Thomas Roulé
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View article: PRC2 Diversity in Neuronal Differentiation and Developmental Disorders
PRC2 Diversity in Neuronal Differentiation and Developmental Disorders Open
Advances in genetic studies have not only improved the diagnosis and treatment of neurodevelopmental disorders but also uncovered human-specific aspects of nervous system development. The generation of neuronal diversity in the human brain…
View article: A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution
A single-cell rice atlas integrates multi-species data to reveal cis-regulatory evolution Open
Cis -regulatory elements (CREs) are essential for regulating gene expression, yet their evolutionary dynamics in plants remain elusive. Here we constructed a single-cell chromatin accessibility atlas for Oryza sativa from 103,911 nuclei re…
View article: YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast
YAP1 and QSER1 are Key Modulators of Embryonic Signaling Pathways in the Mammalian Epiblast Open
YAP1 signaling is essential for development but its specific roles in early embryogenesis remain poorly understood. To shed light on this, we analyzed YAP1’s role in regulating the pluripotency of the mammalian epiblast, using scRNAseq app…
View article: A retinoic acid:YAP1 signaling axis controls atrial lineage commitment
A retinoic acid:YAP1 signaling axis controls atrial lineage commitment Open
In cardiac progenitor cells (CPCs), retinoic acid (RA) signaling induces atrial lineage gene expression and acquisition of an atrial cell fate. To achieve this, RA coordinates a complex regulatory network of downstream effectors that is no…
View article: IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency
IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency Open
Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use m…
View article: A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment
A Retinoic Acid:YAP1 signaling axis controls atrial lineage commitment Open
Vitamin A/Retinoic Acid (Vit A/RA) signaling is essential for heart development. In cardiac progenitor cells (CPCs), RA signaling induces the expression of atrial lineage genes while repressing ventricular genes, thereby promoting the acqu…
View article: Single-Cell RNA Sequencing of Mutant Whole Mouse Embryos: From the Epiblast to the End of Gastrulation
Single-Cell RNA Sequencing of Mutant Whole Mouse Embryos: From the Epiblast to the End of Gastrulation Open
Over the last decade, single-cell approaches have become the gold standard for studying gene expression dynamics, cell heterogeneity, and cell states within samples. Before single-cell advances, the feasibility of capturing the dynamic cel…
View article: Single-cell RNA sequencing of mutant whole mouse embryos: from the epiblast to the end of gastrulation
Single-cell RNA sequencing of mutant whole mouse embryos: from the epiblast to the end of gastrulation Open
Over the last decade, single-cell approaches have become the gold standard for studying gene expression dynamics, cell heterogeneity, and cell states within samples. Before single-cell advances, the feasibility of capturing the dynamic cel…
View article: Altered lipid homeostasis is associated with cerebellar neurodegeneration in SNX14 deficiency
Altered lipid homeostasis is associated with cerebellar neurodegeneration in SNX14 deficiency Open
Dysregulated lipid homeostasis is emerging as a potential cause of neurodegenerative disorders. However, evidence of errors in lipid homeostasis as a pathogenic mechanism of neurodegeneration remains limited. Here, we show that cerebellar …
View article: IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency
IMPDH2 filaments protect from neurodegeneration in AMPD2 deficiency Open
Metabolic dysregulation is one of the most common causes of pediatric neurodegenerative disorders. However, how the disruption of ubiquitous and essential metabolic pathways predominantly affect neural tissue remains unclear. Here we use m…
View article: Evolution of plant cell-type-specific<i>cis</i>-regulatory elements
Evolution of plant cell-type-specific<i>cis</i>-regulatory elements Open
Cis -regulatory elements (CREs) are critical in regulating gene expression, and yet understanding of CRE evolution remains challenging. Here, we constructed a comprehensive single-cell atlas of chromatin accessibility in Oryza sativa , int…
View article: The long intergenic noncoding <scp>RNA <i>ARES</i></scp> modulates root architecture in Arabidopsis
The long intergenic noncoding <span>RNA <i>ARES</i></span> modulates root architecture in Arabidopsis Open
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 prot…
View article: High density SNP array and reanalysis of genome sequencing uncovers CNVs associated with neurodevelopmental disorders in KOLF2.1J iPSCs
High density SNP array and reanalysis of genome sequencing uncovers CNVs associated with neurodevelopmental disorders in KOLF2.1J iPSCs Open
Summary The KOLF2.1J iPSC line was recently proposed as a reference iPSC to promote the standardization of research studies in the stem cell field. Due to overall good performance differentiating to neural cell lineages, high gene editing …
View article: The Role and Activity of SWI/SNF Chromatin Remodelers
The Role and Activity of SWI/SNF Chromatin Remodelers Open
SWITCH deficient SUCROSE NONFERMENTING (SWI/SNF) class chromatin remodeling complexes (CRCs) use the energy derived from ATP hydrolysis to facilitate access of proteins to the genomic DNA for transcription, replication, and DNA repair. Uni…
View article: Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data
Greenscreen: A simple method to remove artifactual signals and enrich for true peaks in genomic datasets including ChIP-seq data Open
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to identify factor binding to genomic DNA and chromatin modifications. ChIP-seq data analysis is affected by genomic regions that generate ultra-high artifactua…
View article: Regulatory long non-coding RNAs in root growth and development
Regulatory long non-coding RNAs in root growth and development Open
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…
View article: ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture Open
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 int…
View article: ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture
ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture Open
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 int…
View article: The lncRNA<i>MARS</i>modulates the epigenetic reprogramming of the marneral cluster in response to ABA
The lncRNA<i>MARS</i>modulates the epigenetic reprogramming of the marneral cluster in response to ABA Open
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 …
View article: Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation
Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation Open
Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may c…
View article: Two ecotype-related long non-coding RNAs in the environmental control of root growth
Two ecotype-related long non-coding RNAs in the environmental control of root growth Open
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 e…