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

RNA processing, silencing and chromatin regulation

Thu, 01 Oct 2026 00:00:00 +0000

Gene expression in plants is controlled by interconnected layers of chromatin organisation, RNA processing and RNA silencing. We study how chromatin remodellers and histone modifiers shape transcriptional programmes: BAF60, a SWI/SNF subunit, represses cytokinin production and promotes root meristem activity; GCN5 regulates H3K14 acetylation and salicylic-acid homeostasis; and HSFA1b coordinates developmental and stress-response genes. We also contributed to the analysis of wheat nuclear architecture, revealing genome territories and transcription factories in a polyploid genome.

Related publications

— A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture
— GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5′ and 3′ ends of its target genes
— Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b regulates multiple developmental genes under benign and stress conditions
— Wheat chromatin architecture is organized in genome territories and transcription factories

At the RNA level, we investigate alternative splicing, transcript maturation and quality control. We showed that MPK4 is required for pathogen-associated molecular pattern-triggered alternative splicing, used nanopore sequencing to resolve the complexity of plastid transcript processing, and demonstrated that the spliceosome components PRP39a and SmD1b act in post-transcriptional transgene silencing.

Related publications

— Role of MPK4 in pathogen-associated molecular pattern-triggered alternative splicing in Arabidopsis
— Full Length Transcriptome Highlights the Coordination of Plastid Transcript Processing
— Synergistic action of the Arabidopsis spliceosome components PRP39a and SmD1b in promoting posttranscriptional transgene silencing

We are particularly interested in how RNA quality control and silencing machineries select their targets. We showed that SGS3 is recruited to chromatin by the remodeller CHR11 to select RNAs that initiate siRNA production, and that the SUPERKILLER complex subunit 3 mediates miR172-directed cleavage of Nodule Number Control 1 during Medicago nodulation. Together, this work provides the mechanistic context in which long non-coding RNAs and other regulatory RNAs operate.

Related publications

— Arabidopsis SGS3 is recruited to chromatin by CHR11 to select RNA that initiate siRNA production
— Subunit 3 of the SUPERKILLER complex mediates microRNA172-directed cleavage of Nodule Number Control 1 in Medicago truncatula

Alternative Splicing | Thomas Blein

Long non-coding RNAs as regulators of gene expression

RNA processing, silencing and chromatin regulation