title: Non-referenced genome assembly from epigenomic short-read data.
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.
authors.affiliation: a Epigenetics in Human Health and Disease Laboratory ; Baker IDI Heart and Diabetes Institute ; The Alfred Medical Research and Education Precinct ; Melbourne , Victoria , Australia ;
authors.forename: Antony
authors.initials: A
authors.lastname: Kaspi
authors.forename: Mark
authors.initials: M
authors.lastname: Ziemann
authors.forename: Samuel T
authors.initials: ST
authors.lastname: Keating
authors.forename: Ishant
authors.initials: I
authors.lastname: Khurana
authors.forename: Timothy
authors.initials: T
authors.lastname: Connor
authors.forename: Briana
authors.initials: B
authors.lastname: Spolding
authors.forename: Adrian
authors.initials: A
authors.lastname: Cooper
authors.forename: Ross
authors.initials: R
authors.lastname: Lazarus
authors.forename: Ken
authors.initials: K
authors.lastname: Walder
authors.forename: Paul
authors.initials: P
authors.lastname: Zimmet
authors.forename: Assam
authors.initials: A
authors.lastname: El-Osta
mesh_terms: D000818:Animals; D019295:Computational Biology; D019175:DNA Methylation; D004331:Drosophila melanogaster; D057890:Epigenomics / Q000379:methods*; D005849:Gerbillinae / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D008297:Male; D051379:Mice; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
keywords: ChIP-seq; ChIP-seq, immunoprecipitated chromatin sequencing; DMR, differentially methylated region; DNA methylation; High-throughput sequencing; MBD-seq; MBD-seq, methyl binding domain protein sequencing; MeDIP-seq; methylated DNA immunoprecipitation sequencing; Psammomys obesus; RNA-seq, RNA sequencing; de novo assembly; epigenomic integration