Cargando…
Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data
CpG islands are typically located in the 5′ end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Hindawi Publishing Corporation
2012
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303704/ https://www.ncbi.nlm.nih.gov/pubmed/22474411 http://dx.doi.org/10.1155/2012/598987 |
_version_ | 1782226774234497024 |
---|---|
author | Du, Xin Han, Leng Guo, An-Yuan Zhao, Zhongming |
author_facet | Du, Xin Han, Leng Guo, An-Yuan Zhao, Zhongming |
author_sort | Du, Xin |
collection | PubMed |
description | CpG islands are typically located in the 5′ end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level. |
format | Online Article Text |
id | pubmed-3303704 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Hindawi Publishing Corporation |
record_format | MEDLINE/PubMed |
spelling | pubmed-33037042012-04-03 Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data Du, Xin Han, Leng Guo, An-Yuan Zhao, Zhongming Comp Funct Genomics Research Article CpG islands are typically located in the 5′ end of genes and considered as gene markers because they play important roles in gene regulation via epigenetic change. In this study, we compared the features of CpG islands identified by several major algorithms by setting the parameter cutoff values in order to obtain a similar number of CpG islands in a genome. This approach allows us to systematically compare the methylation and gene expression patterns in the identified CpG islands. We found that Takai and Jones' algorithm tends to identify longer CpG islands but with weaker CpG island features (e.g., lower GC content and lower ratio of the observed over expected CpGs) and higher methylation level. Conversely, the CpG clusters identified by Hackenberg et al.'s algorithm using stringent criteria are shorter and have stronger features and lower methylation level. In addition, we used the genome-wide base-resolution methylation profile in two cell lines to show that genes with a lower methylation level at the promoter-associated CpG islands tend to express in more tissues and have stronger expression. Our results validated that the DNA methylation of promoter-associated CpG islands suppresses gene expression at the genome level. Hindawi Publishing Corporation 2012 2012-03-04 /pmc/articles/PMC3303704/ /pubmed/22474411 http://dx.doi.org/10.1155/2012/598987 Text en Copyright © 2012 Xin Du et al. https://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Du, Xin Han, Leng Guo, An-Yuan Zhao, Zhongming Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title | Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title_full | Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title_fullStr | Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title_full_unstemmed | Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title_short | Features of Methylation and Gene Expression in the Promoter-Associated CpG Islands Using Human Methylome Data |
title_sort | features of methylation and gene expression in the promoter-associated cpg islands using human methylome data |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3303704/ https://www.ncbi.nlm.nih.gov/pubmed/22474411 http://dx.doi.org/10.1155/2012/598987 |
work_keys_str_mv | AT duxin featuresofmethylationandgeneexpressioninthepromoterassociatedcpgislandsusinghumanmethylomedata AT hanleng featuresofmethylationandgeneexpressioninthepromoterassociatedcpgislandsusinghumanmethylomedata AT guoanyuan featuresofmethylationandgeneexpressioninthepromoterassociatedcpgislandsusinghumanmethylomedata AT zhaozhongming featuresofmethylationandgeneexpressioninthepromoterassociatedcpgislandsusinghumanmethylomedata |