Zebrafish eda and edar mutants reveal conserved and ancestral roles of ectodysplasin signaling in vertebrates

The genetic basis of the development and variation of adult form of vertebrates is not well understood. To address this problem, we performed a mutant screen to identify genes essential for the formation of adult skeletal structures of the zebrafish. Here, we describe the phenotypic and molecular characterization of a set of mutants showing loss of adult structures of the dermal skeleton, such as the rays of the fins and the scales, as well as the pharyngeal teeth. The mutations represent adult-viable, loss of function alleles in the ectodysplasin (eda) and ectodysplasin receptor (edar) genes. These genes are frequently mutated in the human hereditary disease hypohidrotic ectodermal dysplasia (HED; OMIM 224900, 305100) that affects the development of integumentary appendages such as hair and teeth. We find mutations in zebrafish edar that affect similar residues as mutated in human cases of HED and show similar phenotypic consequences. eda and edar are not required for early zebrafish development, but are rather specific for the development of adult skeletal and dental structures. We find that the defects of the fins and scales are due to the role of Eda signaling in organizing epidermal cells into discrete signaling centers of the scale epidermal placode and fin fold. Our genetic analysis demonstrates dose-sensitive and organ-specific response to alteration in levels of Eda signaling. In addition, we show substantial buffering of the effect of loss of edar function in different genetic backgrounds, suggesting canalization of this developmental system. We uncover a previously unknown role of Eda signaling in teleosts and show conservation of the developmental mechanisms involved in the formation and variation of both integumentary appendages and limbs. Lastly, our findings point to the utility of adult genetic screens in the zebrafish in identifying essential developmental processes involved in human disease and in morphological evolution.     

An ecologist's guide for studying DNA methylation variation in wild vertebrates

The field of molecular biology is advancing fast with new powerful technologies, sequencing methods and analysis software being developed constantly. Commonly used tools originally developed for research on humans and model species are now regularly used in ecological and evolutionary research. There is also a growing interest in the causes and consequences of epigenetic variation in natural populations. Studying ecological epigenetics is currently challenging, especially for vertebrate systems, because of the required technical expertise, complications with analyses and interpretation, and limitations in acquiring sufficiently high sample sizes. Importantly, neglecting the limitations of the experimental setup, technology and analyses may affect the reliability and reproducibility, and the extent to which unbiased conclusions can be drawn from these studies. Here, we provide a practical guide for researchers aiming to study DNA methylation variation in wild vertebrates. We review the technical aspects of epigenetic research, concentrating on DNA methylation using bisulfite sequencing, discuss the limitations and possible pitfalls, and how to overcome them through rigid and reproducible data analysis. This review provides a solid foundation for the proper design of epigenetic studies, a clear roadmap on the best practices for correct data analysis and a realistic view on the limitations for studying ecological epigenetics in vertebrates. This review will help researchers studying the ecological and evolutionary implications of epigenetic variation in wild populations.     

Characterization of a microsomal retinol dehydrogenase gene from amphioxus: retinoid metabolism before vertebrates

Amphioxus, a member of the subphylum Cephalochordata, is thought to be the closest living relative to vertebrates. Although these animals have a vertebrate-like response to retinoic acid, the pathway of retinoid metabolism remains unknown. Two different enzyme systems - the short chain dehydrogenase/reductases and the cytosolic medium-chain alcohol dehydrogenases (ADHs) - have been postulated in vertebrates. Nevertheless, recent data show that the vertebrate-ADH1 and ADH4 retinol-active forms originated after the divergence of cephalochordates and vertebrates. Moreover, no data has been gathered in support of medium-chain retinol active forms in amphioxus. Then, if the cytosolic ADH system is absent and these animals use retinol, the microsomal retinol dehydrogenases could be involved in retinol oxidation. We have identified the genomic region and cDNA of an amphioxus Rdh gene as a preliminary step for functional characterization. Besides, phylogenetic analysis supports the ancestral position of amphioxus Rdh in relation to the vertebrate forms.     

Characterization of a microsomal retinol dehydrogenase gene from amphioxus: retinoid metabolism before vertebrates

Amphioxus, a member of the subphylum Cephalochordata, is thought to be the closest living relative to vertebrates. Although these animals have a vertebrate-like response to retinoic acid, the pathway of retinoid metabolism remains unknown. Two different enzyme systems — the short chain dehydrogenase/reductases and the cytosolic medium-chain alcohol dehydrogenases (ADHs) — have been postulated in vertebrates. Nevertheless, recent data show that the vertebrate-ADH1 and ADH4 retinol-active forms originated after the divergence of cephalochordates and vertebrates. Moreover, no data has been gathered in support of medium-chain retinol active forms in amphioxus. Then, if the cytosolic ADH system is absent and these animals use retinol, the microsomal retinol dehydrogenases could be involved in retinol oxidation. We have identified the genomic region and cDNA of an amphioxus Rdh gene as a preliminary step for functional characterization. Besides, phylogenetic analysis supports the ancestral position of amphioxus Rdh in relation to the vertebrate forms.     

The evolving functions of DNA methylation

DNA methylation is an ancient process found in all domains of life. Although the enzymes that mediate methylation have remained highly conserved, DNA methylation has been adapted for a variety of uses throughout evolution, including defense against transposable elements and control of gene expression. Defects in DNA methylation are linked to human diseases, including cancer. Methylation has been lost several times in the course of animal and fungal evolution, thus limiting the opportunity for study in common model organisms. In the past decade, plants have emerged as a premier model system for genetic dissection of DNA methylation. A recent combination of plant genetics with powerful genomic approaches has led to a number of exciting discoveries and promises many more.     

Beta-Arrestins: new roles in regulating heptahelical receptors' functions

The last few years have seen a marked expansion in appreciation of the diversity of roles played by the betaArrestins in regulating GPCR functions. Originally discovered as molecules that desensitize such receptors, the roles of betaArrestins have expanded to include acting as signalling adapters or intermediates that recruit other key molecules to the GPCRs in an agonist-regulated fashion. For example, interactions with components of the endocytic machinery, such as clathrin, the adapter protein AP-2 and the N-ethylmaleimide sensitive fusion protein (NSF), demonstrate the ability of betaArrestins to act as adapters to facilitate the clathrin-mediated endocytosis of certain members of the GPCR family. BetaArrestins have also been shown to serve as signalling molecules. The Ras-dependent activation of ERK1/2 may involve the betaArrestin-dependent recruitment of c-Src to the beta2-adrenergic receptor (beta2-AR). More recently, betaArrestins have been shown to act as molecular scaffolds that coordinate the assembly of certain MAP kinase complexes that lead to the stimulation of either ERK1/2 or JNK3. Finally, long-term accumulation of arrestin-rhodopsin complexes, in photoreceptor cells has been shown to trigger apoptosis.     

昆虫DNA甲基化的特点和功能

DNA甲基化为表观遗传修饰的一种主要形式, 对基因表达的调控具有重要作用。近年来随着有关昆虫DNA甲基化的研究和报道增多, 发现昆虫DNA甲基化除了与高等哺乳动物有一定的相似性之外, 还具有独特的特点和功能。本文就昆虫DNA甲基化的主要特点和功能进行了综述, 以期为进一步研究昆虫DNA甲基化提供借鉴和参考。不同昆虫所具有的DNA甲基转移酶种类和性质差异较大, 且昆虫DNA甲基化具有甲基化水平较低、主要发生在基因区等特点, 其功能主要涉及到调节胚胎发育、参与基因组印迹、调控级型和翅型分化、影响性别决定、介入抗药性形成等。     

Genetic basis for an evolutionary shift from ancestral preaxial to postaxial limb polarity in non-urodele vertebrates

1. Download : Download high-res image (165KB)
2. Download : Download full-size image

     

Developmental origins of transgenerational sperm DNA methylation epimutations following ancestral DDT exposure

Epigenetic alterations in the germline can be triggered by a number of different environmental factors from diet to toxicants. These environmentally induced germline changes can promote the epigenetic transgenerational inheritance of disease and phenotypic variation. In previous studies, the pesticide DDT was shown to promote the transgenerational inheritance of sperm differential DNA methylation regions (DMRs), also called epimutations, which can in part mediate this epigenetic inheritance. In the current study, the developmental origins of the transgenerational DMRs during gametogenesis have been investigated. Male control and DDT lineage F3 generation rats were used to isolate embryonic day 16 (E16) prospermatogonia, postnatal day 10 (P10) spermatogonia, adult pachytene spermatocytes, round spermatids, caput epididymal spermatozoa, and caudal sperm. The DMRs between the control versus DDT lineage samples were determined at each developmental stage. The top 100 statistically significant DMRs at each stage were compared and the developmental origins of the caudal epididymal sperm DMRs were assessed. The chromosomal locations and genomic features of the different stage DMRs were analyzed. Although previous studies have demonstrated alterations in the DMRs of primordial germ cells (PGCs), the majority of the DMRs identified in the caudal sperm originated during the spermatogonia stages in the testis. Interestingly, a cascade of epigenetic alterations initiated in the PGCs is required to alter the epigenetic programming during spermatogenesis to obtain the sperm epigenetics involved in the epigenetic transgenerational inheritance phenomenon.     

Chromosomal mapping of ANTP class homeobox genes in amphioxus: piecing together ancestral genomes

Homeobox genes encode DNA-binding proteins, many of which are implicated in the control of embryonic development. Evolutionarily, most homeobox genes fall into two related clades: the ANTP and the PRD classes. Some genes in ANTP class, notably Hox, ParaHox, and NK genes, have an intriguing arrangement into physical clusters. To investigate the evolutionary history of these gene clusters, we examined homeobox gene chromosomal locations in the cephalochordate amphioxus, Branchiostoma floridae. We deduce that 22 amphioxus ANTP class homeobox genes localize in just three chromosomes. One contains the Hox cluster plus AmphiEn, AmphiMnx, and AmphiDll. The ParaHox cluster resides in another chromosome, whereas a third chromosome contains the NK type homeobox genes, including AmphiMsx and AmphiTlx. By comparative analysis we infer that clustering of ANTP class homeobox genes evolved just once, during a series of extensive cis-duplication events of genes early in animal evolution. A trans-duplication event occurred later to yield the Hox and ParaHox gene clusters on different chromosomes. The results obtained have implications for understanding the origin of homeobox gene clustering, the diversification of the ANTP class of homeobox genes, and the evolution of animal genomes.     

Polyploidy and DNA methylation: new tools available

Most plant species are recent or ancient polyploids (displaying at least one round of genome duplication in their history). Cultivated species (e.g. wheat, cotton, canola, sugarcane, coffee) and invasive species are often relatively recent polyploids, and frequently of hybrid origin (i.e. allopolyploids). Despite the genetic bottleneck occurring during the allopolyploid speciation process, the formation of such species from two divergent lineages leads to fixed heterozygosity decisive to their success. New phenotypes and new niche occupation are usually associated with this mode of speciation, as a result of both genomic rearrangements and gene expression changes of different magnitudes depending on the different polyploid species investigated. These gene expression changes affecting newly formed polyploid species may result from various, interconnected mechanisms, including (i) functional interactions between the homoeologous copies and between their products, that are reunited in the same nucleus and cell; (ii) the fate of duplicated copies, selective pressure on one of the parental copy being released which could lead to gene loss, pseudogenization, or alternatively, to subfunctionalization or neofunctionalization; and (iii) epigenetic landscape changes that in turn affect gene expression. As one of the interrelated processes leading to epigenetic regulation of gene expression, the DNA methylation status of newly formed species appears to be consistently affected following both hybridization and genome doubling. In this issue, Verhoeven et al. have investigated the fate of DNA methylation patterns that could affect naturally occurring new asexual triploid lineages of dandelions. As a result of such a ploidy level change, the authors demonstrate stably transmitted DNA methylation changes leading to unique DNA methylation patterns in each newly formed lineage. Most studies published to date on plant DNA methylation polymorphism were performed using restriction enzymes sensitive to methylation. Recently, new high‐throughput methods were made available, thanks to the development of ‘next‐generation sequencing’ techniques. The combination of these methods offers powerful and promising tools to investigate epigenetic variation in both model and non‐model systems.     

Transposon diversity is higher in amphioxus than in vertebrates: functional and evolutionary inferences

Transposable elements (TEs) are main components of eukaryote genomes-up to 50% in some vertebrates-which can replicate and jump to new locations. TEs contribute to shape genome evolution, actively by creating new genes (or exons) or altering gene expression as consequence of transposition, and passively by serving as illegitimate recombinational hotspots. Analysis of amphioxus TEs can help to shed light on the ancestral status of chordate TEs and to understand genome evolution in cephalochordates and early vertebrates. The Branchiostoma floridae genome project has revealed that TE content constitutes ～28% of the amphioxus genome. Amphioxus TEs belong to more than 30 superfamilies, which represent a higher diversity than in vertebrates. Amphioxus TE families are also highly heterogeneous as generally none of their members are drastically more abundant than others, and none of the TEs seems to have suffered any massive expansion. Such diversity and heterogeneity make the amphioxus genome not to be particularly prone to major evolutionary changes mediated by TEs, and therefore favoring genomic evolutionary stasis. Comparison of TE diversity and content between amphioxus and vertebrates allows us to discuss whether or not a burst of TEs happened after the two rounds of whole-genome duplication that occurred during early vertebrate evolution.     

Gene regulation by histone H1: new links to DNA methylation

Linker histones of the H1 family are among the most abundant components of chromatin. In this issue of Cell, the effect of H1 downregulation on gene expression is examined. Although a 50% reduction of histone H1 levels in embryonic stem cells affects chromatin structure globally, the expression of very few genes is altered. Intriguingly, this study reveals a new link between H1 and DNA methylation.     

Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates.

The complete nucleotide sequence of the mitochondrial DNA of the amphioxus Branchiostoma lanceolatum has been determined. This mitochondrial genome is small (15 076 bp) because of the short size of the two rRNA genes and the tRNA genes. In addition, this genome contains a very short non-coding region (57 bp) with no sequence reminiscent of a control region. The organisation of the coding genes, as well as of the two rRNA genes, is identical to that of the sea lamprey. Some differences in the repartition of the tRNA genes occur when compared to the lamprey. The mitochondrial codon usage of the amphioxus is reminiscent of that of urochordates since the AGA codon is read as a glycine and not as a stop codon as in vertebrates. Moreover, the base composition at the wobble positions of the codon is strongly biased toward guanine. Altogether, these data clearly emphasise the close relationships between amphioxus and vertebrates, and reinforce the notion that prochordates may be viewed as the brother group of vertebrates.