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Publications (100)
Thyroid hormones are involved in many biological processes such as neurogenesis, metabolism, and development. However, compounds called endocrine disruptors can alter thyroid hormone signaling and induce unwanted effects on human and ecosystems health. Regulatory tests have been developed to detect these compounds but need to be significantly impro...
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three dis...
Thyroid hormones (TH) and glucocorticoids (GC) are involved in numerous developmental and physiological processes. The effects of individual hormones are well documented, but little is known about the joint actions of the two hormones. To decipher the crosstalk between these two hormonal pathways, we conducted a transcriptional analysis of genes re...
Frogs are an ecologically diverse and phylogenetically ancient group of living amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus . Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis , along with draft chromosome-scale sequences of three d...
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...
Thyroid hormones (THs) are important regulators of growth, development, and homeostasis of all vertebrates. There are many environmental contaminants that are known to disrupt TH action, yet their mechanisms are only partially understood. While the effects of Endocrine Disrupting Chemicals (EDCs) are mostly studied as “hormone system silos”, the pr...
Amphibians display very diverse life cycles and development can be direct, where it occurs in ovo and a juvenile hatches directly, or biphasic, where an aquatic larva hatches and later undergoes metamorphosis followed by sexual maturation. In both cases, metamorphosis, corresponds to the post embryonic transition (PETr). A third strategy, only foun...
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 addr...
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 Xenopu...
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 coor...
Amphibian post-embryonic development and Thyroid Hormones (TH) signaling are deeply and intimately connected. In anuran amphibians, TH induce the spectacular and complex process known as metamorphosis. In paedomorphic salamanders, at similar development time, raising levels of TH fail to induce proper metamorphosis, as many “larval” tissues (e.g.,...
Thyroid hormones are pleiotropic hormones involved in chordates physiology. Understanding their functions and mechanisms is also instrumental to diagnose dys-regulations and get a predictive power that can applied to medicine, ecology, etc. Today, high-throughput sequencing technologies offer the opportunity to address this issue not only in model...
Proper gene expression involves communication between the regulatory elements and promoters of genes. Because regulatory elements can be located over a large range of genomic distances (from as close as a few hundred bp to as much as several Mb away), contact and communication between regulators and the core transcriptional machinery at promoters a...
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 s...
Previous work identified a transcribed locus, Str. 34945, induced by the frog stress hormone corticosterone (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 specifi...
Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution...
Cooperative, synergistic gene regulation by nuclear receptors (NRs) can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Kr )ppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse...
There is increasing evidence that the thyroid hormone (TH) receptors (THRs) can play a role in aging, cancer and degenerative diseases. In this paper, we demonstrate that binding of TH T3 (triiodothyronine) to THRB induces senescence and deoxyribonucleic acid (DNA) damage in cultured cells and in tissues of young hyperthyroid mice. T3 induces a rap...
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 matrix is still poorly understood. One efficient way to tackle this issue is to compare the expression, between vertebrate species, of osteoblas...
Amphibian metamorphosis is marked by dramatic thyroid hormone (T(3))-induced changes including de novo morphogenesis, tissue remodeling, and organ resorption through programmed cell death. These changes involve cascades of gene regulation initiated by thyroid hormone (TH). TH functions by regulating gene expression through TH receptors (TR). TR are...
Background:
Thyroid hormone (TH) receptor (TR) plays critical roles in vertebrate development. However, the in vivo mechanism of TR action remains poorly explored.
Scope of review:
Frog metamorphosis is controlled by TH and mimics the postembryonic period in mammals when high levels of TH are also required. We review here some of the findings on...
The diversity of thyroid hormone T(3) effects in vivo makes their molecular analysis particularly challenging. Indeed, the current model of the action of T(3) and its receptors on transcription does not reflect this diversity. Here, T(3)-dependent amphibian metamorphosis was exploited to investigate, in an in vivo developmental context, how T(3) di...
Genome annotation files for viewing in Artemis and ACT genome browsers.
(25.93 MB ZIP)
Synteny diagrams of the ORF landscapes surrounding each of the 114 α-rightY128T repeats. The ORF landscape surrounding each of the 114 α-rightY128T repeats in strains Z2491, MC58, and FAM18 are shown. On each page the target element, or bait, is shown in the middle together with a repeat density track. The homologous loci in the other two strains a...
The coordinates and sequences of the 20 bp sequence tags flanking each of the 114 a-rightY128T repeats in strains Z2491, MC58, and FAM18.
(0.10 MB PDF)
Correia αY128T right repeat distribution in the genome of N. meningitidis serogroup B strain MC58.
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Correia αY128T right repeat distribution in the genome of N. meningitidis serogroup C strain FAM18.
(0.06 MB PDF)
Instructions for loading Dataset S1 into Artemis and ACT.
(0.03 MB PDF)
Neisseria meningitidis is the primary causative agent of bacterial meningitis. The genome is rich in repetitive DNA and almost 2% is occupied by a diminutive transposon called the Correia element. Here we report a bioinformatic analysis defining eight subtypes of the element with four distinct types of ends. Transcriptional analysis, using PCR and...
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 sim...
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...
Table S1. Statistics of genome assemblies. For a few species (grayed name), the estimated ChIP-Seq and ChIP-PET mapping efficiency is particularly low.
Figure S1. Genome sequences are often fragmented in many scaffolds containing unsequenced gaps. For each genome assembly available at ENSEMBL, the size and the unsequenced percent of each scaffold has been plotted.
ChIP-Seq and ChIP-PET can potentially be used with any genome for genome wide profiling of protein-DNA interaction sites. Unfortunately, it is probable that most genome assemblies will never reach the quality of the human genome assembly. Therefore, it remains to be determined whether ChIP-Seq and ChIP-PET are practicable with genome sequences othe...
Promoter DNA methylation of MAPK12 and GSTU10 genes was also analyzed after different numbers of passages in Arabidopsis cell suspensions (ACS): IMP, intermediate passages; LP, late passages. Black and white dots indicate methylated and unmethylated CpGs, respectively.
(0.02 MB PDF)
Transcription levels of MET1 in WT callus and drm2 mutant. Transcript levels were analyzed by quantitative RT-PCR and results are expressed as a value relative to the expression in WT callus.
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Sequence context of some of the DNA methylation found in Arabidopsis cell suspensions and leaves.
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Bisulfite genomic sequencing of twelve individual clones of nine representative genes unmethylated in leaves and Arabidopsis wild type callus. Black and white dots indicate methylated and unmethylated CpGs, respectively. Lower panels, representative electropherograms.
(0.05 MB PDF)
Promoter hypermethylation in cell suspensions is dependent on combined phytohormone action and is associated with histone hypoacetylation and gene repression. Bisulfite genomic sequencing of the TTG1, GSTF5, and SUVH8 promoters in the presence or absence of the demethylating drug ADC, and the phytohormones NAA and kinetin in Arabidopsis cell suspen...
Bisulfite genomic sequencing of twelve individual clones of TTG1 (A), GSTF5 (B), and SUVH8 (C) genes in cell suspensions derived from WT and DNA methyltransferase mutants of Arabidopsis thaliana (L.). Black and white dots indicate methylated and unmethylated CpGs, respectively.
(0.03 MB PDF)
Bisulfite genomic sequencing of twelve clones of the TTG1 (three regions) 5′-regulatory region in Arabidopsis cell suspensions at 300, 330, and 400 passages. Schematic representations of the methylation status of each CpG dinucleotide. Black and white dots indicate methylated and unmethylated CpGs, respectively.
(0.03 MB PDF)
Bisulfite genomic sequencing of twelve individual clones of six representative genes unmethylated in leaves and Arabidopsis cell suspensions (ACS). Black and white dots indicate methylated and unmethylated CpGs, respectively. Lower panels, representative electropherograms.
(0.04 MB PDF)
List of candidate genes selected for validation with bisulfite sequencing analysis.
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List of Arabidopsis thaliana genes upregulated after treatment with ADC.
(0.02 MB PDF)
Primer sequences and annealing temperatures.
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Genetic identification of methylated genes in dedifferentiated Arabidopsis cells.
(0.02 MB PDF)
Transposable elements (TEs) are ubiquitous components of eukaryotic genomes that impact many aspects of genome function. TE detection in genomic sequences is typically performed using similarity searches against a set of reference sequences built from previously identified TEs. Here, we demonstrate that this process can be improved by designing ref...
Maintaining and acquiring the pluripotent cell state in plants is critical to tissue regeneration and vegetative multiplication. Histone-based epigenetic mechanisms are important for regulating this undifferentiated state. Here we report the use of genetic and pharmacological experimental approaches to show that Arabidopsis cell suspensions and cal...
TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) is the only Arabidopsis protein with overall sequence similarity to the HETEROCHROMATIN PROTEIN 1 (HP1) family of metazoans and S. pombe. TFL2/LHP1 represses transcription of numerous genes, including the flowering-time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC), as well as...
Mixture Models Used to Identify IP/INPUT Values Reporting Significant Enrichment
Distribution of IP and IP/INPUT values are indicated for each biological replicate in the left and right panels, respectively. Gaussians are indicated in navy blue, light blue, red, and yellow in order of increasing means. Hybridization and IP/INPUT thresholds are indi...
Correlation of H3K27me3 in Untransformed and 35S::TFL2/LHP1:HA Transgenic Seedlings
PCR was carried out on ChIP samples obtained with anti-H3K27me3 antibodies, using 23 different primer pairs. IP/INPUT ratios are plotted against each other. The data show that over-expression TFL2/LHP1 does not affect H3K27me3 distribution.
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List of Genes Associated with H3K27me3
(91 KB XLS)
Genome Browser View of Epigenomic Maps
The entire set of epigenomic maps that was produced in this work is presented in consecutive 1-Mb panels. Biological replicates are shown below each other. IP/INPUT ratios (log2) reporting significant association are marked in dark colors.
(4.4 MB PDF)
List of Tiles Associated with TFL2/LHP1
(239 KB XLS)
Extent of Overlap between TFL2/LHP1 Target Genes and Genes Marked by H3K9me2, H3K9me3 or H3K27me3
(32 KB DOC)
List of PCR Primers
(30 KB XLS)
Confirmation of ChIP-Chip Results by ChIP-PCR
ChIP-PCR was carried out based on 33 randomly selected tiles that showed by ChIP-chip either no association with TFL2/LHP1 and H3K27me3, or association with both. Fifteen out of the 17 tiles declared “negative” and 13 out of 16 tiles declared “positive” by ChIP-chip were validated by PCR in independent...
List of Genes Associated with TFL2/LHP1
(61 KB XLS)
List of Tiles Associated with H3K27me3
(389 KB XLS)
List of Tiles Associated with H3K9me2
(335 KB XLS)
List of Genes Associated with H3K9me2
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List of Genes Associated with H3K9me3
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List of Tiles Associated with H3K9me3
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Extent of Overlap between Biological Replicates
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Transposons have contributed protein coding sequences to a unexpectedly large number of human genes. Except for the V(D)J
recombinase and telomerase, all remain of unknown function. Here we investigate the activity of the human SETMAR protein,
a highly expressed fusion between a histone H3 methylase and a mariner family transposase. Although SETMAR...
TERMINAL FLOWER 2/LIKE HETEROCHROMATIN PROTEIN 1 (TFL2/LHP1) is the only Arabidopsis protein with overall sequence similarity to the HETEROCHROMATIN PROTEIN 1 (HP1) family of metazoans and S. pombe. TFL2/LHP1 represses transcription of numerous genes, including the flowering-time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC), as well as...
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...