Biology subjects

Clark, E. G.

Publications and source records attributed to Clark, E. G..

5 recordsLinked to original sources

bioRxiv2026

DDR and TMEM132 genes control progenitor targeting and regenerative assembly of the planarian eye

How progenitors can faithfully self-assemble to build new organs in adulthood is a central unsolved problem in regeneration biology. The planarian eye is a model for uncovering principles of de novo organogenesis during regeneration. In this process, pluripotent adult stem cells specify into ovo+ migratory progenitors which target to the eye field due to Wnt and FGFRL signals produced from bodywall muscle, then differentiate into photoreceptor neurons (PRNs) and pigmented optic cup (OC) cells, followed by organization of these two cell types in an opposing pattern that completes eye organ maturation. We used scRNA-seq to characterize eye progenitor transcriptomes during regeneration, followed by FISH validation, and RNAi screening to identify regulators of eye regeneration. This uncovered a function for the discoidin domain receptor ddr-1 in preventing the premature terminal differentiation of migratory eye progenitors. DDRs encode collagen receptors, and bodywall muscle is the major source of collagen in planarians, suggesting eye progenitors likely interface with muscle ECM for their proper deployment in regeneration. We further identified a novel eye morphogenesis phenotype from knockdown of tmem132-1, causing failed heterotypic adhesion between eye cell types. TMEM132 factors are conserved cell-surface receptors that mediate adhesion and regulate migration, and human TMEM132 mutations are associated with several neurobehavioral diseases. Therefore, planarian tmem132-1 likely directly regulates the capture and assembly of migratory progenitors into mature eyes during regeneration. Together, these results define new steps in the eye regeneration pathway and suggest ancient roles for DDR and TMEM132 in progenitor migration and coordinated organ assembly.

developmental biology↗

bioRxiv2023

BMP suppresses WNT to integrate patterning of orthogonal body axes in adult planarians.

Adult regeneration restores patterning of orthogonal body axes after damage in a post-embryonic context. Planarians regenerate using distinct body-wide signals primarily regulating each axis dimension: anteroposterior Wnts, dorsoventral BMP, and mediolateral Wnt5 and Slit determinants. How regeneration can consistently form perpendicular tissue axes without symmetry-breaking embryonic events is unknown, and could either occur using fully independent, or alternatively, integrated signals defining each dimension. Here, we report that the planarian dorsoventral regulator bmp4 suppresses the posterior determinant wnt1 to pattern the anteroposterior axis. Double-FISH identified distinct anteroposterior domains within dorsal midline muscle that express either bmp4 or wnt1. Homeostatic inhibition bmp4 and smad1 expanded the wnt1 expression anteriorly, while elevation of BMP signaling through nog1;nog2 RNAi reduced the wnt1 expression domain. BMP signal perturbation broadly affected anteroposterior identity as measured by expression of posterior Wnt pathway factors, without affecting head regionalization. Therefore, dorsal BMP signals broadly limit posterior identity. Furthermore, bmp4 RNAi caused medial expansion of the lateral determinant wnt5 and reduced expression of the medial regulator slit. Double RNAi of bmp4 and wnt5 resulted in lateral ectopic eye phenotypes, suggesting bmp4 acts upstream of wnt5 to pattern the mediolateral axis. Therefore, bmp4 acts at the top of a patterning hierarchy both to control dorsoventral information and also, through suppression of Wnt signals, to regulate anteroposterior and mediolateral identity. These results reveal that adult pattern formation involves integration of signals controlling individual orthogonal axes. Author SummarySystems that coordinate long-range communication across axes are likely critical for enabling tissue restoration in regenerative animals. While individual axis pathways have been identified, there is not yet an understanding of how signal integration allows repatterning across 3-dimensions. Here, we report an unanticipated linkage between anteroposterior, dorsoventral, and mediolateral systems in planarians through BMP signaling. We find that dorsally expressed BMP restricts posterior and lateral identity by suppressing distinct Wnt signals in adult planarians. These results demonstrate that orthogonal axis information is not fully independent and suggest a potentially ancient role of integrated axis patterning in generating stable 3-dimensional adult forms.

developmental biology↗

bioRxiv2020

Kctd15 regulates nephron segment development by repressing Tfap2a activity

A functional vertebrate kidney relies on structural units called nephrons, which are epithelial tubules that contain a sequence of segments each expressing a distinct repertoire of solute transporters. To date, the transcriptional codes driving regional specification, solute transporter program activation, and terminal differentiation of segment populations remain poorly understood. We demonstrate for the first time that the KCTD15 paralogs, kctd15a and kctd15b, function in concert to restrict distal early (DE)/thick ascending limb (TAL) segment lineage assignment in the developing zebrafish pronephros by repressing Tfap2a activity. During renal ontogeny, expression of these factors co-localized with tfap2a in distal tubule precursors. kctd15 loss primed nephron cells to adopt distal fates by driving expansions in slc12a1, kcnj1a.1, and stc1 marker expression. These phenotypes were resultant of Tfap2a hyperactivity, where kctd15a/b-deficient embryos exhibited increased abundance of this transcription factor. Interestingly, tfap2a reciprocally promoted kctd15 transcription, unveiling a circuit of autoregulation operating in nephron progenitors. Concomitant kctd15b knockdown with tfap2a overexpression produced genetic synergy and further expanded the DE population. Our study provides strong evidence that a transcription factor-repressor feedback module employs tight regulation of Tfap2a and Kctd15 kinetics to control nephron segment fate choice and differentiation during kidney development.

developmental biology↗

bioRxiv2019

Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing the Drosophila Segmentation Network

Because regulatory networks of transcription factors drive embryonic patterning, it is possible that chromatin accessibility states impact how networks interact with information encoded in DNA. To determine the interplay between chromatin states and regulatory network function, we performed ATAC seq on Drosophila embryos over the period spanning the establishment of the segmentation network, from zygotic genome activation to gastrulation. Chromatin accessibility states are dynamic over this period, and establishment of the segmentation network requires maturation of the ground chromatin state. Elimination of all maternal patterning information allows identification of patterning-dependent and -independent dynamic chromatin regions. A significant proportion of patterning-dependent accessibility stems from pioneer activity of the pair-rule factor Odd-paired (opa). While opa is necessary to drive late opening of segmentation network cis-regulatory elements, competence for opa to pioneer is regulated over time. These results indicate that dynamic systems for chromatin regulation directly impact the interpretation of embryonic patterning information.

developmental biology↗

bioRxiv2018

Tfap2a is a novel gatekeeper of differentiation in renal progenitors during kidney development

Renal functional units known as nephrons undergo patterning events during development that create a segmental array of cellular populations with discrete physiological tasks. Knowledge about the terminal differentiation programs of each nephron segment has central importance for understanding kidney disease and to advance regenerative medicine, as mammalian nephrons grown in organoid cultures from pluripotent cells fail to terminally differentiate. Here, from a novel forward genetic screen using zebrafish we report the discovery that transcription factor AP-2 alpha (tfap2a) coordinates a gene regulatory network that controls the progression of nephron distal segment progenitors into the differentiated state. Overexpression of tfap2a rescued differentiation in mutants and caused ectopic expression of distal segment markers in wild-type nephrons, indicating tfap2a is sufficient to instigate the distal segment differentiation program. tfap2a/2b deficiency exacerbated distal nephron segment differentiation defects, revealing functional redundancy where tfap2a has a dominant role upstream of its family member. With further genetic studies, we assembled a blueprint of the tfap2a gene regulatory network during nephrogenesis. We demonstrate that tfap2a acts downstream of Iroquois homeobox 3b, a conserved distal lineage transcription factor. tfap2a controls a circuit consisting of irx1a, tfap2b, and genes encoding solute transporters that dictate the specialized metabolic functions of the distal nephron segments, and we show for the first time that this regulatory node is distinct from the pathway circuits controlling aspects such as apical-basal polarity and ciliogenesis during the differentiation process. Thus, our studies reveal new insights into the genetic control of differentiation, where tfap2a regulates the suite of segment transporter traits. These findings have relevance for understanding renal birth defects, as well as efforts to recapitulate nephrogenesis in vivo to make functional units that can facilitate organoid applications such as drug discovery and regenerative therapies.\n\nSummary StatementHere, we report for the first time that transcription factor AP-2 alpha (tfap2a) controls the progression from nephron progenitor into the fully differentiated state. This fundamentally deepens our knowledge about the genetic control of kidney development.

developmental biology↗