C. Charlier - Academia.edu (original) (raw)

Papers by C. Charlier

Research paper thumbnail of Breakpoint mapping positions the callipyge gene within a 450-kilobase chromosome segment containing the DLK1 and GTL2 genes

Research paper thumbnail of Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing

Genome Research, 2010

The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygou... more The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans effect, we used high-throughput sequencing to exhaustively catalog miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1–GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis (∼3.2-fold increase) as well as in trans (∼1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1–GTL2 domain account for ∼20% of miRNAs in skeletal muscle. We show that the CLPG genotype affects the levels of A-to-I ...

Research paper thumbnail of Polymorphic Polymorphic MicroRNA-Target Interactions: A Novel Source of Phenotypic Variation

Cold Spring Harbor Symposia on Quantitative Biology, 2006

Research paper thumbnail of Toward Molecular Understanding of Polar Overdominance at the Ovine Callipyge Locus

Cold Spring Harbor Symposia on Quantitative Biology, 2004

Research paper thumbnail of Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy

Animal Genetics, 2012

SummaryWe used the data from a recently performed genome‐wide association study using the Illumin... more SummaryWe used the data from a recently performed genome‐wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with recurrent laryngeal neuropathy (RLN), an important equine upper airway disease compromising performance. A total of 2797 CNVs were detected for 477 horses, covering 229 kb and seven SNPs on average. Overlapping CNVs were merged to define 478 CNV regions (CNVRs). CNVRs, particularly deletions, were shown to be significantly depleted in genes. Fifty‐two of the 67 common CNVRs (frequency ≥ 1%) were validated by association mapping, Mendelian inheritance, and/or Mendelian inconsistencies. None of the 67 common CNVRs were significantly associated with RLN when accounting for multiple testing. However, a duplication on chromosome 10 was detected in 10 cases (representing three breeds) and two unphenotyped parents but in none of the controls. The duplication was embedded in an 8‐Mb haplo...

Research paper thumbnail of Development of a method for haplotype-based association analysis of binary traits in structured populations

Research paper thumbnail of Microsatellite mapping of the bovine roan locus: A major determinant of White Heifer Disease

Mammalian Genome, 1996

In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single ... more In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single autosomal locus, the roan locus, characterized by a pair of codominant alleles: r + (black) and R (white). Heterozygous r + R animals have intermingled black and white hairs, yielding the ''blue'' phenotype typical of the breed. Major interest for the roan locus stems from its pleiotropic effect on fertility, owing to the critical role of the R allele in the determinism of White Heifer Disease. We describe the linkage mapping of the roan locus to bovine Chromosome (Chr) 5, in the interval between microsatellite markers BPI and AGLA293, with an associated lodscore of 11.2. Moreover, we map a candidate gene, the Steel locus coding for the mast cell growth factor, to bovine Chr 5.

Research paper thumbnail of NGS-based Reverse Genetic Screen Reveals Loss-of-function Variants Compromising Fertility in Cattle

We herein report the results of a large-scale reverse genetic screen, based on next generation se... more We herein report the results of a large-scale reverse genetic screen, based on next generation sequencing (NGS) of the exome or whole genome of more than 500 animals, to identify highly deleterious mutations that cause embryonic lethality in domestic cattle. We first demonstrate that -as in human -domestic cattle carry of the order of 100 loss-of-function (LoF) variants per genome. We then present evidence for significant depletion in homozygosity for at least tens of candidate deleterious variants in Belgian Blue Cattle, strongly suggesting that these act as embryonic lethal (EL) or at least juvenile lethal (JL) mutations. We finally formally demonstrate the embryonic/juvenile lethality of a handful of common LoF variants compromising fertility in domestic cattle of Belgium and New Zealand.

Research paper thumbnail of Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

Nucleic Acids Research, 2009

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) tha... more The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate 'Patrocles DSPs', including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.

Research paper thumbnail of Towards interbreed IBD fine mapping of the mh locus: Double-muscling in the Asturiana de los Valles breed involves the same locus as in the Belgian Blue cattle breed

Mammalian Genome, 1997

The Spanish ''Asturiana'' cattle breed is characterized by the segregation of a genetically deter... more The Spanish ''Asturiana'' cattle breed is characterized by the segregation of a genetically determined muscular hypertrophy referred to as double-muscling or ''culones''. We demonstrate by linkage analysis that this muscular hypertrophy involves the mh locus previously shown to cause double-muscling in the Belgian Blue cattle breed, pointing towards locus homogeneity of this trait across both breeds. Moreover, using a twopoint and multipoint maximum likelihood approach, we show that flanking microsatellite markers are in linkage disequilibrium with the mh locus in both breeds albeit with different alleles. Finally, we discuss how allelic homogeneity across breeds might be exploited to achieve efficient genetic fine-mapping of the mh locus. BBCB: The pedigrees used for linkage analysis with the mh locus in BBCB are as described (Charlier et al. 1995

Research paper thumbnail of Comparative Sequence Analysis of the Imprinted Dlk1–Gtl2 Locus in Three Mammalian Species Reveals Highly Conserved Genomic Elements and Refines Comparison with the Igf2–H19 Region

Genome Research, 2001

The Dlk1–Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potent... more The Dlk1–Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common features involved in imprinting control. We have sequenced this conserved region in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and identification of highly conserved sequence elements, some of which we have shown previously to be differentially methylated in the mouse. Additionally, this analysis facilitated identification of a CpG-rich tandem repeat array located ∼13–15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extendedDlk1 transcripts. Because Dlk1 and Gtl2share many of the imprinting properties of the well-characterizedIgf2–H19 domain, it has been proposed that t...

Research paper thumbnail of Human–Ovine Comparative Sequencing of a 250-kb Imprinted Domain Encompassing the Callipyge (clpg) Locus and Identification of Six Imprinted Transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8

Genome Research, 2001

Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and repres... more Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of theMULGE5-OY3 marker interval known to contain the clpglocus, were completely sequenced. The resulting genomic sequence was aligned with its human ortholog and extensively annotated. Six transcripts, four of which were novel, were predicted to originate from within the analyzed region and their existence confirmed experimentally: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. RT-PCR experiments performed on a range of tissues sampled from an 8-wk-old animal demonstrated the preferential expression of all six transcripts in skeletal muscle, which suggests that they are under control of common regulatory elements. The six transcripts were also shown to be subject to parental imprinting: DLK1, DAT, andPEG11 were shown to be paternally expressed and GTL2,antiPEG11, and MEG8 to be maternally expressed.[The sequence data described in this paper have been submitted to the GenBank d...

Research paper thumbnail of Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification

Bioinformatics, 2012

Motivation: In many situations, genome-wide association studies are performed in populations pres... more Motivation: In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. Results: The method was shown to properly account for stratification under various simulated scenari presenting population and/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM.

Research paper thumbnail of Construction and characterization of an ovine BAC contig spanning the callipyge locus

Animal Genetics, 2000

We describe the construction of an ovine BAC contig spanning a 4•6 centimorgan (cM) chromosome se... more We describe the construction of an ovine BAC contig spanning a 4•6 centimorgan (cM) chromosome segment known to contain the callipyge (CLPG) locus. The contig comprises 21 ovine BAC clones jointly covering approximately 900 kilobases (Kb). Two gaps in the BAC contig, spanning 10 and 7•5 Kb, respectively, were bridged by long range PCR. The corresponding chromosome region was shown to be characterized by an unusually low Kb to cM ratio (164 Kb/cM) and a high density of NotI sites (1:126 Kb) possibly reflecting a high gene density in the corresponding chromosome region. Equivalent amplification of 64 sequence tagged sites spanning the corresponding region from homozygous + / + and CLPG/CLPG individuals disproves the hypothesis of a major deletion causing the CLPG mutation.

Research paper thumbnail of Identity-by-descent mapping of recessive traits in livestock: application to map the bovine syndactyly locus to chromosome 15

Genome Research, 1996

Twelve animals affected with syndactyly or mulefoot were sampled in the Dutch black-and-white cat... more Twelve animals affected with syndactyly or mulefoot were sampled in the Dutch black-and-white cattle population. Analysis of the pedigree data reveal that all of these individuals traced back to a single acknowledged carrier founder individual. Between seven and nine generations separated the founder from its 12 affected descendents. The 12 affected offspring were genotyped for a battery of 213 microsatellites spanning the 29 bovine autosomes. The resulting genotypes were analyzed using a maximum likelihood approach searching for shared homozygous haplotypes among affected individuals. Three candidate regions for the syndactyly locus emerged from this initial screening. syndactyly was shown to map to one of these candidate regions on chromosome 15 by genotyping 29 additional individuals linking founder and affected offspring and performing a conventional linkage analysis with the LINKAGE programs. This study illustrates the potential of identity-by-descent mapping in livestock popul...

Research paper thumbnail of The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis

Proceedings of the National Academy of Sciences, 2006

The callipyge mutation (CLPG) is an A to G transition that affects a muscle-specific long-range c... more The callipyge mutation (CLPG) is an A to G transition that affects a muscle-specific long-range control element located in the middle of the 90-kb DLK1-GTL2 intergenic (IG) region. It causes ectopic expression of a 327-kb cluster of imprinted genes in skeletal muscle, resulting in the callipyge muscular hypertrophy and its non-Mendelian inheritance pattern known as polar overdominance. We herein demonstrate that the CLPG mutation alters the muscular epigenotype of the DLK1-GTL2 IG region in cis, including hypomethylation, acquisition of novel DNase-I hypersentivite sites, and, most strikingly, strongly enhanced bidirectional, longrange IG transcription. The callipyge phenotype thus emerges as a unique model to study the functional significance of IG transcription, which recently has proven to be a widespread, yet elusive, feature of the mammalian genome.

Research paper thumbnail of Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

Nucleic Acids Research, 2010

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) tha... more The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate 'Patrocles DSPs', including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.

Research paper thumbnail of The mh gene causing double-muscling in cattle maps to bovine Chromosome 2

Mammalian Genome, 1995

While the hereditary nature of the "double-muscling" phenotype (a generalized muscular hypertroph... more While the hereditary nature of the "double-muscling" phenotype (a generalized muscular hypertrophy documented in several cattle breeds) is well established, its precise segregation mode has remained controversial. Both monogenic models (autosomal dominant or recessive) and oligogenic models have been proposed. Using a panel of 213 bovine microsatellite markers, and an experimental pedigree obtained by backcrossing "doublemuscled (Belgian Blue) x conventional (Friesian)" F 1 darns to double-muscled sire, we have mapped a locus on bovine Chromosome (Chr) 2 that accounts for all the phenotypic variance in the backcross generation. This locus, referred to as mh (muscular hypertrophy), has been positioned with respect to a map composed of seven Chr 2-specific microsatellites, at 2 cM from the closest marker. This result confirms the validity in the Belgian Blue population of the monogenic model involving an autosomal mh locus, characterized by a wild-type "+" and a recessive "mh" allele, causing the double-muscling phenotype in the homozygous condition. The linkage relationship between the mh locus and the Chr 2 markers was confirmed in three informative pedigrees collected from the general Belgian Blue Cattle population, reinforcing the notion Of genetic homogeneity of the double-muscling trait in this breed. This work paves the way towards marker-assisted selection for or against the double-muscling trait, and towards positional cloning of the corresponding gene.

Research paper thumbnail of Polymorphic Polymorphic MicroRNA-Target Interactions: A Novel Source of Phenotypic Variation

Cold Spring Harbor Symposia on Quantitative Biology, 2006

Research paper thumbnail of Breakpoint mapping positions the callipyge gene within a 450-kilobase chromosome segment containing the DLK1 and GTL2 genes

Research paper thumbnail of Assessing the effect of the CLPG mutation on the microRNA catalog of skeletal muscle using high-throughput sequencing

Genome Research, 2010

The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygou... more The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans effect, we used high-throughput sequencing to exhaustively catalog miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1–GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis (∼3.2-fold increase) as well as in trans (∼1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1–GTL2 domain account for ∼20% of miRNAs in skeletal muscle. We show that the CLPG genotype affects the levels of A-to-I ...

Research paper thumbnail of Polymorphic Polymorphic MicroRNA-Target Interactions: A Novel Source of Phenotypic Variation

Cold Spring Harbor Symposia on Quantitative Biology, 2006

Research paper thumbnail of Toward Molecular Understanding of Polar Overdominance at the Ovine Callipyge Locus

Cold Spring Harbor Symposia on Quantitative Biology, 2004

Research paper thumbnail of Detection of copy number variants in the horse genome and examination of their association with recurrent laryngeal neuropathy

Animal Genetics, 2012

SummaryWe used the data from a recently performed genome‐wide association study using the Illumin... more SummaryWe used the data from a recently performed genome‐wide association study using the Illumina Equine SNP50 beadchip for the detection of copy number variants (CNVs) and examined their association with recurrent laryngeal neuropathy (RLN), an important equine upper airway disease compromising performance. A total of 2797 CNVs were detected for 477 horses, covering 229 kb and seven SNPs on average. Overlapping CNVs were merged to define 478 CNV regions (CNVRs). CNVRs, particularly deletions, were shown to be significantly depleted in genes. Fifty‐two of the 67 common CNVRs (frequency ≥ 1%) were validated by association mapping, Mendelian inheritance, and/or Mendelian inconsistencies. None of the 67 common CNVRs were significantly associated with RLN when accounting for multiple testing. However, a duplication on chromosome 10 was detected in 10 cases (representing three breeds) and two unphenotyped parents but in none of the controls. The duplication was embedded in an 8‐Mb haplo...

Research paper thumbnail of Development of a method for haplotype-based association analysis of binary traits in structured populations

Research paper thumbnail of Microsatellite mapping of the bovine roan locus: A major determinant of White Heifer Disease

Mammalian Genome, 1996

In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single ... more In the Belgian Blue Cattle breed, coat color variation is mainly under the influence of a single autosomal locus, the roan locus, characterized by a pair of codominant alleles: r + (black) and R (white). Heterozygous r + R animals have intermingled black and white hairs, yielding the ''blue'' phenotype typical of the breed. Major interest for the roan locus stems from its pleiotropic effect on fertility, owing to the critical role of the R allele in the determinism of White Heifer Disease. We describe the linkage mapping of the roan locus to bovine Chromosome (Chr) 5, in the interval between microsatellite markers BPI and AGLA293, with an associated lodscore of 11.2. Moreover, we map a candidate gene, the Steel locus coding for the mast cell growth factor, to bovine Chr 5.

Research paper thumbnail of NGS-based Reverse Genetic Screen Reveals Loss-of-function Variants Compromising Fertility in Cattle

We herein report the results of a large-scale reverse genetic screen, based on next generation se... more We herein report the results of a large-scale reverse genetic screen, based on next generation sequencing (NGS) of the exome or whole genome of more than 500 animals, to identify highly deleterious mutations that cause embryonic lethality in domestic cattle. We first demonstrate that -as in human -domestic cattle carry of the order of 100 loss-of-function (LoF) variants per genome. We then present evidence for significant depletion in homozygosity for at least tens of candidate deleterious variants in Belgian Blue Cattle, strongly suggesting that these act as embryonic lethal (EL) or at least juvenile lethal (JL) mutations. We finally formally demonstrate the embryonic/juvenile lethality of a handful of common LoF variants compromising fertility in domestic cattle of Belgium and New Zealand.

Research paper thumbnail of Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

Nucleic Acids Research, 2009

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) tha... more The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate 'Patrocles DSPs', including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.

Research paper thumbnail of Towards interbreed IBD fine mapping of the mh locus: Double-muscling in the Asturiana de los Valles breed involves the same locus as in the Belgian Blue cattle breed

Mammalian Genome, 1997

The Spanish ''Asturiana'' cattle breed is characterized by the segregation of a genetically deter... more The Spanish ''Asturiana'' cattle breed is characterized by the segregation of a genetically determined muscular hypertrophy referred to as double-muscling or ''culones''. We demonstrate by linkage analysis that this muscular hypertrophy involves the mh locus previously shown to cause double-muscling in the Belgian Blue cattle breed, pointing towards locus homogeneity of this trait across both breeds. Moreover, using a twopoint and multipoint maximum likelihood approach, we show that flanking microsatellite markers are in linkage disequilibrium with the mh locus in both breeds albeit with different alleles. Finally, we discuss how allelic homogeneity across breeds might be exploited to achieve efficient genetic fine-mapping of the mh locus. BBCB: The pedigrees used for linkage analysis with the mh locus in BBCB are as described (Charlier et al. 1995

Research paper thumbnail of Comparative Sequence Analysis of the Imprinted Dlk1–Gtl2 Locus in Three Mammalian Species Reveals Highly Conserved Genomic Elements and Refines Comparison with the Igf2–H19 Region

Genome Research, 2001

The Dlk1–Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potent... more The Dlk1–Gtl2 domain on mouse chromosome 12 contains reciprocally imprinted genes with the potential to contribute to our understanding of common features involved in imprinting control. We have sequenced this conserved region in the mouse and sheep and included the human sequence in a three species comparison. This analysis resulted in a precise conservation map and identification of highly conserved sequence elements, some of which we have shown previously to be differentially methylated in the mouse. Additionally, this analysis facilitated identification of a CpG-rich tandem repeat array located ∼13–15 kb upstream of Gtl2. Furthermore, we have identified a third imprinted transcript that overlaps with the last Dlk1 exon in the mouse. This transcript lacks a conserved open reading frame and is probably generated by cleavage of extendedDlk1 transcripts. Because Dlk1 and Gtl2share many of the imprinting properties of the well-characterizedIgf2–H19 domain, it has been proposed that t...

Research paper thumbnail of Human–Ovine Comparative Sequencing of a 250-kb Imprinted Domain Encompassing the Callipyge (clpg) Locus and Identification of Six Imprinted Transcripts: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8

Genome Research, 2001

Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and repres... more Two ovine BAC clones and a connecting long-range PCR product, jointly spanning ∼250 kb and representing most of theMULGE5-OY3 marker interval known to contain the clpglocus, were completely sequenced. The resulting genomic sequence was aligned with its human ortholog and extensively annotated. Six transcripts, four of which were novel, were predicted to originate from within the analyzed region and their existence confirmed experimentally: DLK1, DAT, GTL2, PEG11, antiPEG11, and MEG8. RT-PCR experiments performed on a range of tissues sampled from an 8-wk-old animal demonstrated the preferential expression of all six transcripts in skeletal muscle, which suggests that they are under control of common regulatory elements. The six transcripts were also shown to be subject to parental imprinting: DLK1, DAT, andPEG11 were shown to be paternally expressed and GTL2,antiPEG11, and MEG8 to be maternally expressed.[The sequence data described in this paper have been submitted to the GenBank d...

Research paper thumbnail of Ancestral haplotype-based association mapping with generalized linear mixed models accounting for stratification

Bioinformatics, 2012

Motivation: In many situations, genome-wide association studies are performed in populations pres... more Motivation: In many situations, genome-wide association studies are performed in populations presenting stratification. Mixed models including a kinship matrix accounting for genetic relatedness among individuals have been shown to correct for population and/or family structure. Here we extend this methodology to generalized linear mixed models which properly model data under various distributions. In addition we perform association with ancestral haplotypes inferred using a hidden Markov model. Results: The method was shown to properly account for stratification under various simulated scenari presenting population and/or family structure. Use of ancestral haplotypes resulted in higher power than SNPs on simulated datasets. Application to real data demonstrates the usefulness of the developed model. Full analysis of a dataset with 4600 individuals and 500 000 SNPs was performed in 2 h 36 min and required 2.28 Gb of RAM.

Research paper thumbnail of Construction and characterization of an ovine BAC contig spanning the callipyge locus

Animal Genetics, 2000

We describe the construction of an ovine BAC contig spanning a 4•6 centimorgan (cM) chromosome se... more We describe the construction of an ovine BAC contig spanning a 4•6 centimorgan (cM) chromosome segment known to contain the callipyge (CLPG) locus. The contig comprises 21 ovine BAC clones jointly covering approximately 900 kilobases (Kb). Two gaps in the BAC contig, spanning 10 and 7•5 Kb, respectively, were bridged by long range PCR. The corresponding chromosome region was shown to be characterized by an unusually low Kb to cM ratio (164 Kb/cM) and a high density of NotI sites (1:126 Kb) possibly reflecting a high gene density in the corresponding chromosome region. Equivalent amplification of 64 sequence tagged sites spanning the corresponding region from homozygous + / + and CLPG/CLPG individuals disproves the hypothesis of a major deletion causing the CLPG mutation.

Research paper thumbnail of Identity-by-descent mapping of recessive traits in livestock: application to map the bovine syndactyly locus to chromosome 15

Genome Research, 1996

Twelve animals affected with syndactyly or mulefoot were sampled in the Dutch black-and-white cat... more Twelve animals affected with syndactyly or mulefoot were sampled in the Dutch black-and-white cattle population. Analysis of the pedigree data reveal that all of these individuals traced back to a single acknowledged carrier founder individual. Between seven and nine generations separated the founder from its 12 affected descendents. The 12 affected offspring were genotyped for a battery of 213 microsatellites spanning the 29 bovine autosomes. The resulting genotypes were analyzed using a maximum likelihood approach searching for shared homozygous haplotypes among affected individuals. Three candidate regions for the syndactyly locus emerged from this initial screening. syndactyly was shown to map to one of these candidate regions on chromosome 15 by genotyping 29 additional individuals linking founder and affected offspring and performing a conventional linkage analysis with the LINKAGE programs. This study illustrates the potential of identity-by-descent mapping in livestock popul...

Research paper thumbnail of The callipyge mutation enhances bidirectional long-range DLK1-GTL2 intergenic transcription in cis

Proceedings of the National Academy of Sciences, 2006

The callipyge mutation (CLPG) is an A to G transition that affects a muscle-specific long-range c... more The callipyge mutation (CLPG) is an A to G transition that affects a muscle-specific long-range control element located in the middle of the 90-kb DLK1-GTL2 intergenic (IG) region. It causes ectopic expression of a 327-kb cluster of imprinted genes in skeletal muscle, resulting in the callipyge muscular hypertrophy and its non-Mendelian inheritance pattern known as polar overdominance. We herein demonstrate that the CLPG mutation alters the muscular epigenotype of the DLK1-GTL2 IG region in cis, including hypomethylation, acquisition of novel DNase-I hypersentivite sites, and, most strikingly, strongly enhanced bidirectional, longrange IG transcription. The callipyge phenotype thus emerges as a unique model to study the functional significance of IG transcription, which recently has proven to be a widespread, yet elusive, feature of the mammalian genome.

Research paper thumbnail of Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates

Nucleic Acids Research, 2010

The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) tha... more The Patrocles database (http://www.patrocles.org/) compiles DNA sequence polymorphisms (DSPs) that are predicted to perturb miRNA-mediated gene regulation. Distinctive features include: (i) the coverage of seven vertebrate species in its present release, aiming for more when information becomes available, (ii) the coverage of the three compartments involved in the silencing process (i.e. targets, miRNA precursors and silencing machinery), (iii) contextual information that enables users to prioritize candidate 'Patrocles DSPs', including graphical information on miRNA-target coexpression and eQTL effect of genotype on target expression levels, (iv) the inclusion of Copy Number Variants and eQTL information that affect miRNA precursors as well as genes encoding components of the silencing machinery and (v) a tool (Patrocles finder) that allows the user to determine whether her favorite DSP may perturb miRNA-mediated gene regulation of custom target sequences. To support the biological relevance of Patrocles' content, we searched for signatures of selection acting on 'Patrocles single nucleotide polymorphisms (pSNPs)' in human and mice. As expected, we found a strong signature of purifying selection against not only SNPs that destroy conserved target sites but also against SNPs that create novel, illegitimate target sites, which is reminiscent of the Texel mutation in sheep.

Research paper thumbnail of The mh gene causing double-muscling in cattle maps to bovine Chromosome 2

Mammalian Genome, 1995

While the hereditary nature of the "double-muscling" phenotype (a generalized muscular hypertroph... more While the hereditary nature of the "double-muscling" phenotype (a generalized muscular hypertrophy documented in several cattle breeds) is well established, its precise segregation mode has remained controversial. Both monogenic models (autosomal dominant or recessive) and oligogenic models have been proposed. Using a panel of 213 bovine microsatellite markers, and an experimental pedigree obtained by backcrossing "doublemuscled (Belgian Blue) x conventional (Friesian)" F 1 darns to double-muscled sire, we have mapped a locus on bovine Chromosome (Chr) 2 that accounts for all the phenotypic variance in the backcross generation. This locus, referred to as mh (muscular hypertrophy), has been positioned with respect to a map composed of seven Chr 2-specific microsatellites, at 2 cM from the closest marker. This result confirms the validity in the Belgian Blue population of the monogenic model involving an autosomal mh locus, characterized by a wild-type "+" and a recessive "mh" allele, causing the double-muscling phenotype in the homozygous condition. The linkage relationship between the mh locus and the Chr 2 markers was confirmed in three informative pedigrees collected from the general Belgian Blue Cattle population, reinforcing the notion Of genetic homogeneity of the double-muscling trait in this breed. This work paves the way towards marker-assisted selection for or against the double-muscling trait, and towards positional cloning of the corresponding gene.

Research paper thumbnail of Polymorphic Polymorphic MicroRNA-Target Interactions: A Novel Source of Phenotypic Variation

Cold Spring Harbor Symposia on Quantitative Biology, 2006