Biology subjects

Zayas, R. M.

Publications and source records attributed to Zayas, R. M..

5 recordsLinked to original sources

bioRxiv2026

Ephrin Signaling Patterns Sensory Neurons During Tissue Homeostasis in Planarians

Eph and ephrin genes encode receptor-ligand pairs that mediate contact-dependent cell signaling and are essential for nervous system development. However, less is known about the role of Ephrin signaling during adult tissue homeostasis and regeneration. Here, we investigated the role of Ephrin signaling in neural patterning in the planarian Schmidtea mediterranea. We discovered that RNAi against the Eph receptor EphR1 led to striking ectopic expression of the mechanosensory neuron markers pkd1L-2 and hmcn-1-L, without obvious disruption of the overall architecture of the central nervous system. To investigate the basis of this phenotype, we identified additional Eph receptor homologs and four putative ephrin ligands and assessed their function. An RNAi screen revealed that ephrin-1 phenocopies the defects of EphR1 RNAi. Temporal analyses of EphR1 and ephrin-1 inhibition revealed a progressive increase in pkd1L-2+ and hmcn-1-L+ cells, indicating an unappreciated role for Ephrin signaling in regulating neural patterning and cell number during adult tissue homeostasis. Together, these findings provide a framework for dissecting Ephrin-dependent mechanisms in adult tissue maintenance and regeneration.

developmental biology↗

bioRxiv2025

SoxB1-Mediated Chromatin Remodeling Promotes Sensory Neuron Differentiation in Planarians

Understanding how adult stem cells generate neurons is critical for advancing regenerative medicine. However, few in vivo models enable studying how stem cell fates are specified as neurons in an adult body. The planarian Schmidtea mediterranea provides a powerful system for investigating these mechanisms, owing to its abundant adult pluripotent stem cells, termed neoblasts, and its capacity to regenerate a molecularly complex nervous system. The SoxB1 family of transcription factors is broadly implicated in ectodermal lineage commitment. In planarians, the SoxB1 homolog soxB1-2 has been shown to promote neural and epidermal differentiation. However, the mechanisms by which soxB1-2 influences chromatin dynamics and transcriptional programs during adult neurogenesis remain unknown. To address this, we performed ATAC-seq and RNA-seq on neural-rich head tissues to assess how soxB1-2 RNAi knockdown alters chromatin accessibility and gene expression. Disrupting soxB1-2 resulted in reduced chromatin accessibility and transcriptional downregulation at neural and epidermal loci, consistent with a pioneer-like role in chromatin priming. We identified 31 candidate downstream targets with concordant accessibility and expression changes, including the transcription factors castor and mecom, which regulate mechanosensory and ion transport genes. Head tissue sampling enabled the detection of soxB1-2-responsive genes within rare neural subtypes that were missed in our previous whole-body RNA-seq experiments. These findings offer mechanistic insight into adult ectodermal lineage specification and establish a framework for understanding chromatin-mediated neurogenesis in regenerative systems.

developmental biology↗

bioRxiv2025

Smed-pou4-2 regulates mechanosensory neuron regeneration and function in planarians

POU4 homologs are involved in the development of sensory cell types across diverse species, including cnidarians, ascidians, and mammals. Whether these developmental regulators are redeployed during adult tissue maintenance and regeneration is an open question in regenerative biology. Here, we investigate the role of the Schmidtea mediterranea BRN3/POU4 homolog, Smed-pou4-2 (pou4-2), in the regeneration of mechanosensory neurons. We find that pou4-2 is regulated by the SoxB1 homolog, soxB1-2, and is expressed in a distinct population of ciliated sensory cells that detect water flow. Transcriptomic analysis of pou4-2-deficient planarians reveals enrichment for conserved genes associated with human auditory and vestibular function, suggesting that planarian rheosensory neurons share molecular features with mammalian inner ear hair cells. Expression of these conserved genes is significantly reduced following RNAi-mediated knockdown of pou4-2. To determine whether these transcriptional changes have functional consequences for mechanosensory neuron identity or behavior, we assessed the impact of pou4-2 knockdown on sensory function. pou4-2 RNAi results in impaired mechanosensation in both uninjured and regenerating planarians. Together with the loss of terminal differentiation markers in mechanosensory neurons, these findings identify Smed-pou4-2 as a key regulator of mechanosensory neuron identity in planarians and support the idea that conserved sensory specification programs are redeployed during adult tissue regeneration.

developmental biology↗

bioRxiv2024

The role of polycystic kidney disease-like homologs in planarian nervous system regeneration and function

Planarians are an excellent model for investigating molecular mechanisms necessary for regenerating a functional nervous system. Numerous studies have led to the generation of extensive genomic resources, especially whole-animal single-cell RNA-seq resources. These have facilitated in silico predictions of neuronal subtypes, many of which have been anatomically mapped by in situ hybridization. However, our knowledge of the function of dozens of neuronal subtypes remains poorly understood. Previous investigations identified that polycystic kidney disease (pkd)-like genes in planarians are strongly expressed in sensory neurons and have roles in mechanosensation. Here, we examine the expression and function of all the pkd genes found in the Schmidtea mediterranea genome and map their expression in the asexual and hermaphroditic strains. Using custom behavioral assays, we test the function of pkd genes in response to mechanical stimulation and in food detection. Our work provides insight into the physiological function of sensory neuron populations and protocols for creating inexpensive automated setups for acquiring and analyzing mechanosensory stimulation in planarians.

developmental biology↗

bioRxiv2021

RNAi screening of RING/U-box domain ubiquitin ligases identifies critical regulators of stem cells and tissue regeneration in planarians

Regenerative processes depend on the interpretation of signals to coordinate cell behaviors. The role of ubiquitin-mediated signaling is known to be important in many cellular and biological contexts, but its role in regeneration is not well understood. To investigate how ubiquitylation impacts tissue regeneration in vivo, we are studying planarians that are capable of regenerating after nearly any injury using a population of stem cells. Here we used RNAi to screen RING/U-box E3 ubiquitin ligases that are highly expressed in planarian stem cells and stem cell progeny. RNAi screening identified nine genes with functions in regeneration, including the spliceosomal factor prpf19 and histone modifier rnf2; based on their known roles in developmental processes, we further investigated these two genes. We found that prpf19 was required for animal survival but not for stem cell maintenance, suggesting a role in promoting cell differentiation. Because RNF2 is the catalytic subunit of the Polycomb Repressive Complex 1 (PRC1), we also examined other putative members of this complex (CBX and PHC). We observed a striking phenotype of regional tissue misspecification in cbx and phc RNAi planarians. To identify genes regulated by PRC1, we performed RNA-seq after knocking down rnf2 or phc. Although these proteins are predicted to function in the same complex, we found that the set of genes differentially expressed in rnf2 versus phc RNAi were largely non-overlapping. Using in situ hybridization, we showed that rnf2 regulates gene expression levels within a tissue type, whereas phc is necessary for the spatial restriction of gene expression, findings consistent with their respective in vivo phenotypes. This work not only uncovered roles for RING/U-box E3 ligases in stem cell regulation and regeneration, but also identified differential gene targets for two putative PRC1 factors required for maintaining cell-type-specific gene expression in planarians.

developmental biology↗