Hamrud E, Leese J, Thiery AP
… +4 more, Buzzi AL, Vigilante A, Briscoe J, Streit A
Development
· 2025 Dec · PMID 41235466
·
Publisher ↗
During development, dynamic changes in gene expression and chromatin architecture drive the transition from progenitors to specialised cell types. Here, we use single cell ATAC sequencing (scATAC-seq) to investigate chan...During development, dynamic changes in gene expression and chromatin architecture drive the transition from progenitors to specialised cell types. Here, we use single cell ATAC sequencing (scATAC-seq) to investigate changes in chromatin accessibility as chick neural plate border cells segregate into neural, neural crest and placode cells. We developed a Nextflow pipeline, 'single cell Advanced Chromatin Exploration', which integrates scATAC-seq and scRNA-seq data to identify cell-state-specific accessibility profiles and groups of chromatin regions with coordinated dynamic behaviour, termed accessibility modules. We find that neural plate border and adjacent cells are characterised by broadly open chromatin, reflecting their broad potential to generate any ectodermal derivative. As development proceeds, cell-type-specific chromatin signatures are established. Inferring an enhancer-centric gene regulatory network, we predict Foxk2 as new regulator for placode specification and verify this prediction experimentally. Foxk2 target enhancers are open in placodal cells, but not any other ectodermal cells. This finding suggests that, on a regulatory level, cells can use different strategies to control fate choice: differential accessibility of enhancers and broad accessibility controlled by differentially expressed transcription factors.
Gillespie WB, Zhang Y, Ruiz OE
… +12 more, Cerda J, Ortiz-Guzman J, Sherman M, Turner WD, Largoza G, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD
Development
· 2025 Nov · PMID 41230856
·
Full text
Here, we present MultiSite Assembly of Gateway Induced Clones (MAGIC), which leverages Gateway-based recombinatorial cloning technology for rapid, modular assembly of plasmids to facilitate transgenesis in cells and vert...Here, we present MultiSite Assembly of Gateway Induced Clones (MAGIC), which leverages Gateway-based recombinatorial cloning technology for rapid, modular assembly of plasmids to facilitate transgenesis in cells and vertebrate animal models. The MAGIC collection of plasmids spans a range of in vitro and in vivo uses, from tools for optically and chemically tunable gene expression, to simultaneous expression of microRNAs and fluorescent reporters, to a suite of distinct subcellular compartmental fluorescent reporters, to Cre and Dre recombinase-dependent gene expression. MAGIC system components are compatible with existing MultiSite Gateway Tol2 systems currently used in zebrafish and mammalian lentiviral and adenoviral Destination vectors, allowing rapid cross-species experimentation. The kit also includes novel vectors for stable transgene integration into host genomes in vitro or in vivo when used with piggyBac transposase, I-Sce meganuclease or Tol2 transposase. Collectively, the MAGIC system facilitates transgenesis in cultured mammalian cells, mouse, chick and zebrafish embryos, enabling the rapid generation of innovative DNA constructs for biological research due to a shared, common plasmid platform.
Development
· 2025 Dec · PMID 41221768
·
Full text
Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux...Plants continuously produce lateral organs, such as leaves and flowers, from the shoot apical meristem (SAM). This process is guided by the accumulation of the plant hormone auxin and the polar localization of the efflux protein PIN-FORMED1 (PIN1). The transcription factor MONOPTEROS (MP) plays a crucial role in orienting PIN1 polarity, thereby facilitating auxin-driven organogenesis. In this study, we investigate genes downstream of MP that may regulate PIN1 polarity and organogenesis, discovering that the downstream vascular transcription factor TMO5 can promote PIN1 polarity convergence non-cell-autonomously and that TMO5 and its family members promote organ initiation in the SAM. By examining the role of auxin and cytokinin downstream of these genes, we provide evidence that the TMO5-like genes control PIN1 polarity and drive organogenesis by coordinating multiple hormonal signalling pathways.
Uttley K, Jüllig HJ, De Angelis C
… +4 more, Auer JMT, Ozga E, Bengani H, Long HK
Development
· 2025 Nov · PMID 41208708
·
Full text
Human facial appearance is a highly variable morphological trait, with both rare and common genetic variants shaping craniofacial morphology between individuals and in disease. Deletions encompassing an enhancer cluster...Human facial appearance is a highly variable morphological trait, with both rare and common genetic variants shaping craniofacial morphology between individuals and in disease. Deletions encompassing an enhancer cluster 1.45 megabases upstream of SOX9 (EC1.45) cause Pierre Robin sequence, a craniofacial disorder characterised by underdevelopment of the lower jaw and associated with cleft palate. We hypothesised therefore that single nucleotide variants within EC1.45 may cause more subtle alterations in facial form. Leveraging recent human evolution, and the distinct jaw morphology of Neanderthals, we investigated the impact of three Neanderthal-derived variants on EC1.45 function. Using zebrafish dual enhancer-reporters, we observed higher activity of Neanderthal EC1.45 in neural crest-derived progenitor cells during a specific developmental window. These EC1.45-active cells reside proximal to and are transcriptionally related to precartilaginous condensations that contribute to craniofacial skeletal development. Mimicking the observed increase in enhancer activity, we overexpressed human SOX9 in EC1.45-active cells and detected an expanded volume of developing cartilaginous precursors. Our work implicates Neanderthal-derived variants in increasing regulatory activity for a disease-associated enhancer, with the potential to impact craniofacial morphology across recent hominin evolution.
Cetin R, Picco G, van Staalduinen J
… +11 more, Bindels E, Hoogenboezem R, van Beek G, Sanders MA, Fidan Y, Korkmaz A, Gribnau J, van Haren J, Huylebroeck D, Mulugeta E, Grosveld F
Development
· 2025 Dec · PMID 41200855
·
Full text
Hematopoiesis occurs in three consecutive overlapping waves in mammals, regulated by transcription factors. We investigated the role of three relatively poorly studied transcription factors in early embryonic hematopoiet...Hematopoiesis occurs in three consecutive overlapping waves in mammals, regulated by transcription factors. We investigated the role of three relatively poorly studied transcription factors in early embryonic hematopoietic development at single-cell resolution: Atf3, Zfp711 and Bcl6b. These transcription factors are upregulated early in development, when hematopoietic and endothelial lineages separate from cardiac and other mesodermal lineages. We combined multiplexed single-cell RNA sequencing and flow cytometric analysis with knockouts in in vitro differentiating mouse embryonic stem cells to dissect the function of these transcription factors in lineage specification. ΔAtf3 cells showed increased mesodermal differentiation but decreased endothelial cells and erythro-myeloid progenitors, accompanied by aberrant interferon signaling. Mechanistically, loss of Atf3 disrupted key hematopoietic regulatory genes (Runx1, Egr1, Jun, Fos, Mafb and Batf3) required for the formation of erythro-myeloid progenitors. ΔZfp711 cells exhibited increased blood progenitors and erythroid cells, but decreased endothelial cells, with a striking shift from Hoxa+ mesoderm (allantois and limb mesoderm) to Hoxb+ mesoderm (mesenchyme and epicardium). Notably, Zfp711 binds the Atf3 promoter, suggesting a hierarchical regulation. In contrast, ΔBcl6b had no observable effects on early hematopoiesis, despite specific expression in hemato-endothelial progenitors.
Tenger-Trolander A, Amiri E, Gantz V
… +4 more, Kwan CW, Yadav H, Sanders SA, Schmidt-Ott U
Development
· 2025 Nov · PMID 41159449
·
Full text
The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism Drosophila melanogaster and the ability to cost-effectively rear many species...The order Diptera (true flies) holds promise as a model taxon in evolutionary developmental biology due to the inclusion of the model organism Drosophila melanogaster and the ability to cost-effectively rear many species in laboratories. One of these dipteran species, the scuttle fly Megaselia abdita (Phoridae), has been used in evolutionary developmental biology for 30 years and is an excellent phylogenetic intermediate between fruit flies and mosquitoes, but remains underdeveloped in genomic resources. Here, we present a de novo chromosome-level assembly and annotation of M. abdita and transcriptomes of nine embryonic and four post-embryonic stages. We also compare nine stage-matched embryonic transcriptomes between M. abdita and D. melanogaster. Our analysis of these resources reveals extensive chromosomal synteny with D. melanogaster; 24 orphan genes with embryo-specific expression, including a novel F-box LRR gene in M. abdita; and conserved and diverged features of gene expression dynamics between M. abdita and D. melanogaster. Collectively, our results provide a new resource for studying the diversification of developmental processes in flies.
Bian F, Golestaneh K, Davis E
… +8 more, Khan A, Nicholson B, Daghsni M, Flohr K, Liu S, da Silva S, Pennacchio L, Aldiri I
Development
· 2024 Dec · PMID 41159420
·
Full text
Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides...Retinal neurogenesis is mediated by the coordinated activities of a complex gene regulatory network (GRN) of transcription factors (TFs) in multipotent retinal progenitor cells (RPCs). How this GRN mechanistically guides neural competence remains poorly understood. In this study, we present integrated transcriptional, genetic and genomic analyses to uncover the regulatory mechanisms of SOX2, a key factor in establishing neural identity in RPCs. We show that SOX2 is preferentially enriched in the RPC-specific enhancer landscape associated with essential regulators of retinogenesis. Disruption of SOX2 expression impairs retinogenesis, marked by a selective loss of enhancer activity near genes essential for RPC proliferation and lineage specification. We identified the RPC transcription factor VSX2 as a binding partner for SOX2 and, together, SOX2 and VSX2 co-target a core, retina-specific chromatin repertoire characterized by enhanced TF binding and robust chromatin accessibility. This cooperative binding establishes a shared SOX2-VSX2 transcriptional code that promotes the expression of crucial regulators of neurogenesis while repressing the acquisition of alternative lineage cell fate. Our data illuminate fundamental biological insights on how transcription factors act in concert to drive chromatin-based genetic programs underlying retinal neural identity.
Ogita K, Fukasawa N, Wang R
… +4 more, Fujisaki T, Katagiri K, Uemura T, Tanaka H
Development
· 2025 Nov · PMID 41122808
·
Publisher ↗
The plant hormone auxin is directionally transported in plant tissues by the actions of the auxin transport proteins. PIN-FORMED (PIN) family proteins asymmetrically localize at the plasma membrane, and facilitate auxin...The plant hormone auxin is directionally transported in plant tissues by the actions of the auxin transport proteins. PIN-FORMED (PIN) family proteins asymmetrically localize at the plasma membrane, and facilitate auxin efflux, thereby promoting cell-to-cell polar auxin transport. In previous studies, we have identified the trans-Golgi network-localized ARF GEF BEN1 (BIG5) and the Sec1/Munc18 protein BEN2 (VPS45) as membrane-trafficking components involved in PIN protein localization and auxin-dependent development. Here, we address the role of VPS45-interacting SYP4 Qa-SNARE proteins and the genetic relationship between VPS45 and SYP4 proteins. We show that ben2 and syp4 mutations affect the subcellular localization of SYP4 proteins and VPS45, respectively. Genetic interference of SYP42 and SYP43 genes results in PIN-trafficking defects and developmental alterations, such as decreased root meristem size and cotyledon venation defects, which are qualitatively reminiscent of those of ben2 and/or ben1; ben2 mutants. In addition, the ben2 mutation, which is assumed to compromise VPS45 activity, strongly enhances the developmental defects of the syp4 mutants. These results suggest that VPS45 and SYP4 Qa-SNARE proteins jointly play an important role in auxin-dependent plant development.
Carroll SH, Schafer S, Richman AS
… +5 more, Wang P, Ahsan MU, Tsay L, Wang K, Liao EC
Development
· 2025 Nov · PMID 41111330
·
Full text
The pituitary gland produces several hormones that regulate growth, metabolism, stress response, reproduction and homeostasis. Congenital hypopituitarism is a deficiency in one or more pituitary hormones and encompasses...The pituitary gland produces several hormones that regulate growth, metabolism, stress response, reproduction and homeostasis. Congenital hypopituitarism is a deficiency in one or more pituitary hormones and encompasses a spectrum of clinical conditions. The pituitary has a complex embryonic origin, with the oral ectoderm contributing the anterior lobe, and the neural ectoderm generating the posterior lobe. Pituitary abnormalities and growth deficiencies are associated with cleft palate; however, the developmental genetic connection between pituitary and orofacial cleft malformations remains to be determined. The epithelial RNA splicing regulators Esrp1 and Esrp2 (Esrp1/2) are required for orofacial development in zebrafish, mice and humans, and loss of function of these genes results in a cleft palate. Here, we present a detailed developmental analysis of the genetic requirement for Esrp1/2 in pituitary morphogenesis in mouse and zebrafish. Further, we describe an individual with cleft palate and hypopituitarism who harbors a nucleotide variant in the RNA-binding domain of ESRP2. The discovery of this key function for Esrp1/2 in pituitary formation has significant fundamental and clinical implications for understanding congenital hypopituitarism and craniofacial anomalies.
Warren S, El Farran B, Kang S
… +4 more, Choudhuri A, Xiong S, Brendel VP, Baizabal JM
Development
· 2025 Nov · PMID 41105133
·
Publisher ↗
Chromatin regulation of transcriptional enhancers plays a central role in cell fate specification and differentiation. However, how the coordinated activity of transcription factors and chromatin-modifying enzymes regula...Chromatin regulation of transcriptional enhancers plays a central role in cell fate specification and differentiation. However, how the coordinated activity of transcription factors and chromatin-modifying enzymes regulates enhancers in neural stem cells and dictates subsequent stages of neuronal differentiation and migration is not well understood. The histone methyltransferase PRDM16 is expressed in neural stem cells of the developing mouse and human cerebral cortex, and is essential for determining the position of upper-layer cortical neurons. Here, we report that PRDM16 interacts with C-terminal binding protein 1 (CtBP1) and CtBP2 to control the transcriptional programs of cortical neurogenesis and regulate upper-layer neuron migration. PRDM16 and CtBP1/2 co-regulate enhancers by interacting with histone deacetylase 1 (HDAC1), HDAC2 and lysine-specific demethylase 1 (LSD1). In addition, our results suggest that the CCCTC-binding factor CTCF plays a key role in recruiting CtBP1/2 to cortical enhancers. These findings underscore that reduced interactions between PRDM16 and ubiquitous chromatin regulators may contribute to neurodevelopmental deficits in individuals with PRDM16 haploinsufficiency.
Development
· 2025 Oct · PMID 41099309
·
Full text
Planarian muscle produces key wound signal patterning whole-body regeneration. Within muscle, generic induction of wnt1 promotes tail regeneration, while polarized expression of the Wnt inhibitor notum at anterior-facing...Planarian muscle produces key wound signal patterning whole-body regeneration. Within muscle, generic induction of wnt1 promotes tail regeneration, while polarized expression of the Wnt inhibitor notum at anterior-facing wounds drives head regeneration. Classic experiments indicate that microtubules are also involved in blastema fating, but the cell biology of planarian muscle is still poorly understood. We raised an antibody to muscle-expressed TUBA-2 and found that planarian muscle possesses a microtubule network linking contractile fibers with their mononucleated cell bodies. Microtubules were required for muscle fiber regrowth across wound sites at times that correlated with expression of wound-induced genes. Expression profiling found that sublethal colchicine treatment disrupted a subset of muscle-expressed injury-induced genes, with strongest effects on wnt1 and notum. Higher colchicine doses (>200 µg/ml) prevented wnt1 and notum expression, while, surprisingly, lower doses (125 µg/ml) elevated notum at posterior-facing wounds, thereby implicating microtubules in both the activation and polarization of genes expressed from injured muscle. Furthermore, microtubules functionally interact with Wnts to control head/tail determination. Together, planarian microtubules act in specific regulatory pathways to express key muscle-expressed and injury-induced factors used for blastema fating.
Miliard Y, Moreno S, Cote LE
… +1 more, Reddien PW
Development
· 2025 Oct · PMID 41099308
·
Full text
A central problem in regeneration is how the identity of new tissues is specified. A classic example is the head-versus-tail regeneration decision in planarians. notum is wound induced at anterior-facing planarian wounds...A central problem in regeneration is how the identity of new tissues is specified. A classic example is the head-versus-tail regeneration decision in planarians. notum is wound induced at anterior-facing planarian wounds, where it triggers head regeneration through inhibition of canonical Wnt signaling. This represents the earliest known asymmetric regeneration step between anterior- and posterior-facing wounds. Wound-induced notum is specific to longitudinal (anterior-posterior-axis oriented) muscle cells, suggesting these fibers might harbor polarity harnessed for the head-tail regeneration decision. The processes that occur within longitudinal muscle after injury for preferential notum activation at anterior-facing wounds are poorly understood. We utilized single-cell RNA sequencing to identify multiple wound-induced genes in longitudinal muscle cells and identified processes required for wound-induced notum asymmetry. Egalitarian-like-1 (Egal-1) is wound induced in longitudinal muscle and has some domain similarity with Drosophila Egalitarian, which facilitates asymmetric RNA localization. Both egal-1 RNAi animals and animals with destabilized microtubules (via colchicine or nocodazole treatment) show ectopic notum expression at posterior-facing wounds. We suggest that Egal-1 and microtubules are together required for longitudinal muscle fibers to promote planarian regeneration polarity.
Development
· 2025 Oct · PMID 41078247
·
Publisher ↗
Hox genes, such as Drosophila Abdominal-B (Abd-B), regulate the morphogenesis of specific anatomical regions along the anteroposterior axis in vertebrates. In their work, Olga Kyrchanova and colleagues find that specific...Hox genes, such as Drosophila Abdominal-B (Abd-B), regulate the morphogenesis of specific anatomical regions along the anteroposterior axis in vertebrates. In their work, Olga Kyrchanova and colleagues find that specific initiator sequences control the activity states of the regulatory domains that direct Abd-B expression in the designated segments during Drosophila development. To know more about their work, we spoke to Ksenia Kudryashova and the corresponding author, Olga Kyrchanova, Group Leader, Institute of Gene Biology, Russian Academy of Sciences, Russia.
Sproston CJ, Rak JE, Marin EC
… +2 more, Kondo S, Williams DW
Development
· 2025 Nov · PMID 41065014
·
Publisher ↗
During development, populations of neuronal stem cells generate neurons in a modular fashion to produce a striking diversity of subtypes. Within the Drosophila central nervous system, a stereotyped, segmentally repeated...During development, populations of neuronal stem cells generate neurons in a modular fashion to produce a striking diversity of subtypes. Within the Drosophila central nervous system, a stereotyped, segmentally repeated array of stem cells, called neuroblasts, generate identifiable lineages of neurons, each comprising two hemilineages. Here, we show that a key part of early fate determination within a hemilineage is selective neuronal cell death. This precise deletion of neurons occurs throughout the nervous system, removing neurons of every transmitter type in a segment-specific fashion. Using hybridisation chain reaction in situ (HCR) we reveal the proapoptotic RHG genes reaper and grim, but not hid, are transcribed within doomed neurons. Novel T2A-GAL4 knock-in reporters for reaper and grim reveal complex but repeatable expression patterns within hemilineages. These data support functional analysis with null mutants showing that reaper and grim play a complex role in sculpting lineage populations. We show that segmental and sex-specific differences in neuronal subtypes is mediated by a temporal switching to death within identified hemilineages during neurogenesis to shape adult networks.
Dear HS, Franks NE, Markley EE
… +9 more, Holtz AM, Song JY, Johnson CN, Medina-Cabrera PI, Hernandez D, Joel P, Pasca di Magliano M, Wellik DM, Allen BL
Development
· 2025 Nov · PMID 41058551
·
Full text
GLI proteins (GLI1-3) are the transcriptional effectors of mammalian hedgehog (HH) signaling. However, studies of GLI function have been hampered by the lack of robust GLI antibodies. To address this, we utilized CRISPR-...GLI proteins (GLI1-3) are the transcriptional effectors of mammalian hedgehog (HH) signaling. However, studies of GLI function have been hampered by the lack of robust GLI antibodies. To address this, we utilized CRISPR-based gene editing to generate endogenous epitope-tagged Gli alleles for each Gli gene (Gli1FLAG, Gli2HA, Gli3V5). Through breeding, we established a novel mouse model, Gli1FLAG/FLAG;Gli2HA/HA;Gli3V5/V5, referred to as GliFHV. Importantly, GliFHV animals are viable and fertile with no overt phenotypes. Sanger and long-range DNA sequencing confirmed proper editing of each Gli allele, while qPCR and western blot analysis confirmed similar gene expression and protein levels, respectively, between wild-type and GliFHV animals. We utilized these mice to assess GLI localization in the developing limb, finding that all three GLIs localize to primary cilia with distinct distributions. Finally, we generated immortalized GliFHV mouse embryonic fibroblasts, demonstrating that these cells are HH responsive and that GLIs localize to primary cilia and nuclei in a HH-dependent fashion. These animals and cell lines provide a valuable resource for analyses of GLI processing, localization and function throughout embryogenesis, postnatal development, and in adults.
Development
· 2025 Sep · PMID 41020402
·
Publisher ↗
The plant circadian clock aligns developmental processes with environmental cycles, a function traditionally attributed to a unified, systemic oscillator. However, this view is challenged by observations that mutations i...The plant circadian clock aligns developmental processes with environmental cycles, a function traditionally attributed to a unified, systemic oscillator. However, this view is challenged by observations that mutations in specific clock genes can cause major developmental phenotypes without a proportional disruption to systemic rhythms. This Hypothesis proposes that clock genes perform dual roles: they act not only as components of the systemic oscillator that generates rhythmicity, but also as specific, context-dependent regulators that control the timing of key developmental events. We argue that this gene-centric perspective extends and refines the classical oscillator model, positing that the pleiotropic nature of clock genes reflects their evolutionary history, whereby transcription factors with pre-existing developmental roles were co-opted for timekeeping. Understanding this functional duality - how individual clock components are deployed in specific tissues and conditions - offers a new perspective for dissecting the complex interplay between timekeeping and development.
Kyrchanova O, Kudryashova K, Ibragimov A
… +3 more, Dubrovskaya V, Schedl P, Georgiev P
Development
· 2025 Oct · PMID 41020347
·
Publisher ↗
Drosophila homeotic gene Abdominal-B (Abd-B) is controlled throughout development by four infraabdominal (iab) regulatory domains, the active or repressed state of which is determined by initiators that have parasegment-...Drosophila homeotic gene Abdominal-B (Abd-B) is controlled throughout development by four infraabdominal (iab) regulatory domains, the active or repressed state of which is determined by initiators that have parasegment-specific enhancer activity at an early stage of embryonic development. For this reason, it has long been assumed that the enhancer activity and initiation function of these elements are synonymous. Here, we studied two initiators that regulate the activity of the iab-5 and iab-6 domains responsible for Abd-B expression in embryonic parasegment PS10 (adult segment A5) and PS11(A6), respectively. In both initiators, core regions were identified that do not stimulate reporter gene transcription, but retain the ability to establish the appropriate activity state of the corresponding iab domains. Other initiator sequences are responsible for parasegment-specific reporter activation in early embryos and enhance the activity of the core initiators. Taken together, our results indicate that initiators represent a new type of regulatory element that function as on/off switches for regulatory domains controlling segment-specific Abd-B expression during Drosophila development.
Mahapatra S, Gomez J, Batzorig U
… +4 more, Liu Y, Fernández-Méndez C, Chen Y, Sen GL
Development
· 2025 Oct · PMID 40960263
·
Full text
Dermal white adipose tissue (dWAT) is crucial for skin homeostasis, contributing to hair follicle regeneration, immune defense and skin wound healing. dWAT is formed and maintained by the differentiation of adipocyte pre...Dermal white adipose tissue (dWAT) is crucial for skin homeostasis, contributing to hair follicle regeneration, immune defense and skin wound healing. dWAT is formed and maintained by the differentiation of adipocyte precursors found in the dermis of the skin. While transcription factors that control adipocyte differentiation have been well characterized, other aspects of transcription control, such as pausing/elongation, are poorly understood. Here, we show that deletion of the transcriptional pause factor, Nelfb, from preadipocyte lineages in mice led to a failure of dWAT and other fat depot formation, perinatal lethality and reduced expression of adipogenic genes. Nelfb promotes an open chromatin structure and stabilizes RNA Polymerase II binding to Pparg, Cebpa, Krox20 and Stat3 to allow their transcription, which is necessary for adipocyte differentiation. Retroviral expression of Pparg in Nelfb-depleted cells restored adipocyte differentiation in cultured cells, while treatment of Nelfb-deleted mice with the Pparg agonist, rosiglitazone, allowed for dWAT formation and prolonged lifespan. These findings highlight the essential role of Nelfb in promoting the expression of key adipogenic genes that are necessary for dWAT formation and adipocyte differentiation.
Lee Y, Jenniches C, Metry R
… +5 more, Renaudin G, Kling S, Tjeerdema E, Jackson EW, Hamdoun A
Development
· 2025 Sep · PMID 40960013
·
Full text
Despite the reach of in situ hybridization (ISH) in developmental biology, it is rarely used at scale. The major bottleneck is the throughput of the assay, which relies upon labor-intensive manual steps. The goal of this...Despite the reach of in situ hybridization (ISH) in developmental biology, it is rarely used at scale. The major bottleneck is the throughput of the assay, which relies upon labor-intensive manual steps. The goal of this study was to develop a high-throughput, automated hybridization chain reaction (HCR) pipeline for the sea urchin (Lytechinus pictus). Our method, which we term high-throughput (HT)-HCR, can process 192 gene probe sets on whole-mount embryos within 32 h. The physical properties of sea urchin embryos enabled us to utilize a 96-well plate format, miniaturized reaction volumes, a general-purpose robotic liquid handler and automated confocal microscopy. Using this approach, we produced high quality localization data for 101 target genes across three developmental stages. The results reveal the localization of previously undescribed physiological genes, as well as canonical developmental transcription factors. HT-HCR represents an order of magnitude increase in the throughput of spatial expression profiling studies utilizing the sea urchin. This will enable more-sophisticated perturbation analyses and drug-screening efforts in this emerging animal model.
Didi V, Arnaud D, Melnikava A
… +16 more, Pacinková A, Jupa R, Cegan R, Vasickova J, Benitez M, Unda F, Dobisova T, Riber W, Dostalova Z, Novak O, Strnad M, Hobza R, Mansfield SD, Gloser V, Budinska E, Hejatko J
Development
· 2025 Sep · PMID 40959891
·
Publisher ↗
Spatiotemporal control over developmental programs is vital to all organisms. Here, we show that deficiency in cytokinin signaling or biosynthesis leads to early secondary cell wall (SCW) formation in Arabidopsis inflore...Spatiotemporal control over developmental programs is vital to all organisms. Here, we show that deficiency in cytokinin signaling or biosynthesis leads to early secondary cell wall (SCW) formation in Arabidopsis inflorescence stem that associates with precocious upregulation of an SCW transcriptional cascade controlled by NAC transcription factors (NSTs/VNDs). Cytokinin signaling through AHK2/3 and the ARR1/10/12 suppresses the expression of several NST genes and SCW formation. Exogenous cytokinin application led to fast downregulation of NST1 and NST3 (NST1/3) in the wild type and reconstituted both proper development and the apical-basal gradient of NST1/3 expression in a cytokinin-deficient mutant. AHK2 and AHK3 require functional NST1 or NST3 to control SCW initiation in the interfascicular fibers, demonstrating that cytokinins act upstream of NSTs. The premature onset of a rigid SCW biosynthesis and altered expression of NSTs due to cytokinin deficiency led to the formation of smaller tracheary elements and impaired hydraulic conductivity. We conclude that cytokinins downregulate NST genes to inhibit premature SCW formation in the apical part of the inflorescence stem, facilitating thus the development of fully functional tracheary elements and interfascicular fibers.