Thomas Blein

• Ph. D.
• Researcher at French National Centre for Scientific Research

Root developmental plasticity relies on transcriptional reprogramming, which largely depends on the activity of transcription factors (TFs). NF‐YA2 and NF‐YA10 (nuclear factor A2 and A10) are downregulated by the specific miRNA isoform miR169defg. Here, we analyzed the role of the Arabidopsis thaliana TF NF‐YA10 in the regulation of lateral root (L...

Legumes and rhizobia establish a nitrogen-fixing symbiosis that involves the formation of a lateral root organ, the nodule, and the infection process that allows intracellular accommodation of rhizobia within nodule cells. This process involves significant gene expression changes regulated at the transcriptional and post-transcriptional levels. We...

In plants, aberrant RNAs produced by endogenous genes or transgenes are normally degraded by the nuclear and cytosolic RNA quality control (RQC) pathways. Under certain biotic or abiotic stresses, RQC is impaired, and aberrant RNAs are converted into siRNAs that initiate post-transcriptional gene silencing (PTGS) in the cytosol. How aberrant RNAs a...

As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the tra...

Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression in plants. They have been linked to a wide range of molecular mechanisms, including epigenetics, miRNA activity, RNA processing and translation, and protein localization or stability. In Arabidopsis, characterized lncRNAs have been implicated in several physiologi...

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of eight annotation resources, we defined 6,599 hig...

Root developmental plasticity relies on transcriptional reprogramming, which largely depends on the activity of transcription factors (TFs). NF-YA2 and NF-YA10 (Nuclear Factor A2 and A10) are down-regulated by the specific miRNA isoform miR169defg, in contrast to miR169a. Here, we analyzed the role of the Arabidopsis thaliana TF NF-YA10 in the regu...

Besides regulating splicing, the conserved spliceosome component SmD1b promotes posttranscriptional silencing of sense transgenes (S-PTGS). Here, we show that the conserved spliceosome component PRP39a also plays a role in S-PTGS in Arabidopsis thaliana. However, PRP39a and SmD1b actions appear distinct in both splicing and S-PTGS. Indeed, RNAseq-b...

Thousands of long intergenic noncoding RNAs (lincRNAs) have been identified in plant genomes. While some lincRNAs have been characterized as important regulators in different biological processes, little is known about the transcriptional regulation for most plant lincRNAs. Through the integration of eight annotation resources, we defined 6,599 hig...

In this paper, we propose a novel and efficient two-stage variable selection approach for sparse GLARMA models, which are pervasive for modeling discrete-valued time series. Our approach consists in iteratively combining the estimation of the autoregressive moving average (ARMA) coefficients of GLARMA models with regularized methods designed for pe...

Background RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP ( APOLO ), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Results Here, we show that in addition to the PRC1-component LIKE HETEROCHROMATIN...

Besides regulating splicing, the spliceosome component SmD1 promotes posttranscriptional silencing of sense transgenes (S-PTGS). Here, we show that the spliceosome component PRP39a also plays a role in S-PTGS. However, PRP39a and SmD1 actions appear distinct. Indeed, RNA-seq analysis identified different sets of deregulated mRNAs and non-coding RNA...

In this paper, we propose a novel and efficient two-stage variable selection approach for sparse GLARMA models, which are pervasive for modelling discrete-valued time series. Our approach consists in iteratively combining the estimation of the autoregressive moving average (ARMA) coefficients of GLARMA models with regularized methods designed for p...

Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. Here we identified the long noncoding RNA (lncRNA) MARneral Silencing (MARS), localized inside th...

As sessile organisms, plants have evolved sophisticated mechanisms of gene regulation to cope with changing environments. Among them, long non-coding RNAs (lncRNAs) are a class of RNAs regulating gene expression at both transcriptional and post-transcriptional levels. They are highly responsive to environmental cues or developmental processes and a...

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short-read RNA-Seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is crucial...

Plastid gene expression involves many post-transcriptional maturation steps resulting in a complex transcriptome composed of multiple isoforms. Although short read RNA-seq has considerably improved our understanding of the molecular mechanisms controlling these processes, it is unable to sequence full-length transcripts. This information is however...

Background: Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot...

RNA-DNA hybrid (R-loop)-associated long noncoding RNAs (lncRNAs), including the Arabidopsis lncRNA AUXIN-REGULATED PROMOTER LOOP (APOLO), are emerging as important regulators of three-dimensional chromatin conformation and gene transcriptional activity. Here, we showed that in addition to the PRC1-component LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1), AP...

Carrot (Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical rol...

Background Deep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot,...

Carrot ( Daucus carota L.) is one of the most cultivated vegetable in the world and of great importance in the human diet. Its storage organs can accumulate large quantities of anthocyanins, metabolites that confer the purple pigmentation to carrot tissues and whose biosynthesis is well characterized. Long non-coding RNAs (lncRNAs) play critical ro...

Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. Here we identified the long noncoding RNA (lncRNA) MARneral Silencing (MARS) , localized inside t...

Root architecture varies widely between species, and even between ecotypes of the same species, despite the strong conservation of the coding portion of their genomes. By contrast, non-coding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long non-coding RNAs (lncRNAs) are known t...

The modification of histones by acetyl groups has a key role in the regulation of chromatin structure and transcription. The Arabidopsis thaliana histone acetyltransferase GCN5 regulates histone modifications as part of the Spt-Ada-Gcn5 Acetyltransferase (SAGA) transcriptional coactivator complex. GCN5 was previously shown to acetylate lysine 14 of...

Polyploidy is ubiquitous in eukaryotic plant and fungal lineages, and it leads to the co-existence of several copies of similar or related genomes in one nucleus. In plants, polyploidy is considered a major factor in successful domestication. However, polyploidy challenges chromosome folding architecture in the nucleus to establish functional struc...

Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated...

Alternative splicing (AS) is a major source of transcriptome diversity. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through different molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRs interact with the ALTERNATIVE SPLICING COMPETITOR (ASCO) lncRNA. Here, we analyze the effect of the knock-down and overexpressi...

White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a...

In eukaryotes, three-dimensional genome organization is critical for transcriptional regulation of gene expression. Long noncoding RNAs (lncRNAs) can modulate chromatin conformation of spatially related genomic locations within the nucleus. Here, we show that the lncRNA APOLO (AUXIN-REGULATED PROMOTER LOOP) recognizes multiple distant independent l...

Alternative splicing (AS) is a major source of transcriptome and proteome diversity in higher organisms. Long noncoding RNAs (lncRNAs) have emerged as regulators of AS through a range of molecular mechanisms. In Arabidopsis thaliana, the AS regulators NSRa and b, which affect auxin-driven lateral root formation, can interact with the ALTERNATIVE SP...

White lupin (Lupinus albus L.) is a legume that produces seeds recognized for their high protein content and good nutritional value (lowest glycemic index of all grains, high dietary fiber content, and zero gluten or starch). White lupin can form nitrogen-fixing nodules but has lost the ability to form mycorrhizal symbiosis with fungi. Nevertheless...

Cell division and growth are the major cellular mechanisms that determine the size and shape of plant organs such as leaves. How these mechanisms are orchestrated during leaf morphogenesis remains unknown. Our objective here is to quantify 3D cell parameters during leaf development.

Background: Root architecture varies widely between species and even between ecotypes of the same species despite the strong conservation of the protein-coding portion of their genomes. In contrast, non-coding RNAs evolved rapidly between ecotypes and may control their differential responses to the environment as several long non-coding RNAs (lncRN...

Alternative splicing (AS) of pre-mRNAs in plants is an important mechanism of gene regulation in environmental stress tolerance but plant signals involved are essentially unknown. Pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) is mediated by mitogen-activated protein kinases and the majority of PTI defense genes are regulated...

Advances in deciphering the functional architecture of eukaryotic genomes have been facilitated by recent breakthroughs in sequencing technologies, enabling a more comprehensive representation of genes and repeat elements in genome sequence assemblies, as well as more sensitive and tissue-specific analyses of gene expression. Here we show that PacB...

Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in Arabidopsis thaliana. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named Alternative Splicing Comp...

(A) Pearson correlation matrix heatmap with dendograms showing the relative distance between each poly(A)+ RNA-seq samples. (B) PCA analysis showing the effect of auxin and genotype on the variance between samples.

(A) Pearson correlation matrix heatmap with dendograms showing the relative distance between each sample of the RIP-seq experiments. (B) PCA analysis showing the effect the variance between samples.

(A) Proximal and (B) distal variant relative abundance normalized to an housekeeping transcript (PP2C). Error bars correspond to ± the standard deviation of three biological replicates. Significance was determined using a Student’s t-test (∗∗∗p-value < 0.001).

Sequence of primers used in this study.

Summary of RNA-seq and RIP-seq data analysis. (A) Description of spreadsheet tab. (B) Differential gene expression analysis. (C) RNA prof analysis. (D) Expression and usage of all isoforms from genes containing at least one isoforms switching event. (E) NSRa targets identified by RIP. (F) Transcription Factor identified in NSRa targets.

Large-scale methods and robust algorithms are needed for a quantitative analysis of cells status/geometry in situ. It allows the understanding the cellular mechanisms that direct organ growth in response to internal and environmental cues. Using advanced whole-stack imaging in combination with pattern analysis, we have developed a new approach to i...

In Arabidopsis thaliana, HEAT SHOCK TRANSCRIPTION FACTORA1b (HSFA1b), controls resistance to environmental stress and is a determinant of reproductive fitness by influencing seed yield. To understand how HSFA1b achieves this, we surveyed its genome-wide targets (ChIP-seq) and its impact on the transcriptome (RNA-seq) under non-stress (NS), heat str...

The CUP-SHAPED COTYLEDON (CUC) transcription factors control plant boundary formation, thus allowing the emergence of novel growth axes. While the developmental roles of the CUC genes in different organs and across species are well characterized, upstream and downstream events that contribute to their function are still poorly understood. To identi...

Morphogenesis is a complex process that integrates several mechanisms from the molecular to the organ scales. In plants, division and growth are the two fundamental cellular mechanisms that drive morphogenesis. However, little is known about how these mechanisms are coordinated to establish functional tissue structure. A fundamental bottleneck is t...

Development in plants is a continuous process during which new tissues and organs are formed all along its life cycle. Development involves the coordination of both time and space of complex cellular processes such as proliferation, expansion and differentiation following endogenous programmes and in response to environmental signals. Since their d...

Chromatin architecture determines transcriptional accessibility to DNA and consequently gene expression levels in response to developmental and environmental stimuli. Recently, chromatin remodelers such as SWI/SNF complexes have been recognized as key regulators of chromatin architecture. To gain insight into the function of these complexes during...

In plants, roots are essential for water and nutrient acquisition. Micro RNA s (mi RNA s) regulate their target m RNA s by transcript cleavage and/or inhibition of protein translation and are known as major post‐transcriptional regulators of various developmental pathways and stress responses. In A rabidopsis thaliana , four isoforms of mi R 169 ar...

The histogram of oriented gradients (HOG) is widely used for image description and proves to be very effective. In many vision problems, rotation-invariant analysis is necessary or preferred. Popular solutions are mainly based on pose normalization or learning, neglecting some intrinsic properties of rotations. This paper presents a method to build...

To achieve a detailed understanding of processes in biological systems, cellular features must be quantified in the three-dimensional (3D) context of cells and organs. We introduce the intrinsic Root Coordinate System (iRoCS) as a reference model for the root apical meristem (RAM) of plants. iRoCS enables direct and quantitative comparison between...

not my publication

Background Absorption and refraction induced signal attenuation can seriously hinder the extraction of quantitative information from confocal microscopic data. This signal attenuation can be estimated and corrected by algorithms that use physical image formation models. Especially in thick heterogeneous samples, current single view based models are...

In this paper, we aim for detection and segmentation of Arabidopsis thaliana cells in volumetric image data. To this end, we cluster the training samples by their size and aspect ratio and learn a detector and a shape model for each cluster. While the detector yields good cell hypotheses, additionally aligning the shape model to the image allows to...

In this paper, we aim for detection and segmentation of Arabidopsis thaliana cells in volumetric image data. To this end, we cluster the training samples by their size and aspect ratio and learn a detector and a shape model for each cluster. While the detector yields good cell hypotheses, additionally aligning the shape model to the image allows to...

We present an approach to recover attenuation-free intensities of a thick sample, that is imaged by a standard confocal microscope from two views (top and bottom). A variational approach simultaneously estimates the local signal attenuation and the real attenuation-free intensity at each position. Compared to earlier work we introduce a refined imag...

Leaves show a wide range of shapes that results from the combinatory variations of two main parameters: the relative duration of the morphogenetic phase and the pattern of dissection of the leaf margin. To further understand the mechanisms controlling leaf shape, we have studied the interactions between several loci leading to increased dissection...

This paper presents a discrete energy minimization approach to integrate different prior knowledge and image cues for simultaneous cell segmentation and classification. When there are multiple types of cells to segment, the segmentation of cells and the classification of the cell types are dependent on each other. The presented approach selects the...

Rho GTPase modifying bacterial protein toxins are useful for analysis of Rho signalling in animal cells, but these toxins cannot be taken up by plant cells. We demonstrate in vitro deamidation of Arabidopsis Rop4 by Escherichia coli Cytotoxic Necrotizing Factor 1 (CNF1) and glucosylation by Clostridium difficile toxin B. Expression of the catalytic...

CUP-SHAPED COTYLEDON2 (CUC2) and the interacting microRNA miR164 regulate leaf margin dissection. Here, we further investigate the evolution and the specific roles of the CUC1 to CUC3 genes during Arabidopsis thaliana leaf serration. We show that CUC2 is essential for dissecting the leaves of a wide range of lobed/serrated Arabidopsis lines. Inacti...

Rotation-invariant descriptions are required in many 3D volumetric image analysis tasks. The histogram-of-oriented-gradient (HOG) is widely used in 2D images and proves to be a very robust local description. This paper concentrates on how to use the HOG feature in 3D volumetric images when rotation-invariance is concerned. This is challenging becau...

Leaves, which play an essential role in plant photosynthesis, share common features such as being flat structures, but also show an impressive variability in their sizes and shapes. Following its initiation in the meristems, leaf development is patterned along three polarization axes to establish its basic architecture. This process is further comp...

Formation of dissected compound leaves involves the transient maintenance of an indeterminate environment and the generation of new growth axes that will generate leaflets. Recent work has revealed additional multi-layered mechanisms controlling the activities of the KNOXI homeodomains factors that play a prominent role in the control of indetermin...

Diversity in leaf shape is produced by alterations of the margin: for example, deep dissection leads to leaflet formation and less-pronounced incision results in serrations or lobes. By combining gene silencing and mutant analyses in four distantly related eudicot species, we show that reducing the function of NAM/CUC boundary genes (NO APICAL MERI...

Aerial architecture in higher plants is established post-embryonically by the inception of new meristems in the axils of leaves. These axillary meristems develop into side shoots or flowers. In Arabidopsis, the NAC domain transcription factors CUP SHAPED COTYLEDON1 (CUC1), CUC2 and CUC3 function redundantly in initiating the shoot apical meristem a...

CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conse...