Attenuated sensing of SHH underlies adaptive evolution of bovine limbs
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE52988 | GEO | 2014/06/19
SECONDARY ACCESSION(S): PRJNA230633
REPOSITORIES: GEO
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Project description:Artiodactyls display skeletal adaptations for cursorial (running) locomotion. In these animals, the distal limb skeleton is symmetric, which facilitates walking on the tips of the two central digits, while lateral digits are reduced or lost. We have identified that one primary molecular alteration during the formation of the bovine limb is that, in contrast to mouse, the posterior limb bud mesenchyme does not upregulate Ptch1 expression in response to SHH. We have tracked down this dissimilarity to a cis-regulatory SHH-responsive element that is functionally altered in bovine and established a causal link between lack of upregulation of Ptch1 and acquisition of a symmetric distal autopod. A high resolution 4C-seq protocol involving two restriction digests was applied to viewpoint in Ptch1 promoter (mm9 chr13:63,667,995-63,669,157) in three different tissues, allowing robust detection of physical interactions between regulatory DNA elements.
2014-06-19 | E-GEOD-52988 | biostudies-arrayexpress
Project description:Development of the complex structure of the vertebrate limb requires carefully orchestrated interactions between multiple regulatory pathways and proteins. Among these, precise regulation of 5’ Hox transcription factor expression is essential for proper limb bud patterning and development. Here, we identified Geminin (Gmnn) as a novel regulator of this process. A conditional model of Gmnn deficiency resulted in loss or severe reduction of forelimb skeletal elements, while both the forelimb autopod and hindlimb were unaffected. 5’ Hox gene expression expanded into more proximal and anterior regions of embryonic forelimb buds in this Gmnn-deficient model. A second conditional model of Gmnn deficiency instead caused a similar but less severe reduction of hindlimb skeletal elements and hindlimb polydactyly, while not affecting the forelimb. An ectopic posterior Shh signaling center was evident in the anterior hindlimb bud of Gmnn-deficient embryos in this model. This center ectopically expressed Hoxd13, the Hoxd13 target Shh, and the Shh target Ptch1, while these mutant hindlimb buds also had reduced levels of the cleaved, repressor form of Gli3, a Shh pathway antagonist. Together, this work delineates a new role for Gmnn in modulating Hox expression to pattern the vertebrate limb.
2020-06-05 | GSE143211 | GEO
Project description:Limb-specific expression of Shh is regulated by the long-range (~one megabasepair distant) ZRS enhancer. In the mouse, murine limb bud restricted spatiotemporal expression of Shh occurs from ~E10 until E11.5 at the distal posterior margin is essential for the correct formation of the autopod. Here, we have analyzed the higher-order chromatin conformation of Shh in expressing and non-expressing tissues, both by fluorescence in situ hybridization (FISH) and by chromosome conformation capture (5C). Conventional and super-resolution light microscopy identified significantly elevated frequences of Shh/ZRS co-localization only in the Shh expressing regions of the limb bud consistent with the formation of an enhancer-promoter loop. However, Shh-ZRS spatial distances were consistently shorter than intervening distances to a neural enhancer in all tissues and developmental stages analyzed – regardless of Shh expression. 5C also identified a topologically associating domain (TAD) over the Shh-ZRS genomic region and enriched interactions between Shh and ZRS, but in the head, body and limb buds of E11.5 embryos, so also not linked to Shh expression. We show that gene-enhancer (Shh/ZRS) co-localization correlates with the spatiotemporal domain of limb bud-specific Shh expression, but that close Shh/ZRS proximity in the nucleus occurs regardless of whether the gene or enhancer is active. We suggest that this constrained chromatin configuration optimises the opportunity for the active enhancer to locate and instigate Shh expression.
2016-05-03 | GSE79947 | GEO
Project description:In vitro models allow for the study of developmental processes outside of the embryo. To gain access to the cells mediating digit and joint development, we identified a unique property of undifferentiated mesenchyme isolated from the distal early autopod to autonomously re-assemble forming multiple autopod structures including: digits, interdigital tissues, joints, muscles and tendons. Single cell transcriptomic analysis of these developing structures revealed distinct cell clusters that express canonical markers of distal limb development including: Col2a1, Col10a1, and Sp7 (phalanx formation) Thbs2 and Col1a1, (perichondrium), Gdf5, Wnt5a, and Jun (joint interzone), Aldh1a2 and Msx1 (interdigital tissues), Myod1 (muscle progenitors), Prg4 (articular perichondrium/articular cartilage), and Scx and Tnmd (tenocytes/tendons). Analysis of the gene expression patterns for these signature genes indicates that developmental timing and tissue-specific localization were also recapitulated in a manner similar to the initiation and maturation of the developing murine autopod. Finally, the in vitro digit system also recapitulates congenital malformations associated with genetic mutations as in vitro cultures of Hoxa13 mutant mesenchyme produced defects present in Hoxa13 mutant autopods including digit fusions, reduced phalangeal segment numbers, and poor mesenchymal condensation. These findings demonstrate the robustness of the in vitro digit system to recapitulate digit and joint development. As an in vitro model of murine digit and joint development, this innovative system will provide access to developing limb tissues facilitating studies to discern how digit and articular joint formation is initiated and how undifferentiated mesenchyme is patterned to establish individual digit morphologies. The in vitro digit system also provides a platform to rapidly evaluate treatments aimed at stimulating the repair or regeneration of mammalian digits impacted by congenital malformation, injury, or disease.
2023-02-23 | GSE221883 | GEO
Project description:The free limb is subdivided into three anatomical domains along the proximodistal axis: the stylopod, zeugopod and autopod. These domains possess a specific number and pattern of the bones and each bone possesses unique morphology and length. During limb development, the mesenchymal cells of limb bud first forms precartilaginous aggregates which eventually grow and differentiate into the limb cartilage. Expression of Hox genes belonging to the Abd-B family, Hox9-13, is closely related to the anatomical domains of the limb bones and crucial for controlling morphogenesis and patterning of the limb cartilage. Hoxa13 and Hoxd13 are expressed in the autopodal mesenchyme and double KO mice have smaller autopods during the embryonic stage and a fan-shaped cartilage develops instead of the normal five digits. Thus, Hoxa13 and Hoxd13 are crucial for the cartilage patterning in the autopod. Since Hox encodes a transcription factor, Hox target genes function in region/compartment-specific formation of the precartilaginous condensation, cellular differentiation and proliferation of the cartilage. We used microarray to identified downstream genes of Hox13 in the autopod as exhibiting changes in the expression in the Hox13dKO mutant embryos.
2019-03-28 | GSE118640 | GEO
Project description:During limb development, fibroblast growth factors (FGFs) govern proximal-distal outgrowth and patterning. FGFs also synchronize developmental patterning between the proximal-distal and anterior-posterior axes by maintaining sonic hedgehog (SHH) expression in cells of the zone of polarizing activity (ZPA) in the distal posterior mesoderm. SHH, in turn, maintains FGFs in the apical ectodermal ridge (AER) which caps the distal tip of the limb bud. Crosstalk between FGF and SHH signaling is critical for patterned limb development, but the mechanisms underlying this feedback loop are not well characterized. Implantation of FGF beads in the proximal posterior limb bud can maintain SHH expression in the former ZPA domain (evident 3hrs after application), while prolonged exposure (24hrs) can induce SHH outside of this domain. Although temporally and spatially disparate, comparative analysis of transcriptome data from these different populations enriched molecules required for FGF-mediated SHH regulation.
2018-12-18 | GSE114661 | GEO
Project description:Shh and its receptor Ptch1 define two adjacent mutually exclusive domains: Shh+Ptch1- and Shh-Ptch1+ of E11.5 mouse brain. Gata3 ChIP-seq experiments and RNA-seq assays on Gata3-knockdown cells revealed that Gata3 up-regulates genes enriched in Shh-Ptch1+ domain. Our work is the first genome-wide characterization of gene regulatory mechanisms in Shh pathway underlying the pattern formation of early mouse brain.
2013-11-30 | E-MTAB-2008 | biostudies-arrayexpress
Project description:The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here we performed genome-wide profiling of HOX13 by chromatin immunoprecipitation and analyzed the transcriptome and chromatin state of wild type early and late-distal limb buds, as well as Hoxa13-/-;Hoxd13-/- compound mutant limb buds. Our results show that inactivation of HOX13 impairs the activation and repression of putative cis-regulatory modules specific to the late-distal limb cells. Loss of HOX13 also disrupts the specific, spatial patterning of gene expression along the proximal-distal axis of the developing limb buds. These results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
2016-12-14 | GSE81357 | GEO
Project description:The combinatorial expression of the Hox genes along the body axes, referred to as the HOX code, is a major determinant of cell fate and plays a prevailing role in generating the animal body plan. In developing limb buds, the paralogous group 13 genes of the HoxA and HoxD clusters are essential for patterning the distal-most limb structures, the digits. Inactivation of HOXA13 and HOXD13 transcription factors (HOX13) leads to complete digit agenesis in mice, but how HOX13 regulate transcriptional outcomes and confer identity to the distal-most limb cells has remained elusive. Here we performed genome-wide profiling of HOX13 by chromatin immunoprecipitation and analyzed the transcriptome and chromatin state of wild type early and late-distal limb buds, as well as Hoxa13-/-;Hoxd13-/- compound mutant limb buds. Our results show that inactivation of HOX13 impairs the activation and repression of putative cis-regulatory modules specific to the late-distal limb cells. Loss of HOX13 also disrupts the specific, spatial patterning of gene expression along the proximal-distal axis of the developing limb buds. These results show that proper termination of the early limb transcriptional program and activation of the late-distal limb program are coordinated by the dual action of HOX13 on cis-regulatory modules.
2016-12-14 | GSE81356 | GEO
Project description:The evolution of tetrapod limbs from fish fins enabled the conquest of land by vertebrates and thus represents a key step in evolution. Despite the use of comparative gene expression analyses, critical aspects of this transformation remain controversial, in particularly the origin of digits. Hoxa and Hoxd genes are essential for the specification of the different limb segments and their functional abrogation leads to large truncations of the appendages. Here we show that the selective transcription of mouse Hoxa genes in proximal and distal limbs is related to a bimodal higher order chromatin structure, similar to that reported for Hoxd genes, thus revealing a generic regulatory strategy implemented by both gene clusters during limb development. We found the same bimodal chromatin architecture in fish embryos, indicating that the regulatory strategy used to pattern tetrapod limbs predates the divergence between fish and tetrapods. However, when assessed in mice, both fish regulatory domains triggered transcription in proximal, rather than distal limb territories, supporting an evolutionary scenario whereby digits arose as true tetrapod novelties through genetic retrofitting of a preexisting bimodal chromatin framework. We discuss the possibility to consider regulatory circuitries, rather than expression patterns, as essential parameters to define evolutionary synapomorphies. Circular Chromosome Conformation Capture (4C seq) at the mouse HoxA and HoxD loci in proximal and distal forelimbs and forebrain at E12.5 and at the zebrafish HoxAa, HoxAb and HoxDa loci in 5 dpf whole embryos.
2014-01-21 | E-GEOD-47644 | biostudies-arrayexpress