Mauricio Alberto Reynoso

University of California, Riverside | UCR · Department of Botany and Plant Sciences

In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data were mapped to the version 5 of the M....

Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, c...

Video-presentation. Abstract: Legumes and rhizobia establish a nitrogen-fixing symbiosis that involves the formation of a lateral root organ, the nodule, and the suppression of the immune response of the plant, which allows the rhizobia to infect the root tissue. The activation and coordination of these two genetic programs requires the reprogrammi...

Plant species have evolved myriads of solutions, including complex cell type development and regulation, to adapt to dynamic environments. To understand this cellular diversity, we profiled tomato root cell type translatomes. Using xylem differentiation in tomato, examples of functional innovation, repurposing, and conservation of transcription fac...

Post-transcriptional control of gene expression allows plants to rapidly adapt to changes in their environment. Under low nitrogen conditions, legume plants engage into a symbiosis with soil bacteria that results in the formation of root nodules, where bacteria are allocated and fix atmospheric nitrogen for the plant’s benefit. Recent studies highl...

Translating ribosome affinity purification (TRAP) technology allows the isolation of polysomal complexes and the RNAs associated with at least one 80S ribosome. TRAP consists of the stabilization and affinity purification of polysomes containing a tagged version of a ribosomal protein. Quantitative assessment of the TRAP RNA is achieved by direct s...

Plant species have evolved myriads of solutions to adapt to dynamic environments, including complex cell type development and regulation. To understand this diversity, we profiled tomato root cell type translatomes and chromatin accessibility. Using xylem differentiation in tomato, relative to Arabidopsis, examples of functional innovation, repurpo...

Legume plants establish a symbiosis with soil bacteria known as rhizobia, which results in the formation of a new organ specialized in nitrogen fixation, the nodule. The development of functional nodules requires a reprogramming of gene expression in root cells that are committed for symbiosis, leading to the activation of two highly coordinated mo...

Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied TRAP (Translating Ribosome Affinity Purification) combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen...

Flood-resistance from gene regulation Some plants tolerate flooding better than others. Reynoso et al. compared gene regulatory networks activated by flooding in rice, which is adapted to flooding, with those in species less adapted to flooding. Flood-related gene regulation was characterized according to chromatin accessibility as well as transcri...

The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant spe...

The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how many cis -regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant sp...

Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of Nuclei from TAgged specific Cell Types (INTACT) to the monocot rice (Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer nucle...

Isolated nuclei provide access to early steps in gene regulation involving chromatin as well as transcript production and processing. Here we describe transfer of the Isolation of N uclei from TA gged specific C ell T ypes (INTACT) to the monocot rice ( Oryza sativa L.). The purification of biotinylated nuclei was redesigned by replacing the outer...

Legume roots form two types of post-embryonic organs, lateral roots and symbiotic nodules. Nodule formation is the result of the interaction of legumes with rhizobia, and requires the mitotic activation and differentiation of root cells, as well as an independent, but coordinated, program that allows infection by rhizobia. MicroRNA390 (miR390) is a...

Gene expression is dynamically regulated on many levels, including chromatin accessibility and transcription. In order to study these nuclear regulatory events, we describe our method to purify nuclei with Isolation of Nuclei in TAgged Cell Types (INTACT). As nuclear RNA is low in polyadenylated transcripts and conventional pulldown methods would n...

Gene expression is controlled at transcriptional and post-transcriptional levels including decoding of mRNA into polypeptides via ribosome-mediated translation. Translational regulation has been intensively studied in the model dicot plant Arabidopsis thaliana, and in this study, we assessed the translational status (proportion of steady-state mRNA...

Translating Ribosome Affinity Purification (TRAP) is a technology to isolate the population of mRNAs associated with at least one 80S ribosome, referred as the translatome. TRAP is based on the expression of an epitope-tagged version of a ribosomal protein and the affinity purification of ribosomes and associated mRNAs using antibodies conjugated t...

Agrobacterium rhizogenes or Rhizobium rhizogenes is able to transform plant genomes and induce the production of "hairy roots". We describe the use of A. rhizogenes in tomato to rapidly assess gene expression and function. Gene expression is indistinguishable in plants transformed by A. tumefaciens as compared to A. rhizogenes. A root cell-type and...

Medicago truncatula (barrel medic) is a species native to the Mediterranean that has been adopted as a model organism for temperate legumes due to its relatively small size, short generation time, small diploid genome and the capacity to reproduce by self- and out-crossing. It is a close relative of alfalfa (M. sativa), which is used as forage, but...

Common bean (Phaseolus vulgaris) is a legume plant original from America. It was domesticated independently in the Mesoamerican and Andean geographical centers. From there, it was disseminated to the rest of the world, becoming the most important grain legume in terms of human alimentation. Beans from this plant are the most important source of pro...

During the past ten years, changes in the transcriptome have been assessed at different stages of the legume-rhizobia association by the use of DNA microarrays and, more recently, by RNA sequencing technologies. These studies allowed the identification of hundred or thousand of genes whose steady-state mRNA levels increase or decrease upon bacteria...

Phaseolus vulgaris (common bean) is an agronomic important legume crop native to America, where two centres of genetic diversification (GD) are recognised, one in Mesoamerica and the other in the south Andes. Mesoamerican bean accessions have preferential and more efficient nodulation with Rhizobium etli strains carrying the allele nodC type-α, whi...

Translation of mRNAs is a key regulatory step that contributes to the coordination and modulation of eukaryotic gene expression during development or adaptation to the environment. mRNA stability or translatability can be regulated by the action of small regulatory RNAs (sRNAs), which control diverse biological processes. Under low nitrogen conditi...