\nFebruary 14, 2023<\/span><\/p>\n
![\"Science](\"https:\/\/scitechdaily.com\/images\/DNA-Virus-Vaccine-Research-Concept.jpg?ezimgfmt=ng%3Awebp%2Fngcb2%2Frs%3Adevice%2Frscb2-1\" "\\"Science")
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The new approach is called iDEMS (isolation of DNA by EdU labeling for Mass Spectrometry).<\/p>\n<\/div>\n
A recent technical report in Nature Cell Biology<\/em> has introduced a novel method to examine specific alterations in DNA<\/div>\n ” data-gt-translate-attributes=”[{“attribute”:”data-cmtooltip”, “format”:”html”}]”>DNA<\/span> following replication. Scientists have devised a highly sensitive, quantitative method utilizing mass spectrometry known as iDEMS (isolation of DNA by EdU labeling for Mass Spectrometry).<\/p>\n \u201cThe novelty in our work is that we didn\u2019t use sequencing methods widely used in this field, instead we used mass spectrometry, which is the first time this approach has been used to measure DNA modifications on purified, replicated DNA,\u201d says Dr. Stewart-Morgan, co-first author of the report, from the Groth laboratory at the Novo Nordisk Foundation Center for Protein Research (CPR) at the University of Copenhagen<\/a>.<\/p>\n This unique approach is the result of a joint project with the Hajkova laboratory at MRC London Institute of Medical Sciences (LMS). \u201cIn the Groth laboratory we have expertise in replication and the Hajkova laboratory has expertise in studying DNA methylation by mass spectrometry. I think this multidisciplinary collaboration is a large part of the reason why the project has been so successful,\u201d Dr. Stewart-Morgan explains. \u201cThe results of our research using iDEMS are definitive and open new avenues for future research.\u201d<\/p>\n The genome is the entire set of DNA instructions found in a cell. Virtually all cells in an organism contain the same genetic information \u2013 but which genes are expressed is based on the cell\u2019s function. This cell-specific gene expression is regulated by the cell\u2019s epigenome, which consists of proteins bound to DNA, as well as direct chemical modifications to DNA. One of the most important epigenetic regulators is DNA methylation \u2013 a chemical marker which turns off regions of the genome that should not be expressed. The pattern of these markers is very important in maintaining a cell\u2019s stability and identity: for example, DNA methylation in a liver cell will differ from the DNA methylation pattern in a blood cell.<\/p>\n When DNA is replicated during cell division, the epigenetic marks associated with the DNA, including DNA methylation, are diluted. The newly created DNA strands need to re-establish the level and pattern of methylation to maintain control of gene expression, genomic stability, and the epigenetic memory of the cell\u2019s identity.<\/p>\n However, much about this process is unknown, and loss of DNA methylation is a common feature in cells that have divided many times, such as cancer cells which are very proliferative and aged cells that have replicated many times over the course of a person\u2019s lifespan. In recent years several groups have tried to investigate this process using sequencing methods, however, the exact kinetics of post-replicative methylation maintenance remained unclear.<\/p>\n Using iDEMS, the researchers found that DNA methylation levels increase steadily after replication, and after 4 hours the levels on replicated DNA and the genomic DNA were equal. This indicates that this process proceeds at a steady, slow pace. However, it is outpaced by cell division.<\/p>\n \u201cOver time cells don\u2019t have long enough to re-establish their methylation after replication, and the methylation of the genome is eventually diluted. This is the first time very clear kinetics for methylation re-establishment have been shown. Furthermore, we saw absolute quantification of the levels of DNA methylation, enabling us to distinguish which methylation marks were newly established. This gave us confidence in our kinetic measurements,\u201d Dr. Stewart-Morgan reports.<\/p>\n The researchers also used iDEMS to study a second marker \u2013 DNA hydroxymethylation \u2013 which is a much rarer genomic marker than methylation. Their results corroborated earlier research, says Dr Stewart-Morgan: \u201cWe found that one DNA strand, the template or \u2018parental\u2019 strand, always has more hydroxymethylation than the other \u2018daughter\u2019 strand, supporting earlier work which indicated that this marker distinguishes DNA strands based on age,\u201d she says.<\/p>\n \u201cHowever, we also discovered that there is no point at which the levels of hydroxymethylation are equal between the parental and daughter strands throughout the cell cycle. This opens new questions about how this difference between strands may be used by cells, for example during DNA repair.\u201d<\/p>\n By directly quantifying DNA modifications on replicated DNA, iDEMS resolves DNA methylation and hydroxymethylation kinetics following DNA replication. \u201ciDEMS is a dynamic and informative tool for addressing important questions in epigenome maintenance and DNA modification biology,\u201d Dr. Stewart-Morgan says.<\/p>\n Looking to the future, iDEMS will be useful in profiling methylation and hydroxymethylation dynamics in different cellular contexts, including aging and cancer evolution. Compared with sequencing data, mass spectrometry provides a simple, fast readout, and iDEMS could therefore be useful where efficiency is key, such as in medical settings and drug discovery studies.<\/p>\n \u201cOur results highlight how important new methods are for understanding biology through more than one lens. iDEMS is extremely flexible, as it can be combined with other established methods used in molecular biology to look at the epigenome. This method, therefore, adds an important tool to the suite of technologies investigating epigenome stability,\u201d concludes Dr. Stewart-Morgan.<\/p>\n Reference: \u201cQuantifying propagation of DNA methylation and hydroxymethylation with iDEMS\u201d by Kathleen R. Stewart-Morgan, Cristina E. Requena, Valentin Flury, Qian Du, Zoe Heckhausen, Petra Hajkova and Anja Groth, 12 January 2023, Nature Cell Biology<\/em>.DNA modifications and cell stability<\/h4>\n
Methylation re-establishment<\/h4>\n
A second chemical marker<\/h4>\n
The potential of iDEMS<\/h4>\n
DOI: 10.1038\/s41556-022-01048-x<\/a><\/p>\n<\/div>\n