Swammerdam Institute for Life Sciences

Predicting transcriptional enhancers in the maize genome

17 August 2017

An international team of moleculair biologists and bio-informatics scientists succeeded in the genome wide identification of transcriptional enhancers in the maize genome. With this study, an important step is taken in unravelling the regulatory code of the important crop plant maize.

The UvA researchers Rurika Oka, Blaise Weber, Maike Stam and Huub Hoefsloot of the Swammerdam Institute for Life Sciences and Franziska Turck and Johan Zicola from the Max Planck Institute for Plant Breeding Research Germany published the results of their work in a special issue of Genome Biology on plant epigenomics.

Maize transcriptional enhancers

Image: UvA

The differentiation of cells and their response to external signals such as light, temperature and pathogens is largely accomplished through the activation and repression of regulatory DNA sequences, such as transcriptional enhancers. Enhancers are non-coding DNA sequences that activate the transcription of genes, and these enhancers can be located in close vicinity to, but also very far away from the genes they regulate.

Crucial

Knowledge on the transcriptional regulatory code is crucial for the functional annotation of the genome and the selection of desirable traits for plant breeding. Many genome-wide studies have been performed on animals, identifying thousands of enhancer sequences. The regulatory code of plants, especially that of crop plants, is, however, still largely unknown. A number of plant enhancers have been discovered and one by one experimentally characterised but so far the genome-wide identification has been lagging behind. With this study, an important step is taken in unravelling the regulatory code of the important crop plant maize.

Genome-wide prediction of enhancers in maize

From genome-wide animal studies, it is well known that specific epigenetic marks and chromatin structures are associated with the activation and repression of genes and regulatory elements. For example, to identify active enhancers in animals, acetylation of histone protein 3 aminoacid lysine on position 27 (H3K27ac), together with low DNA methylation and open chromatin regions are widely used. The animal data and the characterisation of a few plant enhancers at the chromatin level inferred that plant enhancers should be characterised by similar epigenetic marks. Hence, to predict transcriptional enhancers in the crop plant maize, we integrated available genome-wide DNA methylation data with newly generated maps of chromatin accessibility and histone 3 lysine 9 acetylation (H3K9ac, another active DNA mark) enrichment in two different tissues. Approximately 1500 regions were classified as enhancer candidates, which included three known and putative enhancers previously reported. About half of the enhancer candidates were located more than 10 kb away from putative target genes. Intriguingly, the chromatin profiles of these enhancer candidates show similarities, but also differences with animal enhancers. Current work is focussed on the verification and further characterisation of the identified enhancer candidates. The published work not only provides a better understanding of the gene regulatory code in plants, but also enlarges the toolbox for the functional annotation of complex plant genomes, and suggests novel targets for informed breeding in crop species. 

Publication details

Oka, R., Zicola, J., Weber, B., Anderson, S.N., Hodgman, C., Gent, J.I., Wesselink, J-J., Springer, N.M., Hoefsloot, H.C.J., Turck, F., Stam, M. (2017). Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biology, 18(1), 137. http://doi.org/10.1186/s13059-017-1273-4

Funding

Published by  Swammerdam Institute