Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns
DNA methyltransferases establish methylation patterns in cells and transmit these patterns over cell generations, thereby influencing each cell's epigenetic states. Three primary DNA methyltransferases have been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in vitro studies have in...
| Main Authors: | , , , , , |
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| Format: | Article |
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Public Library of Science
2012
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| Online Access: | https://eprints.nottingham.ac.uk/2604/ |
| _version_ | 1848790827863638016 |
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| author | Fu, Audrey Q. Genereux, Diane P. Stöger, Reinhard Burden, Alice F. Laird, Charles D. Stephens, Matthew |
| author_facet | Fu, Audrey Q. Genereux, Diane P. Stöger, Reinhard Burden, Alice F. Laird, Charles D. Stephens, Matthew |
| author_sort | Fu, Audrey Q. |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | DNA methyltransferases establish methylation patterns in cells and transmit these patterns over cell generations, thereby influencing each cell's epigenetic states. Three primary DNA methyltransferases have been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in vitro studies have investigated key properties of these enzymes, namely their substrate specificity and processivity. Here we study these properties in vivo, by applying novel statistical analysis methods to double-stranded DNA methylation patterns collected using hairpin-bisulfite PCR. Our analysis fits a novel Hidden Markov Model (HMM) to the observed data, allowing for potential bisulfite conversion errors, and yields statistical estimates of parameters that quantify enzyme processivity and substrate specificity. We apply this model to methylation patterns established in vivo at three loci in humans: two densely methylated inactive X (Xi)-linked loci ( and ), and an autosomal locus (), where methylation densities are tissue-specific but moderate. We find strong evidence for a high level of processivity of DNMT1 at and , with the mean association tract length being a few hundred base pairs. Regardless of tissue types, methylation patterns at are dominated by DNMT1 maintenance events, similar to the two Xi-linked loci, but are insufficiently informative regarding processivity to draw any conclusions about processivity at that locus. At all three loci we find that DNMT1 shows a strong preference for adding methyl groups to hemi-methylated CpG sites over unmethylated sites. The data at all three loci also suggest low (possibly 0) association of the de novo methyltransferases, the DNMT3s, and are consequently uninformative about processivity or preference of these enzymes. We also extend our HMM to reanalyze published data on mouse DNMT1 activities in vitro. The results suggest shorter association tracts (and hence weaker processivity), and much longer non-association tracts than human DNMT1 in vivo. |
| first_indexed | 2025-11-14T18:18:48Z |
| format | Article |
| id | nottingham-2604 |
| institution | University of Nottingham Malaysia Campus |
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| last_indexed | 2025-11-14T18:18:48Z |
| publishDate | 2012 |
| publisher | Public Library of Science |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-26042020-05-04T16:32:47Z https://eprints.nottingham.ac.uk/2604/ Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns Fu, Audrey Q. Genereux, Diane P. Stöger, Reinhard Burden, Alice F. Laird, Charles D. Stephens, Matthew DNA methyltransferases establish methylation patterns in cells and transmit these patterns over cell generations, thereby influencing each cell's epigenetic states. Three primary DNA methyltransferases have been identified in mammals: DNMT1, DNMT3A and DNMT3B. Extensive in vitro studies have investigated key properties of these enzymes, namely their substrate specificity and processivity. Here we study these properties in vivo, by applying novel statistical analysis methods to double-stranded DNA methylation patterns collected using hairpin-bisulfite PCR. Our analysis fits a novel Hidden Markov Model (HMM) to the observed data, allowing for potential bisulfite conversion errors, and yields statistical estimates of parameters that quantify enzyme processivity and substrate specificity. We apply this model to methylation patterns established in vivo at three loci in humans: two densely methylated inactive X (Xi)-linked loci ( and ), and an autosomal locus (), where methylation densities are tissue-specific but moderate. We find strong evidence for a high level of processivity of DNMT1 at and , with the mean association tract length being a few hundred base pairs. Regardless of tissue types, methylation patterns at are dominated by DNMT1 maintenance events, similar to the two Xi-linked loci, but are insufficiently informative regarding processivity to draw any conclusions about processivity at that locus. At all three loci we find that DNMT1 shows a strong preference for adding methyl groups to hemi-methylated CpG sites over unmethylated sites. The data at all three loci also suggest low (possibly 0) association of the de novo methyltransferases, the DNMT3s, and are consequently uninformative about processivity or preference of these enzymes. We also extend our HMM to reanalyze published data on mouse DNMT1 activities in vitro. The results suggest shorter association tracts (and hence weaker processivity), and much longer non-association tracts than human DNMT1 in vivo. Public Library of Science 2012-03-19 Article PeerReviewed Fu, Audrey Q., Genereux, Diane P., Stöger, Reinhard, Burden, Alice F., Laird, Charles D. and Stephens, Matthew (2012) Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns. PLoS ONE, 7 (3). e32225/1-e32225/11. ISSN 1932-6203 http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032225 doi:10.1371/journal.pone.0032225 doi:10.1371/journal.pone.0032225 |
| spellingShingle | Fu, Audrey Q. Genereux, Diane P. Stöger, Reinhard Burden, Alice F. Laird, Charles D. Stephens, Matthew Statistical inference of in vivo properties of human DNA methyltransferases from double-stranded methylation patterns |
| title | Statistical inference of in vivo properties of human
DNA methyltransferases from double-stranded
methylation patterns |
| title_full | Statistical inference of in vivo properties of human
DNA methyltransferases from double-stranded
methylation patterns |
| title_fullStr | Statistical inference of in vivo properties of human
DNA methyltransferases from double-stranded
methylation patterns |
| title_full_unstemmed | Statistical inference of in vivo properties of human
DNA methyltransferases from double-stranded
methylation patterns |
| title_short | Statistical inference of in vivo properties of human
DNA methyltransferases from double-stranded
methylation patterns |
| title_sort | statistical inference of in vivo properties of human
dna methyltransferases from double-stranded
methylation patterns |
| url | https://eprints.nottingham.ac.uk/2604/ https://eprints.nottingham.ac.uk/2604/ https://eprints.nottingham.ac.uk/2604/ |