Biology subjects

Panara, V.

Publications and source records attributed to Panara, V..

3 recordsLinked to original sources

bioRxiv2026

Reconstruction of the Prox gene family evolution in vertebrates reveals multiple lineage-specific gene losses

Prospero-related homeobox (Prox) genes encode a family of transcription factors that play essential roles in the development of several organs and systems, including the central nervous system, lymphatic endothelium, musculature, and liver. Despite their developmental importance, the evolutionary history of the vertebrate Prox gene family remains poorly understood. In this study we combined phylogenetic and synteny analysis to characterise the evolution of the Prox family in vertebrates. Our results reveal that two to three Prox subfamilies were already present in the last common ancestor of jawed vertebrates. We clarify the identity and evolutionary relationships of well-studied members of this family and identify multiple independent losses of Prox2 and Prox3 genes in specific vertebrate lineages. Furthermore, we uncover evidence for the existence of a fourth Prox gene in the ancestral vertebrate genome, which was subsequently lost. Overall, this study provides the first comprehensive analysis of the evolutionary history of the vertebrate Prox gene family and establishes a foundations for future studies on the functional roles of these genes.

genomics↗

bioRxiv2025

Distinct topologically associated domains underlie the regulatory logic in lymphatic endothelial cells contributing to proper cell differentiation

The activation and repression of genes is a fundamental part of proper embryonic development and functional tissue formation, ensuring that unique molecular codes are set up to orchestrate cell differentiation. Changes in chromatin organisation dictate accessibility to gene regulatory elements and control gene expression. Several molecular factors regulating lymphatic endothelial cell (LEC) specification and differentiation have been identified. However, it remains to be defined how chromatin is organised in lymphatic endothelium and how it orchestrates lymphatic vessel network formation. In this study, we combined Hi-C and ATAC-sequencing to characterise 3D chromatin architecture and accessibility in LECs and blood endothelial cells (BECs). We have identified cell type-specific topologically associated domains (TADs) in LECs and BECs. Specifically, our data revealed changes in the TAD boundaries and differentially segregating enhancers regions in lymphatic-associated loci, such as prox1a and tbx1. This multi-omic approach also defined the regulatory logic for nine genes whose expression is enriched in LECs. In vivo validation of their short- and long-range enhancers confirmed their LEC-confined activity. Leveraging these datasets, we reconstructed mafba tissue-specific regulatory networks and identified a genetic interaction with tfe3a in vivo necessary to limit ectopic vessel formation. Overall, our work provides a powerful resource of multi-omic datasets that can be used to systematically determine the regulatory networks governing LEC identity and genes linked to lymphatic disease.

developmental biology↗

bioRxiv2023

Multiple cis-regulatory elements control prox1a expression in distinct lymphatic vascular beds

Lymphatic vessels play a role in several physiological and pathological processes including tissue fluid homeostasis, dietary fat absorption, immunosurveillance, and immunomodulation. During embryonic development, lymphatic endothelial cell (LEC) precursors are distinguished from blood endothelial cells by the expression of the transcription factor Prospero-related homeobox 1 (PROX1). PROX1 is essential for lymphatic vascular network formation in mouse and zebrafish. The initiation of PROX1 expression precedes LEC sprouting and migration, serving as the definitive marker of specified LECs. Despite its crucial role in lymphatic development, the upstream regulation of PROX1 in LECs remains to be uncovered. SOX18 and COUP-TFII are thought to regulate Prox1 expression in mice by binding to its promoter region. However, how the specificity of Prox1 expression to LECs is achieved remains to be studied in detail. In this study, we analysed evolutionary conservation and chromatin accessibility to identify enhancer sequences located in the proximity of zebrafish prox1a active in developing LECs. We confirmed the functional role of the identified sequences through CRISPR/Cas9 mutagenesis of a lymphatic valve enhancer. The deletion of this genomic region results in impaired valve morphology and function. Overall, our results reveal the intricate control of prox1a expression through a collection of enhancers. Ray-finned fish-specific distal enhancers drive pan-lymphatic expression, while vertebrate-conserved proximal enhancers refine expression in functionally distinct subsets of lymphatic vessels. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=89 SRC="FIGDIR/small/550483v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@fed780org.highwire.dtl.DTLVardef@f62a8dorg.highwire.dtl.DTLVardef@163b04corg.highwire.dtl.DTLVardef@1cb7f87_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗