Shh and Gremlin1 chromosomal landscapes in development and disease

Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes

Limbs originated from paired fish fins are an important innovation in Gnathostomata. Many studies have focused on limb development-related genes, of which the T-box transcription factor 4 gene (tbx4) has been considered as one of the most essential factors in the regulation of the hindlimb development. We previously confirmed pelvic fin loss in tbx4-knockout zebrafish. Here, we report a high-quality genome assembly of the Japanese eel (Anguilla japonica), which is an economically important fish without pelvic fins. The assembled genome is 1.13 Gb in size, with a scaffold N50 of 1.03 Mb. In addition, we collected 24 tbx4 sequences from 22 teleost fishes to explore the correlation between tbx4 and pelvic fin evolution. However, we observed complete exon structures of tbx4 in several pelvic-fin-loss species such as Ocean sunfish (Mola mola) and ricefield eel (Monopterus albus). More interestingly, an inversion of a special tbx4 gene cluster (brip1-tbx4-tbx2b- bcas3) occurred twice independently, which coincides with the presence of fin spines. A nonsynonymous mutation (M82L) was identified in the nuclear localization sequence (NLS) of the Japanese eel tbx4. We also examined variation and loss of hindlimb enhancer B (HLEB), which may account for pelvic fin loss in Tetraodontidae and Diodontidae. In summary, we generated a genome assembly of the Japanese eel, which provides a valuable genomic resource to study the evolution of fish tbx4 and helps elucidate the mechanism of pelvic fin loss in teleost fishes. Our comparative genomic studies, revealed for the first time a potential correlation between the tbx4 gene cluster and the evolutionary development of toxic fin spines. Because fin spines in teleosts are usually venoms, this tbx4 gene cluster may facilitate the genetic engineering of toxin-related marine drugs.

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution. PAPERCLIP.

Variant detection and runs of homozygosity in next generation sequencing data elucidate the genetic background of Lundehund syndrome

BACKGROUND

The Lundehund is a highly specialized breed characterized by a unique flexibility of the joints and polydactyly in all four limbs. The extremely small population size and high inbreeding has promoted a high frequency of diseased dogs affected by the Lundehund syndrome (LS), a severe gastro-enteropathic disease.

RESULTS

Comprehensive analysis of bead chip and whole-genome sequencing data for LS in the Lundehund resulted in a genome-wide association signal on CFA 34 and LS-specific runs of homozygosity (ROH) in this region. Filtering analysis for variants with predicted high or moderate effects revealed a missense mutation in LEPREL1 1.2 Mb proximal to the region of the genome-wide association, which was shown to be significantly associated with LS. LS-affected Lundehund harbored the mutant LEPREL1:g.139212C>G genotype A/A whereas all controls of other breeds showed the C/C wild type. In addition, ROH analysis for the Lundehund indicated a high enrichment of genes in potential signatures of selection affecting protein activation and immunoregulatory processes like NOD1 potentially involved in LS breed disposition.

CONCLUSIONS

Sequencing results for Lundehund specific traits reveal a potential causative mutation for LS in the neuropeptide operating gene LEPREL1 and suggests it as a precursor of the inflammatory process. Analyses of ROH regions give an insight into the genetic background of characteristic traits in the Lundehund that remain to be elucidated in the future.

Advances in the Molecular Genetics of Non-syndromic Syndactyly

Syndactyly, webbing of adjacent digits with or without bony fusion, is one of the most common hereditary limb malformations. It occurs either as an isolated abnormality or as a component of more than 300 syndromic anomalies. There are currently nine types of phenotypically diverse nonsyndromic syndactyly. Non-syndromic syndactyly is usually inherited as an autosomal dominant trait, although the more severe presenting types and subtypes may show autosomal recessive or X-linked pattern of inheritance. The phenotype appears to be not only caused by a main gene, but also dependant on genetic background and subsequent signaling pathways involved in limb formation. So far, the principal genes identified to be involved in congenital syndactyly are mainly involved in the zone of polarizing activity and sonic hedgehog pathway. This review summarizes the recent progress made in the molecular genetics, including known genes and loci responsible for non-syndromic syndactyly, and the signaling pathways those genetic factors involved in, as well as clinical features and animal models. We hope our review will contribute to the understanding of underlying pathogenesis of this complicated disorder and have implication on genetic counseling.

Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds

Background

Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1) is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1) locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds.

Results

Three highly conserved regions (HMCO1-3) were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9 kb region located ~70 kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1), is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1 genomic landscape locate to the DNAse I hypersensitive sites identified in this genomic region by the ENCODE consortium.

Conclusions

This study establishes that distant cis-regulatory regions scattered through a larger genomic landscape control the highly dynamic expression of Grem1, which is key to normal progression of mouse limb bud development.

The molecular basis of human congenital limb malformations

This review focuses predominantly on the human congenital malformations caused by alterations affecting the morphoregulatory gene networks that control early limb bud patterning and outgrowth. Limb defects are among the most frequent congenital malformations in humans that are caused by genetic mutations or teratogenic effects resulting either in abnormal, loss of, or additional skeletal elements. Spontaneous and engineered mouse models have been used to identify and study the molecular alterations and disrupted gene networks that underlie human congenital limb malformations. More recently, mouse genetics has begun to reveal the alterations that affect the often-large cis-regulatory landscapes that control gene expression in limb buds and cause devastating effects on limb bud development. These findings have paved the way to identifying mutations in cis-regulatory regions as causal to an increasing number of congenital limb malformations in humans. In these cases, no mutations in the coding region of a presumed candidate were previously detected. This review highlights how the current understanding of the molecular gene networks and interactions that control mouse limb bud development provides insight into the etiology of human congenital limb malformations.

Polydactyl inheritance in the pig

Two pigs were identified having "extra feet" (preaxial polydactyly) within a purebred population of Yorkshire pigs. Polydactyly is an inherited disorder in many species that may be controlled by either recessive or dominant genes. Experimental matings were conducted using pigs that had produced affected offspring with the result of 12 polydactyl offspring out of 95 piglets. One polydactyl-producing boar was also mated to 4 Duroc sows and 8 distantly related Yorkshire sows to produce 129 unaffected offspring. Together, these results suggest a recessive mode of inheritance, possibly with incomplete penetrance. Candidate genes, LMBR1, EN2, HOXA10-13, GLI3, WNT2, WNT16, and SHH, were identified based on association with similar phenotypes in other species. Homologues for these genes are all found on SSC18. Sequencing and linkage studies showed no evidence for association with HOXA10-13, WNT2, and WNT16. Results for the regions including GLI3, LMBR1, and SHH, however, were inconclusive. A whole genome scan was conducted on DNA samples from 10 affected pigs and 12 close relatives using the Illumina PorcineSNP60 BeadChip and compared with 69 more distantly related animals in the same population. No evidence was found for a major gene causing polydactyly. However, a 25-Mb stretch of homozygosity on SSC8 was identified as fairly unique to the family segregating for this trait. Therefore, this chromosome segment may play a role in development of polydactyly in concert with other genes.

Hedgehog signalling: emerging evidence for non-canonical pathways

Hedgehog (HH) signalling is involved in the development of numerous embryonic tissues. In humans,germline mutations in hedgehog pathway components cause congenital malformations and somatic mutations are associated with cancers. The basic framework of the HH pathway was elucidated in the fruitfly, Drosophila melanogaster, and this pathway is largely conserved in vertebrates, although some important differences have been noted. The current paradigm of the "canonical" pathway views HH signalling as a series of repressive interactions which culminates in GLI-mediated transcriptional regulation of a variety of cellular processes. Definitions of "non-canonical" signalling stem from examples where the response to HH morphogen deviates from this paradigm and, according to current reports, three general scenarios of noncanonical HH signalling can be defined: (1) Signalling that involves HH pathway components but which is independent of GLI-mediated transcription; (2) Direct interaction of HH signalling components with components of other molecular pathways; and (3) "Non-contiguous" or "atypical" interaction of core HH pathway components with one another. Currently, the evidence supporting non-canonical HH signalling is not conclusive. However, Sonic hedgehog (SHH) has been shown to regulate cell migration and axon guidance in several contexts, and some of these processes are independent of downstream components of the HH pathway, and presumably the transcriptional response to morphogen. Furthermore, biochemical studies have shown that the HH receptor, PTCH1, can directly interact both with Cyclin B1 and caspases, to inhibit cell proliferation and to promote apoptosis, respectively, and that these functions are inhibited in the presence of morphogen. Genetic analysis of orthologues of the HH pathway in nematode worms further supports the notion that PTCH1-related molecules can function independently of other components of the canonical HH pathway, and the phenotypes of mice with point mutations in the Ptch1 gene offer clues as to the processes that non-canonical HH signalling might regulate. While none of these evidences are conclusive,collectively they point to the existence of added complexity in the HH pathway in the form of non-canonical pathways. A major difficulty in studying this problem is that canonical and non-canonical pathways are likely to act in parallel, and so in many situations it will not be possible to implicate non-canonical responses in certain cellular processes simply by excluding a role for the canonical pathway-directed analyses of non-canonical HH signalling are therefore necessary. The aim of this review is to present the cumulative evidence supporting non-canonical HH signalling, with the hope of promoting further enquiry into this area.

Formin1 disruption confers oligodactylism and alters Bmp signaling

Proper limb development requires concerted communication between cells within the developing limb bud. Several molecules have been identified which contribute to the formation of a circuitry loop consisting in large part of secreted proteins. The intracellular actin nucleator, Formin 1 (Fmn1), has previously been implicated in limb development, but questions remain after the identification of a Gremlin transcriptional enhancer within the 3' end of the Fmn 1 locus. To resolve this issue, a knockout mouse devoid of Fmn1 protein was created and characterized. The mice exhibit a reduction of digit number to four, a deformed posterior metatarsal, phalangeal soft tissue fusion as well as the absence of a fibula to 100% penetrance in the FVB genetic background. Importantly, this mutant allele does not genetically disrupt the characterized Gremlin enhancer, and indeed Gremlin RNA expression is upregulated at the 35 somite stage of development. Our data reveal increased Bone Morphogenetic Protein (Bmp) activity in mice which carry a disruption in Fmn1, as evidenced by upregulation of Msx1 and a decrease in Fgf4 within the apical ectodermal ridge. Additionally, these studies show enhanced activity downstream of the Bmp receptor in cells where Fmn1 is perturbed, suggesting a role for Fmn1 in repression of Bmp signaling.

A second wave of Sonic hedgehog expression during the development of the bat limb

Sonic hedgehog (Shh) plays an integral role in both the anterior-posterior (A-P) patterning and expansion of developing vertebrate limbs through a feedback loop involving Fgfs, Bmps, and Gremlin. In bat limbs A-P patterning and the size of the digital field are unique. The posterior digits of the forelimb are elongated and joined by tissue, whereas the thumb is short. The hindlimb digits often are uniform in length. Here, we reveal novel expression patterns for Shh and its target, Patched 1 (Ptc1), during limb development in two bat species. Early Shh expression in the zone of polarizing activity is wider in the bat forelimb than in the mouse forelimb, correlating with the reported expansion of Fgf8 expression in the apical ectodermal ridge and the early loss of symmetry in the bat forelimb. Later in limb development, Shh and Ptc1 expression is reinitiated in the interdigital tissue. Shh is graded along the A-P axis in forelimb and is expressed uniformly at a lower level across the hindlimb interdigital tissue. We also show that the reported Fgf8 expression in the interdigital tissue precedes the expression of Shh. We propose that the reinitiation of Shh and Fgf8 expression in bat limbs reactivates the Shh-Fgf feedback loop in the interdigital tissue of stage 16 bat embryos. The cell survival and proliferation signals provided by the Shh-Fgf signaling loop probably contribute to the lengthening of the posterior forelimb digits, the survival of the forelimb interdigital webbing, and the extension of the hindlimb digits to a uniform length.