Stage Master2 : Impact des éléments transposables sur l'expression des gènes de maïs

 Stage · Stage M2  · 6 mois    Bac+3 / Licence   GQE - Le Moulon · Gif sur Yvette (France)  577.40 €

 Date de prise de poste : 15 février 2022

Mots-Clés

cis-regulatory sequences, transposable elements, transcriptomics, comparative genomics, comparative epigenomics

Description

Context

Plant development and responses to environmental and hormonal cues are carefully regulated by precise orchestration of gene transcription programs. A large part of this spatiotemporal gene transcriptional regulation is controlled by gene-distal cis-regulatory elements or enhancers. Their regulatory effect is mediated by the binding of transcription factors (TFs), which interact with target gene promoters through 3D-loops and drastically alter the rate and quantity of its mRNA biosynthesis. Transposable Elements (TEs) of various superfamilies have been shown to participate in the rewiring of gene regulatory networks for some key tissue-specific biological functions in animals. In plants, examples of enhancer elements derived from a particular TE have been described and a more general contribution of TEs to cis-regulatory elements has been highlighted in a few species. Despite these findings, how enhancers TF binding sites arise from TE sequences and how they rewire the gene regulatory network in plants remains unclear.


Goals

In a recent study (Fagny et al., Frontiers in Genetics, 2021), we used a systems biology approach to investigate the enhancer-driven regulatory network of two maize tissues at different stages: leaves at seedling stage and ear-covering leaves at flowering. We found that husk-specific enhancers are enriched in miniature inverted-repeat transposable elements (MITEs, a group of non-autonomous DNA transposons) of the Pif-Harbinger superfamily. Investigation of these MITE sequences revealed that some particular families show high enrichment in the TFBS. In these families, over 50% of the MITE insertions overlap with regions of low methylation, suggesting their functional role. We now would like to investigate the impact of sequence and DNA methylation polymorphism at these MITEs on gene expression, using a set of 8 maize genotypes.


Work to do

1) Analysis of the molecular functions sustained by MITEs’ target genes

Using the information given by the gene regulatory network, the student will extract all genes potentially regulated by the MITE TFBS, and will analyze their transcriptional level across 18 tissues/conditions (mRNA-seq data already available) to highlight in which tissues they are the most expressed. He/she will then analyze the functions sustained by these genes, using a gene ontology approach.

2) Conservation of TBFS-containing MITEs across maize lines

We have generated full genome sequence assemblies for 7 other maize genotypes, and generated molecular anchors to locally connect all assemblies in pairwise fashion. The student will use this information to analyze the polymorphism of the TFBS-bearing MITE sequences, and will test whether the TFBSs are more conserved when they are potentially functional.

3) Detection of potential regulatory regions in other genotypes

Using bisulfite-seq data generated on the 8 genotypes, the student will characterize all regions devoid of methylation, which are considered as potential regulatory regions. He/she will then cross this information with the position of the TFBS, to test whether the potential functionality of these sequences is conserved across genotypes.

4) Impact of sequence and methylation polymorphisms on gene expression

We generated mRNA-seq expression data for the 8 genotypes in 18 tissues/conditions. The student will analyze the gene expression profile of the MITE-targeted genes across the 8 genotypes to decipher whether these differ among maize genotypes. He/she will then combine sequence and DNA methylation polymorphisms to expression data and will test for association of these polymorphisms with the gene expression.


Host laboratory

The internship will take place at UMR Génétique Quantitative et Évolution - Le Moulon (http://moulon.inrae.fr/en/), in Paris Saclay. The student will join the GEvAD team (http://moulon.inrae.fr/en/equipes/gevad/), specialized in genetics and adaptation of domesticated plants.

Duration: 4 to 6 months, between February and March 2022.

Candidature

Procédure : Send an email to clementine.vitte@inrae.fr

Date limite : 15 janvier 2022

Contacts

Clémentine Vitte

 clNOSPAMementine.vitte@inrae.fr

Offre publiée le 19 novembre 2021, affichage jusqu'au 15 janvier 2022