Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
Abstract
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 present methylscaper, a visualization framework for simultaneous analysis of DNA methylation and chromatin accessibility landscapes. Methylscaper implements a weighted principal component analysis that orders DNA molecules, 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-BGS) 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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 14, 2021
- Source ID
- 10.1093/bioinformatics/btab438
Entities
People
- Alberto Riva
- Carolina E Pardo
- Eliza Morton
- Hadley Browder
- Kevin Kapadia
- Marie-pierre L Gauthier
- Michael P. Kladde
- Parker Knight
- Rhonda Bacher
- Russell P Darst
Organizations
- Defense Threat Reduction Agency
- National Institutes of Health
- University of Florida
- University of Florida Health