Biology subjects

Libault, M.

Publications and source records attributed to Libault, M..

7 recordsLinked to original sources

bioRxiv2024

Tabula Glycine: The whole-soybean single-cell resolution transcriptome atlas

Soybean (Glycine max) is an essential source of protein and oil with high nutritional value for human and animal consumption. To enhance our understanding of soybean biology, it is essential to have accurate information regarding the expression of each of its 55,897 protein-coding genes. Here, we present "Tabula Glycine", the soybean single-cell resolution transcriptome atlas. This atlas is composed of single-nucleus RNA-sequencing data of nearly 120,000 nuclei isolated from 10 different Glycine max organs and morphological structures comprising the entire soybean plant. These nuclei are grouped into 157 different clusters based on their transcriptomic profiles. Among genes, the pattern of activity of transcription factor genes is sufficient to define most cell types and their organ/morphological structure of origin, suggesting that transcription factors are key determinants of cell identity and function. This unprecedented level of resolution makes the Tabula Glycine a unique resource for the plant and soybean communities.

plant biology↗

bioRxiv2024

Identification and characterization of a temperature sensitive chlorotic soybean mutant

Screening a transposon-mutagenized soybean population led to the discovery of a recessively inherited chlorotic phenotype. This "vir1" phenotype results in smaller stature, weaker stems, and a smaller root system with smaller nodules. Genome sequencing identified 15 candidate genes with mutations likely to result in a loss of function. Amplicon sequencing of a segregating population was then used to narrow the list to a single candidate mutation, a single-base change in Glyma.07G102300 that disrupts splicing of the second intron. Single cell transcriptomic profiling indicates that this gene is expressed primarily in mesophyll cells and RNA sequencing data indicates it is upregulated in germinating seedlings by cold stress. Previous studies have shown that mutations to Os05g34040, the rice homolog of Glyma.07G102300, produced a chlorotic phenotype that was more pronounced in cool temperatures. Growing soybean vir1 mutants at lower temperatures also resulted in a more severe phenotype. In addition, transgenic expression of wild type Glyma.07G102300 in the knockout mutant of the Arabidopsis homolog At4930720 rescues the chlorotic phenotype, further supporting the hypothesis that the mutation in Glyma.07G102300 is causal of the vir1 phenotype.

plant biology↗

bioRxiv2024

DIRT/μ - Automated extraction of root hair traits using combinatorial optimization

Similar to any microscopic appendages, such as cilia or antennae, phenotyping of root hairs has been a challenge due to their complex intersecting arrangements in two-dimensional (2D) images and the technical limitations of automated measurements. Digital Imaging of Root Traits at Microscale (DIRT/) addresses this issue by computationally resolving intersections and extracting individual root hairs from 2D microscopy images. This solution enables automatic and precise trait measurements of individual root hairs. DIRT/ rigorously defines a set of rules to resolve intersecting root hairs and minimizes a newly designed cost function to combinatorically identify each root hair in the microscopy image. As a result, DIRT/ accurately measures traits such as root hair length (RHL) distribution and root hair density (RHD), which are impractical for manual assessment. We tested DIRT/ on three datasets to validate its performance and showcase potential applications. By measuring root hair traits in a fraction of the time manual methods require, DIRT/ eliminates subjective biases from manual measurements. Automating individual root hair extraction accelerates phenotyping and quantifies trait variability within and among plants, creating new possibilities to characterize root hair function and their underlying genetics.

plant biology↗

bioRxiv2022

Isolation and Transfection of Rice Egg Cells and Zygotes for Cellular Localization

Due to the difficulty in accessing to gametes and zygotes in flowering plants, which are controlled in single cells deeply embedded in multiple tissues, little is known about how the initiation of plant embryogenesis may reflect or contrast from such systems in other eukaryotes. In this study we has developed an approach of isolation and transfection of rice egg cells and zygotes for cellular localization of rice cell cycle factors (KRP5, KRP4 and FB3), which opened a pathway to monitor protein expression in rice egg cells and zygotes at different developmental stages. The advantageous feature of isolated rice cells may serve as an ideal system for studying the molecular mechanism underlying the rice zygotic division to initiate seed formation.

cell biology↗

bioRxiv2022

A CDKB/KRP/FB3 cell cycle core complex functions in rice gametes and zygotes

The cell cycle controls division and proliferation of all eukaryotic cells and is tightly regulated at multiple checkpoints by complexes of core cell cycle proteins. Due to the difficulty in accessing female gametes and zygotes of flowering plants, little is known about the molecular mechanisms underlying initiation embryogenesis despite the crucial importance of this process for seed crops. In this study, we reveal four levels of factors involved in rice zygotic cell cycle control and characterize their functions and regulation. Protein-protein interaction studies, including within zygote cells, and in vitro biochemical analyses delineate a model of the zygotic cell cycle core complex for rice. In this model, CDKB1, a major regulator of plant mitosis, is a cyclin (CYCD5)-dependent kinase; its activity is coordinately inhibited by two cell cycle inhibitors, KRP4 and KRP5; and both KRPs are regulated via F-box protein 3 (FB3)-mediated proteolysis. Supporting their critical role in controlling the rice zygotic cell cycle, mutations in KRP4, KRP5, and FB3 result in the compromised function of sperm cells and abnormal organization of female germ units, embryo and endosperm, thus significantly reducing seed-set rates. This work helps reveals regulatory mechanisms controlling the zygotic cell cycle toward seed formation in angiosperms.

cell biology↗

bioRxiv2021

Isolating and Cryo-Preserving Pig Skin Cells for Single Cell RNA Sequencing Study

The Pigskin architecture and physiology are similar to these of humans. Thus, the pig model is valuable for studying skin biology and testing therapeutics for skin diseases. The single-cell RNA sequencing technology allows quantitatively analyzing cell types, cell states, signaling, and receptor-ligand interactome at single-cell resolution and at high throughput. scRNA-Seq has been used to study mouse and human skins. However, studying pigskin with scRNA-Seq is still rare. Here we described a robust method for isolating and cryo-preserving pig single cells for scRNA-Seq. We showed that pigskin could be efficiently dissociated into single cells with high cell viability using the Miltenyi Human Whole Skin Dissociation kit and the Miltenyi gentleMACS Dissociator. Also, we showed that the subsequent single cells could be cryopreserved using DMSO without causing additional cell death, cell aggregation, or changes in gene expression profiles. Using the developed protocol, we were able to identify all the major skin cell types. The protocol and results from this study will be very valuable for the skin research scientific community.

cell biology↗

bioRxiv2020

The impact of chromatin remodeling on gene expression at the single cell level in Arabidopsis thaliana

Similar to other complex organisms, plants consist of diverse and highly specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs and their associated regulatory mechanisms. Recently, single cell transcriptomic approaches have been applied on Arabidopsis thaliana root protoplasts allowing the accurate characterization of the transcriptional profiles of the cell-types composing seedling roots. As a first step in gaining a deeper understanding of the regulatory mechanisms controlling Arabidopsis gene expression, we report the use of single nucleus RNA sequencing (sNucRNA-seq) and single nucleus Assay for Transposase Accessible Chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single nuclei transcriptomes to previously published protoplast transcriptomes validated the use of nuclei as biological entities to establish cell-type specific transcriptomes from multicellular organs. Furthermore, our sNucRNA-seq results uncovered the transcriptome of additional cell subtypes not identified by scRNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters suggesting the differential remodeling of the chromatin between groups of cells according to their identity. To reveal the impact of chromatin remodeling on gene transcription, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes also display cell-type-specific pattern of chromatin accessibility. Our data suggest that the differential remodeling of the chromatin is a critical mechanism to regulate gene activity at the cell-type level.

plant biology↗