Non-referenced genome assembly from epigenomic short-read data

Antony Kaspi, Mark Ziemann, Samuel T. Keating, Ishant Khurana, Timothy Connor, Briana Spolding, Adrian Cooper, Ross Lazarus, Ken Walder, Paul Zimmet, Assam El-Osta

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.

Original languageEnglish
Pages (from-to)1329-1338
Number of pages10
JournalEpigenetics
Volume9
Issue number10
DOIs
Publication statusPublished - 1 Jan 2014

Keywords

  • ChIP-seq
  • DNA methylation
  • De novo assembly
  • Epigenomic integration
  • High-throughput sequencing
  • MBD-seq
  • Psammomys obesus

ASJC Scopus subject areas

  • Molecular Biology
  • Cancer Research

Cite this

Kaspi, A., Ziemann, M., Keating, S. T., Khurana, I., Connor, T., Spolding, B., ... El-Osta, A. (2014). Non-referenced genome assembly from epigenomic short-read data. Epigenetics, 9(10), 1329-1338. https://doi.org/10.4161/15592294.2014.969610