Publications by authors named "Milda Narmonte"
Article Synopsis
- The Mx-TOP method allows for profiling three key epigenetic layers—chromatin accessibility, DNA modification, and DNA hydroxymethylation—from a single sample using a specialized tagging and sequencing technique.
- Validation tests showed that Mx-TOP is highly sensitive and informative in exploring how chromatin and DNA modifications influence gene transcription.
- The method was used to investigate epigenetic changes during neuronal differentiation, revealing that gene body hydroxymethylation (5hmC) plays a crucial role in maintaining promoter accessibility and resisting global changes in chromatin structure.
Article Synopsis
- Fanconi anemia (FA) is a rare genetic disease caused by mutations in certain genes that help fix DNA.
- Cells with FA are very sensitive to certain types of DNA damage and struggle with copying their DNA when it gets blocked.
- The study found that two specific molecules can cause serious DNA damage in FA cells without a protein called FANCD2, but another protein called PARP1 helps protect against this damage.
Neuroblastoma (NB) is a pediatric cancer of the developing sympathetic nervous system that exhibits significant variation in the stage of differentiation and cell composition of tumors. Global loss of DNA methylation and genomic 5-hydroxymethylcytosine (5hmC) is a hallmark of human cancers. Here, we used our recently developed single-base resolution approaches, hmTOP-seq and uTOP-seq, for construction of 5hmC maps and identification of large partially methylated domains (PMDs) in different NB cell subpopulations.
View Article and Find Full Text PDFBackground: Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of high cost. Building upon previous knowledge that placenta, the main source of fetal circulating DNA, is hypomethylated in comparison to maternal tissue counterparts of cfDNA, we propose that targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches fetal genetic material and reduces numbers of required analytical sequencing reads thereby decreasing cost of a test.
View Article and Find Full Text PDF5-hydroxymethylcytosine (5hmC) is the most prevalent intermediate on the oxidative DNA demethylation pathway and is implicated in regulation of embryogenesis, neurological processes, and cancerogenesis. Profiling of this relatively scarce genomic modification in clinical samples requires cost-effective high-resolution techniques that avoid harsh chemical treatment. Here, we present a bisulfite-free approach for 5hmC profiling at single-nucleotide resolution, named hmTOP-seq (5hmC-specific tethered oligonucleotide-primed sequencing), which is based on direct sequence readout primed at covalently labeled 5hmC sites from an in situ tethered DNA oligonucleotide.
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