fileUNF]
Analysis of flanking sequence preference with a randomized substrate and bioinformatic data For analysis of the flanking sequence preference, substrate with different target sites sites in a 9 or 10 bp randomized sequence context were prepared as described (Dukatz, et al. 2020; Dukatz, et al. 2022). Substrate methylation reactions were performed wi... |
Aug 12, 2024
Jeltsch, Albert; Bashtrykov, Pavel; Rajaram, Nivethika, 2024, "NGS data related to Rajaram et al.: Allele specific DNA demethylation ...", https://doi.org/10.18419/DARUS-4230, DaRUS, V2
Method overview To achieve targeted locus and allele-specific DNA demethylation, HEK293 cells were transfected with two plasmids. One plasmid contains, dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter protein. The other plasmid is a multiguide plasmid wi... |
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 Cloning Kit (Stratagene) into a StrataClone Vector Mix amp/kan (Stratagen... |
Jan 12, 2024
Jeltsch, Albert; Bashtrykov, Pavel; Rajaram, Nivethika, 2023, "NGS data related to Rajaram et al.: Development of super-specific epigenome editing by targeted allele-specific DNA methylation", https://doi.org/10.18419/DARUS-3581, DaRUS, V2
Method overview To achieve targeted ASM, transient transfection of the dCas9-10X SunTag-BFP, scFv-DNMT3A-3L-sfGFP, and sgRNA-DsRed plasmids was performed in HEK293 cells. Control experiments were conducted with a scrambled sgRNA that does not have a binding site in the human genome. Initial studies showed that cells positive for all three plasmids... |
Jan 10, 2024
Jeltsch, Albert; Bashtrykov, Pavel; Albrecht, Claudia, 2024, "NGS data related to Albrecht et al.: Locus specific and stable DNA demethylation at the H19/IGF2 ICR1 by epigenome editing using a dCas9-SunTag system and the catalytic domain of TET1", https://doi.org/10.18419/DARUS-3790, DaRUS, V1
Method overview For targeted DNA demethylation of the H19/IGF2 ICR1, HEK293 cells were transfected with two plasmids, one containing dCas9 fused to a SunTag with five repeats of the GCN4 peptide, separated by 22 aa long linkers, and scFv-fused TET1CD, as well as a GFP reporter protein. The second plasmid encodes five sgRNAs targeting the ICR1 and a... |
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 mutated CXXC domain was taken from Bashtrykov, et al. (2012). Synthesis long... |
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. |
Jeltsch, Albert; Bashtrykov, Pavel; Adam, Sabrina, 2021, "Deep enzymology data related to Adam et al.: Flanking sequences influence the activity of TET1 and TET2 methylcytosine dioxygenases and affect genomic 5hmC patterns", https://doi.org/10.18419/DARUS-2114, DaRUS, V2
Experimental procedures for deep enzymology reactions with randomized substrates: For analysis of flanking sequence preferences of the TET enzymes, a similar approach as described for DNMTs (Emperle et al., 2019; Gao et al., 2020; Adam et al., 2020; Dukatz et al., 2020) was used. Briefly, the following single-stranded oligonucleotides containing a... |
Nov 25, 2021
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 remove residual unbound DNA. Afterwards, DNMT3A2 or DNMT3AC was added to... |
