Abstract
Array-based comparative genomic hybridization identified a 2.3-Mb microdeletion of 17p13.2p13.1 in a boy presenting with moderate mental retardation, intractable epilepsy and dysmorphic features. This deletion region was overlapped with the previously proposed shortest region overlapped for microdeletion of 17p13.1 in patients with mental retardation, microcephaly, microretrognathia and abnormal magnetic resonance imaging (MRI) findings of cerebral white matter, in which at least 17 known genes are included. Among them, DLG4/PSD95, GPS2, GABARAP and KCTD11 have a function in neuronal development. Because of the functional importance, we paid attention to DLG4/PSD95 and GABARAP, and analyzed zebrafish in which the zebrafish homolog of human DLG4/PSD95 and GABARAP was knocked down and found that gabarap knockdown resulted in small head and hypoplastic mandible. This finding would be similar to the common findings of the patients with 17p13.1 deletions. Although there were no pathogenic mutations in DLG4/PSD95 or GABARAP in a cohort study with 142 patients with idiopathic developmental delay with/without epilepsy, further studies would be required for genes included in this region.
Similar content being viewed by others
Introduction
Neurodevelopmental disorders are generally characterized by neurological symptoms that occur during stages of rapid development of the nervous system. These disorders encompass a variety of symptoms, including cognitive impairment, which can range from learning disabilities to mental retardation, neuromotor dysfunction and seizure disorders. In the post-genomic era, the availability of the human genome sequence for genome-wide analysis has revealed a high frequency of neurodevelopmental disorders that result not only from genomic sequence mutations but also from genomic copy-number aberrations.1
Recently, the use of whole-genome scanning with array-based comparative genome hybridization (aCGH) has enabled the more accurate delineation of subtle chromosomal rearrangements.2, 3, 4, 5 Many novel microdeletion and duplication syndromes have been characterized using this revolutionary cytogenetic testing;6, 7 for example, 1q41q42 deletion syndrome,8 15q13.3 deletion syndrome,9 16p11.2 deletion syndrome,10, 11 17q12 deletion syndrome12 and 17q21.31 deletion/duplication syndrome.13, 14, 15 Despite its small size as compared with other chromosomes, chromosome 17 is associated with many newly characterized genomic syndromes. Chromosome 17 stands out among the human chromosomes in many respects. It is the largest human autosome with orthology to only a single mouse chromosome, mapping entirely to the distal half of mouse chromosome 11. Chromosome 17 is rich in protein-coding genes, having the second-highest gene density among the human chromosomes. It is also enriched in segmental duplications, ranking third in density among the autosomes. For these reasons, human chromosome 17 has been implicated in a wide range of human diseases.16
The proximal chromosome 17p arm, in which >23% of the genomic sequence consists of low-copy repeats, is associated with a wide variety of recurrent chromosomal aberrations resulting from nonallelic homologous recombination between low-copy repeats, including four well-known genomic disorders: Charcot–Marie–Tooth type1A disease; hereditary neuropathy with liability to pressure palsies, which results from reciprocal duplication or deletion of 17p12;17 Smith–Magenis syndrome and the Potocki–Lupski syndrome, which is associated with deletion or duplication of 17p11.2.18, 19, 20, 21 Miller–Dieker syndrome characterized by lissencephaly and characteristic facial features is caused by subtelomeric deletion of 17p, in which PAFAH1B/LIS1 is included,22 and heterozygous duplication of PAFAH1B/LIS1 has been reported to cause neurodevelopmental delays.7, 23
Recently, four mentally retarded patients with chromosomal microdeletions sharing an overlapping segment of 180 kb in 17p13.1 was reported.24 Although the phenotypes of the patients were variable because of the variable deletion sizes, the common features were mental retardation, microcephaly and abnormal magnetic resonance imaging (MRI) findings of the cerebral white matter.24 We identified a new patient with a microdeletion of 17p13.1, who shared common features. In the overlapping deletion region, some candidate genes for the phenotype are included. As little is known about their contribution to the phenotype, we analyzed DLG4/PSD95 and GABARAP using zebrafish embryos with morpholino knockdown system as a model organism. We also performed a cohort study in which we looked for human mutations in DLG4/PSD95 and GABARAP.
Materials and methods
Subjects
The indicated patient was diagnosed as having a chromosomal deletion by our cohort study for genomic copy-number aberrations. After obtaining informed consent from patients’ families based on the permission from the ethical committee of the institution, total of 300 peripheral blood samples were obtained from patients with idiopathic mental retardation and/or epilepsy whose etiology were unknown and were used to investigate genomic copy-number aberrations using aCGH. Then, the samples with no genomic copy-number aberrations were used to screen for candidate gene mutations. A total of 142 samples derived from patients with neurological symptoms including developmental delay with/without epilepsy were used for the second screening. Genomic DNA was extracted from peripheral blood using a QIAquick DNA extraction kit (Qiagen, Hilden, Germany).
aCGH analysis
aCGH analysis was performed using a Human Genome CGH Microarray 244 chip (Agilent Technologies, Santa Clara, CA, USA).25 Genomic copy numbers were visualized using CGH Analytics version 3.5 software (Agilent Technologies).
Fluorescence in situ hybridization analysis
Metaphase or prometaphase chromosomes were prepared from phytohemagglutinin-stimulated peripheral blood lymphocytes according to the standard technique and used for fluorescence in situ hybridization (FISH) as described elsewhere.25 Fifteen BAC clones, RP11-104O19, RP11-1038H1, RP11-198F11, RP11-305G1, RP11-46I8, RP11-457I18, RP11-104N2, RP11-61B20, CTD-2015K4, RP11-542C16, RP11-104H15, RP11-1081A10, RP11-89D11, RP11-1099M24 and RP11-1D5, all of which mapped around 7p13.2p13.1, and RP11-153A23, which mapped on 17q25.3 and used as a marker, were selected from the UCSC Human genome browser, March 2006 (http://genome.ucsc.edu/) (Table 1).
Microsatellite marker analyses
Microsatellite marker analyses were performed to determine the origin of the deletion using six microsatellite markers, D17S1832, D17S938, D17S796, GATA158H04, D17S1881 and D17S578 (Table 1), which were selected from the web site of Marshfield Clinic Research Foundation (http://www.marshfieldclinic.org/chg/pages/default.aspx). The information of the markers primers was obtained from the UCSC Human genome browser, March 2006 (http://genome.ucsc.edu/). Polymerase chain reaction (PCR) amplification was performed according to the standard method. The amplicons were visualized by ethidium bromide staining after separation by electrophoresis on a 12% acrylamide gel.25
Maintenance of zebrafish
Adult zebrafish (Danio rerio) were maintained at 28.5 °C under 14-h light/10-h dark cycle conditions. Fertilized eggs from natural crosses were collected a few minutes after spawning and cultured at 28.5 °C in water containing 0.006% NaCl, 0.00025% methylene blue and 0.003% N-phenylthiourea. Embryos were staged according to morphology and hours post-fertilization (hpf).26
Sequence analyses of dlg4 and gabarap in zebrafish
The 5′ untranslated region (UTR) of dlg4 in our zebrafish strain was cloned using the 5′ RACE method with primers (Supplementary Table 1) that were designed according to the reported dlg4 sequence (NM_214728). The partial fragment of zebrafish gabarap that contains incomplete 5′ and 3′ UTRs and a complete open reading frame was also amplified by reverse transcribed (RT)-PCR with primers (Supplementary Table 1) that was designed according to the reported zebrafish gabarap (Accession #BC065894). This PCR product was cloned into the pGEM-T vector (Promega, Madison, WI, USA), and the resulting plasmid, pGEM-gabarap, was served as a template for RNA probe synthesis. Total RNA was extracted from 24 hpf embryos using the RNeasy Mini kit (Qiagen). cDNA was synthesized using an Omniscript RT kit (Qiagen). All PCR reactions were performed with KOD plus DNA polymerase (Toyobo, Osaka, Japan). For 5′ RACE, the 5′-Full RACE Core Set (TAKARA, Otsu, Japan) was used.
Whole-mount in situ hybridization
Whole-mount in situ hybridization was performed as described.27 The antisense RNA probe for gabarap was synthesized using T7 RNA polymerase (TAKARA, Otsu, Japan), and the pGEM-gabarap clone described above was used as the template.
Morpholinos and microinjection
Morpholino antisense oligos (MOs) were purchased from GENE TOOLS (Philomath, OR, USA) (Supplementary Table 1). Storage and microinjection were performed as described.27
Preparation of zebrafish head sections
Zebrafish embryos at appropriate stages were fixed with 4% paraformaldehyde in PBS at 4 °C overnight. The fixed embryos were gradually dehydrated with ethanol, soaked in xylene, transferred to Paraplast Plus embedding medium (McCormick Scientific, St Louis, MO, USA), and embedded in Paraplast Plus under microscopic observation. Specimens were cut into serial sections (7 μm) and stained with Mayer's hematoxylin and eosin solution.
Sequence analyses of DLG4/PSD95 and GABARAP
All DLG4/PSD95 and GABARAP exons from the indicated patient and 142 patients with neurological symptoms were amplified with PCR using originally designed primers located in both neighboring intronic sequences (Supplementary Table 2) according to the standard method. All amplicons were subjected to direct sequencing using the BigDye Terminator Cycle Sequencing kit (Applied Biosystems, Foster city, CA, USA). Sequencing reactions were analyzed with a 3130 × l Genetic Analyzer (Applied Biosystems).
RESULTS
Molecular cytogenetic analysis
We identified a 2.3-Mb microdeletion spanning from 17p13.2 to p13.1 in a patient with developmental delay and epilepsy (Figures 1a and b; Table 1). Two-color FISH analysis using BAC clones confirmed the deletion region (Figure 2a). There was no deletion in his parents’ DNA, indicating a de novo deletion in the patient. According to the March 2006 human reference sequence (NCBI Build 36.1), the final karyotype of this patient was arr 17p13.2p13.1 (4 937 065–7 203 194) × 1.ich (RP11–104O19+, RP11–1038H1+, RP11–198F11+, RP11–305G1+, RP11–46I8+, RP11–457I18−, RP11–104N2−, RP11–61B20−, CTD–2015K4−, RP11–542C16−, RP11–104H15+, RP11–1081A10+, RP11–89D11+, RP11–1099M24+, RP11–1D5+, RP11–153A23+) dn (Table 1). Among the six microsatellite markers used, only D17S1881 was informative, and showed that this patient had bands in common only with his mother (Figure 2b; Table 1). Thus, we deduced that the paternally derived allele at this locus was deleted in the patient.
Patient report
A 5-year-old boy was born spontaneously at a gestational age of 39 weeks and 1 day after an uneventful pregnancy. At his birth, his father was 33 years old and his mother was 31 years old. Both parents were healthy and nonconsanguineous. A 9-month-old younger sister was healthy. The proband's birth weight was 2480 g (<10th percentile), his birth length was 49.0 cm (50th percentile), and his head circumference was 33 cm (50th percentile). The amniotic fluid was contaminated by meconium, and amniotic fluid aspiration by tracheal incubation was performed. Because of the asphyxic respiration, he was admitted to the neonatal intensive care unit. Electrocardiography and ultrasound examination showed no abnormality of the heart or abdominal organs, except for a slightly dilated uteropelvic region. Measurement of the auditory brainstem response revealed no abnormality.
His cryptorchidism was surgically repaired at the age of 16 months. He showed gross motor delay, establishing head control at 5 months, turning over at 8 months, sitting alone at 11 months, walking alone at 2 years and speaking his first word at 14 months. Electroencephalography was performed at 17 months because of the developmental delay, and no obvious abnormality was observed at this time.
At the age of 2 years, he developed cataplectic attack seizures that sometimes produced unconsciousness. He received valproic acid at 2 years 5 months of age, but his seizures were not controlled with this treatment. An electroencephalography revealed hypsarrhythmia with diffuse polyspikes and waves burst (Supplementary Figure 1). He was admitted to the hospital for adrenocorticotropic hormone therapy to control his epileptic attacks at the age of 2 years and 11 months.28 At this time, his height was 87.8 cm (10th percentile), his weight was 11 kg (3rd percentile) and his head circumference was 48.1 cm (<25th percentile). Dysmorphic features including, a broad nasal root, a high arched palate, low-set ears, rough hair, telecanthus, microretrognathia (Figure 3), and flat feet were noted. His development quotient was 46 according to the Enjoji Scale of Psychological Development.29 Blood cell counts, glucose, urinalysis, amino acid studies, liver and thyroid function studies and cerebrospinal fluid were normal. After adrenocorticotropic hormone therapy, the incidence of the epileptic attacks was reduced. G-banded chromosomal analysis showed a normal male karyotype of 46,XY. To survey the etiology of developmental of this patient, the patient's blood sample was supplied for this study. Brain MRI at his age of 5 years showed mild white matter volume reduction (Supplementary Figure 2).
Injection of dlg4–MO shows no distinct defects in brain development
In the deleted region of chromosome 17p13.1 of this patient, two genes, DLG4/PSD95430 and GABARAP31 may be responsible for this patient's developmental delays because the earlier studies showed the involvement of these two genes in neurological functions.
Zebrafish dlg4 is expressed in developing and adult brain, in a manner similar to the expression of its homolog in both human and mouse,32, 33, 34 suggesting that zebrafish can be used as a model animal to examine this gene. Therefore, we first focused on the function of dlg4 during cerebral development in zebrafish. Although a zebrafish homolog of dlg4 has been reported (NM_214728), sequence information of the 5′ UTR in our zebrafish strain was needed for functional analysis with gene knockdown using MOs. Thus, we performed 5′ RACE and obtained a 12-nucleotide fragment that corresponds to the upstream region of the translation initiation site, which was found to be identical to the reported sequence (data not shown). Then, to determine whether deletion of the DLG4/PSD954 locus resulted in brain growth impairment, we performed gene knockdown of dlg4 in zebrafish. Microinjection of a translation-blocking type morpholino against dlg4 (dlg4-MO), however, resulted in various types of defects that differed from one individual to the next with no obvious tendency (Supplementary Figure 3). As we could not confirm a possible relationship between the phenotype of our patient and deletion of the DLG4/PSD954 locus, we abandoned further investigation of the participation of dlg4 in zebrafish brain development.
gabarap is involved in cerebral development
Using the zebrafish, we next investigated whether gabarap, another gene that could be responsible for the symptoms of this patient, has any functions in brain development, because this could be responsible for the symptoms of 17p13.1 microdeletion syndrome. First, the gene expression pattern of gabarap during development in zebrafish was determined. At 24 hpf, gabarap was expressed in the head, especially in the telencephalon, hindbrain and rhombomere (Figure 4a). Later in development, at 72 hpf, expression was observed in the ventral central nervous system through the forebrain to the hindbrain (Figure 4b). As these expression patterns of gabarap in the developing head indicated possible functions of this gene in brain development, we performed gene knockdown of gabarap. When 3 ng of gabarap-MO1, a translation-blocking MO, was injected into each embryo, the most of morphants (88%, n=150) showed slight dwarfism of the entire body with a severely hypoplastic head and mandible (Figures 4g and h). Although generalized growth retardation may be involved, it is also possible that these prominently hypoplastic head and mandible indicate the microcephaly and microretrognathia seen in the previously reported patients with 17p13.1 microdeletion syndrome.24 To confirm whether this defect was a specific effect of the gene knockdown of gabarap, gabarap-MO2, another translation-blocking MO with different sequence, was used. When 3 ng of gabarap-MO2 was injected, approximately two thirds of the morphants (63%, n=90) of gabarap-MO2 showed a similar phenotype as did those of gabarap-MO1 (Figures 4i and j). This phenotypes was hardly observed in wildtype (1.3%, n=300) or control-MO injected (6.7%, n=90) embryo (Figures 4c–f). These results indicated that the hypoplastic head and mandible were caused by the gene knockdown of gabarap, and that gabarap is required for normal development of anterior structures. Although we tried the mRNA rescue experiment using mRNA of GABARAP, we could not obtain compelling consistent results (data not shown).
To examine whether gabarap-MO morphants show histological abnormalities of the brain, cross-sections of the head were prepared. On the basis of the expression pattern of gabarap, we focused on sections that included the forebrain. In normal cerebral development of the zebrafish, the brain ventricle narrows as development progresses and almost fills up at 72 hpf (Figures 4k and l). Compared to that, the ventricle in both gabarap morphants was clearly retained in sections from the same relative positions of both wild-type and control morphants (Figures 4m and n). Overall, these results strongly suggest that gabarap has important functions in normal brain development in zebrafish.
Mutation screening for DLG4/PSD95 and GABARAP
No disease-causing mutations in DLG4/PSD95 and GABARAP were found in the remaining allele of the indicated patient and other 142 patients with neurodevelopmental disorders.
DISCUSSION
A microdeletion of 17p13.2p13.1 was identified in our patient who showed characteristic dysmorphic features, developmental delay and intractable epilepsy. This deletion was overlapped with previously reported microdeletions of 17p13.1 (Figure 1).24 The reported four patients showed common clinical manifestations including mental retardation, microcephaly, abnormal brain MRI findings with delayed myelination and some dysmorphic findings including epicanthic folds, low nasal bridge and microretrognathia, despite the variability of deletion size. As the deletion end breakpoint identified in our patient was on the most telomeric region compared with the previously reported deletions, this narrowed the shortest region overlapped (SRO) to chr17 (7 054 400–7 203 194), from 178.3 to 148.8 kb (Table 2; Figure 1).24 The overlapping clinical manifestation between our patient and the previously reported patients are mental retardation, MRI abnormalities and distinctive facial features including epicanthic folds, low nasal bridge and microretrognathia (Supplementary Table 3). Thus, the responsible genes for these manifestations would be included in the narrowed SRO. Compared with the clinical phenotypes of four patients,24 our patient is unique with intractable epilepsy but no microcephaly.
Mapping genomic rearrangements in patients with multiple congenital anomalies has increased our understanding of the etiology of diseases and has led to the identification of a number of disease-causing genes, including CHD735 and STXBP1.36 The narrowed SRO of 17p13.1 is small with the size 148.8 kb but is gene rich and includes 17 genes (known protein-coding genes taken from mRNA reference sequences, UCSC Human Genome Browser March 2006; Figure 1b, Supplementary Table 4). The genes in this SRO were analyzed, and picked up four genes, DLG4/PSD95, GPS2, GABARAP and KCTD11 as the candidates for causing mental retardation.24 DLG4/PSD95 encodes a member of the membrane-associated guanylate kinase family, which is highly expressed in excitatory glutamatergic synapses in the brain.37 DLG4/PSD95 is important for coupling the N-methyl-D-aspartate receptor to pathways that control bidirectional synaptic plasticity and learning.38 However, several studies have reported that DLG4/PSD95 knockout mice do not show an essential function in synaptic development for DLG4/PSD95.39 Likewise, our knockdown zebrafish showed no morphological abnormalities. A possible function for this protein in neurodevelopment cannot, however, be ruled out without further examination. KCTD11 is a suppressor of the Sonic Hedgehog signaling, which is known to be deregulated in medulloblastoma.40 Hedgehog signaling has been described as having a critical function in brain morphogenesis by regulating the ventral patterning of the neural tube.41 GPS2 interacts with regulatory factor X4 variant 3 (RFX4_v3) to modulate transactivation of genes involved in brain morphogenesis and mutagenesis in mice shows that Rfx4_v3 is crucial for normal brain development.42 From these reasons, haploinsufficiency of these genes may also contribute to the phenotype of this patient.
Regarding candidate genes for brain developmental delay, we paid attention to GABARAP in the deletion region. GABA(A) receptors are ligand-gated chloride channels that mediate inhibitory neurotransmission. By screening a cDNA library using GABA(A) receptor γ-2S subunit as a bait, GABARAP was identified as a potential linker between GABA(A) receptors and microtubules.31, 43 Currently, a more general function is emerging for GABARAP, including transport of GABA(A) receptors to and from the cell surface, organization of GABA(A) receptors into post-synaptic clusters, and regulation of steady-state receptor density.43 We analyzed expression patterns of the genes included in the SRO by use of in silico library (UCSC genome browser), and GABARAP showed higher expression levels in the brain. As little is known about the functions of GABARAP, we paid attention to that as a potential candidate gene for neuronal development. To confirm the contribution of this to the phenotype of the patient, we used the gene knockdown technique in zebrafish. As the results showed hypoplastic brain and mandible in gabarap knockdown zebrafish that correlate with common phenotypes of the patient with 17p13.1 deletion, human GABARAP is likely to contribute to the development of anterior structure. Among the patients with 17p13.1 deletion, only our patient showed intractable epilepsy. As there may be an unmasked mutation of GABARAP, we analyzed the sequence of GABARAP in the remaining allele of our patient, but there was no pathogenic mutation. Thus, the reason of the phenotypic difference among the patients with 17p13.1 deletion is unknown. We analyzed 142 DNA samples derived from patients with mental retardation with/without epilepsy, and there were no pathogenic nucleotide alterations in patients with neurodevelopmental disorders. It is, however, still possible that nucleotide mutations in DLG4/PSD95 and GABARAP are the pathogenic cause of neurodevelopmental delay and epilepsy.
As there are other powerful candidate genes, including GPS2, and KCTD11, for neurodevelopmental delay and epilepsy in this region, further studies for the genes including in this region would be required.
References
Lee, J. A. & Lupski, J. R. Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders. Neuron 52, 103–121 (2006).
Emanuel, B. S. & Saitta, S. C. From microscopes to microarrays: dissecting recurrent chromosomal rearrangements. Nat. Rev. Genet. 8, 869–883 (2007).
Shaffer, L. G., Bejjani, B. A., Torchia, B., Kirkpatrick, S., Coppinger, J. & Ballif, B. C. The identification of microdeletion syndromes and other chromosome abnormalities: cytogenetic methods of the past, new technologies for the future. Am. J. Med. Genet. C Semin. Med. Genet. 145, 335–345 (2007).
Shaikh, T. H. Oligonucleotide arrays for high-resolution analysis of copy number alteration in mental retardation/multiple congenital anomalies. Genet. Med. 9, 617–625 (2007).
Stankiewicz, P. & Beaudet, A. L. Use of array CGH in the evaluation of dysmorphology, malformations, developmental delay, and idiopathic mental retardation. Curr. Opin. Genet. Dev. 17, 182–192 (2007).
Slavotinek, A. M. Novel microdeletion syndromes detected by chromosome microarrays. Hum. Genet. 124, 1–17 (2008).
Gu, W. & Lupski, J. R. CNV and nervous system diseases--what's new? Cytogenet. Genome Res. 123, 54–64 (2008).
Shaffer, L. G., Theisen, A., Bejjani, B. A., Ballif, B. C., Aylsworth, A. S., Lim, C. et al. The discovery of microdeletion syndromes in the post-genomic era: review of the methodology and characterization of a new 1q41q42 microdeletion syndrome. Genet. Med. 9, 607–616 (2007).
Sharp, A. J., Mefford, H. C., Li, K., Baker, C., Skinner, C., Stevenson, R. E. et al. A recurrent 15q13.3 microdeletion syndrome associated with mental retardation and seizures. Nat. Genet. 40, 322–328 (2008).
Ballif, B. C., Hornor, S. A., Jenkins, E., Madan-Khetarpal, S., Surti, U., Jackson, K. E. et al. Discovery of a previously unrecognized microdeletion syndrome of 16p11.2-p12.2. Nat. Genet. 39, 1071–1073 (2007).
Kumar, R. A., KaraMohamed, S., Sudi, J., Conrad, D. F., Brune, C., Badner, J. A. et al. Recurrent 16p11.2 microdeletions in autism. Hum. Mol. Genet. 17, 628–638 (2008).
Mefford, H. C., Clauin, S., Sharp, A. J., Moller, R. S., Ullmann, R., Kapur, R. et al. Recurrent reciprocal genomic rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy. Am. J. Hum. Genet. 81, 1057–1069 (2007).
Koolen, D. A., Vissers, L. E., Pfundt, R., de Leeuw, N., Knight, S. J., Regan, R. et al. A new chromosome 17q21.31 microdeletion syndrome associated with a common inversion polymorphism. Nat. Genet. 38, 999–1001 (2006).
Sharp, A. J., Hansen, S., Selzer, R. R., Cheng, Z., Regan, R., Hurst, J. A. et al. Discovery of previously unidentified genomic disorders from the duplication architecture of the human genome. Nat. Genet. 38, 1038–1042 (2006).
Shaw-Smith, C., Pittman, A. M., Willatt, L., Martin, H., Rickman, L., Gribble, S. et al. Microdeletion encompassing MAPT at chromosome 17q21.3 is associated with developmental delay and learning disability. Nat. Genet. 38, 1032–1037 (2006).
Zody, M. C., Garber, M., Adams, D. J., Sharpe, T., Harrow, J., Lupski, J. R. et al. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. Nature 440, 1045–1049 (2006).
Chance, P. F., Abbas, N., Lensch, M. W., Pentao, L., Roa, B. B., Patel, P. I. et al. Two autosomal dominant neuropathies result from reciprocal DNA duplication/deletion of a region on chromosome 17. Hum. Mol. Genet. 3, 223–228 (1994).
Potocki, L., Chen, K. S., Park, S. S., Osterholm, D. E., Withers, M. A., Kimonis, V. et al. Molecular mechanism for duplication 17p11.2− the homologous recombination reciprocal of the Smith-Magenis microdeletion. Nat. Genet. 24, 84–87 (2000).
Stankiewicz, P., Shaw, C. J., Dapper, J. D., Wakui, K., Shaffer, L. G., Withers, M. et al. Genome architecture catalyzes nonrecurrent chromosomal rearrangements. Am. J. Hum. Genet. 72, 1101–1116 (2003).
Chen, K. S., Manian, P., Koeuth, T., Potocki, L., Zhao, Q., Chinault, A. C. et al. Homologous recombination of a flanking repeat gene cluster is a mechanism for a common contiguous gene deletion syndrome. Nat. Genet. 17, 154–163 (1997).
Shaw, C. J., Shaw, C. A., Yu, W., Stankiewicz, P., White, L. D., Beaudet, A. L. et al. Comparative genomic hybridisation using a proximal 17p BAC/PAC array detects rearrangements responsible for four genomic disorders. J. Med. Genet. 41, 113–119 (2004).
Cardoso, C., Leventer, R. J., Ward, H. L., Toyo-Oka, K., Chung, J., Gross, A. et al. Refinement of a 400-kb critical region allows genotypic differentiation between isolated lissencephaly, Miller-Dieker syndrome, and other phenotypes secondary to deletions of 17p13.3. Am. J. Hum. Genet. 72, 918–930 (2003).
Bi, W., Sapir, T., Shchelochkov, O. A., Zhang, F., Withers, M. A., Hunter, J. V. et al. Increased LIS1 expression affects human and mouse brain development. Nat. Genet. 41, 168–177 (2009).
Krepischi-Santos, A. C., Rajan, D., Temple, I. K., Shrubb, V., Crolla, J. A., Huang, S. et al. Constitutional haploinsufficiency of tumor suppressor genes in mentally retarded patients with microdeletions in 17p13.1. Cytogenet. Genome Res. 125, 1–7 (2009).
Shimojima, K., Adachi, M., Tanaka, M., Tanaka, Y., Kurosawa, K. & Yamamoto, T. Clinical features of microdeletion 9q22.3 (pat). Clin. Genet. 75, 384–393 (2009).
Kimmel, C. B., Ballard, W. W., Kimmel, S. R., Ullmann, B. & Schilling, T. F. Stages of embryonic development of the zebrafish. Dev. Dyn. 203, 253–310 (1995).
Razzaque, M. A., Nishizawa, T., Komoike, Y., Yagi, H., Furutani, M., Amo, R. et al. Germline gain-of-function mutations in RAF1 cause Noonan syndrome. Nat. Genet. 39, 1013–1017 (2007).
Hamano, S., Yamashita, S., Tanaka, M., Yoshinari, S., Minamitani, M. & Eto, Y. Therapeutic efficacy and adverse effects of adrenocorticotropic hormone therapy in west syndrome: differences in dosage of adrenocorticotropic hormone, onset of age, and cause. J. Pediatr. 148, 485–488 (2006).
Hokama, T., Gushi Ken, M. & Nosoko, N. Iron deficiency anaemia and child development. Asia Pac. J. Public Health 17, 19–21 (2005).
Ying, Z., Bingaman, W. & Najm, I. M. Increased numbers of coassembled PSD-95 to NMDA-receptor subunits NR2B and NR1 in human epileptic cortical dysplasia. Epilepsia 45, 314–321 (2004).
Wang, H., Bedford, F. K., Brandon, N. J., Moss, S. J. & Olsen, R. W. GABA(A)-receptor-associated protein links GABA(A) receptors and the cytoskeleton. Nature 397, 69–72 (1999).
Meyer, M. P., Trimmer, J. S., Gilthorpe, J. D. & Smith, S. J. Characterization of zebrafish PSD-95 gene family members. J. Neurobiol. 63, 91–105 (2005).
Porter, K., Komiyama, N. H., Vitalis, T., Kind, P. C. & Grant, S. G. Differential expression of two NMDA receptor interacting proteins, PSD-95 and SynGAP during mouse development. Eur. J. Neurosci. 21, 351–362 (2005).
Stathakis, D. G., Hoover, K. B., You, Z. & Bryant, P. J. Human postsynaptic density-95 (PSD95): location of the gene (DLG4) and possible function in nonneural as well as in neural tissues. Genomics 44, 71–82 (1997).
Vissers, L. E., van Ravenswaaij, C. M., Admiraal, R., Hurst, J. A., de Vries, B. B., Janssen, I. M. et al. Mutations in a new member of the chromodomain gene family cause CHARGE syndrome. Nat. Genet. 36, 955–957 (2004).
Saitsu, H., Kato, M., Mizuguchi, T., Hamada, K., Osaka, H., Tohyama, J. et al. De novo mutations in the gene encoding STXBP1 (MUNC18-1) cause early infantile epileptic encephalopathy. Nat. Genet. 40, 782–788 (2008).
Beique, J. C., Lin, D. T., Kang, M. G., Aizawa, H., Takamiya, K. & Huganir, R. L. Synapse-specific regulation of AMPA receptor function by PSD-95. Proc. Natl Acad. Sci. USA 103, 19535–19540 (2006).
Migaud, M., Charlesworth, P., Dempster, M., Webster, L. C., Watabe, A. M., Makhinson, M. et al. Enhanced long-term potentiation and impaired learning in mice with mutant postsynaptic density-95 protein. Nature 396, 433–439 (1998).
McGee, A. W., Topinka, J. R., Hashimoto, K., Petralia, R. S., Kakizawa, S., Kauer, F. W. et al. PSD-93 knock-out mice reveal that neuronal MAGUKs are not required for development or function of parallel fiber synapses in cerebellum. J. Neurosci. 21, 3085–3091 (2001).
Di Marcotullio, L., Ferretti, E., De Smaele, E., Argenti, B., Mincione, C., Zazzeroni, F. et al. REN(KCTD11) is a suppressor of Hedgehog signaling and is deleted in human medulloblastoma. Proc. Natl Acad. Sci. USA 101, 10833–10838 (2004).
Di Marcotullio, L., Ferretti, E., De Smaele, E., Screpanti, I. & Gulino, A. Suppressors of hedgehog signaling: linking aberrant development of neural progenitors and tumorigenesis. Mol. Neurobiol. 34, 193–204 (2006).
Zhang, D., Harry, G. J., Blackshear, P. J. & Zeldin, D. C. G-protein pathway suppressor 2 (GPS2) interacts with the regulatory factor X4 variant 3 (RFX4_v3) and functions as a transcriptional co-activator. J. Biol. Chem. 283, 8580–8590 (2008).
Coyle, J. E. & Nikolov, D. B. GABARAP: lessons for synaptogenesis. Neuroscientist 9, 205–216 (2003).
Acknowledgements
This work was supported by the International Research and Educational Institute for Integrated Medical Sciences and the Tokyo Women's Medical University, which is supported by the Program for Promoting the Establishment of Strategic Research Centers; Special Coordination Funds for Promoting Science and Technology; and Ministry of Education, Culture, Sports, Science and Technology (Japan).
Author information
Authors and Affiliations
Corresponding author
Additional information
Supplementary Information accompanies the paper on Journal of Human Genetics website (http://www.nature.com/jhg)
Supplementary information
Rights and permissions
About this article
Cite this article
Komoike, Y., Shimojima, K., Liang, JS. et al. A functional analysis of GABARAP on 17p13.1 by knockdown zebrafish. J Hum Genet 55, 155–162 (2010). https://doi.org/10.1038/jhg.2010.1
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/jhg.2010.1
Keywords
This article is cited by
-
Family-based genome-wide copy number scan identifies five new genes of dyslexia involved in dendritic spinal plasticity
Journal of Human Genetics (2013)
-
Zebrafish: a model for the study of addiction genetics
Human Genetics (2012)