Biography

My research focuses on the regulation of plants response to environment at the molecular level. In particular, I am interested in the regulation of gene expression. I study how the networks regulating the expression of genes are rewired in response to environment, and which forces are driving their evolution. During my postdoctoral studies, I was awarded a Marie Skłodowska-Curie Individual Fellowship Marie Skłodowska-Curie Individual Fellowship to assess the role of polygenic adaptation that targets the regulation of gene expression in the evolution of polygenic characters, by using a combination of systems biology and population genetics approaches. I am now working at INRAE in the GQE-Le Moulon laboratory, where I mainly use maize response to abiotic constraints such as water deficit and nitrogen deficit as a model. I recently was awarded a Young Researcher ANR ANR grant to tackle the question of whether better understanding gene regulatory networks rewiring in maize in response to water deficit will help build more accurate yield prediction models.

  • Population Genomics
  • Polygenic Adaptation
  • Epigenomics
  • Transcriptomics
  • Systems Biology
  • Gene Regulatory Networks
  • Biostatistics

Recent News

ANR JCJC NETWITS is starting soon!

I got an ANR JCJC to fund the NETWITS project

Grants from INRAE and Universite Paris-Saclay

I got starting grants from INRAE and Universite Paris-Saclay.

Starting at INRAE as Researcher today!

I’m now a junior researcher at INRAE, working at GQE-Le Moulon.

Meet the Team

Principal Investigators

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Maud Fagny

Researcher

Population Genomics, Polygenic Adaptation, Epigenomics, Transcriptomics, Systems Biology, Gene Regulatory Networks, Biostatistics

Grad Students

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Thomas-Sylvestre Michau

Grad Student

Transcriptomics, Systems Biology, Gene Regulatory Networks, Bioinformatics

Projects

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NETWITS (starting in 2024)

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.

WIREMAIZE - Maize GRN and water deficit (2021-)

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, 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.

PATTERNS (2020 - 2021)

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.

Role of Enhancers in Maize Leaf Development Gene Regulatory Networks (2019-2021)

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.

Characterizing cancer-risk mutations (2015-2017)

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.

PhD thesis - Humans in an Adaptive World : Genetic and Epigenetic Responses to Environmental Challenges (2011-2015)

I did my PhD in population genomics and epigenomics. I studied the impact of the global environment on the genetic and epigenetic diversity of human populations. I investigated the role of a particular type of positive selection, selective sweeps, in shaping the human genome diversity. I also assessed the relative impact of genetic and environmental factors on the variation in DNA methylation profiles between human populations living in contrasted environments.

Experience

 
 
 
 
 

Chargée de Recherche (Researcher)

GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, 91190, Gif-sur-Yvette, France

Jul 2021 – Present Gif-sur-Yvette, France
I investigate the regulation of plants response to environmental constraints.
 
 
 
 
 

Post-doctoral Fellow

UMR7206 Eco-Anthropologie, MNHN, CNRS, Université de Paris, 75016 Paris, France

Apr 2020 – Jun 2021 Paris, France
I investigated the extent of local polygenic selection targeting the regulation of gene expression in complex genomes by combining theoretical work and OMICS data analysis.
 
 
 
 
 

Post-doctoral Fellow

GQE - Le Moulon, Université Paris-Saclay, INRAE, CNRS, AgroParisTech, 91190, Gif-sur-Yvette, France

Jan 2019 – Mar 2020 Gif-sur-Yvette, France
I investigated the role of structural variations in non-coding regions in wiring the tissue-specific gene regulatory network of maize leaf during development using bipartite networks approaches.
 
 
 
 
 

Post-doctoral Fellow

LEE, CNRGH, CEA, 91000 Evry, France

Jan 2018 – Oct 2018 Gif-sur-Yvette, France Evry, France
I worked on the role of miRNAs in deregulating gene expression in the contexte of autoimmune diseases.
 
 
 
 
 

Post-doctoral Fellow

Department of Biostatistics, Harvard T.H. Chan School of Public Helath, Boston MA 02115, United States

Nov 2015 – Dec 2017 Gif-sur-Yvette, France
I characterized the regulatory role of non-coding mutations increasing the risk to develop cancer in humans using bipartite network approaches.
 
 
 
 
 

PhD student

Human Evolutionary Genetics, Institut Pasteur, CNRS UMR2000, Paris, France

Sep 2011 – Sep 2015 Paris, France
I investigated the impact of lifestyle and environment on the genetics and epigenetics variability of human genome.

Publications

Identification of key tissue-specific, biological processes by integrating enhancer information in maize gene regulatory networks
Sex differences in gene expression and regulatory networks across twenty-nine human tissues
Differential DNA methylation in experienced meditators after an intensive day of mindfulness-based practice: Implications for immune-related pathways
PUMA: PANDA Using MicroRNA Associations

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