Biology subjects

Mayran, A.

Publications and source records attributed to Mayran, A..

13 recordsLinked to original sources

bioRxiv2026

Engineered dual-gastruloid model for foregut-pharyngeal mesoderm co-development

During mammalian gastrulation, progenitors of craniofacial and cardiopharyngeal muscles arise from anterior mesoderm adjacent to foregut endoderm, and they are controlled by gene regulatory networks and signalling pathways distinct from those of trunk mesoderm. While in vitro models capture aspects of posterior and heart development, a spatially organised interface between foregut-like endoderm and cranial-mesoderm-like tissue has not been described. Here we introduce a dual-aggregate gastruloid model, formed by fusing two mouse embryonic stem cell aggregates patterned under distinct Nodal, FGF, and Wnt signalling. These structures reproducibly establish an anterior-posterior axis and position a Foxa2/Sox17/Cdh1 foregut-like epithelium proximal to Pax1/Pax9 pharyngeal-like endoderm and Tbx1 cranial-mesoderm-like cells, resembling the E8.5 pharyngeal region. Reciprocal chimeras and Foxa2 loss-of-function indicate that Foxa2 endoderm is required for Tbx1 expression in adjacent anterior mesoderm. Pharmacological perturbation of Hedgehog disrupts Foxa2 and Tbx1 expression. The model provides a tractable platform for dissecting endoderm-mesoderm signalling and congenital craniofacial disease mechanisms.

developmental biology↗

bioRxiv2026

MULTIPLE DEFECTS IN MOUSE STEM CELL BASED EMBRYO MODELS LACKING ALL HOX FUNCTION

Mammals have four genomic copies of an ancestral Hox cluster, with a total of 39 genes. While gene inactivation approaches and full cluster deletions have revealed their critical functions during early development, the effect of removing all Hox function has remained elusive due to both biological and technological challenges. We have used mouse gastruloids, an ES cells-derived embryo model where Hox genes are properly activated in time and space, to assess the effect of their complete absence. We report that gastruloids lacking Hox function can still elongate and reach a general shape resembling their control counterparts, with a well-established AP polarity. However, unlike controls, they fail to produce any endoderm and are unable to properly segment their presomitic mesoderm into persistent somite-like structures. Instead, they produce a type of mesoderm with a more anterior identity. We thus propose that, in this system at least, HOX proteins are necessary to posteriorize an existing anterior ground-state structure, in part by promoting and/or maintaining the epithelialization of cellular condensations. Multiomes analysis revealed range of modifications in chromatin accessibility in the absence of any HOX proteins, involving in particular variations in the binding of the co-factor PBX1. In contrast, neuro-mesodermal progenitor (NMP) cells are not overtly affected in mutant gastruloids, even though they normally initiate strong Hox gene transcription, suggesting that these cells are used as vehicles to translate a temporal sequence of activation into an AP colinear transcript distribution, which becomes functional at a later stage only.

Developmental Biology↗

bioRxiv2025

Fine-tuning mechanical constraints uncouple patterning and gene expression in murine pseudo-embryos

The interplay between mechanical forces and genetic programs is fundamental to embryonic development, yet how these factors independently or jointly influence morphogenesis and cell fate decisions remains poorly understood. Here, we fine-tune the mechanical environment of murine gastruloids, three-dimensional in vitro models of early embryogenesis, by embedding them in bioinert hydrogels with precisely tunable stiffness and timing of application. This approach reveals that external constraints can selectively influence transcriptional profiles, patterning, or morphology, depending on the level and timing of mechanical modulation. Gastruloids embedded in ultra-soft hydrogels (< 30 Pa) elongate robustly, preserving both anteroposterior patterning and transcriptional profiles. In contrast, embedding at higher stiffness disrupts polarization while leaving gene expression largely unaffected. Conversely, earlier embedding significantly impacts transcriptional profiles independently of polarization defects, highlighting the uncoupling of patterning and transcription. These findings suggest that distinct cellular states respond differently to external constraints. Live imaging and cell tracking imply that impaired cell motility underlies polarization defects, underscoring the role of mechanical forces in shaping morphogenesis independently of transcriptional changes. By allowing precise control over external mechanical boundaries, our approach provides a powerful platform to dissect how physical and biochemical factors interact to orchestrate early embryonic development.

developmental biology↗

bioRxiv2024

WNT signaling coordinately controls mouse limb bud outgrowth and establishment of the digit-interdigit pattern

Self-organization, such as the emergence of a pattern from a homogenous state, is a fascinating property of biological systems. Early limb bud outgrowth and patterning in mice are controlled by a robust and self-regulatory signaling system, and initiation of the periodic digit-interdigit pattern appears under control of a self-regulatory Turing system. Previous studies established the requirement of WNT and BMP signaling for both early limb bud and digit-interdigit morphogenesis, but the molecular changes underlying the transition from early limb bud signaling to the digit-interdigit patterning system remained unknown. Here, we use small molecule inhibitors to rapidly but transiently block WNT signaling to identify the early transcriptional targets that are altered during disruption and recovery of limb bud and digit development. Together, this study highlights the overarching role of WNT signaling in controlling early limb bud outgrowth and patterning, and establishment of the periodic digit-interdigit pattern. Finally, the transient WNT signaling disruption approach reveals the plasticity and robustness of these self-organizing limb bud and digit patterning systems.

developmental biology↗

bioRxiv2024

Size-dependent temporal decoupling of morphogenesis and transcriptional programs in gastruloids

Understanding the interplay between cell fate specification and morphogenetic changes remains a central challenge in developmental biology. Gastruloids, self-organizing stem cell-based models of post-implantation mammalian development, provide a powerful platform to address this question. Here, we show that physical parameters, particularly system size, critically influence the timing and outcomes of morphogenetic processes. Larger gastruloids exhibit delayed symmetry breaking, increased multipolarity, and prolonged axial elongation, with morphogenesis driven by system size. Despite these variations, transcriptional programs and cell fate composition remain remarkably stable across a broad size range. Notably, extreme sizes show distinct transcriptional modules and clear shifts in gene expression patterns. Intriguingly, size perturbation experiments rescued the morphogenetic and pattern phenotypes observed in extreme sizes, demonstrating the remarkable adaptability of gastruloids to their effective system size. These findings establish gastruloids as versatile models for studying spatiotemporal dynamics in mammalian embryogenesis and reveal how physical constraints decouple transcriptional from morphogenetic programs.

developmental biology↗

bioRxiv2024

CTCF-DEPENDENT INSULATION OF Hoxb13 AND THE HETEROCHRONIC CONTROL OF TAIL LENGTH

In mammals, tail length is controlled by several genetic determinants, amongst which Hox13 genes located at the posterior extremities of Hox clusters, whose main function are to terminate the extension of the body axis. In this view, the precise timing in the transcriptional activation of these genes may impact upon body length. Unlike other Hox clusters, HoxB lacks all posterior genes between Hoxb9 and Hoxb13, two genes separated by a ca. 70 kb large DNA segment containing an unusually high number of CTCF sites, suggesting it isolates Hoxb13 from the rest of the cluster, thereby delaying its negative impact on trunk extension. We deleted the spacer DNA to induce a potential heterochronic gain of function of Hoxb13 at physiological concentration and observed a shortening of the tail as well as other abnormal phenotypes, which were all rescued by inactivating Hoxb13 in-cis with the deletion. A comparable gain of function was observed in mutant ES cells grown as pseudo-embryos in vitro, which allowed us to examine in details the importance of both the number and the orientation of CTCF sites in the insulating activity of the DNA spacer. A short cassette containing all the CTCF sites was sufficient to insulate Hoxb13 from the rest of HoxB and additional modifications of this CTCF cassette showed that two CTCF sites in convergent orientations are already capable of importantly delaying Hoxb13 activation in these conditions. We discuss the relative importance of genomic distance versus number and orientation of CTCF sites in preventing Hoxb13 to be activated too early during trunk extension and hence to modulate tail length.

developmental biology↗

bioRxiv2023

Cadherins modulate the self-organizing potential of gastruloids

Gastruloids have recently emerged as an efficient four-dimensional model for studying some aspects of post-implantation embryonic patterning. They undergo gastrulation-like processes leading to the self-organization into highly reproducible biological objects. Here, we sought to uncover the molecular and cellular mechanism underlying this remarkable property. We report that self-organization competence is associated with a cell-specific coordination of a Cadherin switch. We find that N-Cadherin hinders gastruloids morphogenetic competence, for its inactivation leads to the formation of trunk-like structures in absence of extra-cellular matrix analogues. In contrast, E-Cadherin repression by Snai1 is critical for self-organization: Snai1 establishes a cell-specific repressive pace by triggering the repression of a pluripotency-associated transcription program and its chromatin landscape, thus allowing a proper transition from E-to N-Cadherin to occur. Altogether, this work establishes a molecular mechanism that integrates the exit from pluripotency and the pace of cell differentiation, leading to the observed self-organizing potential of gastruloids.

developmental biology↗

bioRxiv2021

Polycomb Repressive Complexes occupancy reveals PRC2-independent PRC1 critical role in the control of limb development

The Polycomb Repressive Complexes (PRC) are key players in the regulation of tissue-specific gene expression through their ability to epigenetically silence developmental genes. They are subdivided into two multicomponent complexes, PRC1 and PRC2, functioning through post-translational modifications of histone tails. A large body of work revealed functional interactions between PRC1 and PRC2, whereby trimethylation of lysine 27 on histone H3 (H3K27me3) by PRC2 contributes to the recruitment of canonical PRC1 (cPRC1). In parallel, a PRC2-independent binding of PRC1 has been uncovered and referred to as non-canonical PRC1 or variant PRC1 (vPRC1), in which PRC1-dependent ubiquitination of lysine 119 on histone H2A is involved in recruiting PRC2/propagating PRC2-dependent H3K27 trimethylation. While it was initially assumed that cPRC1 and vPRC1 bind distinct targets, subsequent evidence pointed to cPRC1 and vPRC1 sharing a significant subset of targets. How the functional interplay between PRC2, cPRC1 and vPRC1 contributes to gene regulation remains partially understood. Here, we show that, in the developing limb, PRC2 inactivation barely affects PRC1 occupancy, as the majority of PRC2- bound loci are bound by vPRC1 (RYBP-PRC1), both in wild type and PRC2 mutant limbs. Consistent with this, we found that loci bound by CBX2, a PRC1 subunit involved in the recognition of H3K27me3 and thereby recruitment of cPRC1, are, for the vast majority, also bound by vPRC1. Intriguingly, analysis of PRC2 mutant limbs revealed that while a large part of CBX2 occupancy is lost in absence of PRC2 function, as expected from the absence of H3K27me3, there is a significant number of genes retaining CBX2 occupancy as well as a few genes with apparent gain of CBX2 binding. Importantly, among these genes, 56 of them correspond to developmental genes known for playing a key role in limb morphogenesis. Based on the importance of vPRC1 in gene silencing, our findings emphasize the primary role of PRC2-independent PCR1 function in regulating developmental genes and questions the role of PRC2/cPRC1 in controlling developmental programs.

developmental biology↗

bioRxiv2020

Pax7 pioneer factor action requires both paired and homeo DNA binding domains

The pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 had shown that each DBD can bind a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed binding sites for both paired and homeo domains. The present work investigated the implication of both DBDs in pioneer action. We now show that the composite sequence is a higher affinity Pax7 binding site compared to either paired or homeo binding sites and that efficient binding to this site involves both DBDs. We also show that a Pax7 monomer binds composite sites and that methylation of cytosines within the binding site does not affect binding, which is consistent with pioneer action exerted at methylated DNA sites within nucleosomal heterochromatin. Finally, introduction of single amino acid mutations in either the paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites. Significance StatementPioneer transcription factors have the unique ability to recognize DNA target sites within closed heterochromatin and to trigger chromatin opening. Only a fraction of the heterochromatin recruitment sites of pioneers are subject to chromatin opening. The molecular basis for this selectivity is unknown and the present work addressed the importance of DNA sequence affinity for selection of sites to open. The pioneering ability of the pioneer factor Pax7 is not strictly determined by affinity or DNA sequence of binding sites, nor by number or methylation status of DNA sites. Mutation analyses showed that recruitment to heterochromatin is primarily dependent on the Pax7 paired domain whereas the ability to open chromatin requires both paired and homeo DNA binding domains.

molecular biology↗

bioRxiv2020

Analysis of Polycomb Repressive Complexes binding dynamics during limb development reveals the prevalence of PRC2-independent PRC1 occupancy

The Polycomb group (PcG) proteins are key players in the regulation of tissue-specific gene expression through their known ability to epigenetically silence developmental genes. The PcG proteins form two multicomponent complexes, Polycomb Repressive Complex 1 and 2 (PRC1 and PRC2), whereby the hierarchical model of recruitment postulates that PRC2 triggers the trimethylation of Histone H3 lysine 27 (H3K27me3) leading to the recruitment of PRC1. Here we report on the genome-wide binding dynamics of components from both PRC1 and PRC2 in the developing limb. We show that a large proportion of PRC-bound promoters are occupied exclusively by PRC1, suggesting a more extensive PRC1-specific activity than anticipated. We found that PRC1 (RING1B) and PRC2 (SUZ12) co-occupy the promoters of developmental genes, for which a subset become up-regulated upon the inactivation of PRC2. Strikingly, we found that RING1B occupancy is largely unaffected by the loss of PRC2, revealing a complex functional relationship between these two complexes in regulating gene expression and possibly an expansive functional interplay between canonical and non-canonical PRC1.

developmental biology↗

bioRxiv2019

HOX13-dependent chromatin accessibility modulates the target repertoires of the HOX factors

Hox genes encode essential transcription factors that control patterning during embryonic development. Distinct combinations of nested Hox expression domains establish cell and tissue identities1-3. Consequently, spatial or temporal de-regulation of Hox genes can cause severe alterations of the body plan3. While HOX factors have very similar DNA binding motifs, their binding specificity is, in part, mediated by co-factors4-6. Yet, the interplay between HOX binding specificities and the cellular context remains largely elusive. To gain insight into this question, we took advantage of developing limbs for which the differential expression of Hox genes is well-characterized7. We show that the transcription factors HOXA13 and HOXD13 (hereafter referred as HOX13) allow another HOX factor, HOXA11, to bind loci initially assumed to be HOX13-specific. Importantly, HOXA11 is unable to bind these loci in distal limbs lacking HOX13 function indicating that HOX13 modulates HOXA11 target repertoire. In addition, we find that the HOX13 factors implement the distal limb developmental program by triggering chromatin opening, a defining property of pioneer factors8,9. Finally, single cell analysis of chromatin accessibility reveals that HOX13 factors pioneer chromatin opening in a lineage specific manner. Together, our data uncover a new mechanism underlying HOX binding specificity, whereby tissue-specific variations in the target repertoire of HOX factors rely, at least in part, on HOX13-dependent chromatin accessibility.

developmental biology↗

bioRxiv2018

Pioneer and nonpioneer cooperation drives lineage specific chromatin opening

Pioneer transcription factors are coined as having the unique property of "opening closed chromatin sites" for implementation of cell fates. We previously showed that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire: this allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigated the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes were defined by scRNAseq and chromatin accessibility profiling. We found that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors.

genomics↗

bioRxiv2018

Cell-autonomous transcriptional mechanism for enhancement of translation capacity in secretory cells

Translation is a basic cellular process and its capacity is adapted to cell function. In particular, secretory cells achieve high protein synthesis levels without triggering the protein stress response. It is unknown how and when translation capacity is increased during differentiation. Here, we show that the transcription factor Creb3l2 is a scaling factor for translation capacity in secretory cells and that it directly binds ~75% of regulatory and effector genes for translation. In parallel with this cell-autonomous mechanism, implementation of the physiological UPR pathway prevents triggering the protein stress response. The pituitary differentiation factor Tpit activates Creb3l2 expression, the Creb3l2-dependent regulatory network as well as the physiological UPR pathway. Thus, Creb3l2 implements high basal translation levels through direct targeting of translation effector genes acting downstream of signaling pathways that otherwise regulate protein synthesis. Expression of Creb3l2 may be a useful means to enhance production of therapeutic proteins.

cell biology↗