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.

LanguageEnglish
Pages1329-1338
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
Kaspi, Antony ; Ziemann, Mark ; Keating, Samuel T. ; Khurana, Ishant ; Connor, Timothy ; Spolding, Briana ; Cooper, Adrian ; Lazarus, Ross ; Walder, Ken ; Zimmet, Paul ; El-Osta, Assam. / Non-referenced genome assembly from epigenomic short-read data. In: Epigenetics. 2014 ; Vol. 9, No. 10. pp. 1329-1338.
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Kaspi, A, Ziemann, M, Keating, ST, Khurana, I, Connor, T, Spolding, B, Cooper, A, Lazarus, R, Walder, K, Zimmet, P & El-Osta, A 2014, 'Non-referenced genome assembly from epigenomic short-read data', Epigenetics, vol. 9, no. 10, pp. 1329-1338. https://doi.org/10.4161/15592294.2014.969610

Non-referenced genome assembly from epigenomic short-read data. / Kaspi, Antony; Ziemann, Mark; Keating, Samuel T.; Khurana, Ishant; Connor, Timothy; Spolding, Briana; Cooper, Adrian; Lazarus, Ross; Walder, Ken; Zimmet, Paul; El-Osta, Assam.

In: Epigenetics, Vol. 9, No. 10, 01.01.2014, p. 1329-1338.

Research output: Contribution to journalArticle

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Kaspi A, Ziemann M, Keating ST, Khurana I, Connor T, Spolding B et al. Non-referenced genome assembly from epigenomic short-read data. Epigenetics. 2014 Jan 1;9(10):1329-1338. https://doi.org/10.4161/15592294.2014.969610