Biology subjects

Raimundo, J.

Publications and source records attributed to Raimundo, J..

4 recordsLinked to original sources

bioRxiv2025

Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries

O_LIZygomorphic flowers in Antirrhinum majus arise from coordinated patterning along the dorsoventral and proximal-distal axes, but the transcriptional programs that pattern these axes to generate the complex corolla morphology remain poorly understood. C_LIO_LIWe performed comparative transcriptomic analyses of dorsal and ventral petals across developmental stages, combined with expression profiling in floral symmetry mutants, to identify genes potentially associated with dorsal identity (AmCYC-dependent) and ventral identity (AmDIV-dependent), and to map their spatial dynamics along the proximal-distal axis. Axis-specific and boundary-localized expression patterns were validated by in situ hybridisation. C_LIO_LIWe identified dorsal-specific candidate targets of AmCYC and ventral-specific genes regulated by AmDIV, including factors with regionally restricted expression along the proximal-distal axis. We further found that a conserved NGATHA-LIKE1-BRASSINAZOLE-RESISTANT 1-miR164 module, known for primordia growth regulation in Arabidopsis, has been co-opted in Antirrhinum to act as a potential spatiotemporal regulator of AmCUP, a target of AmDIV, thereby contributing to the complex shape of the Antirrhinum flower. C_LIO_LIOur results provide new insight into the gene regulatory landscape underlying zygomorphic flower development and highlight specific regulatory modules that may coordinate axis patterning with boundary establishment in the corolla. This work establishes a framework for further understanding how developmental gene networks shape a complex corolla morphology and offers new targets for functional and evolutionary investigation of floral diversity. C_LI

plant biology↗

bioRxiv2021

Optogenetic control of the Bicoid morphogen reveals fast and slow modes of gap gene regulation

Developmental patterning networks are regulated by multiple inputs and feedback connections that rapidly reshape gene expression, limiting the information that can be gained solely from slow genetic perturbations. Here we show that fast optogenetic stimuli, real-time transcriptional reporters, and a simplified genetic background can be combined to reveal quantitative regulatory dynamics from a complex genetic network in vivo. We engineer light-controlled variants of the Bicoid transcription factor and study their effects on downstream gap genes in embryos. Our results recapitulate known relationships, including rapid Bicoid-dependent expression of giant and hunchback and delayed repression of Kruppel. In contrast, we find that the posterior pattern of knirps exhibits a quick but inverted response to Bicoid perturbation, suggesting a previously unreported role for Bicoid in suppressing knirps expression. Acute modulation of transcription factor concentration while simultaneously recording output gene activity represents a powerful approach for studying how gene circuit elements are coupled to cell identification and complex body pattern formation in vivo.

developmental biology↗

bioRxiv2020

DeepArk: modeling cis-regulatory codes of model species with deep learning

To enable large-scale analyses of regulatory logic in model species, we developed DeepArk (https://DeepArk.princeton.edu), a set of deep learning models of the cis-regulatory codes of four widely-studied species: Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, and Mus musculus. DeepArk accurately predicts the presence of thousands of different context-specific regulatory features, including chromatin states, histone marks, and transcription factors. In vivo studies show that DeepArk can predict the regulatory impact of any genomic variant (including rare or not previously observed), and enables the regulatory annotation of understudied model species.

bioinformatics↗

bioRxiv2019

The nuclear to cytoplasmic ratio directly regulates zygotic transcription in Drosophila

Early embryos must rapidly generate large numbers of cells to form an organism. Many species accomplish this through a series of rapid, reductive, and transcriptionally silent cleavage divisions. Previous work has demonstrated that the number of divisions before both cell cycle elongation and zygotic genome activation (ZGA) is regulated by the ratio of nuclear content to cytoplasm (N/C). To understand how the N/C ratio affects the timing of ZGA, we directly assayed the behavior of several previously identified N/C-ratio-dependent genes using the MS2-MCP reporter system in living Drosophila embryos with altered ploidy and cell cycle durations. For every gene that we examined, we found that nascent RNA output per cycle is delayed in haploid embryos. Moreover, we found that the N/C ratio influences transcription through three separate modes of action. For some genes (knirps and snail) the effect of ploidy can be entirely accounted for by changes in cell cycle duration. However, for other genes (giant, bottleneck and fruhstart) the N/C ratio directly affects ZGA. For giant and bottleneck, the N/C ratio regulates the kinetics of transcription activation, while for fruhstart it controls the probability of transcription initiation. Our data demonstrate that the regulatory elements of N/C-ratio-dependent genes respond directly to the N/C ratio, through multiple modes of regulation, independent of interphase length.

developmental biology↗