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: Genome Research

Article Title: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

doi: 10.1101/gr.213660.116

Figure Lengend Snippet: Methodology for the placement of the PCFs on chromosomes. ( A ) Dual-color FISH of universal BAC clones, ( B ) cytogenetic map of the falcon chromosome 8 (FPE8) with indication of the relative positions of the BAC clones along the chromosome, and ( C ) assembled chromosome containing PCFs 7a, 7b, and 13b_13a. Blue blocks indicate positive (+) orientation of tracks compared with the falcon chromosome; red blocks, negative (−) orientation; and gray blocks, unknown (?) orientation.

Article Snippet: On the other hand, the development of advanced mapping and sequencing techniques (e.g., Dovetail, BioNano, or PacBio) will eventually provide an opportunity to replace RACA PCFs with longer and more complete subchromosomal-sized superscaffolds or sequence contigs requiring fewer BACs to anchor them to chromosomes.

Techniques: Clone Assay

Journal: Genome Research

Article Title: Upgrading short-read animal genome assemblies to chromosome level using comparative genomics and a universal probe set

doi: 10.1101/gr.213660.116

Figure Lengend Snippet: Ideogram of pigeon ( A ) and peregrine falcon ( B ) chromosomes. Numbered rectangles represent chromosomes, and colored blocks inside represent regions of homeology with chicken chromosomes. Lines within the colored blocks represent block orientation. Pigeon chromosomes 1–9 and Z were numbered according to the method of and the remaining chromosomes according to their chicken homeologs. Falcon chromosomes 1–13 and Z were numbered accordingly to the method of . The remaining chromosomes were numbered by decreasing combined length of the placed PCFs. Triangles above the falcon chromosomes point to the positions of falcon-specific fusions; below chromosomes, the positions of fissions. Black filling within the triangles point to the EBR boundaries used in the CNE analysis.

Article Snippet: On the other hand, the development of advanced mapping and sequencing techniques (e.g., Dovetail, BioNano, or PacBio) will eventually provide an opportunity to replace RACA PCFs with longer and more complete subchromosomal-sized superscaffolds or sequence contigs requiring fewer BACs to anchor them to chromosomes.

Techniques: Blocking Assay