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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

Authors

Rurika Oka

Johan Zicola

Blaise Weber

Sarah N. Anderson

CHARLIE HODGMAN charlie.hodgman@nottingham.ac.uk
Professor of Bioinformatics and Systems Biology

Jonathan I. Gent

Jan-Jaap Wesselink

Nathan M. Springer

Hubb C.J. Hoefsloot

Franziska Turck

Maike Stam



Abstract

© 2017 The Author(s). 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.

Journal Article Type Article
Publication Date Jul 21, 2017
Journal Genome Biology
Print ISSN 1474-760X
Electronic ISSN 1465-6906
Publisher Springer Verlag
Peer Reviewed Peer Reviewed
Volume 18
Article Number 137
APA6 Citation Oka, R., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., …Stam, M. (2017). Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology, 18, https://doi.org/10.1186/s13059-017-1273-4
DOI https://doi.org/10.1186/s13059-017-1273-4
Keywords Transcriptional enhancer, Gene regulation, Chromatin accessibility, Histone acetylation, DNAmethylation, Zea mays
Publisher URL https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1273-4
Copyright Statement Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0

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Copyright Statement
Copyright information regarding this work can be found at the following address: http://creativecommons.org/licenses/by/4.0





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