Epigenetics - Part 1

A long time coming, but here it is! - **Introduction:** https://medlineplus.gov/genetics/understanding/howgeneswork/epigenome/ - **Mechanisms:** https://en.wikipedia.org/wiki/Epigenetics - **DNA packaging:** https://www.nature.com/scitable/topicpage/dna-packaging-nucleosomes-and-chromatin-310/ - **Chromatin and gene regulation:** https://learn.genetics.utah.edu/content/epigenetics/control/ - **Histone writers, erasers and readers:** https://www.nature.com/articles/emm201711 - **DNA methylation, DNMTs and SAM:** https://www.nature.com/articles/npp2012112 - **Modified bases (5mC, N6-mA):** https://en.wikipedia.org/wiki/DNA\_methylation - **Active DNA demethylation (TET/TDG/BER):** https://www.tandfonline.com/doi/full/10.1080/17501911.2025.2586452 <!--THE END--> - **Bisulfite sequencing (WGBS):** https://www.illumina.com/techniques/sequencing/methylation-sequencing/bisulfite-sequencing.html - **WGBS alignment benchmarking:** https://www.sciencedirect.com/science/article/pii/S2001037022003853 - **Illumina 5-base methylome sequencing:** https://www.illumina.com/techniques/sequencing/methylation-sequencing/methylome-genome.html - **MethylationEPIC v2.0 array:** https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html - **Infinium 450K datasheet:** https://www.illumina.com/content/dam/illumina-marketing/documents/products/datasheets/datasheet\_humanmethylation450.pdf <!--THE END--> - **PacBio HiFi methylation detection:** https://www.pacb.com/revio/ - **SMRT direct methylation detection:** https://www.pacb.com/publications/direct-detection-of-dna-methylation-during-single-molecule-real-time-sequencing/ - **Fiber-seq and cancer research:** https://www.pacb.com/blog/what-a-clearer-view-of-epigenetics-can-mean-for-cancer-research/ - **PacBio epigenetics overview:** https://www.pacb.com/products-and-services/applications/epigenetics/ - **Sequencing 101: Epigenetics:** https://www.pacb.com/blog/sequencing-101-epigenetics/ - **Oxford Nanopore modified-base calling:** https://nanoporetech.com/applications/investigations/epigenetics-and-methylation-analysis - **Nanopore sequencing accuracy:** https://nanoporetech.com/platform/accuracy - **Nanopore chromatin accessibility (EPI2ME):** https://epi2me.nanoporetech.com/chromatin-acc-hg002/ - **Nanopore 5mC/5hmC detection:** https://www.nature.com/articles/s42003-025-07681-0 <!--THE END--> - **Ultima Genomics (bisulfite, EM-seq, TAPS+):** https://www.ultimagenomics.com/focus-areas/methylation-profiling/ - **Watchmaker TAPS+:** https://www.watchmakergenomics.com/taps.html - **Element AVITI methylation sequencing:** https://www.elementbiosciences.com/applications/dna-sequencing/methylation-sequencing - **MGI DNBSEQ bisulfite sequencing:** https://link.springer.com/article/10.1186/s13148-023-01543-4 <!--THE END--> - **NEBNext EM-seq v2:** https://www.neb.com/en-us/products/e8015-nebnext-enzymatic-methyl-seq-v2-kit - **NEBNext enzymatic 5hmC-seq:** https://www.neb.com/en-us/products/e3350nebnext-enzymatic-methyl-seq-5hmc-kit - **5hmC detection overview:** https://www.neb.com/en-us/products/epigenetics/methylation-analysis/5hmc-hydroxymethylation - **meCUT&RUN:** https://www.epicypher.com/product/cutana-mecutrun-kit-for-dna-methylation-sequencing/ - **Fiber-seq chromatin profiling:** https://www.epicypher.com/fiber-seq-long-read-sequencing/ - **Fiber-seq + PacBio HiFi:** https://www.pacb.com/blog/how-pairing-epicyphers-fiber-seq-with-hifi-sequencing-delivers-an-all-in-one-multiomic-view/ - **MeDIP:** https://www.activemotif.com/catalog/736/medip - **LINE-1 global methylation assay:** https://www.activemotif.com/catalog/1043/global-dna-methylation-assay-line-1 - **RRBS:** https://www.nature.com/articles/nprot.2010.190 <!--THE END--> - **DNA methylation biomarkers in liquid biopsies:** https://www.nature.com/articles/s41388-025-03624-5 Epigenetics fundamentalsConversion-based sequencingNative/direct methylation detectionOther sequencing platformsEnzymatic and targeted methodsFrom bench to clinic