Conservation and evolution of lncRNAs

Tue, 03 Aug 2021 18:20:46 +0200

Unlike protein-coding genes, lncRNAs show limited sequence conservation, which makes orthology assignment and functional transfer difficult. We investigate alternative levels of conservation—expression, genomic position, secondary structure and function—to understand how lncRNAs evolve and contribute to plant adaptation. Comparing two Arabidopsis accessions under phosphate starvation, we found that lncRNAs are far more variable between accessions than coding genes, even when their DNA sequence is conserved, and identified ecotype-specific lncRNAs linked to root responses. At the genome-wide level, we analysed the evolutionary age, sequence conservation and transcriptional regulation of Arabidopsis lincRNAs, revealing a root-specific transcription-factor network and distinct selective pressures across lincRNA age classes.

Related publications

— Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
— Transcription factors KANADI 1, MYB DOMAIN PROTEIN 44, and PHYTOCHROME INTERACTING FACTOR 4 regulate long intergenic noncoding RNAs expressed in Arabidopsis roots

Conservation can also be functional rather than sequence-based. APOLO and the human UPAT lncRNA share neither sequence nor structure, yet both are recognised by the conserved VIM1/LHP1 machinery in plants, illustrating how lncRNA function can be preserved through conserved protein interactions. We have synthesised these findings in reviews on lncRNA conservation and on their contribution to environmental adaptation.

Related publications

— The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
— From environmental responses to adaptation: the roles of plant lncRNAs

More broadly, the same evolutionary question applies to other multigenic and regulatory loci. In apple, we contributed to a haplotype-resolved analysis of the S-locus showing that long-term balancing selection preserves multigenic S-haplotype architectures despite extensive structural divergence and transposable-element accumulation. This broader perspective will help us connect lncRNA evolution to the evolution of plant genomes, regulatory sequences and adaptive traits.

Related publications

— Innovation within stability: balancing selection preserves multigenic S-haplotype architecture in apple

Non-coding RNAs regulatory networks controlling lateral root organogenesis across Brassicaceae – RESOLAT

Wed, 01 Jan 2025 00:00:00 +0000

Long non-coding RNAs (lncRNAs) are now recognized as regulators of gene expression, from chromatin conformation to protein translation, playing a key role in a variety of biological processes. However, their mode of action remains poorly understood, due to the lack of known characteristics that can determine their mechanism of action. Their integration within biological networks remains largely unknown, in particular lateral root development.

The multidisciplinary RESOLAT project aims to understand the impact of lncRNAs on the gene network regulating lateral root development in Brassicaceae. Using time-series RNA-seq data, we propose to reconstruct the gene regulatory network controlling lateral root development in eight Brassicaceae, integrating coding and non-coding genes (small and long). This approach will enable us to identify new interactions and regulatory pathways, with particular emphasis on lncRNAs.

To overcome the challenges associated with the functional characterization of lncRNAs, we propose an approach based on the conservation of their function. Based on lateral root development, a highly conserved process in Angiosperms, we will use conservation of position in the regulatory network as a proxy for conservation of function, i.e. regulation of orthologous genes in different species. By integrating data on genomic conservation (genomic synteny, sequence, secondary structure) and expression conservation during lateral root development, we will seek to better understand the conservation features leading to the functionality of long lncRNAs, including their ability to regulate orthologous genes within Brassicaceae.

Using deep learning approaches based on large language models (LLMs) that will combine sequence and network data, we plan to develop a predictive tool to determine whether a lncRNA acts as a regulator of gene expression level.

Finally, we will use functional approaches in several species to validate the function of conserved lncRNAs in the control of lateral root architecture. First, we will use a semi-high-throughput method derived from Perturb-seq to confirm the regulatory action of conserved lncRNAs in A. thaliana. Based on these results, we will further functionally characterize lncRNAs conserved in several Brassicaceae species to validate their role in controlling lateral root architecture. By modifying the expression dynamics of conserved regulators, we should be able to quantitatively modify root architecture and confirm the regulatory links established by gene network inference.

By comparing different species with a common lateral root organogenesis program, this project will reveal evolutionary conserved and specific mechanisms controlling lateral root development in Brassicaceae, including both wild and cultivated species. It will also enable us to identify functionally conserved lncRNAs and analyze the features underlying their conservation.

Brassicaceae | Thomas Blein

Conservation and evolution of lncRNAs

Non-coding RNAs regulatory networks controlling lateral root organogenesis across Brassicaceae – RESOLAT