Folding Keratin Gene Clusters During Skin Specification
Ontology highlight
ABSTRACT:
ORGANISM(S): Gallus gallus
PROVIDER: GSE136224 | GEO | 2020/06/08
REPOSITORIES: GEO
Similar Datasets
Project description:Animals develop skin regional specificities to best adapt to their environments. Birds are excellent models in which to study the epigenetic mechanisms that facilitate these adaptions. Patients suffering from SATB2 mutations exhibit multiple defects including ectodermal dysplasia-like changes. The preferential expression of SATB2, a chromatin regulator, in feather-forming compared to scale-forming regions, suggests it functions in regional specification of chicken skin appendages by acting on either differentiation or morphogenesis. Retrovirus mediated SATB2 misexpression in developing feathers, beaks, and claws causes epidermal differentiation abnormalities (e.g. knobs, plaques) with few organ morphology alterations. Chicken β-keratins are encoded in 5 sub-clusters (Claw, Feather, Feather-like, Scale, and Keratinocyte) on Chromosome 25 and a large Feather keratin cluster on Chromosome 27. Type I and II α-keratin clusters are located on Chromosomes 27 and 33, respectively. Transcriptome analyses showed these keratins 1) are often tuned up or down collectively as a sub-cluster, and 2) these changes occur in a temporo-spatial specific manner. This cluster-level suppression is also seen in MMPs on Chromosome 1. SATB2 alters gene expression changes of most other transcripts without this cluster-level switching. These results suggest an organizing role of SATB2 in cluster-level gene co-regulation during skin regional specification.
2021-08-14 | GSE178651 | GEO
Project description:Folding Keratin Gene Clusters During Skin Specification
| PRJNA561632 | ENA
Project description:The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major more modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze the transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered chromatin opening sites, and they are distributed around. When a key gene is perturbed, many other co-expressed genes in the same module also will be influenced. These findings suggest that these feather / scale fate specification genes form an interconnected network, and rewiring of the gene network can lead to changes of appendage phenotypes. This work shows the key hub positions of Beta catenin and retinoic acid signaling in the hierarchy of the scale / feather fate specification gene networks, opening up new possibilities to understand the control switches of multi-component organ phenotypes.
2018-10-15 | GSE111099 | GEO
Project description:The molecular mechanism controlling regional specific skin appendage phenotypes is a fundamental question that remains unresolved. We recently identified feather and scale primordium associated genes and with functional studies, proposed five major more modules are involved in scale-to-feather conversion and their integration is essential to form today’s feathers. Yet, how the molecular networks are wired and integrated at the genomic level is still unknown. Here, we combine classical recombination experiments and systems biology technology to explore the molecular mechanism controlling cell fate specification. In the chimeric explant, dermal fate is more stable, while epidermal fate is reprogrammed to be similar to the original appendage type of the mesenchyme. We analyze the transcriptome changes in both scale-to-feather and feather-to-scale transition in the epidermis. We found a highly interconnected regulatory gene network controlling skin appendage types. These gene networks are organized around two molecular hubs, β-catenin and retinoic acid (RA), which can bind to regulatory elements controlling downstream gene expression, leading to scale or feather fates. ATAC sequencing analyses revealed about 1000 altered chromatin opening sites, and they are distributed around. When a key gene is perturbed, many other co-expressed genes in the same module also will be influenced. These findings suggest that these feather / scale fate specification genes form an interconnected network, and rewiring of the gene network can lead to changes of appendage phenotypes. This work shows the key hub positions of Beta catenin and retinoic acid signaling in the hierarchy of the scale / feather fate specification gene networks, opening up new possibilities to understand the control switches of multi-component organ phenotypes.
2018-10-15 | GSE111098 | GEO
Project description:Feather evolution enabled feathered dinosaurs and early Mesozoic birds to venture into new ecological niches. Studying how feathers and scales are specified provides insight into how a new organ evolves. We use genome-wide analyses to identify feather-associated genes and test their feather-forming ability by expressing them in chicken and alligator scales. Intermediate morphotypes revealed five cardinal morphogenetic events: localized growth zone, follicle invagination, branching, feather keratin differentiation and dermal papilla formation. In contrast to molecules known to induce feathers on scales (retinoic acid, beta-catenin), we identify novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce only one or several of the five regulatory modules. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, while others demonstrate some characteristics of modern feathers. We propose that at least five morpho-regulatory modules were used to diversify ancient reptile scales. The regulatory combination and hierarchical integration led to extant feather forms.
2017-12-31 | GSE87247 | GEO
Project description:Feather evolution enabled feathered dinosaurs and early Mesozoic birds to venture into new ecological niches. Studying how feathers and scales are specified provides insight into how a new organ evolves. We use genome-wide analyses to identify feather-associated genes and test their feather-forming ability by expressing them in chicken and alligator scales. Intermediate morphotypes revealed five cardinal morphogenetic events: localized growth zone, follicle invagination, branching, feather keratin differentiation and dermal papilla formation. In contrast to molecules known to induce feathers on scales (retinoic acid, beta-catenin), we identify novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce only one or several of the five regulatory modules. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, while others demonstrate some characteristics of modern feathers. We propose that at least five morpho-regulatory modules were used to diversify ancient reptile scales. The regulatory combination and hierarchical integration led to extant feather forms.
2017-12-31 | GSE87248 | GEO
Project description:Feather evolution enabled feathered dinosaurs and early Mesozoic birds to venture into new ecological niches. Studying how feathers and scales are specified provides insight into how a new organ evolves. We use genome-wide analyses to identify feather-associated genes and test their feather-forming ability by expressing them in chicken and alligator scales. Intermediate morphotypes revealed five cardinal morphogenetic events: localized growth zone, follicle invagination, branching, feather keratin differentiation and dermal papilla formation. In contrast to molecules known to induce feathers on scales (retinoic acid, beta-catenin), we identify novel scale-feather converters (Sox2, Zic1, Grem1, Spry2, Sox18) which induce only one or several of the five regulatory modules. Some morphotypes resemble filamentous appendages found in feathered dinosaur fossils, while others demonstrate some characteristics of modern feathers. We propose that at least five morpho-regulatory modules were used to diversify ancient reptile scales. The regulatory combination and hierarchical integration led to extant feather forms.
2017-12-31 | GSE87139 | GEO
Project description:The genetic and developmental mechanisms that control the decision between scale and feather growth â two profoundly different epidermal appendages, and an important developmental shift in the evolution of birds from their dinosaurian ancestors â remain poorly understood. Domestic pigeons display dramatic variation in foot epidermal appendages within a single species, and classical studies suggest that a small number of genes control much of this variation; thus pigeons provide a tractable model to understand skin appendage specification and variation. Here we show that feathered feet in pigeons are the consequence of a partial transformation of limb-type identity mediated by cis-regulatory changes in the hindlimb-specific transcription factor Pitx1 and forelimb-specific transcription factor Tbx5. We also demonstrate that ectopic hindlimb expression of Tbx5 is associated with the development of foot feathers in domestic chickens, suggesting that similar developmental mechanisms underlie phenotypic convergence in avian lineages that diverged over 100 MYA. These results show how qualitative and quantitative changes in expression of regional patterning genes can generate localized changes in organ fate and morphology, and provide a viable molecular mechanism for the evolution of hindlimb scale and feather distribution in dromaeosaurs. Examination of H3K27ac status in embryonic limb buds from two domestic pigeon breeds, racing homer and Indian fantail
2016-04-03 | E-GEOD-67875 | biostudies-arrayexpress
Project description:Regeneration is one of the key factors affecting downy feather production. However, the signals and molecular controlling the progression of feather regeneration was poorly understood. We used a high density microarray to profile the temporal transcriptome dynamics during the regeneration periods. A total of 3540 genes expressed differentially with significant fold changes during feather regeneration. Cluster analysis revealed event specific dynamic expression of genes related to cell cycling, cell migration, cell proliferation, follicle re-growth and fiber elongation. These clusters involved functional clusters like regulation of actin cytoskeleton, focal adhesion and sphingolipid metabolism, and enriched signaling pathways like Wnt signaling pathway, MAPK pathway and TGFβ signaling pathway. In cell cycling, mainly involved genes were cyclin B3, cyclin Y. In TGFβ signaling pathway, mainly involved genes were TGFβ3, BMP7, NOG and BMP2. While Wnt5a, Wnt10a, FZD2, and FZD10 were involved in canonical Wnt/β-catenin pathway. Our study provides a comprehensive genetic blue print of diverse cellular responses during regeneraton of goose feather. The data provide an initial step towards a better understanding of molecular mechanisms underlying feather regeneration process and also suggest that signals or molecular participated in feather regeneration was quite different from the generation of hair in mammals.
2018-02-01 | GSE65852 | GEO
Project description:Transcriptome profiles of skin and feather follicle from two body parts at three physiological stages were constructed to understand the molecular network and excavate the candidate genes associated with the plumulaceous and flight feathers structure. The key series-clusters, many candidate biological processes and genes were identified for the morphogenesis, growth and development of two feather types. Through comparing the results of developmental transcritpomes from plumulaceous and flight feather, we found that DEGs belonging to the family of WNT, FGF and BMP have certain differences; even the consistent DEGs of skin and feather follicle transcriptomes from abdomen and wing have the different expression patterns.
2018-05-07 | GSE104386 | GEO