Search PubMed⌕ Search

Biomedical subjects

Reiner A Veitia

Publications and source records attributed to Reiner A Veitia.

At least 19 recordsLinked to original sources
PubMed2006

Reverse transcriptase template switching and false alternative transcripts.

Reverse transcriptase (RT) can switch from one template to another in a homology-dependent manner. In the study of eukaryotic transcripts, this propensity of RT can produce an artificially deleted cDNA, which can be wrongly interpreted as an alternative transcript. Here, we have investigated the presence of such template-switching artifacts in cDNA databases, by scanning a collection of human splice sites (Information for the Coordinates of Exons, ICE database). We have confirmed several cases at the experimental level. Artifacts represent a significant portion of apparently spliced sequences using noncanonical splice signals but are rare in the context of the whole database. However, care should be taken in the annotation of alternative transcripts, especially when the RT used is poorly thermostable and when the putative intron is flanked by direct repeats, which are the substrate for template switching.

Alternative Splicing↗
PubMed2006

The robustness of the transcriptional response to alterations in morphogenetic gradients.

Sharp sigmoidal transitions of transcription in response to morphogenetic gradients are often involved in the generation of boundaries during development. Here we explore two simple models of transcription that generate sigmoidal outputs. Specifically, we analyse the case of a promoter responding to a single type of activator. We then consider a model where an activator and an inhibitor, distributed as two gradients with opposite slopes, act competitively on the same promoter. This system can produce a sharper response than that obtained with a promoter with the same number of binding sites responding to a similar gradient of activator alone. We also explore how these systems buffer the effect of variations in the dosage of the morphogens. Our results highlight how non-linearities can be a source of robustness and the crucial role of the inhibitor in the generation of a sharp and robust response.

Animals↗
PubMed2006

Partial defects in transcriptional activity of two novel DAX-1 mutations in childhood-onset adrenal hypoplasia congenita.

OBJECTIVE: Mutations in DAX-1, an X-linked gene encoding an orphan nuclear receptor, have been associated with adrenal hypoplasia congenita and hypogonadotropic hypogonadism. Here we describe two novel DAX-1 mutations, Y214X and I361T, associated with childhood-onset primary adrenal failure. We aimed at analysing their effects on protein localization, transcriptional activity and propose a structural-function relationship. DESIGN: We have directly sequenced the DAX-1 gene from PCR-amplified DNA. The effect of the mutations on protein localization was assessed by immunocytochemistry in transfected cells. The impact of mutations on transcriptional activity was determined by transfection using a StAR promoter-luciferase reporter system. RESULTS: The mutation Y214X produces a protein lacking the C-terminal half of DAX-1. The other one, I361T, affects a highly conserved amino acid within the putative ligand-binding domain. The mutant Y214X displayed a wild-type subcellular localization while I361T was partially retained in the cytoplasm. Both mutants retained subtantial transcriptional repressive activity, compared to mutants producing early onset adrenal failure. Interestingly, I361T displayed similar in vitro transcriptional repressive activity to the mutant I439S previously described in a case of late-onset AHC. This shows that molecular alterations of DAX-1 leading to similar in vitro activities may result in very different ages of onset of adrenal failure, which suggests that additional genetic and epigenetic factors are important in determining the clinical course of AHC. CONCLUSIONS: Our results help the understanding of structure-function relationships in the DAX-1 molecule, suggesting that the N-terminal domain is relatively autonomous and add credence to presumed molecular interactions within ligand binding domain of the protein.

Adrenal Glands↗
PubMed2006

Mutations and sequence variants in GDF9 and BMP15 in patients with premature ovarian failure.

BACKGROUND AND OBJECTIVE: Mutations in bone morphogenic protein 15 (BMP15) and growth/differentiation factor 9 (GDF9) lead to altered fertility in animal models. In the human, a heterozygous point mutation of BMP15 has been associated with premature ovarian failure (POF). SUBJECT AND METHODS: We have directly sequenced both genes in a cohort of 203 POF patients presenting with primary or secondary amenorrhea and high FSH levels and in a control population including 54 women with regular menstrual cycles who had at least one child. RESULTS: We have identified several heterozygous variants. One alteration in GDF9 (S186Y) and one in BMP15 (L148P) may have pathogenic effects as both positions are conserved in vertebrate species, ranging from the chicken to mammals. These variants were absent in the control samples. We also found synonymous and neutral substitutions. CONCLUSIONS: We propose that although mutations in BMP15 and GDF9 are not a major cause of ovarian insufficiency, they may be involved in POF.

Adult↗
PubMed2005

Deletions in the polyAlanine-containing transcription factor FOXL2 lead to intranuclear aggregation.

Mutations of FOXL2, a gene encoding a forkhead transcription factor, have been shown to cause the blepharophimosis-ptosis-epicanthus inversus syndrome. This genetic disorder is characterized by eyelid and craniofacial abnormalities associated or not with premature ovarian failure. We have previously shown that mutant FOXL2 with an expanded polyAlanine (polyAla) tract forms large aggregates both in the nucleus and in the cytoplasm of transfected cells, whereas the wild-type protein localizes in the nucleus in a rather diffuse manner. Premature stop codons in FOXL2 have been considered so far as null alleles. However, we demonstrate here that such nonsense mutations may lead to the production of N-terminally truncated proteins by re-initiation of translation downstream of the stop codon. Surprisingly, the truncated proteins strongly aggregate in the nucleus, partially localize in the cytoplasm and retain a fraction of the wild-type protein. We also show that a complete deletion of the polyAla tract of FOXL2 induces a significant intranuclear aggregation. Our results enlarge the spectrum of mutations inducing FOXL2 aggregation.

Amino Acid Sequence↗
PubMed2005

Coding repeats and evolutionary "agility".

The rapid generation of new shapes observed in the living world is the result of genetic variation, especially in "morphological" developmental genes. Many of these genes contain coding tandem repeats. Fondon and Garner have shown that expansions and contractions of these repeats are associated with the great diversity of morphologies observed in the domestic dog, Canis familiaris. In particular, they found that the repeat variations in two genes were significantly associated with changes in limb and skull morphology. These results open the possibility that such a mechanism contributes to the diversity of life.

Animals↗
PubMed2005

Stochasticity or the fatal 'imperfection' of cloning.

The concept of clone is analysed with the aim of exploring the limits to which a phenotype can be said to be determined geneticaly. First of all, mutations that result from the replication, topological manipulation or lesion of DNA introduce a source of heritable variation in an otherwise identical genetic background. But more important, stochastic effects in many biological processes may superimpose a phenotypic variation which is not encoded in the genome. The source of stochasticity ranges from the random selection of alleles or whole chromosomes to be expressed in small cell populations, to fluctuations in processes such as gene expression, due to limiting amounts of the players involved. The picture emerging is that the term clone is a statistical over-simplification representing a series of individuals having essentially the same genome but capable of exhibiting wide phenotypic variation. Finally, to what extent fluctuations in biological processes, usually thought of as noise, are in fact signal is also discussed.

Animals↗
PubMed2005

Dosage balance in gene regulation: biological implications.

Classical studies in genetics involving aneuploidy and ploidy comparisons and sex-determination mechanisms indicated a balance phenomenon such that changes of individual chromosomal dosage altered the phenotype more dramatically than changes in ploidy. Recent evidence suggests that a major contributor to this balance is the behavior of molecular complexes that function in various regulatory processes affecting gene expression. In this article, we discuss the potential contribution of regulatory balance to the control of quantitative traits, hybrid vigor, genome evolution and post-zygotic speciation mechanisms.

Aneuploidy↗
PubMed2005

Sense and antisense Foxl2 transcripts in mouse.

FOXL2 is a forkhead transcription factor involved in eyelid development and in the development and adult function of the ovary in mammals. In mouse, we have previously suggested the existence of two mRNA isoforms of Foxl2 that result from an alternative polyadenylation. In this study, we characterize in depth the structure and expression of these two variants. We also describe an antisense transcript that overlaps the whole Foxl2 transcription unit. This antisense transcript, called Foxl2OS (for opposite strand), yields several isoforms resulting from alternative splicing. No significant coding region was found in the Foxl2OS sequence. Foxl2OS displays a pattern of expression very similar to that of Foxl2 in the gonads during development and at the adult age. RNA FISH experiments show that both transcripts are expressed in the same cells at the same time. We suggest that Foxl2OS is a noncoding antisense RNA that may be involved in the regulation of Foxl2. All in all our results provide new insights about the organization of the murine Foxl2 locus. This might help us understand its regulation and function.

Alternative Splicing↗
PubMed2004

Amino acids runs and genomic compositional biases in vertebrates.

A compositional analysis of a sample of 50 zebrafish proteins containing at least one alanine run and of their open reading frames (ORFs) has been performed. The sample of poly(Ala) proteins showed a tendency to have runs of other amino acids (His/H, Gln/Q, Ser/S, Pro/P). Their ORFs and the first and second codon positions had higher GC contents than a reference gene set. The "universal" correlation between the GC content of the first+second and third codon positions (GC1+2 vs GC3) does not hold, but I provide an explanation in terms of genomic heterogeneity. Significant correlation between AHQS content and GC3 was obtained, reflecting codon bias favoring G/C at the third codon position of these amino acids. A correspondence analysis (COA) of relative synonymous codon usage showed that the poly(Ala) proteins have a biased distribution according to the second axis of the COA, which correlates with gene expression in zebrafish. A comparison with human is undertaken.

Amino Acids↗
PubMed2004

A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs.

We have previously shown that polyAla (A) tract-containing proteins frequently present runs of glycine (G), proline (P), and histidine (H) and that, in their ORFs, GC content at all codon positions is higher than that in the rest of the genome. In this study, we present new analyses of these human proteins/ORFs. We detected striking differences in codon usage for A, G, and P in and out of runs. After dividing the ORFs, we found that 5' halves were richer in runs than 3' halves. Afterward, when removing the runs, we observed that the run-rich halves (grouped irrespectively of their 5' or 3' position) had a marked statistical tendency to have more homo- and hetero-dicodons for A, G, P, and H than the run-poor halves. This suggests that, in addition to the necessary GC-rich genomic background, a specific codon organization is probably required to generate these coding repeats. Homo-dicodons may indeed provide primers for run formation through polymerase slippage. The compositional analysis of human HOX genes, the most polyAla-rich family, and their comparison with their zebrafish homologs, support these hypotheses and suggest possible effects of genomic environment on ORF evolution and organismal diversification.

Amino Acid Sequence↗
PubMed2004

An evolutionary and functional analysis of FoxL2 in rainbow trout gonad differentiation.

FOXL2 is a forkhead transcription factor involved in ovarian development and function. Here, we have studied the evolution and pattern of expression of the FOXL2 gene and its paralogs in fish. We found well conserved FoxL2 sequences (FoxL2a) and divergent genes, whose forkhead domains belonged to the class L2 and were shown to be paralogs of the FoxL2a sequences (named FoxL2b). In the rainbow trout, FoxL2a and FoxL2b were specifically expressed in the ovary, but displayed different temporal patterns of expression. FoxL2a expression correlated with the level of aromatase, the key enzyme in estrogen production, and an estrogen treatment used to feminize genetically male individuals elicited the up-regulation of both paralogs. Conversely, androgens or an aromatase inhibitor down-regulated FoxL2a and FoxL2b in females. We speculate that there is a direct link between estrogens and FoxL2 expression in fish, at least during the period where the identity of the gonad is sensitive to hormonal treatments.

Animals↗
PubMed2003

Nonlinear effects in macromolecular assembly and dosage sensitivity.

Haploinsufficiency refers to dominant abnormal phenotypes resulting from the absence of substantial activity from one allele at a normally diploid locus. Haploinsufficiency may also result from an altered stoichiometry in a macromolecular complex. Higher-than-diploid levels of a gene product can also induce abnormalities that may even resemble the haploinsufficient phenotype. Here, I explore possible non-linearities in the assembly of multimeric molecules from the perspective of dose effects. I propose that for any oligomer assembly reaction, there may be a set of conditions (initial subunit concentrations and equilibrium constants) such that changing the input concentration of one component (0.5 x or 1.5x) will lead to a minimum and non-proportional change of the final oligomer concentration. This buffer effect is a general property of multimeric systems in equilibrium and can be, in principle, exploited by selection to diminish dosage sensitivity. Other effects involving cooperativity or sequential assembly may also play a role in palliating the effect of changes in input amounts of monomers.

Enzymes↗
PubMed2003

A sigmoidal transcriptional response: cooperativity, synergy and dosage effects.

A sigmoidal transcriptional response (STR) is thought to act as a molecular switch to control gene expression. This nonlinear behaviour arises as a result of the cooperative recognition of a promoter/enhancer by transcription factors (TFs) and/or their synergy to attract the basal transcriptional machinery (BTM). Although this cooperation between TFs is additive in terms of energy, it leads to an exponential increase in affinity between the BTM and the pre-initiation complexes. This exponential increase in the strength of interactions is the principle that governs synergistic systems. Here, I propose a minimalist quasi-equilibrium model to explore qualitatively the STR taking into account cooperative recognition of the promoter/enhancer and synergy. Although the focus is on the effect of activators, a similar treatment can be applied to inhibitors. One of the main insights obtained from the model is that generation of a sigmoidal threshold is possible even in the absence of cooperative DNA binding provided the TFs synergistically interact with the BTM. On the contrary, when there is cooperative binding, the impact of synergy diminishes. It will also be shown that a sigmoidal response to a morphogenetic gradient can be used to generate a nested gradient of another morphogen. Previously, I had proposed that halving the amounts of TFs involved in sigmoidal transcriptional switches could account for the abnormal dominant phenotypes associated with some of these genes. This phenomenon, called haploinsufficiency (HI), has been recognised as the basis of many human diseases. Although a formal proof linking HI and a sigmoidal response is lacking, it is tempting to explore the model from the perspective of dosage effects.

Animals↗