long non-coding RNA (lncRNA) | Thomas Blein

Long non-coding RNAs as regulators of gene expression

Thu, 05 Aug 2021 17:52:41 +0200

Long non-coding RNAs are emerging as versatile regulators of plant gene expression, acting at the interface between chromatin, transcription and RNA processing. We have characterised lncRNAs that control chromatin conformation and gene expression in response to developmental and environmental signals. APOLO recognises distant genomic loci through R-loop formation and decoys LHP1 to modulate chromatin loops during lateral root development; it also interacts with VIM1 and LHP1 to regulate DNA and histone methylation at YUCCA2 during thermomorphogenesis, a function shared with the sequence-unrelated human UPAT lncRNA. MARS controls the marneral biosynthetic gene cluster by titrating LHP1 in an ABA-dependent manner, promoting a chromatin loop between MRN1 and a distal enhancer, while ARES modulates lateral root architecture through its neighbouring genes.

Related publications

— R-Loop Mediated trans Action of the APOLO Long Noncoding RNA
— The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants
— The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA
— The long intergenic noncoding RNA ARES modulates root architecture in Arabidopsis

A second axis of our work concerns alternative splicing. ASCO interacts with the splicing regulators NSR and with spliceosome components such as PRP8a and SmD1b, thereby modulating the recognition of specific transcripts. More recently, we identified ACHLYS, a Brassicaceae-conserved lncRNA that interacts with NSRa and GRP7 and modulates biomolecular condensates to regulate alternative splicing during lateral root development.

Related publications

— Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses
— The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors
— The long non-coding RNA ACHLYS modulates biomolecular condensates to regulate alternative splicing in root development

Beyond these model mechanisms, we investigate how lncRNAs contribute to specific biological processes and how their modes of action can be generalised. We identified lncRNAs associated with anthocyanin pigmentation in carrot roots, reviewed the roles of lncRNAs in root growth and development, and synthesised their contributions to environmental responses and adaptation and to chromatin regulation across plants.

Related publications

— Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation
— Regulatory long non-coding RNAs in root growth and development
— From environmental responses to adaptation: the roles of plant lncRNAs
— From non-coding to chromatin regulators: VIVIpary and the rise of lncRNAs in plant biology

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

Drought and Heat Tolerance in Plants through AI-Assisted Long Noncoding RNAs Design – DHARP

Mon, 01 Sep 2025 00:00:00 +0000

Rice is one of the most important food crops globally, but its productivity is highly vulnerable to climate change, especially to increasing episodes of drought and extreme heat. These stresses often occur together and have a significant impact on yield and food security. While traditional breeding has contributed to improving stress tolerance, this process is slow and frequently constrained by trade-offs between growth and resilience. New strategies are needed to help crops respond quickly and efficiently to changing environmental conditions.

This project aims to explore the potential of long noncoding RNAs (lncRNAs), a relatively understudied class of RNA molecules that do not encode proteins but are increasingly recognized as powerful regulators of gene expression. Because lncRNAs can influence how plants respond to stress, often in subtle and finely tuned ways, they represent a promising new layer of control over key survival traits. However, predicting their function remains a major scientific challenge, as they lack the sequence conservation typical of protein-coding genes. Nonetheless, lncRNAs that share similar biological roles often contain short conserved sequence or structural motifs linked to their interactions with protein partners. However, the systematic detection and characterization of these motifs remains a significant computational challenge due to their subtlety, variability, and the complexity of RNA-protein interaction landscapes.

Artificial intelligence (AI) offers a promising solution for identifying patterns and features beyond primary sequence similarity. Therefore, we propose to use deep learning embedding to analyze the structure and patterns of lncRNAs in rice and Arabidopsis, identifying those most likely to be involved in gene regulation in the context of heat and drought response. By combining AI predictions with high throughput functional screening, we aim to pinpoint the most effective lncRNAs and understand how they work in the plant’s stress response networks. Our ultimate goal is to turn this knowledge into practical tools: using synthetic lncRNAs delivered through innovative RNA spray technology to help plants better tolerate high temperatures and water scarcity—without the need for genetic modification.

This project merges cutting-edge artificial intelligence methods with experimental high throughput plant biology to unlock new ways of boosting crop resilience. It aims to lay the foundation for a new generation of RNA-based, climate-smart agricultural solutions.

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.

The Arabidopsis APOLO and human UPAT sequence-unrelated long noncoding RNAs can modulate DNA and histone methylation machineries in plants

Mon, 01 Aug 2022 00:00:00 +0000

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

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

Regulatory long non-coding RNAs in root growth and development

Tue, 01 Feb 2022 00:00:00 +0000

Insights into long non-coding RNA regulation of anthocyanin carrot root pigmentation

Mon, 01 Feb 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

The Arabidopsis lncRNA ASCO modulates the transcriptome through interaction with splicing factors

Fri, 01 May 2020 00:00:00 +0000

R-Loop Mediated trans Action of the APOLO Long Noncoding RNA

Sun, 01 Mar 2020 00:00:00 +0000

Whole-genome landscape of Medicago truncatula symbiotic genes

Sat, 01 Dec 2018 00:00:00 +0000

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions

Tue, 01 May 2018 00:00:00 +0000