Our research focuses on the impact of regulatory non-coding RNAs (such as si/miRNAs or long non-coding RNAs) in developmental mechanisms controlling the plasticity of the root system. Our lab develops two research axes using Arabidopsis thaliana and Medicago truncatula to address key emerging questions on the ncRNA field :
This axis profits from the extensive knowledge of Medicago and Arabidopsis genomes among ecotypes to analyse, at genome-wide level, npcRNA evolution and polymorphism (both on lincRNAs and si/miRNAs). We want to establish correlations between the expression of ncRNAs and phenotypic diversity with a focus on root responses to low phosphate in Arabidopsis and low nitrate/rhizobial symbiosis in Medicago, both interesting agricultural traits.
2. Developmental mechanisms involving ncRNAs
This second axis focuses on specific regulatory mechanisms involving ncRNAs in a defined developmental context.
We have identified a class of lincRNAs (the ASCO RNA, for Alterntive Splicing COmpetitor) that interact with the alternative splicing machinery in Arabidopsis. This results in a significant repression of lateral root formation. Hence, by modulating npcRNA expression, changes in alternative splicing patterns may control developmental transitions such as the organogenesis of a lateral root.
In addition, we have identified a class of lincRNAs that co-localise with 24nt siRNA in the genome. This dual transcription pattern (producing polII ncRNA as well as polV-dependent 24nt siRNAs) of the same locus, named APOLO, correlated with the expression pattern of a distant neighbouring gene. Indeed, we could show that the APOLO lincRNA (for Auxin-driven PrOmoter LOop ncRNA) controls the formation of a chromatin loop encompassing the promoter of the neighbouring gene and determining its epigenetic status in Arabidopsis. These epigenetic changes lead to changes in gene expression during primary root growth and gravitropism. Interestingly, similar type of lincRNAs and 24nt siRNAs have been identified in Medicago truncatula linked to the formation of nodule organogenesis. Hence, epigenetic changes and/or regulation of alternative splicing can be regarded as part of a global analysis of mechanisms involved in adaptation to the environment.