RT Journal Article
SR Electronic
T1 methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.11.13.382465
DO 10.1101/2020.11.13.382465
A1 Parker Knight
A1 Marie-Pierre L. Gauthier
A1 Carolina E. Pardo
A1 Russell P. Darst
A1 Alberto Riva
A1 Michael P. Kladde
A1 Rhonda Bacher
YR 2020
UL http://biorxiv.org/content/early/2020/11/15/2020.11.13.382465.abstract
AB Differential DNA methylation and chromatin accessibility are associated with disease development, particularly cancer. Methods that allow profiling of these epigenetic mechanisms in the same reaction and at the single-molecule or single-cell level continue to emerge. However, a challenge lies in jointly visualizing and analyzing the heterogeneous nature of the data and extracting regulatory insight. Here, we developed methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin landscapes. Methylscaper implements a weighted principle component analysis that orders sequencing reads, each providing a record of the chromatin state of one epiallele, and reveals patterns of nucleosome positioning, transcription factor occupancy, and DNA methylation. We demonstrate methylscaper’s utility on a long-read, single-molecule methyltransferase accessibility protocol for individual templates (MAPit) dataset and a single-cell nucleosome, methylation, and transcription sequencing (scNMT-seq) dataset. In comparison to other procedures, methylscaper is able to readily identify chromatin features that are biologically relevant to transcriptional status while scaling to larger datasets.Availability and implementation Methylscaper, is available on GitHub at https://github.com/rhondabacher/methylscaper.Contact rbacher{at}ufl.eduCompeting Interest StatementThe authors have declared no competing interest.