Projects | Thomas Blein

Root system architecture and plant adaptation

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

Root architecture determines how plants explore the soil for water and nutrients and how they adapt to fluctuating nutrient availability. Our work spans the control of root hair and meristem morphogenesis by Rac/Rop GTPase signalling, the miR169–NF-YA module that adjusts primary root growth and branching, and the role of NF-YA10 in lateral root angle and the area explored by the root system. We also study systemic nitrogen signalling, where the CRA2 pathway coordinates cytokinin and miR399 accumulation to repress root growth and nodulation.

Related publications

— Modification of plant Rac/Rop GTPase signalling using bacterial toxin transgenes
— A miR169 isoform regulates specific NF-YA targets and root architecture in Arabidopsis
— The transcription factor NF-YA10 determines the area explored by Arabidopsis thaliana roots and directly regulates LAZY genes
— The Compact Root Architecture 2 systemic pathway is required for the repression of cytokinins and miR399 accumulation in Medicago truncatula N-limited plants

In legumes, root architecture is tightly linked to symbiotic nitrogen fixation and soil exploration. We contributed to the genome and transcriptome resources of Medicago truncatula, revealing symbiotic islands and thousands of nodule-induced lncRNAs, and to the white lupin genome, which provides a framework to study cluster-root development and phosphate acquisition.

Related publications

— Whole-genome landscape of Medicago truncatula symbiotic genes
— High-quality genome sequence of white lupin provides insight into soil exploration and seed quality

Quantifying these traits requires dedicated phenotyping and imaging approaches. We developed ChronoRoot, an open-hardware and deep-learning system for temporal root-system phenotyping, and ChronoRoot 2.0, which extends it to multi-organ segmentation and higher-throughput analysis. At the cellular scale, we use iRoCS to compare root apical meristems at single-cell resolution, and we have combined 3D imaging with pattern analysis to show how light dynamically regulates root meristem organisation. These studies are supported by image-analysis developments such as rotation-invariant HOG descriptors and attenuation correction for two-view confocal microscopy.

Related publications

— ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
— ChronoRoot 2.0: an open AI-powered platform for 2D temporal plant phenotyping
— The iRoCS Toolbox — 3D analysis of the plant root apical meristem at cellular resolution
— Light dynamically regulates growth rate and cellular organisation of the Arabidopsis root meristem
— Rotation-invariant HOG descriptors using Fourier analysis in polar and spherical coordinates
— Variational attenuation correction in two-view confocal microscopy

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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

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

Leaf development and morphogenesis

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

Leaves are a powerful system to understand how organs acquire their shape. We study the genetic and hormonal control of leaf margin dissection, boundary formation and leaflet individualisation, with a focus on the NAM/CUC transcription factors, miR164 and auxin. We showed that the balance between MIR164A and CUC2 controls leaf margin serration, that miR164, CUC genes and LATERAL SUPPRESSOR interact to control axillary meristem formation, and that NAM/CUC boundary genes promote leaflet formation in distantly related eudicots.

Related publications

— The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis
— Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana
— A conserved molecular framework for compound leaf development

These findings led us to propose that leaf dissection relies on the interplay between boundary domains, KNOX gene activity and auxin gradients. We further reviewed the genetic and molecular networks controlling leaf polarity and the comparison between simple and compound leaves, and analysed the evolution and specific roles of CUC1–CUC3 during Arabidopsis leaf serration.

Related publications

— Leaf development: what it needs to be complex
— A conserved mechanism at the base of leaf dissection
— Leaving the meristem behind: the genetic and molecular control of leaf patterning and morphogenesis
— Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development

More recently, we combined genetics and morphometrics to show that mutations in different pathways can act synergistically to alter leaf dissection, and that GDP-L-fucose is required for boundary definition and differential growth at the leaf margin. Together, this work connects molecular boundary formation to the evolution and diversification of leaf shape.

Related publications

— Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection
— GDP-L-fucose is required for boundary definition in plants