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

doi:10.4161/15592294.2014.969610

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

Aboriginal Health Equity

Research output: Contribution to journal › Article › peer-review

3 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 language	English
Pages (from-to)	1329-1338
Number of pages	10
Journal	Epigenetics
Volume	9
Issue number	10
DOIs	https://doi.org/10.4161/15592294.2014.969610
Publication status	Published or Issued - 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

Access to Document

10.4161/15592294.2014.969610

Cite this

@article{da976fa112df458d88d7362e83edd245,

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.",

keywords = "ChIP-seq, DNA methylation, De novo assembly, Epigenomic integration, High-throughput sequencing, MBD-seq, Psammomys obesus",

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

note = "Publisher Copyright: {\textcopyright} 2014 Taylor & Francis Group, LLC.",

year = "2014",

doi = "10.4161/15592294.2014.969610",

language = "English",

volume = "9",

pages = "1329--1338",

journal = "Epigenetics",

issn = "1559-2294",

publisher = "Taylor and Francis Ltd.",

number = "10",

}

TY - JOUR

T1 - Non-referenced genome assembly from epigenomic short-read data

AU - Kaspi, Antony

AU - Ziemann, Mark

AU - Keating, Samuel T.

AU - Khurana, Ishant

AU - Connor, Timothy

AU - Spolding, Briana

AU - Cooper, Adrian

AU - Lazarus, Ross

AU - Walder, Ken

AU - Zimmet, Paul

AU - El-Osta, Assam

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - ChIP-seq

KW - DNA methylation

KW - De novo assembly

KW - Epigenomic integration

KW - High-throughput sequencing

KW - MBD-seq

KW - Psammomys obesus

UR - http://www.scopus.com/inward/record.url?scp=84922053046&partnerID=8YFLogxK

U2 - 10.4161/15592294.2014.969610

DO - 10.4161/15592294.2014.969610

M3 - Article

C2 - 25437048

AN - SCOPUS:84922053046

SN - 1559-2294

VL - 9

SP - 1329

EP - 1338

JO - Epigenetics

JF - Epigenetics

IS - 10

ER -

Non-referenced genome assembly from epigenomic short-read data

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Cite this