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.

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

Projects

Maize Gene Regulatory Networks Response to Water Deficit (2021-today)

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

Contact

  • maud.fagny@mnhn.fr
  • +33 (0)1 73 78 28 06
  • EcoAnthropology Lab
    UMR 7206 CNRS/MNHN/Universite Paris Diderot
    Muséum National d'Histoire Naturelle
    Site du Musée de l'Homme
    Bureau E202
    17 place du Trocadéro
    75016 Paris
  • Unpredictable due to the post-coronavirus lockdown reopening.
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