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Targeted and genome-scale methylomics reveals gene body signatures in human cell lines
Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock pr...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
2009
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566772/ https://www.ncbi.nlm.nih.gov/pubmed/19329998 http://dx.doi.org/10.1038/nbt.1533 |
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author | Ball, Madeleine Price Li, Jin Billy Gao, Yuan Lee, Je-Hyuk LeProust, Emily Park, In-Hyun Xie, Bin Daley, George Q. Church, George M. |
author_facet | Ball, Madeleine Price Li, Jin Billy Gao, Yuan Lee, Je-Hyuk LeProust, Emily Park, In-Hyun Xie, Bin Daley, George Q. Church, George M. |
author_sort | Ball, Madeleine Price |
collection | PubMed |
description | Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions. |
format | Online Article Text |
id | pubmed-3566772 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
record_format | MEDLINE/PubMed |
spelling | pubmed-35667722013-02-07 Targeted and genome-scale methylomics reveals gene body signatures in human cell lines Ball, Madeleine Price Li, Jin Billy Gao, Yuan Lee, Je-Hyuk LeProust, Emily Park, In-Hyun Xie, Bin Daley, George Q. Church, George M. Nat Biotechnol Article Cytosine methylation, an epigenetic modification of DNA, is a target of growing interest for developing high throughput profiling technologies. Here we introduce two new, complementary techniques for cytosine methylation profiling utilizing next generation sequencing technology: bisulfite padlock probes (BSPPs) and methyl sensitive cut counting (MSCC). In the first method, we designed a set of ~10,000 BSPPs distributed over the ENCODE pilot project regions to take advantage of existing expression and chromatin immunoprecipitation data. We observed a pattern of low promoter methylation coupled with high gene body methylation in highly expressed genes. Using the second method, MSCC, we gathered genome-scale data for 1.4 million HpaII sites and confirmed that gene body methylation in highly expressed genes is a consistent phenomenon over the entire genome. Our observations highlight the usefulness of techniques which are not inherently or intentionally biased in favor of only profiling particular subsets like CpG islands or promoter regions. 2009-03-29 2009-04 /pmc/articles/PMC3566772/ /pubmed/19329998 http://dx.doi.org/10.1038/nbt.1533 Text en http://www.nature.com/authors/editorial_policies/license.html#terms Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms |
spellingShingle | Article Ball, Madeleine Price Li, Jin Billy Gao, Yuan Lee, Je-Hyuk LeProust, Emily Park, In-Hyun Xie, Bin Daley, George Q. Church, George M. Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title | Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title_full | Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title_fullStr | Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title_full_unstemmed | Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title_short | Targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
title_sort | targeted and genome-scale methylomics reveals gene body signatures in human cell lines |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566772/ https://www.ncbi.nlm.nih.gov/pubmed/19329998 http://dx.doi.org/10.1038/nbt.1533 |
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