Change search
ReferencesLink to record
Permanent link

Direct link
Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques
University of Edinburgh, Scotland .
University of Edinburgh, Scotland .
Linköping University, Department of Clinical and Experimental Medicine, Division of Clinical Sciences. Linköping University, Faculty of Health Sciences.
University of Edinburgh, Scotland .
Show others and affiliations
2013 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 41, no 22Article in journal (Refereed) Published
Abstract [en]

The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC.

Place, publisher, year, edition, pages
Oxford University Press (OUP): Policy C - Option B / Oxford University Press , 2013. Vol. 41, no 22
National Category
Medical and Health Sciences
URN: urn:nbn:se:liu:diva-104131DOI: 10.1093/nar/gkt1080ISI: 000329874400005OAI: diva2:694655
Available from: 2014-02-07 Created: 2014-02-07 Last updated: 2014-03-26

Open Access in DiVA

fulltext(10363 kB)66 downloads
File information
File name FULLTEXT01.pdfFile size 10363 kBChecksum SHA-512
Type fulltextMimetype application/pdf

Other links

Publisher's full text

Search in DiVA

By author/editor
Nestor, Colm
By organisation
Division of Clinical SciencesFaculty of Health Sciences
In the same journal
Nucleic Acids Research
Medical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar
Total: 66 downloads
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 36 hits
ReferencesLink to record
Permanent link

Direct link