Arabidopsis Thaliana | Thomas Blein

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

The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA

Sun, 01 May 2022 00:00:00 +0000

Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing

Fri, 01 Oct 2021 00:00:00 +0000

Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation

Wed, 01 Jul 2020 00:00:00 +0000

GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes

Mon, 01 Jun 2020 00:00:00 +0000

Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis

Wed, 01 Apr 2020 00:00:00 +0000

GDP-L-fucose is required for boundary definition in plants

Fri, 01 Dec 2017 00:00:00 +0000

A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis

Sun, 01 Jun 2014 00:00:00 +0000

Modification of plant Rac/Rop GTPase signalling using bacterial toxin transgenes

Tue, 01 Jan 2013 00:00:00 +0000

Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development

Sat, 01 Jan 2011 00:00:00 +0000

Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana

Tue, 01 Jul 2008 00:00:00 +0000

The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis

Wed, 01 Nov 2006 00:00:00 +0000