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TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MA, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP - Nat. Genet. (2015)

Bottom Line: Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism.TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes.Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.

ABSTRACT
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.

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Mutations in TRAIP cause primordial dwarfism(a) Mutations identified in TRAIP. Top, schematic of TRAIP gene structure; middle, TRAIP protein structure; bottom, sequence electropherograms demonstrating (middle, right panels) homozygous nonsense mutations in Patient 1 (P1) and Patient 2 (P2) and (left) a homozygous missense mutation, Arg18Cys in Patient 3 (P3). (b) A physiochemically similar residue is present at codon 18 in all vertebrates. Sequence alignments of Homo sapiens, Pan troglodytes, Mus musculus, Gallus gallus, Xenopus tropicalis and Danio rerio using Clustal W. (c) Patients with TRAIP mutations have prenatal onset severe growth failure with disproportionate microcephaly. Birth weight (BWGT), current height (HGT) and current head circumference (OFC) plotted as z-scores (standard deviations from population mean for age and sex). 97.5% of general population will lie above the dashed line at −2 S.D. Black bars indicate mean values. (d) Cerebral cortical size is markedly reduced with simplification of gyral folding. MRI T2-weighted sagittal and axial images of P3 (age 3 years) compared with control scans of a healthy child (age 3 years 1 month). Scale bar, 2 cm. (e) Photographs of affected individuals with TRAIP mutations demonstrating facial similarities, including an elongated narrow face and micrognathia. Informed consent to publish photographs was obtained from families.
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Figure 1: Mutations in TRAIP cause primordial dwarfism(a) Mutations identified in TRAIP. Top, schematic of TRAIP gene structure; middle, TRAIP protein structure; bottom, sequence electropherograms demonstrating (middle, right panels) homozygous nonsense mutations in Patient 1 (P1) and Patient 2 (P2) and (left) a homozygous missense mutation, Arg18Cys in Patient 3 (P3). (b) A physiochemically similar residue is present at codon 18 in all vertebrates. Sequence alignments of Homo sapiens, Pan troglodytes, Mus musculus, Gallus gallus, Xenopus tropicalis and Danio rerio using Clustal W. (c) Patients with TRAIP mutations have prenatal onset severe growth failure with disproportionate microcephaly. Birth weight (BWGT), current height (HGT) and current head circumference (OFC) plotted as z-scores (standard deviations from population mean for age and sex). 97.5% of general population will lie above the dashed line at −2 S.D. Black bars indicate mean values. (d) Cerebral cortical size is markedly reduced with simplification of gyral folding. MRI T2-weighted sagittal and axial images of P3 (age 3 years) compared with control scans of a healthy child (age 3 years 1 month). Scale bar, 2 cm. (e) Photographs of affected individuals with TRAIP mutations demonstrating facial similarities, including an elongated narrow face and micrognathia. Informed consent to publish photographs was obtained from families.

Mentions: We performed WES to establish a molecular diagnosis for a child with severe microcephalic primordial dwarfism. After filtering to remove common variants (minor allele frequency (MAF) > 0.005), analysis under a recessive inheritance model identified a homozygous nonsense mutation in TRAIP, c.553C>T, resulting in a premature stop codon, p.Arg185* (Fig. 1a). Sanger sequencing confirmed the presence of this mutation and its appropriate segregation in the family, with both parents being heterozygous carriers. The variant was not detected on sequencing of 380 control chromosomes, nor was it present in 1000 Genomes, EVS or EXaC public variant databases, in keeping with it being a rare recessive pathogenic mutation. Sanger resequencing of the coding exons and splice junctions of TRAIP in 262 primary microcephaly and primordial dwarfism patients identified a second patient, homozygous for the same mutation, p.Arg185*. Notably the two patients were born to non-consanguineous parents and originated from different countries with the families having no known relationship. However, high density genome-wide SNP genotyping demonstrated regions of homozygosity surrounding TRAIP in both patients of 4.6 and 8.4Mb respectively, consistent with unrecognized parental relatedness in each family (Supplementary Fig. 1a). As well, analysis of genome-wide SNP genotype data using FEstim20 provided an inbreeding coefficient estimate of 0.003 for P2, equivalent to the inbreeding coefficient of 3rd cousin parents and also consistent with unknown parental consanguinity in this family (Supplementary Fig. 1b). Furthermore a 4.3 Mb homozygous haplotype was shared between P1 and P2 for the region immediately surrounding TRAIP, signifying a distant familial link with shared ancestry many generations previously despite their geographical separation (Supplementary Fig. 1a).


TRAIP promotes DNA damage response during genome replication and is mutated in primordial dwarfism.

Harley ME, Murina O, Leitch A, Higgs MR, Bicknell LS, Yigit G, Blackford AN, Zlatanou A, Mackenzie KJ, Reddy K, Halachev M, McGlasson S, Reijns MA, Fluteau A, Martin CA, Sabbioneda S, Elcioglu NH, Altmüller J, Thiele H, Greenhalgh L, Chessa L, Maghnie M, Salim M, Bober MB, Nürnberg P, Jackson SP, Hurles ME, Wollnik B, Stewart GS, Jackson AP - Nat. Genet. (2015)

Mutations in TRAIP cause primordial dwarfism(a) Mutations identified in TRAIP. Top, schematic of TRAIP gene structure; middle, TRAIP protein structure; bottom, sequence electropherograms demonstrating (middle, right panels) homozygous nonsense mutations in Patient 1 (P1) and Patient 2 (P2) and (left) a homozygous missense mutation, Arg18Cys in Patient 3 (P3). (b) A physiochemically similar residue is present at codon 18 in all vertebrates. Sequence alignments of Homo sapiens, Pan troglodytes, Mus musculus, Gallus gallus, Xenopus tropicalis and Danio rerio using Clustal W. (c) Patients with TRAIP mutations have prenatal onset severe growth failure with disproportionate microcephaly. Birth weight (BWGT), current height (HGT) and current head circumference (OFC) plotted as z-scores (standard deviations from population mean for age and sex). 97.5% of general population will lie above the dashed line at −2 S.D. Black bars indicate mean values. (d) Cerebral cortical size is markedly reduced with simplification of gyral folding. MRI T2-weighted sagittal and axial images of P3 (age 3 years) compared with control scans of a healthy child (age 3 years 1 month). Scale bar, 2 cm. (e) Photographs of affected individuals with TRAIP mutations demonstrating facial similarities, including an elongated narrow face and micrognathia. Informed consent to publish photographs was obtained from families.
© Copyright Policy
Related In: Results  -  Collection

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Figure 1: Mutations in TRAIP cause primordial dwarfism(a) Mutations identified in TRAIP. Top, schematic of TRAIP gene structure; middle, TRAIP protein structure; bottom, sequence electropherograms demonstrating (middle, right panels) homozygous nonsense mutations in Patient 1 (P1) and Patient 2 (P2) and (left) a homozygous missense mutation, Arg18Cys in Patient 3 (P3). (b) A physiochemically similar residue is present at codon 18 in all vertebrates. Sequence alignments of Homo sapiens, Pan troglodytes, Mus musculus, Gallus gallus, Xenopus tropicalis and Danio rerio using Clustal W. (c) Patients with TRAIP mutations have prenatal onset severe growth failure with disproportionate microcephaly. Birth weight (BWGT), current height (HGT) and current head circumference (OFC) plotted as z-scores (standard deviations from population mean for age and sex). 97.5% of general population will lie above the dashed line at −2 S.D. Black bars indicate mean values. (d) Cerebral cortical size is markedly reduced with simplification of gyral folding. MRI T2-weighted sagittal and axial images of P3 (age 3 years) compared with control scans of a healthy child (age 3 years 1 month). Scale bar, 2 cm. (e) Photographs of affected individuals with TRAIP mutations demonstrating facial similarities, including an elongated narrow face and micrognathia. Informed consent to publish photographs was obtained from families.
Mentions: We performed WES to establish a molecular diagnosis for a child with severe microcephalic primordial dwarfism. After filtering to remove common variants (minor allele frequency (MAF) > 0.005), analysis under a recessive inheritance model identified a homozygous nonsense mutation in TRAIP, c.553C>T, resulting in a premature stop codon, p.Arg185* (Fig. 1a). Sanger sequencing confirmed the presence of this mutation and its appropriate segregation in the family, with both parents being heterozygous carriers. The variant was not detected on sequencing of 380 control chromosomes, nor was it present in 1000 Genomes, EVS or EXaC public variant databases, in keeping with it being a rare recessive pathogenic mutation. Sanger resequencing of the coding exons and splice junctions of TRAIP in 262 primary microcephaly and primordial dwarfism patients identified a second patient, homozygous for the same mutation, p.Arg185*. Notably the two patients were born to non-consanguineous parents and originated from different countries with the families having no known relationship. However, high density genome-wide SNP genotyping demonstrated regions of homozygosity surrounding TRAIP in both patients of 4.6 and 8.4Mb respectively, consistent with unrecognized parental relatedness in each family (Supplementary Fig. 1a). As well, analysis of genome-wide SNP genotype data using FEstim20 provided an inbreeding coefficient estimate of 0.003 for P2, equivalent to the inbreeding coefficient of 3rd cousin parents and also consistent with unknown parental consanguinity in this family (Supplementary Fig. 1b). Furthermore a 4.3 Mb homozygous haplotype was shared between P1 and P2 for the region immediately surrounding TRAIP, signifying a distant familial link with shared ancestry many generations previously despite their geographical separation (Supplementary Fig. 1a).

Bottom Line: Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism.TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes.Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.

View Article: PubMed Central - PubMed

Affiliation: MRC Human Genetics Unit, IGMM, University of Edinburgh, Edinburgh, UK.

ABSTRACT
DNA lesions encountered by replicative polymerases threaten genome stability and cell cycle progression. Here we report the identification of mutations in TRAIP, encoding an E3 RING ubiquitin ligase, in patients with microcephalic primordial dwarfism. We establish that TRAIP relocalizes to sites of DNA damage, where it is required for optimal phosphorylation of H2AX and RPA2 during S-phase in response to ultraviolet (UV) irradiation, as well as fork progression through UV-induced DNA lesions. TRAIP is necessary for efficient cell cycle progression and mutations in TRAIP therefore limit cellular proliferation, providing a potential mechanism for microcephaly and dwarfism phenotypes. Human genetics thus identifies TRAIP as a component of the DNA damage response to replication-blocking DNA lesions.

Show MeSH
Related in: MedlinePlus