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BACKGROUND: Chromosomal duplications involving 17p13.3 have recently been defined as a new distinctive syndrome with several diagnosed patients. Some variation is known to occur in the breakpoints of the duplicated region and, consequently, in the phenotype as well. AIMS: We report on a patient, the fifth to our knowledge, a 4-year-old girl with a pure de novo subtelomeric 17p13.2-pter duplication. She presents all of the facial features described so far for this duplication and in addition, a unilateral palmar transversal crease and oculocutaneous albinism which has not been reported previously. METHODS: A detailed molecular description of the reported aberration and correlation with the observed phenotypical features based on a literature review. We discuss the possible molecular etiology of albinism in regard to the mode of inheritance. CONCLUSION: The new data provided here may be useful for further genotype correlations in syndromes with oculocutaneous albinism, especially of autosomal dominant inheritance.
- Klíčová slova
- 17p13.3, albinism, chromosomal duplication,
- MeSH
- albinismus generalizovaný genetika MeSH
- duplikace chromozomů genetika MeSH
- hybridizace in situ fluorescenční MeSH
- lidé MeSH
- lidské chromozomy, pár 19 genetika MeSH
- předškolní dítě MeSH
- Check Tag
- lidé MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
- práce podpořená grantem MeSH
The 17q12 chromosomal region carries the HNF1B gene, mutations of which cause various conditions. When searching for HNF1B/17q12 rearrangements among children with biliary atresia and/or choledochal cysts, we identified a male proband carrying a 17q12 duplication spanning 1698 kb that included 24 genes from TBC1D3C to HNF1B. The boy presented with cholestatic jaundice at the age of 2 weeks due to a choledochal cyst sized 15 ×12 mm (type Ia according to the Todani classification). He underwent a shunt surgery consisting of a hepaticojejunostomy using Roux-en-Y loop at the age of 2 months, which led to a permanent relief of cholestasis. Perioperative liver histology revealed significant hepatic fibrosis and bile ductular proliferation. At 17 years, he has a mildly enlarged liver with decreased elasticity, an upper-normal-sized spleen, normal biochemistry values, and no renal or hepatic cysts. We report the first hepatobiliary phenotype in a patient with an HNF1B overdosage.
- Klíčová slova
- 17q12 chromosomal duplication, choledochal cyst, hepaticojejunoanastomosis, HNF1B overdosage, neonatal jaundice,
- MeSH
- cysta choledochu genetika MeSH
- duplikace chromozomů * MeSH
- genová dávka * MeSH
- hepatocytární jaderný faktor 1-beta genetika MeSH
- jaterní cirhóza patologie MeSH
- játra chirurgie MeSH
- jejunum chirurgie MeSH
- lidé MeSH
- lidské chromozomy, pár 17 genetika MeSH
- novorozenec MeSH
- Rouxova Y-anastomóza MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- hepatocytární jaderný faktor 1-beta MeSH
- HNF1B protein, human MeSH Prohlížeč
BACKGROUND: Recent studies suggest that duplication of the 9p24.3 chromosomal locus, which includes the DOCK8 and KANK1 genes, is associated with autism spectrum disorders (ASD), intellectual disability/developmental delay (ID/DD), learning problems, language disorders, hyperactivity, and epilepsy. Correlation between this duplication and the carrier phenotype needs further discussion. METHODS: In this study, three unrelated patients with ID/DD and ASD underwent SNP aCGH and MLPA testing. Similarities in the phenotypes of patients with 9p24.3, 15q11.2, and 16p11.2 duplications were also observed. RESULTS: All patients with ID/DD and ASD carried the 9p24.3 duplication and showed intragenic duplication of DOCK8. Additionally, two patients had ADHD, one was hearing impaired and obese, and one had macrocephaly. Inheritance of the 9p24.3 duplication was confirmed in one patient and his sibling. In one patient KANK1 was duplicated along with DOCK8. Carriers of 9p24.3, 15q11.2, and 16p11.2 duplications showed several phenotypic similarities, with ID/DD more strongly associated with duplication of 9p24.3 than of 15q11.2 and 16p11.2. CONCLUSION: We concluded that 9p24.3 is a likely cause of ASD and ID/DD, especially in cases of DOCK8 intragenic duplication. DOCK8 is a likely causative gene, and KANK1 aberrations a modulator, of the clinical phenotype observed. Other modulators were not excluded.
- Klíčová slova
- 15q11.2 duplication, 16p11.2 duplication, 9p24.3 duplication, developmental delay,
- MeSH
- adaptorové proteiny signální transdukční genetika MeSH
- chromozomální poruchy genetika patologie MeSH
- cytoskeletální proteiny genetika MeSH
- dítě MeSH
- duplikace chromozomů * MeSH
- fenotyp * MeSH
- lidé MeSH
- lidské chromozomy, pár 9 genetika MeSH
- předškolní dítě MeSH
- výměnné faktory guaninnukleotidů genetika MeSH
- vývojové poruchy u dětí genetika patologie MeSH
- Check Tag
- dítě MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adaptorové proteiny signální transdukční MeSH
- cytoskeletální proteiny MeSH
- DOCK8 protein, human MeSH Prohlížeč
- KANK1 protein, human MeSH Prohlížeč
- výměnné faktory guaninnukleotidů MeSH
Chromosomal band 17q12 is a gene-rich region flanked by segmental duplications, making the region prone to deletions and duplications via the non-allelic homologous recombination mechanism. While deletions cause a well-described disorder with a specific phenotype called renal cysts and diabetes mellitus, the phenotype caused by reciprocal duplications is less specific, primarily because of variable expressivity, and incomplete penetrance. We present an unusual family with four children carrying the 17q12 microduplication inherited from their clinically healthy mother, who was a carrier of both the duplication and, interestingly, also of an atypical deletion of the 17q12 region. The duplication was inherited from her diabetic father and the deletion from her diabetic mother who also suffered from a renal disorder. Clinical manifestations in the family were variable, but all children showed some degree of a neurodevelopmental disorder, such as epilepsy, intellectual disability, delayed speech development, or attention deficit disorder. The simultaneous occurrence of a deletion and duplication in the same chromosomal region in one family is very rare, and to our knowledge, individuals carrying both a deletion and a duplication of this region have never been described.
- Klíčová slova
- 17q12 deletion, 17q12 duplication, LHX1 gene, epilepsy, intellectual disability,
- MeSH
- chromozomální delece MeSH
- duplikace chromozomů genetika MeSH
- fenotyp MeSH
- lidé MeSH
- mentální retardace * genetika MeSH
- mnohočetné abnormality * genetika MeSH
- Check Tag
- lidé MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- kazuistiky MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Česká republika MeSH
Whole genome duplication (WGD) can promote adaptation but is disruptive to conserved processes, especially meiosis. Studies in Arabidopsis arenosa revealed a coordinated evolutionary response to WGD involving interacting proteins controlling meiotic crossovers, which are minimized in an autotetraploid (within-species polyploid) to avoid missegregation. Here, we test whether this surprising flexibility of a conserved essential process, meiosis, is recapitulated in an independent WGD system, Cardamine amara, 17 My diverged from A. arenosa. We assess meiotic stability and perform population-based scans for positive selection, contrasting the genomic response to WGD in C. amara with that of A. arenosa. We found in C. amara the strongest selection signals at genes with predicted functions thought important to adaptation to WGD: meiosis, chromosome remodeling, cell cycle, and ion transport. However, genomic responses to WGD in the two species differ: minimal ortholog-level convergence emerged, with none of the meiosis genes found in A. arenosa exhibiting strong signal in C. amara. This is consistent with our observations of lower meiotic stability and occasional clonal spreading in diploid C. amara, suggesting that nascent C. amara autotetraploid lineages were preadapted by their diploid lifestyle to survive while enduring reduced meiotic fidelity. However, in contrast to a lack of ortholog convergence, we see process-level and network convergence in DNA management, chromosome organization, stress signaling, and ion homeostasis processes. This gives the first insight into the salient adaptations required to meet the challenges of a WGD state and shows that autopolyploids can utilize multiple evolutionary trajectories to adapt to WGD.
- Klíčová slova
- adaptation, convergence, genome duplication, polyploidy,
- MeSH
- Arabidopsis * genetika MeSH
- duplikace genu * MeSH
- genom rostlinný MeSH
- meióza genetika MeSH
- polyploidie MeSH
- segregace chromozomů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Loss of the awn in some cereals, including sorghum, is a key transition during cereal domestication or improvement that has facilitated grain harvest and storage. The genetic basis of awn loss in sorghum during domestication or improvement remains unknown. Here, we identified the awn1 gene encoding a transcription factor with the ALOG domain that is responsible for awn loss during sorghum domestication or improvement. awn1 arose from a gene duplication on chromosome 10 that translocated to chromosome 3, recruiting a new promoter from the neighboring intergenic region filled with "noncoding DNA" and recreating the first exon and intron. awn1 acquired high expression after duplication and represses the elongation of awns in domesticated sorghum. Comparative mapping revealed high collinearity at the awn1 paralog locus on chromosome 10 across cereals, and awn growth and development were successfully reactivated on the rice spikelet by inactivating the rice awn1 ortholog. RNA-seq and DAP-seq revealed that as a transcriptional repressor, AWN1 bound directly to a motif in the regulatory regions of three MADS genes related to flower development and two genes, DL and LKS2, involved in awn development. AWN1 downregulates the expression of these genes, thereby repressing awn elongation. The preexistence of regulatory elements in the neighboring intergenic region of awn1 before domestication implicates that noncoding DNA may serve as a treasure trove for evolution during sorghum adaptation to a changing world. Taken together, our results suggest that gene duplication can rapidly drive the evolution of gene regulatory networks in plants.
- Klíčová slova
- DAP-seq, awn, gene duplication, sorghum domestication and improvement,
- MeSH
- chromozomy rostlin MeSH
- duplikace genu * MeSH
- jedlá semena anatomie a histologie genetika MeSH
- lokus kvantitativního znaku MeSH
- mapování chromozomů MeSH
- promotorové oblasti (genetika) MeSH
- proteinové domény MeSH
- regulace genové exprese u rostlin MeSH
- represorové proteiny genetika fyziologie MeSH
- rostlinné geny * MeSH
- rostlinné proteiny genetika fyziologie MeSH
- Sorghum anatomie a histologie genetika fyziologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- represorové proteiny MeSH
- rostlinné proteiny MeSH
Hybridization is a creative evolutionary force, increasing genomic diversity and facilitating adaptation and even speciation. Hybrids often face significant challenges to establishment, including reduced fertility that arises from genomic incompatibilities between their parents. Whole-genome duplication in hybrids (allopolyploidy) can restore fertility, cause immediate phenotypic changes, and generate reproductive isolation. Yet the survival of polyploid lineages is uncertain, and few studies have compared the performance of recently formed allopolyploids and their parents under field conditions. Here, we use natural and synthetically produced hybrid and polyploid monkeyflowers (Mimulus spp.) to study how polyploidy contributes to the fertility, reproductive isolation, phenotype, and performance of hybrids in the field. We find that polyploidization restores fertility and that allopolyploids are reproductively isolated from their parents. The phenotype of allopolyploids displays the classic gigas effect of whole-genome duplication, in which plants have larger organs and are slower to flower. Field experiments indicate that survival of synthetic hybrids before and after polyploidization is intermediate between that of the parents, whereas natural hybrids have higher survival than all other taxa. We conclude that hybridization and polyploidy can act as sources of genomic novelty, but adaptive evolution is key in mediating the establishment of young allopolyploid lineages.
- Klíčová slova
- Erythranthe, Mimulus, allopolyploid, polyploidy, speciation, whole-genome duplication,
- MeSH
- duplikace genu * MeSH
- fenotyp MeSH
- fertilita genetika MeSH
- genom rostlinný * MeSH
- hybridizace genetická * MeSH
- Mimulus genetika MeSH
- molekulární evoluce * MeSH
- polyploidie * MeSH
- reprodukční izolace MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Hematopoiesis is a precisely orchestrated process regulated by the activity of hematopoietic cytokines and their respective receptors. Due to an extra round of whole genome duplication during vertebrate evolution in teleost fish, zebrafish have two paralogs of many important genes, including genes involved in hematopoiesis. Importantly, these duplication events brought increased level of complexity in such cases, where both ligands and receptors have been duplicated in parallel. Therefore, precise understanding of binding specificities between duplicated ligand-receptor signalosomes as well as understanding of their differential expression provide an important basis for future studies to better understand the role of duplication of these genes. However, although many recent studies in the field have partly addressed functional redundancy or sub-specialization of some of those duplicated paralogs, this information remains to be scattered over many publications and unpublished data. Therefore, the focus of this review is to provide an overview of recent findings in the zebrafish hematopoietic field regarding activity, role and specificity of some of the hematopoietic cytokines with emphasis on crucial regulators of the erythro-myeloid lineages.
- Klíčová slova
- cytokine, erythropoiesis, genome duplication, hematopoiesis, myelopoiesis, zebrafish,
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Adaptive gene flow is a consequential phenomenon across all kingdoms. Although recognition is increasing, there is no study showing that bidirectional gene flow mediates adaptation at loci that manage core processes. We previously discovered concerted molecular changes among interacting members of the meiotic machinery controlling crossover number upon adaptation to whole-genome duplication (WGD) in Arabidopsis arenosa. Here we conduct a population genomic study to test the hypothesis that adaptation to WGD has been mediated by adaptive gene flow between A. arenosa and A. lyrata. We find that A. lyrata underwent WGD more recently than A. arenosa, suggesting that pre-adapted alleles have rescued nascent A. lyrata, but we also detect gene flow in the opposite direction at functionally interacting loci under the most extreme levels of selection. These data indicate that bidirectional gene flow allowed for survival after WGD, and that the merger of these species is greater than the sum of their parts.
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we examined whether this could be explained by a hidden gene duplication. Re-sequencing and manual assembly of the Arabidopsis thaliana SEC10 (At5g12370) locus revealed that this locus, comprising a single gene in the reference genome assembly, indeed contains two paralogous genes in tandem, SEC10a and SEC10b, and that a sequence segment of 7 kb in length is missing from the reference genome sequence. Differences between the two paralogs are concentrated in non-coding regions, while the predicted protein sequences exhibit 99% identity, differing only by substitution of five amino acid residues and an indel of four residues. Both SEC10 genes are expressed, although varying transcript levels suggest differential regulation. Homozygous T-DNA insertion mutants in either paralog exhibit a wild-type phenotype, consistent with proposed extensive functional redundancy of the two genes. By these observations we demonstrate that recently duplicated genes may remain hidden even in well-characterized genomes, such as that of A. thaliana. Moreover, we show that the use of the existing A. thaliana reference genome sequence as a guide for sequence assembly of new Arabidopsis accessions or related species has at least in some cases led to error propagation.
