UNRAVELING CHROMATIN DINAMICS DURING DEETIOLATION

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 the development.
Plants are ideal models 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 research 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. This developmental transition has been extensively used to study mechanisms controlling plant development in response to light. However it is still unclear how the 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. Phillip Lord will mentor the student 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.
Under the guidance of Dr. Lord, the student will construct a statistical and categorical model to integrate the bioinformatic and molecular data. The principal aim of this model is to enable integration of knowledge from multiple data sources, describing the functional characteristics of our candidate genes. This will allow us to uncover unknown relationships and the generation of new hypotheses to better understand how environmental signals modulates development by influencing chromatin organization and thus gene expression. Dr Lord will also help to generate a resear