RP02: The role of repetitive DNA and genome structural variation in mediating environment-epigenome interactions in Populus nigra

  • PhD Supervisor(s): Michele Morgante, Emanuele De Paoli, Federica Cattonaro
  • Host Institution: Institute of Applied Genomics (IGA) -Technology Services, Udine, Italy
  • Duration: 36 months.
  • Fixed start date: 1 April 2018
  • Planned secondment(s): Philipps Universitaet Marburg (DE), Institut National de la Recherche Agronomique (FR)

Different combinations of epigenetic marks mediate the timely expression of genetic determinants and the silencing of detrimental repetitive elements. However, the epigenetic suppression of transposable elements (TEs) can accidentally impact the transcriptional status of neighbouring genes generating epigenetic variants (obligatory or facilitated epialleles) associated with differential phenotypes. To date, these cases provide the most convincing examples of naturally occurring epialleles genetically transmitted by plants. Thus, the capability of environmental stresses to alter the epigenomic landscape and trigger TE activity raises a compelling theme of research focusing on the potential role of TEs in mediating the regulation of gene expression by environmental cues.

In this project we aim to explore the three-way relationship potentially existing between the DNA methylome of poplar (Populus nigra), the highly dynamic transposable element systems that represent a major contributor of plant genomic structural variation and the environmental challenges plants are exposed to. Through the integration of Next Generation Sequencing approaches, single nucleotide polymorphism analysis and genomic maps of structural variants, we aim to produce allele-specific single-base resolution maps of the DNA methylome in poplar emphasizing the effects of the most variable and repetitive component of the genome. The resulting data will be combined with DNA methylation screening in common garden experiments to identify the most reactive TE families and unveil the epigenetic variation that may link TE silencing to gene regulation in an ecologically relevant manner.


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