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International audience; Setmar is a gene specific to simian genomes. The function(s) of its isoforms are poorly understood and their existence in healthy tissues remains to be validated. Here we profiled SETMAR expression and its genome-wide binding landscape in colon tissue. We found isoforms V3 and V6 in healthy and tumour colon tissues as well as incell lines. In two colorectal cell lines SETMAR binds to several thousand Hsmar1 and MADE1 terminal ends, transposons mostly located in non-genic regions of active chromatin including in enhancers. It also binds to a 12-bp motifs similar to an inner motif in Hsmar1 and MADE1 terminal ends. This motif is interspersed throughout the genome and is enriched in GC-rich regions as well as in CpG islands that contain constitutive replication origins. It is also found in enhancers other than those associated with Hsmar1 and MADE1. The role of SETMAR in the expression of genes, DNA replication and in DNA repair are discussed.

Thyroid hormones (TH) act mainly on the expression of the genome. It is well accepted that differential gene expression following treatment with TH recapitulates the expression profiles taking place during natural processes induced by these hormones. Although both processes seem to correlate at the scale of a few target genes, this hasn’t been addressed in a systematic manner. Our objectives were first to compare transcriptome variations after TH treatment with transcriptome variations during a TH controlled natural process and second to evaluate the proportion of the direct TH-response. The measurement of gene expression at genome scale (transcriptome) is obtained by sequencing all the messenger RNAs (RNA-seq). Direct response was sorted out by linking the transcription start sites of target genes using RNA-PET analysis with TR binding sites mapping using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). Indeed, ChIA-PET not only allow to map TR binding sites but also the physical interactions between them and transcription start sites of regulated genes. Our model is one of the striking developmental processes orchestrated by TH: amphibian metamorphosis. Tadpole transformation is marked by dramatic changes including de novo morphogenesis (limb), tissue remodelling (brain, intestine...) and organ resorption through apoptosis (tail). These changes involve cascades of gene regulation initiated by TH and their receptors. Because metamorphosis has close and interesting parallels with the perinatal period in mammals (including human), metamorphosis is thus an attractive model to analyze in a physiological context, the functions and mechanisms of action of TH. Here, we have focused on one Xenopus tropicalis organs, the tail fin skin which will disappear through cell death. We have compared natural metamorphosis with 24h of 10nM triiodothyronine (T3) treatment. We were able to observe several differences between T3 treatment and natural development. First, the genes regulated by T3 only correspond to a proportion of genes differentially expressed during metamorphosis. Second, T3-response genes start to be regulated well before tail regression (several days). Finally, T3-direct target genes represent a few percent of all the genes differentially expressed during tail regression. In conclusion, the comparison of transcriptomes of natural and induced metamorphosis allow us to reach a more precise understanding of TH action

International audience; Methylation of cytosine residues in DNA influences chromatin structure and gene transcription, and its regulation is crucial for brain development. There is mounting evidence that DNA methylation can be modulated by hormone signaling. We analyzed genome-wide changes in DNA methylation and their relationship to gene regulation in the brain of Xenopus tadpoles during metamorphosis, a thyroid hormone-dependent developmental process. We studied the region of the tadpole brain containing neurosecretory neurons that control pituitary hormone secretion, a region that is highly responsive to thyroid hormone action. Using Methylated DNA Capture sequencing (MethylCap-seq) we discovered a diverse landscape of DNA methylation across the tadpole neural cell genome, and pairwise stage comparisons identified several thousand differentially methylated regions (DMRs). During the pre-to pro-metamorphic period, the number of DMRs was lowest (1,163), with demethylation predominating. From pre-metamorphosis to metamorphic climax DMRs nearly doubled (2,204), with methylation predominating. The largest changes in DNA methylation were seen from metamorphic climax to the completion of metamorphosis (2960 DMRs), with 80% of the DMRs representing demethylation. Using RNA sequencing, we found negative correlations between differentially expressed genes and DMRs localized to gene bodies and regions upstream of transcription start sites. DNA demethylation at metamorphosis revealed by MethylCap-seq was corroborated by increased immunoreactivity for the DNA demethylation intermediates 5-hydroxymethylcytosine and 5-carboxymethylcytosine, and the methylcytosine dioxygenase ten eleven translocation 3 that catalyzes DNA demethylation. Our findings show that the genome of tadpole neural cells undergoes significant changes in DNA methylation during metamorphosis, and these changes likely influence chromatin architecture, and gene regulation programs occurring during this developmental period.

International audience; Previous work identified a transcribed locus, Str. 34945, induced by the frog stress hormone corticos-terone (CORT) in Xenopus tropicalis tails. Because thyroid hormone had no influence on its expression, Str. 34945 was dubbed the first ''CORT-only" gene known from tadpoles. Here, we examine the genomic annotation for this transcript, hormone specificity, time course of induction, tissue distribution, and developmental expression profile. The location of Str. 34945 on the X. tropicalis genome lies between the genes ush1g (Usher syndrome 1G) and fads6 (fatty acid desaturase 6). A blast search showed that it maps to the same region on the X. laevis genome, but no hits were found in the human genome. Using RNA-seq data and conventional reverse transcriptase PCR and sequencing, we show that Str. 34945 is part of the 3 0 untranslated region of ush1g. We find that CORT but not aldosterone or thyroid hormone treatment induces Str. 34945 in tadpole tails and that expression of Str. 34945 achieves maximal expression within 12-24 h of CORT treatment. Among tissues, Str. 34945 is induced to the highest degree in tail, with lesser induction in lungs, liver, and heart, and no induction in the brain or kidney. During natural metamorphosis , Str. 34945 expression in tails peaks at metamorphic climax. The role of ush1g in metamorphosis is not understood, but the specificity of its hormone response and its expression in tail make ush1g valuable as a marker of CORT-response gene induction independent of thyroid hormone.

Background: Most work in endocrinology focus on the action of a single hormone, and very little on the cross-talks between two hormones. Here we characterize the nature of interactions between thyroid hormone and glucocorticoid signaling during Xenopus tropicalis metamorphosis. Methods: We used functional genomics to derive genome wide profiles of methylated DNA and measured changes of gene expression after hormonal treatments of a highly responsive tissue, tailfin. Clustering classified the data into four types of biological responses, and biological networks were modeled by system biology. Results: We found that gene expression is mostly regulated by either T3 or CORT, or their additive effect when they both regulate the same genes. A small but non-negligible fraction of genes (12%) displayed non-trivial regulations indicative of complex interactions between the signaling pathways. Strikingly, DNA methylation changes display the opposite and are dominated by cross-talks. Conclusion: Cross-talks between thyroid hormones and glucocorticoids are more complex than initially envisioned and are not limited to the simple addition of their individual effects, a statement that can be summarized with the pseudo-equation: TH ∙ GC &gt, TH + GC. DNA methylation changes are highly dynamic and buffered from genome expression.

Thyroid hormones (TH) have been shown to govern post-embryonic development in vertebrates inducing multiples effects. Recently, TH were shown to regulate the expression of genes coding for DNA methylation modifying enzymes. Acting on DNA methylation is an important means of regulating the expression of gene clusters and a central mechanism for coordinating developmental transitions. However, DNA methylation is dynamic and also integrate signals from the constantly changing environment. Certain variation of DNA methylation at these developmental transitions can confer on the genome a risk situation that can have lifelong consequences (cardiovascular and metabolism diseases, cancer or nervous system associated illness). Our objective is to locate TH induced variation of DNA methylation profiles to characterize potential determinants for certain pathologies and / or adaptation to a variation of the environment. We have thus initiated the mapping of DNA methylation following treatment with T3, using a method for capturing methylated DNA (MethylCap) combined with high-throughput sequencing (MethylCap-Seq). Magnetic beads allow for capture and fractionation of methylated DNA by CpG density. Here, we will focus on the highly methylated fraction of DNA. Our model of developmental transition is the amphibian metamorphosis, a post-embryonic process regulated by TH. Additionally, stress during metamorphosis might also induce potential phenotype propagation to adult forms, highlighting its importance in driving adaptation to fluctuating environments. We have compared TH induced methylation profiles in the hind limb and caudal epidermal, two organs with contrasted fate during metamorphosis (respectively morphogenesis and cell death). The results shown that TH affect the methylome with a strong tendency for DNA methylation marks to be removed. The majority of differential methylated regions (DMR) are tissue specific. However, few DMRs are found in both tissues and show either identical or opposite variations. The DMRs are generally not localize near genes regulated or not by the hormones. In conclusion, at post-embryonic transition in amphibians, TH induce mainly tissues-specific DNA demethylation not directly related to gene transcription.

International audience; PiggyBac(PB)-like elements (pble) are members of a eukaryotic DNA transposon family. This family is of interest to evolutionary genomics because pble transposases have been domesticated at least 9 times in vertebrates. The amino acid sequence of pble transposases can be split into three regions: an acidic N-terminal domain (similar to 100 aa), a central domain (similar to 400 aa) containing a DD[D/E] catalytic triad, and a cysteine-rich domain (CRD; similar to 90 aa). Two recent reports suggested that a functional CRD is required for pble transposase activity. Here we found that two CRD-deficient pble transposases, a PB variant and an isoform encoded by the domesticated PB-derived vertebrate transposase gene 5 (pgbd5) trigger transposition of the Ifp2 pble. When overexpressed in HeLa cells, these CRD-deficient transposases can insert Ifp2 elements with proper and improper transposon ends, associated with deleterious effects on cells. Finally, we found that mouse CRD-deficient transposase Pgbd5, as well as PB, do not insert pbles at random into chromosomes. Transposition events occurred more often in genic regions, in the neighbourhood of the transcription start sites and were often found in genes predominantly expressed in the human central nervous system.

Setmar is a 3-exons gene coding a SET domain fused to a Hsmar1 transposase. Its different transcripts theoretically encode 8 isoforms with SET moieties differently spliced. In vitro, the largest isoform binds specifically to Hsmar1 DNA ends and with no specificity to DNA when it is associated with hPso4. In colon cell lines, we found they bind specifically to two chromosomal targets depending probably on the isoform, Hsmar1 ends and sites with no conserved motifs. We also discovered that the isoforms profile was different between cell lines and patient tissues, suggesting the isoforms encoded by this gene in healthy cells and their functions are currently not investigated.

The emergence of vertebrates is closely associated to the evolution of mineralized bone tissue. However, the molecular basis underlying the origin and subsequent diversification of the skeletal mineralized matrixisstillpoorlyunderstood. Oneefficientway totackle thisissueis tocomparethe expression, between vertebrate species, of osteoblastic genes coding for bone matrix proteins. In this work, wehave focusedon theevolution ofthenetwork formingcollagen familywhichcontains the Col8a1, Col8a2, and Col10a1 genes. Both phylogeny and synteny reveal that these three paralogues are vertebrate-specific and derive from two independent duplications in the vertebrate lineage. To shed light on the evolution of this family, we have analyzed the osteoblastic expression of the network forming collagens in endochondral and intramembraneous skeletal elements of the amphibian Xenopus tropicalis. Remarkably, we find that amphibian osteoblasts express Col10a1 ,a gene strongly expressed in osteoblasts in actinopterygians but not in amniotes. In addition, while Col8a1 is known to be robustly expressed in mammalian osteoblasts, the expression levels of its amphibian orthologue are dramatically reduced. Our work reveals that while a skeletal expression of network forming collagen members is widespread throughout vertebrates, osteoblasts from divergent vertebrate lineages express different combinations of network forming collagen paralogues. J. Exp. Zool. (Mol. Dev. Evol.) 9999B: 1-11, 2013. © 2013 Wiley Periodicals, Inc. How to cite this article: Aldea D, Hanna P, Munoz D, Espinoza J, Torrejon M, Sachs L, Buisine N, Oulion S, Escriva H, Marcellini S. 2013. Evolution of the vertebrate bone matrix: An expression analysisofthenetworkformingcollagenparaloguesinamphibianosteoblasts.J.Exp.Zool.(Mol. Dev. Evol.) 9999:1-11.

The origin of bone and cartilage, and their subsequent diversification in specific vertebrate lineages, is intimately linked to the precise transcriptional control of genes involved in matrix mineralization. It is not yet clear, however, to which extent the osteoblasts, osteocytes, and chondrocytes of each of the major vertebrate groups express similar sets of genes. In this study we have focused on the evolution of two independent families of genes that code for extracellular matrix components of the skeleton and that include secreted protein, acidic, cysteine-rich (SPARC), bone sialoprotein (BSP) and dentin matrix protein 1 (DMP1) paralogues, and the osteocalcin (OC) and matrix gla protein (MGP) paralogues. Analyzing developing Xenopus tropicalis skeletal elements, we show that the expression patterns of these genes are well conserved with mammals. The fact that only a few osteoblasts express DMP1, while only some osteocytes express SPARC and BSP, reveals a significant degree of molecular heterogeneity for these two populations of X. tropicalis cells, similarly to what has been described in mouse. Although the cis-regulatory modules (CRM) of the mammalian OC, DMP1, and BSP orthologs have been functionally characterized, we found no evidence of sequence similarity between these regions and the X. tropicalis genome. Furthermore, these regulatory elements evolve rapidly, as they are only poorly conserved between human and rodents. Therefore, the SPARC/DMP1/BSP and the OC/MGP families provide a good paradigm to study how transcriptional output can be maintained in skeletal cells despite extensive sequence divergence of CRM.

Proper gene expression involves communication between the regulatory elements and promoters of genes. Today, chromosome conformation capture (3C)-based methods efficiently probe chromosome folding in the nucleus and thus provide a molecular description of physical proximity through DNA looping between enhancer(s) and their target promoter(s). One such method, chromatin interaction analysis using paired-end-tag (ChIA-PET) sequencing is a powerful high-throughput method for detection of genome-wide chromatin interactions. Following enrichment of the chromatin complexes with a dedicated antibody, through a process of immunoprecipitation (IP), DNA fragments are end-joined with specifically designed DNA-linkers through proximity ligation. The DNA-linkers contain the binding site for the type II restriction enzyme MmeI, which cleaves 20 bp from each end of the ligated fragments, thus releasing a “paired end tag” (PET): [20 bp tag]-[linker]-[20 bp tag]. The PETs are then deep-sequenced and reads are mapped to the reference genome, revealing both binding sites, as well as remote chromatin interactions mediated by the protein factors of interest. The method detailed here focuses on ChIA-PET library construction and can be completed in 2 wk.

International audience; In most of oviparous animals, vitellogenins (VTG) are the major egg yolk precursors. They are produced in the liver under the control of estrogens. In rainbow trout (Oncorhynchus mykiss), the vtg genes cluster contains an unusually large number of almost identical gene copies. In order to identify the regulatory elements in their promoters, we used a combination of reporter plasmids containing genomic sequences including putative estrogen response elements (EREs) and we performed transient transfection assays in MCF-7 and yeast cells. We found a functional ERE corresponding to the sequence GGGGCAnnnTAACCT (rtvtgERE), which differs from the consensus ERE (ERE(cs)) by three base pairs. This non-palindromic ERE is located in the env gene of a retrotransposon relic, 180 base pairs upstream of the transcriptional start site. Fluorescence anisotropy experiments confirmed that the purified human estrogen receptor alpha (hERalpha) can specifically bind to rtvtgERE. Furthermore, we observe that the stability of hERalpha-ERE(cs) and hERalpha-rtvtgERE complexes is similar with equilibrium dissociation constants of 3.0nM and 6.2nM respectively, under our experimental conditions. Additionally, this rtvtgERE sequence displays a high E2-responsiveness through ER activation in cellulo. In the rainbow trout, the functional ERE (rtvtgERE) lies within promoter sequences which are mostly composed of sequences derived from transposable elements (TEs), which therefore may have acted as an evolutionary buffer to secure the proper expression of these genes.

Transposable elements are ubiquitous genomic parasites with an ancient history of coexistence with their hosts. A few cases have emerged recently where these genetic elements have been recruited for normal function in the host organism. We have identified an expressed hobo/Ac/Tam (hAT) family transposase-like gene in cereal grasses which appears to represent such a case. This gene, which we have called gary, is found in one or two copies in barley, two diverged copies in rice and two very similar copies in hexaploid wheat. No gary homologues are found in Arabidopsis. In all three cereal species, an apparently complete 2.5 kb transposase-like open reading frame is present and nucleotide substitution data show evidence for positive selection, yet the predicted gary protein is probably not an active transposase, as judged by the absence of key amino acids required for transposase function. Gary is expressed in wheat and barley spikes and gary cDNA sequences are also found in rice. oat, rye. maize, sorghum and Sugarcane. The short inverted terminal repeats. flanked by an eight-nucleotide host sequence duplication. which are characteristic of a hAT transposon are absent. Genetic mapping in barley shows that gary is located on the distal end of the long arm of chromosome 2H. Wheat homologues of gary map to the same approximate location on the wheat group 2 chromosomes by physical bin-mapping and the more closely related of the two rice garys maps to the syntenic location near the bottom of rice chromosome 4. These data suggest that gary has resided in a single genomic location for at least 60 Myr and has lost the ability to transpose. yet expresses a transposase-related protein that is being conserved under host selection. We propose that the gary, transposase-like gene has been recruited by the cereal grasses for an unknown function.

Vitellogenins (Vtg) are the major yolk proteins in most oviparous organisms. They are encoded by a small number of genes – between one and four depending on the species. Characterization of the Vtg region in the genome of the rainbow trout reveals unusual features, however, in that this locus contains twenty complete genes and ten pseudogenes per haploid genome. The Vtg genes differ from each other by insertion, deletion and rearrangement events, although, at the sequence level, they show a high degree of similarity. Fluorescent in situ hybridization (FISH), pulsed-field gel electrophoresis (PFGE) and Southern analysis indicate that all gene copies are contained in a single 1500-kb region, and that most of the genes form tandem arrays separated by a conserved 4.5-kb intergenic region. The presence of large reiterated fragments indicates that this region has been subjected to several amplification events. The presence of a retroposon element (called I9) in Vtg intron 9 appears to be responsible for the silencing of at least nine of the ten pseudogenes. Two other incomplete retrotransposons (one LTR- and one LINE-type) and sequences derived from a HIV-like retrovirus are inserted into the conserved intergenic region, very close to the transcription start site. Their presence in all Vtg 5′-flanking regions suggests a possible role in gene amplification at this locus.