Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize
Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcri...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
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BioMed Central
2017
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| Online Access: | https://eprints.nottingham.ac.uk/45076/ |
| _version_ | 1848797064036614144 |
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| author | Oka, Rurika Zicola, Johan Weber, Blaise Anderson, Sarah N. Hodgman, Charlie Gent, Jonathan I. Wesselink, Jan-Jaap Springer, Nathan M. Hoefsloot, Hubb C.J. Turck, Franziska Stam, Maike |
| author_facet | Oka, Rurika Zicola, Johan Weber, Blaise Anderson, Sarah N. Hodgman, Charlie Gent, Jonathan I. Wesselink, Jan-Jaap Springer, Nathan M. Hoefsloot, Hubb C.J. Turck, Franziska Stam, Maike |
| author_sort | Oka, Rurika |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | Background
While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant.
Result
To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes.
Conclusions
Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. |
| first_indexed | 2025-11-14T19:57:56Z |
| format | Article |
| id | nottingham-45076 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:57:56Z |
| publishDate | 2017 |
| publisher | BioMed Central |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-450762020-05-04T18:56:15Z https://eprints.nottingham.ac.uk/45076/ Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize Oka, Rurika Zicola, Johan Weber, Blaise Anderson, Sarah N. Hodgman, Charlie Gent, Jonathan I. Wesselink, Jan-Jaap Springer, Nathan M. Hoefsloot, Hubb C.J. Turck, Franziska Stam, Maike Background While most cells in multicellular organisms carry the same genetic information, in each cell type only a subset of genes is being transcribed. Such differentiation in gene expression depends, for a large part, on the activation and repression of regulatory sequences, including transcriptional enhancers. Transcriptional enhancers can be located tens of kilobases from their target genes, but display characteristic chromatin and DNA features, allowing their identification by genome-wide profiling. Here we show that integration of chromatin characteristics can be applied to predict distal enhancer candidates in Zea mays, thereby providing a basis for a better understanding of gene regulation in this important crop plant. Result To predict transcriptional enhancers in the crop plant maize (Zea mays L. ssp. mays), we integrated available genome-wide DNA methylation data with newly generated maps for chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac) enrichment in young seedling and husk tissue. Approximately 1500 intergenic regions, displaying low DNA methylation, high chromatin accessibility and H3K9ac enrichment, were classified as enhancer candidates. Based on their chromatin profiles, candidate sequences can be classified into four subcategories. Tissue-specificity of enhancer candidates is defined based on the tissues in which they are identified and putative target genes are assigned based on tissue-specific expression patterns of flanking genes. Conclusions Our method identifies three previously identified distal enhancers in maize, validating the new set of enhancer candidates and enlarging the toolbox for the functional characterization of gene regulation in the highly repetitive maize genome. BioMed Central 2017-07-21 Article PeerReviewed Oka, Rurika, Zicola, Johan, Weber, Blaise, Anderson, Sarah N., Hodgman, Charlie, Gent, Jonathan I., Wesselink, Jan-Jaap, Springer, Nathan M., Hoefsloot, Hubb C.J., Turck, Franziska and Stam, Maike (2017) Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology, 18 . p. 137. ISSN 1465-6906 Transcriptional enhancer Gene regulation Chromatin accessibility Histone acetylation DNA methylation Zea mays https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1273-4 doi:10.1186/s13059-017-1273-4 doi:10.1186/s13059-017-1273-4 |
| spellingShingle | Transcriptional enhancer Gene regulation Chromatin accessibility Histone acetylation DNA methylation Zea mays Oka, Rurika Zicola, Johan Weber, Blaise Anderson, Sarah N. Hodgman, Charlie Gent, Jonathan I. Wesselink, Jan-Jaap Springer, Nathan M. Hoefsloot, Hubb C.J. Turck, Franziska Stam, Maike Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title_full | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title_fullStr | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title_full_unstemmed | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title_short | Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize |
| title_sort | genome-wide mapping of transcriptional enhancer candidates using dna and chromatin features in maize |
| topic | Transcriptional enhancer Gene regulation Chromatin accessibility Histone acetylation DNA methylation Zea mays |
| url | https://eprints.nottingham.ac.uk/45076/ https://eprints.nottingham.ac.uk/45076/ https://eprints.nottingham.ac.uk/45076/ |