Non-coding, regulatory elements called enhancers and silencers, that modulate the level of gene expression in the different cells and tissues, are likely to play an important role in crops response to environmental factors. They help establish gene regulatory networks that can affect the expression of numerous genes involved in the same biological functions. However, how the structure of these networks changes in response to the environment, and their role in climate adaptation of crops, is largely unknown. Using maize response to water deficit, a model that is important both for our economy and the sustainability of our agricultural practices, This project will aim at studying how networks are rewired in response to water deficit, how much they already participate to water deficit adaptation, and if these information can help develop more accurate model of maze yield prediction in the context of water deficit.
This project aims at studying how plants gene regulatory networks are rewired in response to abiotic constraints in different tissues. To this end, I will use maize response to water deficit as a model. I will use data from the [AMAZING GeneATLAS project](https://amaizing.fr/), to infer the gene regulatory networks of several tissues in well-watered and water-deficit conditions. I am particularly interested in the role of enhancers in such a response.
Polygenic adaptation, in which small changes in allele frequencies co-occur at multiple variants, has been proposed to be a major adaptive mechanism for polygenic traits. Because 90% of genetic variants associated to polygenic traits are located in non-coding, regulatory regions, I am interested in studying the extent to which polygenic selection targets regulatory regions of the human genome. I propose to combine network biology and population genetics methods in order to develop a new approach to detect signatures of polygenic adaptation in regulatory regions.
This project aims at deciphering the enhancer-mediated tissue-specific regulation of gene expression in maize tissues during leaf development. To this end, I contrasted the gene regulatory networks of two leaf tissues, dividing seedling leaves and mature husk modified leaves that protect the cob. Using a systems biology approach, I showed that these two leaf tissues both share a part of their regulatory network, and feature tissue-specific regulatory modules such as response to growth hormone in seedlings, and stress response in husk. I also investigated the molecular origin of such tissue-specific enhancer-driven regulatory networks, and showed that two different transposable elements from families were shaping the tissue-specific gene regulatory networks of seedlings and husks.
During my first postdoc, I investigated the genetic bases of the regulation of the expression of polygenic traits, using systems biology approaches based on bipartite network representation. I notably characterized the regulatory role of germinal mutations increasing the risk to develop cancers.