Abstract
The study of epigenetic heterogeneity at the level of individual cells and in whole populations is the key to understanding cellular differentiation, organismal development, and the evolution of cancer. We develop a statistical method, epiG, to infer and differentiate between different epi-allelic haplotypes, annotated with CpG methylation status and DNA polymorphisms, from whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq data. We demonstrate the capabilities of the method by inferring allele-specific methylation and nucleosome occupancy in cell lines, and colon and tumor samples, and by benchmarking the method against independent experimental data.
Highlights
The epigenetic state of a particular genomic region is the combined configuration of the epigenetic modifications in the region, including DNA (CpG) methylation, nucleosome positioning, and histone modifications
Various statistical methods exist for drawing inference on epigenetic patterns in general and allele-specific methylation (ASM)
E.g. as implemented in armfinder [9], have been used to identify allele-specific methylated regions (AMRs) from whole-genome bisulfite sequencing (WGBS) data without inferring the structure of the underlying epi-allelic haplotypes. Other methods, such as Bis-single nucleotide polymorphism (SNP) [20] and Bismark [21], infer CpG methylation levels position-wise from WGBS data without distinguishing between epi-alleles
Summary
The epigenetic state of a particular genomic region is the combined configuration of the epigenetic modifications in the region, including DNA (CpG) methylation, nucleosome positioning, and histone modifications. Such states are important regulators of many biological processes in health and disease, and at many different biological levels, for example gene regulation, cellular differentiation, and organismal development [1,2,3]. Heterogeneity occurs at the population level, for example, in relation to cellular development and differentiation [6], and in the evolution of cancer [7, 8] It occurs at the level of individual cells in the form of allele-specific methylation (ASM) [9,10,11,12,13]
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
