Biomedical subjects

Olivier Mathieu

Publications and source records attributed to Olivier Mathieu.

14 recordsLinked to original sources

PubMed2026

Reconstruction of ancestral plant genomes for inter-crop translational research.

We present Ancestral Genome Reconstruction (AGR), an exploratory framework for the automated inference of "paleogenomes" from large-scale comparative datasets. By analyzing 84 extant angiosperm species, we reconstructed 10 key ancestral angiosperm genomes millions of years old. These reconstructed ancestors were instrumental in (1) estimating when angiosperms emerged, when major botanical families originated, and when shared ancestral whole-genome duplication events occurred; and (2) tracing the evolutionary trajectories of ancestral chromosomes and genes, especially those that may have driven the emergence of key life-history traits (e.g., woody vs. herbaceous, aquatic vs. terrestrial, C3 vs. C4, and symbiotic root-nodulating vs. non-nodulating species). We demonstrated that these paleogenomes serve as tractable backbones for inter-crop translational research. Through an open-access web tool, OrthoViewer, we identified orthologs that have retained the same ancestral genomic context, favoring the identification of genes associated with "phenologs"- orthologous genes across species driving analogous phenotypes, traits, or processes-exemplified by FUWA for yield components, FLC for flowering time, and DDM1 for DNA methylation. Taken together, this study provides a testable paleogenomic workflow, opening novel avenues for integrating evolutionary genomics data into modern climate-smart crop breeding and supporting the agroecological transition.

Genome, Plant↗

PubMed2006

MOM1 mediates DNA-methylation-independent silencing of repetitive sequences in Arabidopsis.

The heterochromatic regions around centromeres of animal and plant chromosomes are composed of tandem repetitive sequences, interspersed with transposons and transposon derivatives. These sequences are largely transcriptionally silent and highly methylated, and are associated with specifically modified histones. Although embedded in heterochromatin, Arabidopsis 5S ribosomal RNA genes are among the most highly transcribed genes. However, some 5S genes are silenced, and we show here that this silencing can be suppressed by a reduction in CG methylation. Importantly, we show that mutation of MORPHEUS' MOLECULE 1 (MOM1) releases 5S repeat silencing independently of chromatin properties, as illustrated by the absence of detectable alteration of DNA and histone H3 methylation patterns. MOM1 also prevents transcription of 180-bp satellite repeats and 106B dispersed repeats but not of transposons. Our results provide evidence that transcription of densely methylated and highly repetitive heterochromatic sequences is controlled by two distinct epigenetic silencing pathways, one dependent on and the other independent of DNA methylation.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2006

Epigenetic regulation of transcription in intermediate heterochromatin.

Constitutive heterochromatin is a compact, transcriptionally inert structure formed in gene-poor and repeat- and transposon-rich regions. In Arabidopsis, constitutive heterochromatin is characterized by hypermethylated DNA and histone H3 dimethylated at lysine (K) 9 (H3K9me2) together with depletion of histone H3 dimethylated at lysine 4 (H3K4me2). Here, we describe loci with intermediate properties of heterochromatin in which transcription downregulation is inherited in a manner similar to constitutive heterochromatin, although the loci are associated with opposing histone marks--H3K4me2 and H3K9me2. In the ddm1 (decrease in DNA methylation 1) mutants, their transcriptional activation is accompanied by the expected shift in the H3 modifications--depletion of H3K9me2 and enrichment in H3K4me2. In mom1 (Morpheus' molecule 1) mutants, however, a marked increase in transcription is not accompanied by detectable changes in the levels of H3K4me2 and H3K9me2. Therefore, transcriptional regulation in the intermediate heterochromatin involves two distinct epigenetic mechanisms. Interestingly, silent transgenic inserts seem to acquire properties characteristic of the intermediate heterochromatin.

ATPases Associated with Diverse Cellular Activitie↗

PubMed2006

Image-guided core-needle biopsy of peripheral lymph nodes allows the diagnosis of lymphomas.

It is commonly admitted that the diagnosis of lymphomas can be assessed by the image-guided needle biopsy (IGNB) of deep lymph nodes. However, when peripheral lymph nodes are present, surgical dissection remains the standard strategy. The aim of this study was to evaluate the diagnostic yield of IGNB of peripheral lymph nodes in patients with suspected lymphomas. The records of 180 multisampling IGNBs of peripheral lymph nodes in 180 patients were reviewed. One hundred and twenty-three IGNBs were observed at first diagnosis and 57 at progression using large-cutting core-biopsy needles ranging between 18 G and 14 G in size. Immunohistochemistry studies were performed in all cases and at least one biopsy was systematically frozen. A diagnosis of lymphoma with sufficient information such that a therapeutic decision could be made was obtained in 146 of the 152 patients with lymphoproliferative disorders (96%). IGNB was equally effective in making the correct diagnosis of lymphoma at the time of original diagnosis than at relapse. The results did not depend on the biopsy site, lymph nodes size, or needle type. We recommend that IGNB may be performed as an initial procedure for the diagnosis of lymphomas either in the presence of peripheral or deep lymph nodes, as it avoids surgery.

Adolescent↗

PubMed2006

Liquid chromatography-electrospray mass spectrometry determination of ibogaine and noribogaine in human plasma and whole blood. Application to a poisoning involving Tabernanthe iboga root.

A liquid chromatography/electrospray ionization mass spectrometry (LC-ESI-MS) method was developed for the first time for the determination of ibogaine and noribogaine in human plasma and whole blood. The method involved solid phase extraction of the compounds and the internal standard (fluorescein) from the two matrices using OasisHLB columns. LC separation was performed on a Zorbax eclipse XD8 C8 column (5 microm) with a mobile phase of acetonitrile containing 0.02% (v/v) trimethylamine and 2mM ammonium formate buffer. MS data were acquired in single ion monitoring mode at m/z 311.2, 297.2 and 332.5 for ibogaine, noribogaine and fluorescein, respectively. The drug/internal standard peak area ratios were linked via a quadratic relationship to plasma (0.89-179 microg/l for ibogaine; 1-200 microg/l for noribogaine) and to whole blood concentrations (1.78-358 microg/kg for ibogaine; 2-400 microg/kg for noribogaine). Precision ranged from 4.5 to 13% and accuracy was 89-102%. Dilution of the samples had no influence on the performance of the method. Extraction recoveries were > or =94% in plasma and > or =57% in whole blood. The lower limits of quantitation were 0.89 microg/l for ibogaine and 1 microg/l for noribogaine in plasma, and 1.78 microg/kg for ibogaine and 2 microg/kg for noribogaine in whole blood. In frozen plasma samples, the two drugs were stable for at least 1 year. In blood, ibogaine and noribogaine were stable for 4h at 4 degrees C and 20 degrees C and 2 months at -20 degrees C. The method was successfully used for the analysis of a poisoning involving Tabernanthe iboga root.

Chromatography, Liquid↗

PubMed2006

Distribution of ibogaine and noribogaine in a man following a poisoning involving root bark of the Tabernanthe iboga shrub.

In the present paper, we report for the first time the tissue distribution of ibogaine and noribogaine, the main metabolite of ibogaine, in a 48-year-old Caucasian male, with a history of drug abuse, found dead at his home after a poisoning involving the ingestion of root bark from the shrub Tabernanthe iboga. Ibogaine and noribogaine were quantified in tissues and fluids using a fully validated liquid chromatography-electrospray mass spectrometry method. Apart from cardiac tissue, ibogaine and noribogaine were identified in all matrices investigated. The highest concentrations were found in spleen, liver, brain, and lung. The tissue/subclavian blood concentration ratios averaged 1.78, 3.75, 1.16, and 4.64 for ibogaine and 0.83, 2.43, 0.90, and 2.69 for noribogaine for spleen, liver, brain, and lung, respectively. Very low concentrations of the two drugs were found in the prostatic tissue. Both ibogaine and noribogaine are secreted in the bile and cross the blood-brain barrier. Four other compounds were detected in most of the studied matrices. One of them was identified as ibogamine. Unfortunately, we were not able to positively identify the other three compounds because of the unavailability of reference substances. Two of them could possibly be attributed to the following oxidation products: iboluteine and desmethoxyiboluteine. The third compound could be ibogaline.

Chromatography, Liquid↗

PubMed2005

Liquid chromatography-electrospray mass spectrometry determination of free and total concentrations of ropivacaine in human plasma.

A specific and sensitive liquid chromatography-electrospray ionization mass spectrometry (LC-ESI-MS) method was developed for the determination of free and total ropivacaine in human plasma. The work-up procedure involved a simple precipitation of plasma proteins with methanol. Etidocaine served as the internal standard. After microscale equilibrium-dialysis, measurement of free ropivacaine levels was performed after direct injection of the dialysate into the chromatograph. The system used a Zorbax eclipse XD8 C8 analytical column packed with 5 microm diameter particles as the stationary phase. The mobile phase consisted of a 15-min gradient (mobile phase A: 0.05% (v/v) trimethylamine in acetonitrile, mobile phase B: 2mM ammonium formate buffer (pH 3)). Mass spectrometric data were acquired in single ion monitoring mode at m/z 275 for ropivacaine and m/z 277 for etidocaine. The drug/internal standard peak area ratios (plasma) or peak areas (dialysate) were linked via a quadratic relationship to concentrations. Precision ranged from 1 to 7.6% accuracy was between 92.6 and 109%. The lower limits of quantitation were 1 microg/l in plasma and 2 microg/l in the dialysate. This method was found suitable for the analysis of plasma samples collected during a clinical trial performed in 30 infants undergoing epidural anaesthesia or continuous psoas compartment block.

Amides↗

PubMed2005

Distinct regulation of histone H3 methylation at lysines 27 and 9 by CpG methylation in Arabidopsis.

Transcriptional activity and structure of chromatin are correlated with patterns of covalent DNA and histone modification. Previous studies have revealed that high levels of histone H3 dimethylation at lysine 9 (H3K9me2), characteristic of transcriptionally silent heterochromatin in Arabidopsis, require hypermethylation of DNA at CpG sites. Here, we report that CpG hypermethylation characteristic of heterochromatin specifically prevented H3K27 trimethylation (H3K27me3). H3K27 mono- and dimethylation mark silent heterochromatin independently of DNA methylation. Upon loss of CpG methylation, there was target-specific enrichment of H3K27me3 in heterochromatin that correlated with transcriptional reactivation. Moreover, using the kyp mutant affected in H3K9me2, we showed that changes in H3K27me3 occurred independently of the levels of H3K9me2. Therefore, CpG methylation provides distinct and direct information for a specific subset of histone methylation marks. The observed independence of the regulation of H3K9 and H3K27 methylation by CpG methylation refines the recently proposed combinatorial histone code involving these two marks.

Arabidopsis↗

PubMed2004

RNA-directed DNA methylation.

Double-stranded RNAs (dsRNAs) and their 'diced' small RNA products can guide key developmental and defense mechanisms in eukaryotes. Some RNA-directed mechanisms act at a post-transcriptional level to degrade target messenger RNAs. However, dsRNA-derived species can also direct changes in the chromatin structure of DNA regions with which they share sequence identity. For example, plants use such RNA species to lay down cytosine methylation imprints on identical DNA sequences, providing a fundamental mark for the formation of transcriptionally silent heterochromatin. Thus, RNA can feed backwards to modulate the accessibility of information stored in the DNA of cognate genes. RNA triggers for DNA methylation can come from different sources, including invasive viral, transgene or transposon sequences, and in some cases are derived from single-stranded RNA precursors by RNA-dependent RNA polymerases. The mechanism by which RNA signals are translated into DNA methylation imprints is currently unknown, but two plant-specific types of cytosine methyltransferase have been implicated in this process. RNA can also direct heterochromatin formation in fission yeast and Drosophila, but in these organisms the process occurs in the absence of DNA methylation.

Animals↗

PubMed2003

Changes in 5S rDNA chromatin organization and transcription during heterochromatin establishment in Arabidopsis.

In the Arabidopsis accession Columbia, 5S rDNA is located in the pericentromeric heterochromatin of chromosomes 3, 4, and 5. Both a major and some minor 5S rRNA species are expressed from chromosomes 4 and 5, whereas the genes on chromosome 3 are not transcribed. Here, we show that 5S rDNA methylation is reduced in 2-day-old seedlings versus 4-day-old or older aerial plant tissues, and the minor 5S rRNA species are expressed most abundantly at this stage. Similarly, when 5S rDNA is demethylated by 5-azacytidine treatment or via the decrease in DNA methylation1 (ddm1) mutation, the expression of minor 5S rRNA species is increased. We also show that in leaf nuclei of mature wild-type plants, the transcribed fraction of 5S rDNA forms loops that emanate from chromocenters. These loops, which are enlarged in nuclei of mature ddm1 plants, are enriched for histone H3 acetylated at Lys-9 and methylated at Lys-4 compared with the heterochromatic chromocenters. Up to 4 days after germination, heterochromatin is not fully developed: the 5S rDNA resides in prechromocenters, does not form conspicuous loops, and shows the lowest transcription level. Our results indicate that the expression and chromatin organization of 5S rRNA genes change during heterochromatin establishment.

Arabidopsis↗

PubMed2003

Identification and characterization of transcription factor IIIA and ribosomal protein L5 from Arabidopsis thaliana.

Thus far, no transcription factor IIIA (TFIIIA) from higher plants has been cloned and characterized. We have cloned and characterized TFIIIA and ribosomal protein L5 from Arabidopsis thaliana. Primary sequence comparison revealed a high divergence of AtTFIIIA and a relatively high conservation of AtL5 when compared with other organisms. The AtTFIIIA cDNA encodes a protein with nine Cys(2)-His(2)-type zinc fingers, a 23 amino acid spacer between fingers 1 and 2, a 66 amino acid spacer between fingers 4 and 5, and a 50 amino acid non-finger C-terminal tail. Aside from the amino acids required for proper zinc finger folding, AtTFIIIA is highly divergent from other known TFIIIAs. AtTFIIIA can bind 5S rDNA, as well as 5S rRNA, and efficiently stimulates the transcription of an Arabidopsis 5S rRNA gene in vitro. AtL5 identity was confirmed by demonstrating that this protein binds to 5S rRNA but not to 5S rDNA. Protoplast transient expression assays with green fluorescent protein fusion proteins revealed that AtTFIIIA is absent from the cytoplasm and concentrated at several nuclear foci including the nucleolus. AtL5 protein accumulates in the nucleus, especially in the nucleolus, and is also present in the cytoplasm.

Amino Acid Sequence↗

PubMed2002

Methylation of a euchromatin-heterochromatin transition region in Arabidopsis thaliana chromosome 5 left arm.

Cytosine methylation was studied at the level of the euchromatin/heterochromatin transition genomic region of the Arabidopsis chromosome 5 left arm. It has been shown using a monoclonal antibody against 5-methylcytosines that the density of DNA methylation increases from the euchromatin towards the heterochromatin. YACs mapped along this region were characterized for their repeated sequences content. Some of them, corresponding to euchromatin, euchromatin/heterochromatin border and heterochromatin regions, were used as probes for a Southern blot analysis of methylation. This revealed that the degree of mCmCGG and GATmC methylation increases significantly from the euchromatin towards the heterochromatin. Moreover, an analysis of cytosine methylation levels (% of 5-methylcytosine) of different DNA fragments, inside the same genomic region, was performed using PCR and/or Southern blot approaches. There is a gradual increase of methylation along the genomic region analyzed: CpG methylation in the euchromatic fraction, CpG and CpNpG methylation at the euchromatin/heterochromatin transition and an additional asymmetrical methylation in the repeated-heterochromatic fraction. The most methylated repeated family at CpG, CpNpG and asymmetrical sites is the 5S ribosomal DNA, highly methylated even though it is transcribed.

5-Methylcytosine↗

PubMed2002

5S rRNA genes expression is not inhibited by DNA methylation in Arabidopsis.

Methylation has often been correlated with transcriptional inhibition of genes transcribed by polymerase II, but its role on polymerase III genes is less well understood. Using the genomic sequencing technique, we have analysed the methylation pattern of the different 5S-rDNA arrays of the Arabidopsis genome. Every cytosine position within the 5S sequence is highly methylated whatever the context - CpG, CpNpG or non-symmetrical. The methylation pattern of both transcribed and non-transcribed 5S units is similar, with no preferential methylated or unmethylated site. These results, taken together with 5-azacytidine treatments and in vitro transcription experiments using methylated 5S templates, demonstrate that 5S rRNA gene transcription is not inhibited by methylation. Non-transcribed 5S arrays are more subject to transition mutations resulting from deamination of 5-methylcytosines, leading to CpG depletions and an increasing A + T content. As there were no detectable differences in methylation, this implies more efficient repair and/or selection pressure in transcribed 5S-blocks.

Arabidopsis↗

PubMed2002

Analysis of the 5S RNA pool in Arabidopsis thaliana: RNAs are heterogeneous and only two of the genomic 5S loci produce mature 5S RNA.

One major 5S RNA, 120 bases long, was revealed by an analysis of mature 5S RNA from tissues, developmental stages, and polysomes in Arabidopsis thaliana. Minor 5S RNA were also found, varying from the major one by one or two base substitutions; 5S rDNA units from each 5S array of the Arabidopsis genome were isolated by PCR using CIC yeast artificial chromosomes (YACs) mapped on the different loci. By using a comparison of the 5S DNA and RNA sequences, we could show that both major and minor 5S transcripts come from only two of the genomic 5S loci: chromosome 4 and chromosome 5 major block. Other 5S loci are either not transcribed or produce rapidly degraded 5S transcripts. Analysis of the 5'- and 3'-DNA flanking sequence has permitted the definition of specific signatures for each 5S rDNA array.

Arabidopsis↗