Nicolas Buisine

Nicolas Buisine
Muséum National d'Histoire Naturelle · Département Régulations, développement et diversité moléculaire

About

95
Publications
4,202
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
1,786
Citations

Publications

Publications (95)
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
Full-text available
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.,...
Chapter
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
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...
Article
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...
Article
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...
Article
Full-text available
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...
Data
Genome annotation files for viewing in Artemis and ACT genome browsers. (25.93 MB ZIP)
Data
Full-text available
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...
Data
Full-text available
Plasmids used in this study. (0.06 MB PDF)
Data
Full-text available
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)
Data
Full-text available
Primers for RT-PCR. (0.03 MB PDF)
Data
Full-text available
Correia αY128T right repeat distribution in the genome of N. meningitidis serogroup B strain MC58. (0.07 MB PDF)
Data
Full-text available
Correia αY128T right repeat distribution in the genome of N. meningitidis serogroup C strain FAM18. (0.06 MB PDF)
Data
Full-text available
Instructions for loading Dataset S1 into Artemis and ACT. (0.03 MB PDF)
Article
Full-text available
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...
Article
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...
Article
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...
Data
Table S1. Statistics of genome assemblies. For a few species (grayed name), the estimated ChIP-Seq and ChIP-PET mapping efficiency is particularly low.
Data
Table S2. Outcome of simulated ChIP-Seq mapping.
Data
Table S3. Outcome of simulated ChIP-PET mapping.
Data
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.
Article
Full-text available
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...
Data
Full-text available
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)
Data
Full-text available
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. (0.01 MB PDF)
Data
Full-text available
Sequence context of some of the DNA methylation found in Arabidopsis cell suspensions and leaves. (0.01 MB PDF)
Data
Full-text available
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)
Data
Full-text available
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...
Data
Full-text available
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)
Data
Full-text available
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)
Data
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)
Data
Full-text available
List of candidate genes selected for validation with bisulfite sequencing analysis. (0.03 MB PDF)
Data
Full-text available
List of Arabidopsis thaliana genes upregulated after treatment with ADC. (0.02 MB PDF)
Data
Primer sequences and annealing temperatures. (0.02 MB PDF)
Data
Full-text available
Genetic identification of methylated genes in dedifferentiated Arabidopsis cells. (0.02 MB PDF)
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Data
Full-text available
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...
Data
Full-text available
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. (46 KB PDF)
Data
List of Genes Associated with H3K27me3 (91 KB XLS)
Data
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)
Data
List of Tiles Associated with TFL2/LHP1 (239 KB XLS)
Data
Extent of Overlap between TFL2/LHP1 Target Genes and Genes Marked by H3K9me2, H3K9me3 or H3K27me3 (32 KB DOC)
Data
Full-text available
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...
Data
List of Genes Associated with TFL2/LHP1 (61 KB XLS)
Data
List of Tiles Associated with H3K27me3 (389 KB XLS)
Data
List of Tiles Associated with H3K9me2 (335 KB XLS)
Data
List of Genes Associated with H3K9me2 (53 KB XLS)
Data
List of Genes Associated with H3K9me3 (165 KB XLS)
Data
List of Tiles Associated with H3K9me3 (681 KB XLS)
Data
Extent of Overlap between Biological Replicates (27 KB DOC)
Article
Full-text available
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...