Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

Ravichandran, Mirunalini; Rafalski, Dominik; Davies, Claudia I.; Ortega‐Recalde, Oscar; Nan, Xinsheng; Glanfield, Cassandra R.; Kötter, Annika; Misztal, Katarzyna; Wang, Andrew H.; Wojciechowski, Marek; Rażew, Michał; Mayyas, Issam M; Kardailsky, Olga; Schwartz, Uwe; Zembrzycki, Krzysztof; Morison, Ian M.; Helm, Mark; Weichenhan, Dieter; Jurkowska, Renata Z.; Krueger, Felix; Plass, Christoph; Zacharias, Martin; Bochtler, Matthias; Hore, Timothy A.; Jurkowski, Tomasz P.

doi:10.1126/sciadv.abm2427

Cited by 8 publications

(10 citation statements)

References 51 publications

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“…We hypothesised that discordant readouts could be the result of TET2, a key enzyme in EM-seq, which has reported preferences for converting specific motifs (5’-MCGW-3’) [33, 34]. From our data, TET2 did not seem to display the same motif preferences (Supplementary Fig.…”

Section: Discussionmentioning

confidence: 75%

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Comparing methylation levels assayed in GC-rich regions with current and emerging methods

Guanzon,

Ross,

et al. 2023

Preprint

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DNA methylation is an epigenetic mechanism that regulates gene expression, and for mammals typically occurs on cytosines within CpG dinucleotides. A significant challenge for methylation detection methods is accurately measuring methylation levels within GC-rich regions such as gene promoters, as inaccuracies compromise downstream biological interpretation of the data. To address this challenge, we compared methylation levels assayed using four different methods: Enzymatic Methyl-seq (EM-seq), whole genome bisulphite sequencing (WGBS), Infinium arrays (Illumina MethylationEPIC, “EPIC”), and Oxford Nanopore Technologies nanopore sequencing (ONT) applied to human DNA. Overall, all methods produced comparable and consistent methylation readouts across the human genome. The flexibility offered by current gold standard WGBS in interrogating genome-wide cytosines is surpassed technically by both EM-seq and ONT, as their coverages and methylation readouts are less prone to GC bias. These advantages are tempered by higher costs (EM-seq) and higher complexity (ONT). We further assess the strengths and weaknesses of each method, and provide recommendations in choosing the most appropriate methylation method for specific scientific questions or translational needs.

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Section: Discussionmentioning

confidence: 75%

“…Echoing our motif-related observations, two recent studies have experimentally characterised the preference bias of TET enzymes for specific motifs surrounding methylated CpG dinucleotides [33, 34]. Specifically, TET2 (used in EM-seq) has a binding preference for the 4-mer motif 5’-MCGW-3’, where M=A/C and W=A/T.…”

Section: Resultsmentioning

confidence: 91%

Comparing methylation levels assayed in GC-rich regions with current and emerging methods

Guanzon,

Ross,

et al. 2023

Preprint

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“…Interestingly, both VMPs within enhancers and promoters display enrichment of motifs for JUN, HIF1A and FOS. TET enzymes which are involved in active demethylation, display sequence preferences for these motifs, which indicates a potential mechanistic link between the enrichment of these TFs at VMPs and changes in DNA methylation (38).…”

Section: Resultsmentioning

confidence: 99%

Systematic investigation of interindividual variation of DNA methylation in human whole blood

Grant,

Kumari,

Schalkwyk

et al. 2024

Preprint

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Interindividual genetic variability is well characterised, but we still lack a complete catalogue of loci displaying variable and stable epigenetic patterns. Here, we report a catalogue of stable and variable interindividual DNA methylation in human whole blood by analysing the DNA methylation patterns in 3642 individuals using the IlluminaEPIC array. Our results showed that 41,216 CpGs display stable methylation (SMPs) and 34,972 CpGs display variable methylation levels (VMPs). This catalogue will be a useful resource for interpretation of results when associating epigenetic signals to phenotypes. We observed that SMPs are highly enriched in CpG islands, depleted at CpG shelves and open sea regions of the genome. In addition, we found that the VMPs were under higher genetic control than the SMPs and that trans mQTL pairs are often located in the same TAD or connected by chromatin loops. A subset of these VMPs (784) were classified as putative epialleles and our results demonstrate that these loci located in regulatory regions exhibit a link with gene expression.

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“…The evidence generated in this regard during the grant period is too extensive to even mention all of the high-level publications. Among other things, there was remarkable mechanistic progress in the field of DNA methylation, − as well as its oxidative removal, with synthetic work on target structures providing particularly important foundations, on the basis of which important mechanistic insights were gained, e.g., into the formation and metabolization of hm 5 dC (5-hydroxymethyl-2′-deoxycytidine), f 5 dC (5-formyl-2′-deoxycytidine), and ca 5 dC (5-carboxy-2′-deoxycytidine). − Activities of DNA methyltransferases (DNMTs) and ten–eleven translocation enzymes (TETs) were shown to strongly depend on flanking sequences and the in vitro observed specificity imprints were clearly detected in cellular DNA modification patterns. − Insights from molecular recognition have also been used for targeted manipulation of DNA, again specifically related to the above-mentioned cytidine derivatives. , …”

Section: Results: the Three Guiding Questions: Where How And Why?mentioning

confidence: 99%

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications

Helm,

Bohnsack,

Carell

et al. 2023

ACS Chem. Biol.

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The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field. Pertinent research was funded from mid-2015 to 2022, including an extension related to the coronavirus pandemic. Despite being a detriment to research activity in general, the pandemic has resulted in tremendously boosted interest in the field of RNA and RNA modifications as a consequence of their widespread and successful use in vaccination campaigns against SARS-CoV-2. Funded principal investigators published over 250 pertinent papers with a very substantial impact on the field. The program also helped to redirect numerous laboratories toward this dynamic field. Finally, SPP1784 spawned initiatives for several funded consortia that continue to drive the fields of nucleic acid modification.

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Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function

Cited by 8 publications

References 51 publications

Comparing methylation levels assayed in GC-rich regions with current and emerging methods

Comparing methylation levels assayed in GC-rich regions with current and emerging methods

Systematic investigation of interindividual variation of DNA methylation in human whole blood

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications

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