Biology subjects

Triozzi, P. M.

Publications and source records attributed to Triozzi, P. M..

4 recordsLinked to original sources

bioRxiv2021

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Rhizobia can establish symbiotic associations with legumes to provide plants with nitrogen needed in agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet the extent of chromatin changes and impact on gene expression is unknown. We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with rhizobia lipo-chitooligosaccharides. Using a novel approach, Dynamic Regulatory Module Networks, we predicted gene expression as a function of chromatin accessibility and accessible cis-regulatory elements. This approach identified the cis-regulatory elements and associated transcription factors that most significantly contribute to transcriptomic changes triggered by lipo-chitooligosaccharides. Regulators involved in auxin (IAA4-5,SHY2), ethylene (EIN3, ERF1) and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia. Significance StatementLegumes can fix nitrogen through symbiosis with rhizobia in root nodules, a critical mutualistic relationship for crop productivity and agricultural sustainability. Introducing this symbiotic relationship into non-legume crops is of great interest, but limited knowledge of host genome modifications induced by rhizobia has hampered such efforts. We applied time-course analysis of chromatin accessibility and gene expression of M. truncatula roots treated with rhizobia lipochitooligosaccharides. We show that extensive remodeling of genome accessibility drives a large component of the temporal transcriptome dynamics. By predicting gene expression as a function of accessibility of regulatory features, we identified known and novel regulators that are associated with early nodule development, which may be critical for its engineering into crops.

plant biology↗

bioRxiv2021

Functional and comparative genomics reveals conserved noncoding sequences in the nitrogen-fixing clade

Nitrogen is one of the most inaccessible plant nutrients, but certain species have overcome this limitation by establishing symbiotic interactions with nitrogen-fixing bacteria in the root nodule. This root nodule symbiosis (RNS) is restricted to species within a single clade of angiosperms, suggesting a critical evolutionary event at the base of this clade, which has not yet been determined. While genes implicated in the RNS are present in most plant species (nodulating or not), gene sequence conservation alone does not imply functional conservation - developmental or phenotypic differences can arise from variation in the regulation of transcription. To identify putative regulatory sequences implicated in the evolution of RNS, we aligned the genomes of 25 species capable of nodulation. We detected 3,091 conserved noncoding sequences (CNS) in the nitrogen-fixing clade that are absent from outgroup species. Functional analysis revealed that chromatin accessibility of 452 CNS significantly correlates with the differential regulation of genes responding to lipo-chitooligosaccharides in Medicago truncatula. These included 38 CNS in proximity to 19 known genes involved in RNS. Five such regions are upstream of MtCRE1, Cytokinin Response Element 1, required to activate a suite of downstream transcription factors necessary for nodulation in M. truncatula. Genetic complementation of a Mtcre1 mutant showed a significant association between nodulation and the presence of these CNS, when they are driving the expression of a functional copy of MtCRE1. Conserved noncoding sequences, therefore, may be required for the regulation of genes controlling the root nodule symbiosis in M. truncatula.

plant biology↗

bioRxiv2021

Asc-Seurat - Analytical single-cell Seurat-based web application

SummarySingle-cell RNA sequencing (scRNA-seq) has become a popular approach for studying the transcriptome, providing a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data processing and uncover relevant biological information. We present Asc-Seurat, a feature rich workbench, providing a user-friendly and easy-to-install web application encapsulating the necessary tools for an all-encompassing and fluid scRNA-seq data analysis. Availability and implementationAsc-Seurat is available at https://github.com/KirstLab/asc_seurat/ and released under GNU 3 license. Contactmkirst@ufl.edu Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

A robust method of nuclei isolation for single-cell RNA sequencing of solid tissues from the plant genus Populus

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between the different cell types of a tissue or an organ. It demonstrated its capability to discover the key regulatory elements that determine cell fate during developmental programs such as brain or heart development. Single-cell analysis requires the isolation and labeling of the messenger RNA (mRNA) derived from each cell. These challenges were primarily addressed in mammals by developing microfluidic-based approaches. For plant species whose cells contain cell walls, these approaches have generally required the generation of isolated protoplasts. Many plant tissues secondary cell wall hinders enzymatic digestion required for individual protoplast isolation, resulting in an unequal representation of cell types in a protoplast population. This limitation is especially critical for cell types located in the inner layers of a tissue or the inner tissues of an organ. Consequently, single-cell RNA sequencing (scRNA-seq) studies using microfluidic approaches in plants have mainly been restricted to Arabidopsis roots, for which well-established procedures of protoplast isolation are available. Here we present a simple alternative approach to generating high-quality protoplasts from plant tissue by characterizing the mRNA extracted from individual nuclei instead of whole cells. We developed the protocol using two different plant materials with varying cellular complexity levels and cell-wall structure, Populus shoot apices, and more lignified stems. Using the 10x Genomics Chromium technology, we show that this procedure results in intact mRNA isolation and limited leakage, with a broad representation of individual cell transcriptomes.

plant biology↗