Non-referenced genome assembly from epigenomic short-read data.
Epigenetics
; 9(10): 1329-38, 2014 Oct.
Article
in En
| MEDLINE
| ID: mdl-25437048
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.
Key words
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
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Sequence Analysis, DNA
/
DNA Methylation
/
Epigenomics
Limits:
Animals
/
Humans
/
Male
Language:
En
Journal:
Epigenetics
Journal subject:
GENETICA
Year:
2014
Document type:
Article