scholarly journals The Human Accelerated Region HACNS1 modifies developmental gene expression in humanized mice

2019 ◽  
Author(s):  
Emily V. Dutrow ◽  
Deena Emera ◽  
Kristina Yim ◽  
Severin Uebbing ◽  
Acadia A. Kocher ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Evolution ◽  
Limb Development ◽  
Specific Activity ◽  
Limb Bud ◽  
Humanized Mouse ◽  
Enhancer Activity ◽  
Regulatory Pathways ◽  
Embryonic Limb ◽  
Human Specific

AbstractMorphological innovations that arose during human evolution are ultimately encoded in genetic changes that altered development. Human Accelerated Regions (HARs), which include developmental enhancers that harbor a significant excess of human-specific sequence changes, are leading candidates for driving novel physical modifications in humans. Here we examine the role of the HAR HACNS1 (also known as HAR2) in human limb evolution by directly interrogating its cellular and developmental functions in a humanized mouse model. HACNS1 encodes an enhancer with human-specific activity in the developing limb in transgenic mouse reporter assays, and exhibits increased epigenetic signatures of enhancer activity in the human embryonic limb compared to its orthologs in rhesus macaque and mouse. Here we find that HACNS1 maintains its human-specific enhancer activity compared to its chimpanzee ortholog in the mouse embryonic limb, and that it alters expression of the transcription factor gene Gbx2 during limb development. Using single-cell RNA-sequencing, we demonstrate that Gbx2 is upregulated in humanized limb bud chondrogenic mesenchyme, implicating HACNS1-mediated Gbx2 expression in early skeletal patterning. Our findings establish that HARs direct changes in the level and distribution of gene expression during development, and illustrate how humanized mouse models provide insight into regulatory pathways modified in human evolution.

scholarly journals Pigeon foot feathering reveals conserved limb identity networks

2019 ◽  
Author(s):  
Elena F. Boer ◽  
Hannah F. Van Hollebeke ◽  
Sungdae Park ◽  
Carlos R. Infante ◽  
Douglas B. Menke ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Limb Development ◽  
Limb Bud ◽  
Differentially Expressed ◽  
Evolutionarily Conserved ◽  
Genes Encoding ◽  
Embryonic Limb ◽  
Summary Statement ◽  
Limb Identity

AbstractThe tetrapod limb is a stunning example of evolutionary diversity, with dramatic variation not only among distantly related species, but also between the serially homologous forelimbs (FLs) and hindlimbs (HLs) within species. Despite this variation, highly conserved genetic and developmental programs underlie limb development and identity in all tetrapods, raising the question of how limb diversification is generated from a conserved toolkit. In some breeds of domestic pigeon, shifts in the expression of two conserved limb identity transcription factors,PITX1andTBX5, are associated with the formation of feathered HLs with partial FL identity. To determine how modulation ofPITX1andTBX5expression affects downstream gene expression, we compared the transcriptomes of embryonic limb buds from pigeons with scaled and feathered HLs. We identified a set of differentially expressed genes enriched for genes encoding transcription factors, extracellular matrix proteins, and components of developmental signaling pathways with important roles in limb development. A subset of the genes that distinguish scaled and feathered HLs are also differentially expressed between FL and scaled HL buds in pigeons, pinpointing a set of gene expression changes downstream ofPITX1andTBX5in the partial transformation from HL to FL identity. We extended our analyses by comparing pigeon limb bud transcriptomes to chicken, anole lizard, and mammalian datasets to identify deeply conservedPITX1- andTBX5-regulated components of the limb identity program. Our analyses reveal a suite of predominantly low-level gene expression changes that are conserved across amniotes to regulate the identity of morphologically distinct limbs.Summary statementIn feather-footed pigeons, mutant alleles ofPITX1andTBX5drive the partial redeployment of an evolutionarily conserved forelimb genetic program in the hindlimb.

scholarly journals Geminin is required for Hox gene regulation to pattern the developing limb

2020 ◽  
Author(s):  
Emily M.A. Lewis ◽  
Savita Sankar ◽  
Caili Tong ◽  
Ethan Patterson ◽  
Laura E. Waller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Limb Development ◽  
Complex Structure ◽  
Limb Bud ◽  
Conditional Model ◽  
Regulatory Pathways ◽  
Shh Pathway ◽  
Severe Reduction ◽  
Vertebrate Limb ◽  
Mouse Limb

AbstractDevelopment 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 elaboration of distinct limb skeletal elements. 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 the 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.SummaryThis work identifies a new role for Geminin in mouse limb development. Geminin is a nuclear protein that regulates gene expression to control several other aspects of vertebrate development.

The dominant hemimelia mutation uncouples epithelial-mesenchymal interactions and disrupts anterior mesenchyme formation in mouse hindlimbs

Development ◽  
1999 ◽  
Vol 126 (21) ◽  
pp. 4729-4736
Author(s):  
L. Lettice ◽  
J. Hecksher-Sorensen ◽  
R.E. Hill
Keyword(s):  
Gene Expression ◽  
Pattern Formation ◽  
Limb Development ◽  
Limb Bud ◽  
Mouse Mutation ◽  
Number Of Factors ◽  
Limb Outgrowth ◽  
Gene Functions ◽  
Regulatory Loop ◽  
Limb Initiation

Epithelial-mesenchymal interactions are essential for both limb outgrowth and pattern formation in the limb. Molecules capable of communication between these two tissues are known and include the signaling molecules SHH and FGF4, FGF8 and FGF10. Evidence suggests that the pattern and maintenance of expression of these genes are dependent on a number of factors including regulatory loops between genes expressed in the AER and those in the underlying mesenchyme. We show here that the mouse mutation dominant hemimelia (Dh) alters the pattern of gene expression in the AER such that Fgf4, which is normally expressed in a posterior domain, and Fgf8, which is expressed throughout are expressed in anterior patterns. We show that maintenance of Shh expression in the posterior mesenchyme is not dependent on either expression of Fgf4 or normal levels of Fgf8 in the overlying AER. Conversely, AER expression of Fgf4 is not directly dependent on Shh expression. Also the reciprocal regulatory loop proposed for Fgf8 in the AER and Fgf10 in the underlying mesenchyme is also uncoupled by this mutation. Early during the process of limb initiation, Dh is involved in regulating the width of the limb bud, the mutation resulting in selective loss of anterior mesenchyme. The Dh gene functions in the initial stages of limb development and we suggest that these initial roles are linked to mechanisms that pattern gene expression in the AER.

Sonic hedgehog is not required for polarising activity in the Doublefoot mutant mouse limb bud

Development ◽  
1998 ◽  
Vol 125 (3) ◽  
pp. 351-357 ◽  
Author(s):  
C. Hayes ◽  
J.M. Brown ◽  
M.F. Lyon ◽  
G.M. Morriss-Kay
Keyword(s):  
Gene Expression ◽  
Limb Development ◽  
Target Genes ◽  
Anterior Part ◽  
Expression Patterns ◽  
Ectopic Expression ◽  
Mutant Gene ◽  
Limb Bud ◽  
Active Constituent ◽  
Limb Buds

The mouse mutant Doublefoot (Dbf) shows preaxial polydactyly of all four limbs. We have analysed limb development in this mutant with respect to morphogenesis, gene expression patterns and ectopic polarising activity. The results reveal a gain-of-function mutation at a locus that mediates pattern formation in the developing limb. Shh expression is identical with that of wild-type embryos, i.e. there is no ectopic expression. However, mesenchyme from the anterior aspects of Dbf/+ mutant limb buds, when transplanted to the anterior side of chick wing buds, induces duplication of the distal skeletal elements. Mid-distal mesenchymal transplants from early, but not later, Dbf/+ limb buds are also able to induce duplication. This demonstration of polarising activity in the absence of Shh expression identifies the gene at the Dbf locus as a new genetic component of the Shh signalling pathway, which (at least in its mutated form) is able to activate signal transduction independently of Shh. The mutant gene product is sufficient to fulfil the signalling properties of Shh including upregulation of the direct Shh target genes Ptc and Gli, and induction of the downstream target genes Bmp2, Fgf4 and Hoxd13. The expression domains of all these genes extend from their normal posterior domains into the anterior part of the limb bud without being focused on a discrete ectopic site. These observations dissociate polarising activity from Shh gene expression in the Dbf/+ limb bud. We suggest that the product of the normal Dbf gene is a key active constituent of the polarising region, possibly acting in the extracellular compartment.

scholarly journals Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

2012 ◽  
Vol 22 (6) ◽  
pp. 1069-1080 ◽  
Author(s):  
Justin Cotney ◽  
Jing Leng ◽  
Sunghee Oh ◽  
Laura E. DeMare ◽  
Steven K. Reilly ◽  
...  
Keyword(s):  
Gene Expression ◽  
Chromatin State ◽  
Specific Gene ◽  
Enhancer Activity ◽  
Tissue Specific ◽  
Tissue Specific Gene ◽  
Specific Gene Expression ◽  
Embryonic Limb

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

2020 ◽  
Author(s):  
Claudia Gentile ◽  
Alexandre Mayran ◽  
Fanny Guerard-Millet ◽  
Marie Kmita
Keyword(s):  
Gene Expression ◽  
Limb Development ◽  
Functional Relationship ◽  
Specific Activity ◽  
Polycomb Group ◽  
Specific Gene ◽  
Developmental Genes ◽  
Genome Wide ◽  
Polycomb Repressive Complexes ◽  
Polycomb Repressive Complex 1

AbstractThe 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.

The chick limbless mutation causes abnormalities in limb bud dorsal-ventral patterning: implications for the mechanism of apical ridge formation

Development ◽  
1996 ◽  
Vol 122 (12) ◽  
pp. 3851-3861 ◽  
Author(s):  
U. Grieshammer ◽  
G. Minowada ◽  
J.M. Pisenti ◽  
U.K. Abbott ◽  
G.R. Martin
Keyword(s):  
Gene Expression ◽  
Limb Development ◽  
Positional Information ◽  
Limb Bud ◽  
Local Application ◽  
Chick Embryos ◽  
Limb Buds ◽  
Early Stages ◽  
Potential Link

In chick embryos homozygous for the limbless mutation, limb bud outgrowth is initiated, but a morphologically distinct apical ridge does not develop and limbs do not form. Here we report the results of an analysis of gene expression in limbless mutant limb buds. Fgf4, Fgf8, Bmp2 and Msx2, genes that are expressed in the apical ridge of normal limb buds, are not expressed in the mutant limb bud ectoderm, providing molecular support for the hypothesis that limb development fails in the limbless embryo because of the inability of the ectoderm to form a functional ridge. Moreover, Fgf8 expression is not detected in the ectoderm of the prospective limb territory or the early limb bud of limbless embryos. Since the early stages of limb bud outgrowth occur normally in the mutant embryos, this indicates that FGF8 is not required to promote initial limb bud outgrowth. In the absence of FGF8, Shh is also not expressed in the mutant limb buds, although its expression can be induced by application of FGF8-soaked beads. These observations support the hypothesis that Fgf8 is required for the induction of Shh expression during normal limb development. Bmp2 expression was also not detected in mutant limb mesoderm, consistent with the hypothesis that SHH induces its expression. In contrast, SHH is not required for the induction of Hoxd11 or Hoxd13 expression, since expression of both these genes was detected in the mutant limb buds. Thus, some aspects of mesoderm A-P patterning can occur in the absence of SHH and factors normally expressed in the apical ridge. Intriguingly, mutant limbs rescued by local application of FGF displayed a dorsalized feather pattern. Furthermore, the expression of Wnt7a, Lmx1 and En1, genes involved in limb D-V patterning, was found to be abnormal in mutant limb buds. These data suggest that D-V patterning and apical ridge formation are linked, since they show that the limbless mutation affects both processes. We present a model that explains the potential link between D-V positional information and apical ridge formation, and discuss the possible function of the limbless gene in terms of this model.

BMPR-IA signaling is required for the formation of the apical ectodermal ridge and dorsal-ventral patterning of the limb

Development ◽  
2001 ◽  
Vol 128 (22) ◽  
pp. 4449-4461 ◽  
Author(s):  
Kyung Ahn ◽  
Yuji Mishina ◽  
Mark C. Hanks ◽  
Richard R. Behringer ◽  
E. Bryan Crenshaw
Keyword(s):  
Limb Development ◽  
Apical Ectodermal Ridge ◽  
Bmp Signaling ◽  
Conditional Knockout ◽  
Limb Bud ◽  
Gene Encoding ◽  
Bone Morphogenetic Protein Receptor ◽  
Protein Receptor ◽  
Morphogenetic Protein ◽  
Embryonic Limb

We demonstrate that signaling via the bone morphogenetic protein receptor IA (BMPR-IA) is required to establish two of the three cardinal axes of the limb: the proximal-distal axis and the dorsal-ventral axis. We generated a conditional knockout of the gene encoding BMPR-IA (Bmpr) that disrupted BMP signaling in the limb ectoderm. In the most severely affected embryos, this conditional mutation resulted in gross malformations of the limbs with complete agenesis of the hindlimbs. The proximal-distal axis is specified by the apical ectodermal ridge (AER), which forms from limb ectoderm at the distal tip of the embryonic limb bud. Analyses of the expression of molecular markers, such as Fgf8, demonstrate that formation of the AER was disrupted in the Bmpr mutants. Along the dorsal/ventral axis, loss of engrailed 1 (En1) expression in the non-ridge ectoderm of the mutants resulted in a dorsal transformation of the ventral limb structures. The expression pattern of Bmp4 and Bmp7 suggest that these growth factors play an instructive role in specifying dorsoventral pattern in the limb. This study demonstrates that BMPR-IA signaling plays a crucial role in AER formation and in the establishment of the dorsal/ventral patterning during limb development.

Bone morphogenetic proteins and a signalling pathway that controls patterning in the developing chick limb

Development ◽  
1994 ◽  
Vol 120 (1) ◽  
pp. 209-218 ◽  
Author(s):  
P.H. Francis ◽  
M.K. Richardson ◽  
P.M. Brickell ◽  
C. Tickle
Keyword(s):  
Gene Expression ◽  
Retinoic Acid ◽  
Bone Morphogenetic Proteins ◽  
Limb Development ◽  
Posterior Part ◽  
Signalling Pathway ◽  
Limb Bud ◽  
Bone Morphogenetic Protein 2 ◽  
Close Relationship ◽  
Wing Bud

We show here that bone morphogenetic protein 2 (BMP-2) is involved in patterning the developing chick limb. During early stages of limb development, mesenchymal expression of the Bmp-2 gene is restricted to the posterior part of the bud, in a domain that colocalizes with the polarizing region. The polarizing region is a group of cells at the posterior margin of the limb bud that can respecify the anteroposterior axis of the limb when grafted anteriorly and can activate expression of genes of the HoxD complex. We dissect possible roles of BMP-2 in the polarizing region signalling pathway by manipulating the developing wing bud. Retinoic acid application, which mimics the effects of polarizing region grafts, activates Bmp-2 gene expression in anterior cells. This shows that changes in anteroposterior pattern are correlated with changes in Bmp-2 expression. When polarizing region grafts are placed at the anterior margin of the wing bud, the grafts continue to express the Bmp-2 gene and also activate Bmp-2 expression in the adjacent anterior host mesenchyme. These data suggest that BMP-2 is part of the response pathway to the polarizing signal, rather than being the signal itself. In support of this, BMP-2 protein does not appear to have any detectable polarizing activity when applied to the wing bud. The pattern of Bmp-4 gene expression in the developing wing bud raises the possibility that BMP-2 and BMP-4 could act in concert. There is a close relationship, both temporal and spatial, between the activation of the Bmp-2 and Hoxd-13 genes in response to retinoic acid and polarizing region grafts, suggesting that expression of the two genes might be linked.

scholarly journals Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

2015 ◽  
Author(s):  
Betty M Booker ◽  
Tara Friedrich ◽  
Mandy K Mason ◽  
Julia E VanderMeer ◽  
Jingjing Zhao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Limb Development ◽  
Myotis Lucifugus ◽  
Enhancer Activity ◽  
Mouse Sequence ◽  
Molecular Events ◽  
Mouse Limb ◽  
Morphological Differences ◽  
Drive Gene ◽  
Bat Wing

The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing.

Sign in / Sign up

Export Citation Format

Share Document