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STUDY OF CHROMATIN DINAMICS DURING DEETIOLATION

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  • Full or part time
    Dr de Lucas
    Dr Lord
  • Application Deadline
    No more applications being accepted

Project Description

Eukaryotic genomes must be tightly folded to be contained within cell nuclei. This compacted macromolecule, which consists of DNA, proteins and RNA, is known as chromatin. The structure of the chromatin modulates each process involving DNA accessibility (such as replication, transcription and DNA repair). The basic chromatin unit is the nucleosome, which consists of ~146 base pairs of DNA wrapped in two turn around eight histone proteins (2xH2A, 2xH2B, 2xH3, 2xH4). There are multiple histone posttranscriptional modifications that control genomic functions by affecting chromatin compaction. Despite the extensive epigenetic studies generated to the date, it is still not clear how the different histone posttranscriptional modifications act coordinately during development.
Plants are ideal to study chromatin-regulated processes, primarily because their epigenetic regulators are well conserved among metazoans. Secondly, in contrast to other organisms, their organs are differentiated post-embryonically, which allows studies to be performed in finer detail than is possible in other organisms. One of the most intriguing questions in biology is how the environment affects gene expression. It is known that chromatin organization has direct effects on this process, by influencing DNA availability to regulatory proteins. The main goal of this project is to understand how the environment dynamically regulates chromatin changes during plant development.

When a buried seed germinates, it undergoes a developmental strategy termed skotomorphogenesis, whereby the seedling grows on seed reserves in the absence of chlorophyll accumulation. Upon reaching the soil surface, the seedling undergoes a marked developmental transition, termed deetiolation, toward the normal photomorphogenic pattern of fully green plants. This transition is triggered by light and involves resetting the chromatin modifications that motivate the transcriptional switch that gives rise to the new phase. It is not clear how light induces chromatin reorganization and uncovering the early events controlling this process is key for understanding how plants adapt their growth and development to the continuous changing environment.

Key scientific questions to be addressed are:
Q1. What are the main chromatin modifications happening during deetiolation? Which enzymes are involved? Is there a hierarchical connection between the different chromatin modifications?
Q2. Which genes are the primary targets affected by the chromatin reorganization? What are the functions of these genes?
Q3. What is the mechanism by which light signaling impinges on the chromatin remodelling machinery?"
To address these questions we will perform state-of-the-art next generation sequencing (NGS) techniques to profile chromatin and transcriptional changes during the course of detiolation. The student will be mentored in the use of bioinformatic and statistical tools to perform meta-analysis with the NGS data and identify candidate genes involved in chromatin reorganization in response to light. Function and mode of action of the candidate genes will be studied in Arabidopsis with genetic, molecular biology approaches and state of the art microscopy techniques.

Funding Notes

This project is in competition with others for funding. Success will depend on the quality of applications received, relative to those for competing projects. If you are interested in applying, in the first instance contact the supervisor, with a CV and covering letter, detailing your reasons for applying for the project

References

Ikeuchi, Momoko, Akira Iwase, Bart Rymen, Hirofumi Harashima, Michitaro Shibata, Mariko Ohnuma, Christian Breuer, et al. 2015. “PRC2 Represses Dedifferentiation of Mature Somatic Cells in Arabidopsis.” Nature Plants 1 (7): 15089. doi:10.1038/nplants.2015.89.

Taylor-Teeples, M, L Lin, M de Lucas, G Turco, T W Toal, Allison Gaudinier, N F Young, et al. 2015. “An Arabidopsis Gene Regulatory Network for Secondary Cell Wall Synthesis..” Nature 517 (7536): 571–75. doi:10.1038/nature14099.

Bernardo-Garcia, S, M de Lucas, C Martinez, A Espinosa-Ruiz, J M Daviere, and S Prat. 2014. “BR-Dependent Phosphorylation Modulates PIF4 Transcriptional Activity and Shapes Diurnal Hypocotyl Growth.” Genes & Development 28 (15): 1681–94. doi:10.1101/gad.243675.114.

de Lucas Miguel, and Salomé Prat. 2014. “PIFs Get BRright: PHYTOCHROME INTERACTING FACTORs as Integrators of Light and Hormonal Signals..” The New Phytologist 202 (4): 1126–41. doi:10.1111/nph.12725.

de Lucas Miguel, Jean-Michel Davière, Mariana Rodríguez-Falcón, Mariela Pontin, Juan Manuel Iglesias-Pedraz, Séverine Lorrain, Christian Fankhauser, Miguel Angel Blázquez, Elena Titarenko, and Salomé Prat. 2008. “A Molecular Framework for Light and Gibberellin Control of Cell Elongation.” Nature 451 (7177): 480–84. doi:10.1038/nature06520.

How good is research at Durham University in Biological Sciences?

FTE Category A staff submitted: 39.00

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