Papers by Frederique Pitel
HAL (Le Centre pour la Communication Scientifique Directe), 1999
HAL (Le Centre pour la Communication Scientifique Directe), 1999
HAL (Le Centre pour la Communication Scientifique Directe), 2003
HAL (Le Centre pour la Communication Scientifique Directe), Jul 21, 1996
HAL (Le Centre pour la Communication Scientifique Directe), Aug 20, 2000
HAL (Le Centre pour la Communication Scientifique Directe), May 10, 2006
Genetics Selection Evolution, Apr 15, 2019
Background: In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated w... more Background: In quail, two feather colour phenotypes i.e. fawn-2/beige and yellow are associated with the ASIP locus. The aim of our study was to characterize the structural modifications within this locus that explain the yellow mutation (large deletion) and the fawn-2/beige mutation (assumed to be caused by a different structural modification). Results: For the yellow phenotype, we identified a complex mutation that involves a 141,162-bp long deletion. For the fawn-2/beige phenotype, we identified a 71-kb tandem duplication that comprises one unchanged copy of ASIP and one copy present in the ITCH-ASIP fusion gene, which leads to a transcript coding for a normal ASIP protein. Although this agrees with previous reports that reported an increased level of ASIP transcripts in the skin of mutant animals, we show that in the skin from fawn-2/beige embryos, this level is higher than expected with a simple duplication of the ASIP gene. Thus, we hypothesize that the 5′ region of the ITCH-ASIP fusion gene leads to a higher transcription level than the 5′ region of the ASIP gene. Conclusions: We were able to conclude that the fawn-2 and beige phenotypes are caused by the same allele at the ASIP locus. Both of the associated mutations fawn-2/beige and yellow lead to the formation of a fusion gene, which encodes a transcript for the ASIP protein. In both cases, transcription of ASIP depends on the promoter of a different gene, which includes alternative up-regulating sequences. However, we cannot exclude the possibility that the loss of the 5′ region of the ASIP gene itself has additional impacts, especially for the fawn-2/beige mutation. In addition, in several other species including mammals, the existence of other dominant gain-of-function structural modifications that are localized upstream of the ASIP coding sequences has been reported, which supports our hypothesis that repressors in the 5′ region of ASIP are absent in the fawn-2/beige mutant.
HAL (Le Centre pour la Communication Scientifique Directe), Mar 27, 2001
Frontiers in Genetics
Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction u... more Most single-nucleotide polymorphisms (SNPs) are located in non-coding regions, but the fraction usually studied is harbored in protein-coding regions because potential impacts on proteins are relatively easy to predict by popular tools such as the Variant Effect Predictor. These tools annotate variants independently without considering the potential effect of grouped or haplotypic variations, often called “multi-nucleotide variants” (MNVs). Here, we used a large RNA-seq dataset to survey MNVs, comprising 382 chicken samples originating from 11 populations analyzed in the companion paper in which 9.5M SNPs— including 3.3M SNPs with reliable genotypes—were detected. We focused our study on in-codon MNVs and evaluate their potential mis-annotation. Using GATK HaplotypeCaller read-based phasing results, we identified 2,965 MNVs observed in at least five individuals located in 1,792 genes. We found 41.1% of them showing a novel impact when compared to the effect of their constituent SNPs...
HAL (Le Centre pour la Communication Scientifique Directe), Jan 14, 2006
HAL (Le Centre pour la Communication Scientifique Directe), 2001
Adaptation to heat exposure is required to maintain animal welfare and productivity under high am... more Adaptation to heat exposure is required to maintain animal welfare and productivity under high ambient temperature (AT) conditions. In this study we investigate the effects of chronic heat exposure (5 weeks at a constant temperature of 32°C) on the liver and whole blood transcriptome of brown egg layers from 2 divergent lines selected for low (R-) and high (R+) residual feed intake. The R+ and R- hens were equally distributed among 2 temperature-controlled chambers and reared under thermo-neutrality (22°C). At 28 wk of age the AT of one chamber was increased to 32°C until 33 wk of age, when 32 animals (8 per line and treatment) were slaughtered. Total RNA was obtained from the liver and blood and was sequenced using the Illumina HiSEqn 3000, yielding an average per sample of 90 million paired-end reads. The reads were mapped to the Gallus gallus-5 reference genome by STAR software and counted by RSEM software using the Ensembl V87 GTF annotation. Comparisons between the two AT group...
Scientific Reports, 2021
An amendment to this paper has been published and can be accessed via a link at the top of the pa... more An amendment to this paper has been published and can be accessed via a link at the top of the paper.
BMC Biology, 2020
BackgroundThe Japanese quail (Coturnix japonica) is a popular domestic poultry species and an inc... more BackgroundThe Japanese quail (Coturnix japonica) is a popular domestic poultry species and an increasingly significant model species in avian developmental, behavioural and disease research.ResultsWe have produced a high-quality quail genome sequence, spanning 0.93 Gb assigned to 33 chromosomes. In terms of contiguity, assembly statistics, gene content and chromosomal organisation, the quail genome shows high similarity to the chicken genome. We demonstrate the utility of this genome through three diverse applications. First, we identify selection signatures and candidate genes associated with social behaviour in the quail genome, an important agricultural and domestication trait. Second, we investigate the effects and interaction of photoperiod and temperature on the transcriptome of the quail medial basal hypothalamus, revealing key mechanisms of photoperiodism. Finally, we investigate the response of quail to H5N1 influenza infection. In quail lung, many critical immune genes and...
HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific re... more HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.
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Papers by Frederique Pitel