Visualising Nanopore Methylation Data using NanoMethViz Shian Su Walter and Eliza Hall Institute of Medical Research Abstract Data produced by Oxford Nanopore direct DNA sequencing has been shown to contain information on DNA modifications, providing an effective new tool for high-throughput and high-resolution analysis of genome-wide DNA methylation patterns. I focus on 5-methylcytosine CpG DNA methylation, which plays an important role in the epigenetic regulation of mammalian gene expression. CpG methylation is vital in embryonic development, genomic imprinting, X-inactivation and repression of repetitive elements.
Spiky: standardizing cfMeDIP-seq data with spike-in controls Lauren Marie Harmon,Samantha Lea Wilson,Michael Hoffman,Shu Yi Shen,Justin M Burgener,Scott V Bratman,Daniel D. DeCarvalho,Tim Triche Van Andel Institute Abstract Cell-free methylated DNA immunoprecipitation-sequencing (cfMeDIP-seq) is a sensitive and template-sparing approach to identify genomic regions with DNA methylation using cell-free DNA. cfMeDIP-seq is well-suited for liquid biopsies due to its low input DNA requirement (1ng) and cost-efficiency. Furthermore, cfMeDIP-seq conserves scarce circulating DNA by avoiding bisulfite conversion, and increases diagnostic yield in independent studies when compared to cfDNA variant analysis.
proActiv: Estimating promoter activity from RNA-seq data Joseph Lee,Deniz Demircioğlu,Jonathan Goeke National University of Singapore, Genome Institute of Singapore Abstract Most human protein-coding genes have multiple promoters that control the expression of distinct isoforms. The use of alternative promoters enables the regulation of isoform expression pre-transcriptionally. Alternative promoters have also been found to be important in a wide number of cell types and diseases, and thus the choice of promoter is as important as its level of transcriptional activity.
Short talk: Compartmap: Direct inference of higher-order chromatin structure in individual cells from single-cell RNA-seq & single-cell ATAC-seq
Compartmap: Direct inference of higher-order chromatin structure in individual cells from single-cell RNA-seq & single-cell ATAC-seq Benjamin K Johnson,Jean-Philippe Fortin,Kasper Daniel Hansen,Hui Shen,Tim Triche Van Andel Institute Abstract Single-cell profiling of higher-order chromatin structure remains a challenge due to cost, throughput, and resolution. We introduce compartmap as a method to reconstruct higher-order chromatin domains in individual cells, inferred from single-cell transcriptomic and epigenomic assays. In multiple cell lines and primary human samples, compartmap infers higher-order chromatin structure at least as well as chromatin capture or proximity ligation based methods, while distinguishing clinically relevant structural alterations in single cells.