Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA.
Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA met...
| Main Authors: | , , , , , |
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| Format: | Journal article |
| Language: | English |
| Published: |
Oxford University Press
2012
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| _version_ | 1797078906318094336 |
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| author | Blackledge, N Long, H Zhou, J Kriaucionis, S Patient, R Klose, R |
| author_facet | Blackledge, N Long, H Zhou, J Kriaucionis, S Patient, R Klose, R |
| author_sort | Blackledge, N |
| collection | OXFORD |
| description | Across vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA methylation, but recently an alternative approach based on profiling non-methylated CpGs was developed. This technique, called CxxC affinity purification (CAP), uses a ZF-CxxC (CxxC) domain to specifically capture DNA containing clusters of non-methylated CpGs. Here we describe a new CAP approach, called biotinylated CAP (Bio-CAP), which eliminates the requirement for specialized equipment while dramatically improving and simplifying the CxxC-based DNA affinity purification. Importantly, this approach isolates non-methylated DNA in a manner that is directly proportional to the density of non-methylated CpGs, and discriminates non-methylated CpGs from both methylated and hydroxymethylated CpGs. Unlike conventional CAP, Bio-CAP can be applied to nanogram quantities of genomic DNA and in a magnetic format is amenable to efficient parallel processing of samples. Furthermore, Bio-CAP can be applied to genome-wide profiling of non-methylated DNA with relatively small amounts of input material. Therefore, Bio-CAP is a simple and streamlined approach for characterizing regions of the non-methylated DNA, whether at specific target regions or genome wide. |
| first_indexed | 2024-03-07T00:38:12Z |
| format | Journal article |
| id | oxford-uuid:82248b23-9eaa-4a3d-91f4-18c8fae04e44 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T00:38:12Z |
| publishDate | 2012 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:82248b23-9eaa-4a3d-91f4-18c8fae04e442022-03-26T21:35:14ZBio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:82248b23-9eaa-4a3d-91f4-18c8fae04e44EnglishSymplectic Elements at OxfordOxford University Press2012Blackledge, NLong, HZhou, JKriaucionis, SPatient, RKlose, RAcross vertebrate genomes methylation of cytosine residues within the context of CpG dinucleotides is a pervasive epigenetic mark that can impact gene expression and has been implicated in various developmental and disease-associated processes. Several biochemical approaches exist to profile DNA methylation, but recently an alternative approach based on profiling non-methylated CpGs was developed. This technique, called CxxC affinity purification (CAP), uses a ZF-CxxC (CxxC) domain to specifically capture DNA containing clusters of non-methylated CpGs. Here we describe a new CAP approach, called biotinylated CAP (Bio-CAP), which eliminates the requirement for specialized equipment while dramatically improving and simplifying the CxxC-based DNA affinity purification. Importantly, this approach isolates non-methylated DNA in a manner that is directly proportional to the density of non-methylated CpGs, and discriminates non-methylated CpGs from both methylated and hydroxymethylated CpGs. Unlike conventional CAP, Bio-CAP can be applied to nanogram quantities of genomic DNA and in a magnetic format is amenable to efficient parallel processing of samples. Furthermore, Bio-CAP can be applied to genome-wide profiling of non-methylated DNA with relatively small amounts of input material. Therefore, Bio-CAP is a simple and streamlined approach for characterizing regions of the non-methylated DNA, whether at specific target regions or genome wide. |
| spellingShingle | Blackledge, N Long, H Zhou, J Kriaucionis, S Patient, R Klose, R Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title | Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title_full | Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title_fullStr | Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title_full_unstemmed | Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title_short | Bio-CAP: a versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA. |
| title_sort | bio cap a versatile and highly sensitive technique to purify and characterise regions of non methylated dna |
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