Training in Systems Biology Applied to Flowering

Lead Research Organisation: John Innes Centre
Department Name: Contracts Office


This project focuses on plant reproductive development as a subject to provide interdisciplinary training ranging from developmental genetics to computational analysis and modelling of large biological datasets. We will study how the master regulator of reproductive organ development AGAMOUS (AG) selects different target genes at different stages of development. Target availability may be controlled by chromatin accessibility, which is typically assayed by nuclease sensitivity assays. Based on precedents from other systems, it is also possible that AG acts in combination with stage-specific regulators that interact with specific cis-elements within target genes. Therefore, the work will focus on determining chromatin accessibility at different stages, defining stage-specific target genes of AG and mining the data for cis-elements that could mediate stage-specific expression.
To screen for AG targets, tagged versions of AG will be used for chromatin immunoprecipitation (ChIP) at different time points. For chromatin accessibility assays, nuclei will be purified from ap1 cal AP1GR plants at different stages after induction of organ development and treated with micrococal nuclease or DNAseI. Global analysis of nuclease-sensitive sites will be based on published methods using Affymetrix tiling arrays. The datasets will be mined for cis-elements that may participate in stage-specific expression, based on over-representation in target genes bound by AG at specific stages, on the overlap with chromatin accessibility data and on evolutionary conservation.


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Description A fundamental question in Biology is how genes influence the size and shape of macroscopic structures such as limbs in animals or flowers in plants. In plants, growth of these structures ultimately depends on how their constituent cells grow and divide. In this project, we contributed to this area in two ways:

1. We established methods for accurately measuring cell growth and division in developing flowers. We found that an important regulatory gene (JAGGED) changes growth of floral organs by inducing oriented cell growth, faster cell growth and division, and by modifying the way cell growth and division are coordinated with each other.

2. We found that JAGGED promotes plant organ growth to a large extent by removing a constraint on the progression of cells into DNA synthesis. Apart form revealing fundamental mechanisms that shape plant organs, our results revealed similarities in the control of plant tissue growth during normal development and in response to environmental stresses.
Exploitation Route In the long term, clarifying the rules of plant organ growth will be important for predictive genetic modification of plant shape, which is important for crop performance.
Sectors Agriculture, Food and Drink

Description The findings in this project are of fundamental nature, with potential long-term impact on plant genetic modification for crop improvement. A major aim of this type of grant (EU Marie-Curie Training Network) is staff training, and accordingly staff were trained in cutting edge molecular genetics and image analysis methods. This resulted in a PhD award (the student subsequently progressed on her academic career) and improved the skills of a research assistant who subsequently won a PhD studentship in Denmark.
First Year Of Impact 2014
Sector Agriculture, Food and Drink
Impact Types Cultural