single-molecule long-read accessible chromatin mapping sequencing assay  (SMAC Corp)

Journal: Nucleic Acids Research

Article Title: Simultaneous profiling of chromatin accessibility and DNA methylation in complete plant genomes using long-read sequencing

doi: 10.1093/nar/gkae306

Figure Lengend Snippet: SAM-seq probes simultaneously chromatin accessibility and DNA methylation on plant tissues. ( A ) Workflow of the SAM-seq protocol and assessment of m6A-MTase sequence preferences on gDNA (EcoGII-treated gDNA). ( B ) Strand-specific m6A levels of EcoGII-treated genomic DNA before and after normalisation for m6A-MTase preferences over the five A. thaliana chromosomes. Centromeres are depicted as grey boxes. ( C ) UMAP projections of Arabidopsis 12-mer sequences coloured by m6A/A levels of EcoGII-treated gDNA, A content and AT content. ( D ) Density plots and correlation analysis between ONT sequencing of gDNA and SAM-Seq for mCG, mCHG, and mCHH levels. ( E ) Strand-specific SAM-seq m6A levels before and after normalisation for m6A-MTases preferences. ( F ) Metaplot of Arabidopsis genes displaying ATAC-seq accessibility (Lu et al. 2017) (right Y axis) and SAM-seq chromatin accessibility (m6A/A) obtained from independent experiments using distinct m6A-MTases (EcoGII or Hia5) as well as distinct ONT chemistry (R9.4.1 or R10) (left Y axis).

Article Snippet: Because of the lack of endogenous m6A in most eukaryotes, treatment of chromatin with m6A-MTases followed by ONT sequencing could provide a high-resolution snapshot of chromatin accessibility, as was demonstrated using the single-molecule long-read accessible chromatin mapping (SMAC-seq) sequencing assay in yeast and humans ( ).

Techniques: DNA Methylation Assay, Sequencing

Journal: Nature Reviews. Genetics

Article Title: Beyond assembly: the increasing flexibility of single-molecule sequencing technology

doi: 10.1038/s41576-023-00600-1

Figure Lengend Snippet: Summary of long-read DNA enrichment methods

Article Snippet: The single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq) uses a combination of methyltransferases (including M.CviPI, M.SssI and EcoGII (m6dA on all adenines)) to achieve high-resolution (<5 bp) mapping in order to study chromatin states and the coordination of regulatory elements on single molecules using ONT nanopore sequencing (Fig. ).

Techniques: Multiplex Assay, Hybridization, Sampling, Nanopore Sequencing, Sequencing

Journal: Nature Reviews. Genetics

Article Title: Beyond assembly: the increasing flexibility of single-molecule sequencing technology

doi: 10.1038/s41576-023-00600-1

Figure Lengend Snippet: Summary of long-read footprinting assays

Article Snippet: The single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq) uses a combination of methyltransferases (including M.CviPI, M.SssI and EcoGII (m6dA on all adenines)) to achieve high-resolution (<5 bp) mapping in order to study chromatin states and the coordination of regulatory elements on single molecules using ONT nanopore sequencing (Fig. ).

Techniques: Footprinting, Sequencing, DNA Methylation Assay, Next-Generation Sequencing, Nanopore Sequencing, Methylation, Binding Assay