1
|
Ballios BG, Mandola A, Tayyib A, Tumber A, Garkaby J, Vong L, Heon E, Roifman CM, Vincent A. Deep phenotypic characterization of the retinal dystrophy in patients with RNU4ATAC-associated Roifman syndrome. Eye (Lond) 2023; 37:3734-3742. [PMID: 37225827 PMCID: PMC10697969 DOI: 10.1038/s41433-023-02581-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
PURPOSE To characterize the retinal phenotype in RNU4ATAC-associated Roifman syndrome. METHODS Ten patients (including 8 males) with molecularly confirmed Roifman syndrome underwent detailed ophthalmologic evaluation including fundus imaging, fundus autofluorescence (FAF) imaging, spectral-domain optical coherence tomography (SD-OCT), and electroretinography (ERG). Six patients had follow-up eye exams. All patients also underwent comprehensive examination for features of extra-retinal Roifman syndrome. RESULTS All patients had biallelic RNU4ATAC variants. Nyctalopia was common (7/10). Visual acuity at presentation ranged from 20/20 to 20/200 (Age Range: 5-41 years). Retinal exam revealed features of generalized retinopathy with mid-peripheral pigment epithelial changes. A para or peri-foveal ring of hyper-autofluorescence was the commonest FAF abnormality noted (6/8). The SD-OCT demonstrated relative preservation of the foveal ellipsoid zone in six cases; associated features included cystoid changes (5/10) and posterior staphyloma (3/10). The ERG was abnormal in all patients; nine showed generalized rod-cone dystrophy, whilst one patient with sectoral retinal involvement only had isolated rod dystrophy (20 years old). On follow-up examination (Mean duration: 8.16 years), progressive loss of visual acuity (2/6), mid-peripheral retinal atrophy (3/6) or shortening of ellipsoid zone width (1/6) were observed. CONCLUSION This study has characterized the retinal phenotype in RNU4ATAC-associated Roifman syndrome. Retinal involvement is universal, early-onset, and overall, the retinal and FAF features are consistent with rod-cone degeneration that is slowly progressive over time. The sub-foveal retinal ultrastructure is relatively preserved in majority of patients. Phenotypic variability independent of age exists, and more study of allelic- and sex-based determinants of disease severity are necessary.
Collapse
Affiliation(s)
- Brian G Ballios
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
| | - Amarilla Mandola
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Alaa Tayyib
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anupreet Tumber
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jenny Garkaby
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
| | - Linda Vong
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada
| | - Chaim M Roifman
- Division of Immunology and Allergy, The Hospital for Sick Children and the University of Toronto, Toronto, ON, Canada
- The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, University of Toronto, Toronto, ON, Canada.
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
| |
Collapse
|
2
|
The Names of Things: The 2018 Bernard Sachs Lecture. Pediatr Neurol 2021; 122:41-49. [PMID: 34330614 DOI: 10.1016/j.pediatrneurol.2021.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 11/22/2022]
Abstract
In 2018, I was honored to receive the Bernard Sachs Award for a lifetime of work expanding knowledge of diverse neurodevelopmental disorders. Summarizing work over more than 30 years is difficult but is an opportunity to chronicle the dramatic changes in the medical and scientific world that have transformed the field of Child Neurology over this time, as reflected in my own work. Here I have chosen to highlight five broad themes of my research beginning with my interest in descriptive terms that drive wider understanding and my choice for the title of this review. From there I will go on to contrast the state of knowledge as I entered the field with the state of knowledge today for four human brain malformations-lissencephaly, megalencephaly, cerebellar malformations, and polymicrogyria. For all, the changes have been dramatic.
Collapse
|
3
|
Minor Intron Splicing from Basic Science to Disease. Int J Mol Sci 2021; 22:ijms22116062. [PMID: 34199764 PMCID: PMC8199999 DOI: 10.3390/ijms22116062] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 01/14/2023] Open
Abstract
Pre-mRNA splicing is an essential step in gene expression and is catalyzed by two machineries in eukaryotes: the major (U2 type) and minor (U12 type) spliceosomes. While the majority of introns in humans are U2 type, less than 0.4% are U12 type, also known as minor introns (mi-INTs), and require a specialized spliceosome composed of U11, U12, U4atac, U5, and U6atac snRNPs. The high evolutionary conservation and apparent splicing inefficiency of U12 introns have set them apart from their major counterparts and led to speculations on the purpose for their existence. However, recent studies challenged the simple concept of mi-INTs splicing inefficiency due to low abundance of their spliceosome and confirmed their regulatory role in alternative splicing, significantly impacting the expression of their host genes. Additionally, a growing list of minor spliceosome-associated diseases with tissue-specific pathologies affirmed the importance of minor splicing as a key regulatory pathway, which when deregulated could lead to tissue-specific pathologies due to specific alterations in the expression of some minor-intron-containing genes. Consequently, uncovering how mi-INTs splicing is regulated in a tissue-specific manner would allow for better understanding of disease pathogenesis and pave the way for novel therapies, which we highlight in this review.
Collapse
|
4
|
Abstract
Systematics is described for annotation of variations in RNA molecules. The conceptual framework is part of Variation Ontology (VariO) and facilitates depiction of types of variations, their functional and structural effects and other consequences in any RNA molecule in any organism. There are more than 150 RNA related VariO terms in seven levels, which can be further combined to generate even more complicated and detailed annotations. The terms are described together with examples, usually for variations and effects in human and in diseases. RNA variation type has two subcategories: variation classification and origin with subterms. Altogether six terms are available for function description. Several terms are available for affected RNA properties. The ontology contains also terms for structural description for affected RNA type, post-transcriptional RNA modifications, secondary and tertiary structure effects and RNA sugar variations. Together with the DNA and protein concepts and annotations, RNA terms allow comprehensive description of variations of genetic and non-genetic origin at all possible levels. The VariO annotations are readable both for humans and computer programs for advanced data integration and mining.
Collapse
Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
| |
Collapse
|
5
|
Clinical interpretation of variants identified in RNU4ATAC, a non-coding spliceosomal gene. PLoS One 2020; 15:e0235655. [PMID: 32628740 PMCID: PMC7337319 DOI: 10.1371/journal.pone.0235655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/19/2020] [Indexed: 12/16/2022] Open
Abstract
Biallelic variants in RNU4ATAC, a non-coding gene transcribed into the minor spliceosome component U4atac snRNA, are responsible for three rare recessive developmental diseases, namely Taybi-Linder/MOPD1, Roifman and Lowry-Wood syndromes. Next-generation sequencing of clinically heterogeneous cohorts (children with either a suspected genetic disorder or a congenital microcephaly) recently identified mutations in this gene, illustrating how profoundly these technologies are modifying genetic testing and assessment. As RNU4ATAC has a single non-coding exon, the bioinformatic prediction algorithms assessing the effect of sequence variants on splicing or protein function are irrelevant, which makes variant interpretation challenging to molecular diagnostic laboratories. In order to facilitate and improve clinical diagnostic assessment and genetic counseling, we present i) an update of the previously reported RNU4ATAC mutations and an analysis of the genetic variations affecting this gene using the Genome Aggregation Database (gnomAD) resource; ii) the pathogenicity prediction performances of scores computed based on an RNA structure prediction tool and of those produced by the Combined Annotation Dependent Depletion tool for the 285 RNU4ATAC variants identified in patients or in large-scale sequencing projects; iii) a method, based on a cellular assay, that allows to measure the effect of RNU4ATAC variants on splicing efficiency of a minor (U12-type) reporter intron. Lastly, the concordance of bioinformatic predictions and cellular assay results was investigated.
Collapse
|
6
|
Lardelli RM, Lykke-Andersen J. Competition between maturation and degradation drives human snRNA 3' end quality control. Genes Dev 2020; 34:989-1001. [PMID: 32499401 PMCID: PMC7328512 DOI: 10.1101/gad.336891.120] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 04/29/2020] [Indexed: 12/11/2022]
Abstract
Polymerases and exonucleases act on 3' ends of nascent RNAs to promote their maturation or degradation but how the balance between these activities is controlled to dictate the fates of cellular RNAs remains poorly understood. Here, we identify a central role for the human DEDD deadenylase TOE1 in distinguishing the fates of small nuclear (sn)RNAs of the spliceosome from unstable genome-encoded snRNA variants. We found that TOE1 promotes maturation of all regular RNA polymerase II transcribed snRNAs of the major and minor spliceosomes by removing posttranscriptional oligo(A) tails, trimming 3' ends, and preventing nuclear exosome targeting. In contrast, TOE1 promotes little to no maturation of tested U1 variant snRNAs, which are instead targeted by the nuclear exosome. These observations suggest that TOE1 is positioned at the center of a 3' end quality control pathway that selectively promotes maturation and stability of regular snRNAs while leaving snRNA variants unprocessed and exposed to degradation in what could be a widespread mechanism of RNA quality control given the large number of noncoding RNAs processed by DEDD deadenylases.
Collapse
Affiliation(s)
- Rea M Lardelli
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| | - Jens Lykke-Andersen
- Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA
| |
Collapse
|
7
|
Wang Y, Wu X, Du L, Zheng J, Deng S, Bi X, Chen Q, Xie H, Férec C, Cooper DN, Luo Y, Fang Q, Chen JM. Identification of compound heterozygous variants in the noncoding RNU4ATAC gene in a Chinese family with two successive foetuses with severe microcephaly. Hum Genomics 2018; 12:3. [PMID: 29370840 PMCID: PMC5784706 DOI: 10.1186/s40246-018-0135-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Background Whole-exome sequencing (WES) over the last few years has been increasingly employed for clinical diagnosis. However, one caveat with its use is that it inevitably fails to detect disease-causative variants that occur within noncoding RNA genes. Our experience in identifying pathogenic variants in the noncoding RNU4ATAC gene, in a Chinese family where two successive foetuses had been affected by severe microcephaly, is a case in point. These foetuses exhibited remarkably similar phenotypes in terms of their microcephaly and brain abnormalities; however, the paucity of other characteristic phenotypic features had made a precise diagnosis impossible. Given that no external causative factors had been reported/identified during the pregnancies, we sought a genetic cause for the phenotype in the proband, the second affected foetus. Results A search for chromosomal abnormalities and pathogenic copy number variants proved negative. WES was also negative. These initial failures prompted us to consider the potential role of RNU4ATAC, a noncoding gene implicated in microcephalic osteodysplastic primordial dwarfism type-1 (MOPD1), a severe autosomal recessive disease characterised by dwarfism, severe microcephaly and neurological abnormalities. Subsequent targeted sequencing of RNU4ATAC resulted in the identification of compound heterozygous variants, one being the most frequently reported MOPD1-causative mutation (51G>A), whereas the other was a novel 29T>A variant. Four distinct lines of evidence (allele frequency in normal populations, evolutionary conservation of the affected nucleotide, occurrence within a known mutational hotspot for MOPD1-causative variants and predicted effect on RNA secondary structure) allowed us to conclude that 29T>A is a new causative variant for MOPD1. Conclusions Our findings highlight the limitations of WES in failing to detect variants within noncoding RNA genes and provide support for a role for whole-genome sequencing as a first-tier genetic test in paediatric medicine. Additionally, the identification of a novel RNU4ATAC variant within the mutational hotspot for MOPD1-causative variants further strengthens the critical role of the 5′ stem-loop structure of U4atac in health and disease. Finally, this analysis enabled us to provide prenatal diagnosis and genetic counselling for the mother’s third pregnancy, the first report of its kind in the context of inherited RNU4ATAC variants.
Collapse
Affiliation(s)
- Ye Wang
- Fetal Medicine Centre, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xueli Wu
- Department of Dermatology, Guangzhou Institute of Dermatology, Guangzhou, China
| | - Liu Du
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Ju Zheng
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Songqing Deng
- Fetal Medicine Centre, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Xin Bi
- Guangzhou KingMed Center for Clinical Laboratory, Guangzhou, China
| | - Qiuyan Chen
- Dongguan Women and Children's Hospital, Dongguan, China
| | - Hongning Xie
- Department of Ultrasonic Medicine, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Claude Férec
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", INSERM, EFS - Bretagne, Université de Brest, CHRU Brest, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Yanmin Luo
- Fetal Medicine Centre, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Qun Fang
- Fetal Medicine Centre, Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.
| | - Jian-Min Chen
- UMR1078 "Génétique, Génomique Fonctionnelle et Biotechnologies", INSERM, EFS - Bretagne, Université de Brest, CHRU Brest, Brest, France. .,INSERM UMR1078, EFS, UBO, 22 avenue Camille Desmoulins, 29238, Brest, France.
| |
Collapse
|
8
|
Farach LS, Little ME, Duker AL, Logan CV, Jackson A, Hecht JT, Bober M. The expanding phenotype of RNU4ATAC pathogenic variants to Lowry Wood syndrome. Am J Med Genet A 2017; 176:465-469. [PMID: 29265708 DOI: 10.1002/ajmg.a.38581] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 11/27/2017] [Indexed: 11/10/2022]
Abstract
RNU4ATAC pathogenic variants to date have been associated with microcephalic osteodysplastic primordial dwarfism, type 1 and Roifman syndrome. Both conditions are clinically distinct skeletal dysplasias with microcephalic osteodysplastic primordial dwarfism, type 1 having a more severe phenotype than Roifman syndrome. Some of the overlapping features of the two conditions include developmental delay, microcephaly, and immune deficiency. The features also overlap with Lowry Wood syndrome, another rare but well-defined skeletal dysplasia for which the genetic etiology has not been identified. Characteristic features include multiple epiphyseal dysplasia and microcephaly. Here, we describe three patients with Lowry Wood syndrome with biallelic RNU4ATAC pathogenic variants. This report expands the phenotypic spectrum for biallelic RNU4ATAC disorder causing variants and is the first to establish the genetic cause for Lowry Wood syndrome.
Collapse
Affiliation(s)
- Laura S Farach
- Department of Pediatrics, Division of Medical Genetics, McGovern Medical School, University of Texas Health Science Center, Houston at Houston, Texas
| | - Mary E Little
- Division of Medical Genetics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Angela L Duker
- Division of Medical Genetics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| | - Clare V Logan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jaqueline T Hecht
- Department of Pediatrics, Pediatric Research Center, McGovern Medical School and School of Dentistry, University of Texas Health Science Center at Houston, Houston, Texas
| | - Michael Bober
- Division of Medical Genetics, Nemours/Alfred I. duPont Hospital for Children, Wilmington, Delaware
| |
Collapse
|
9
|
Abstract
PURPOSE OF THE REVIEW This review will provide an overview of the microcephalic primordial dwarfism (MPD) class of disorders and provide the reader comprehensive clinical review with suggested care guidelines for patients with microcephalic osteodysplastic primordial dwarfism, type II (MOPDII). RECENT FINDINGS Over the last 15 years, significant strides have been made in the diagnosis, natural history, and management of MOPDII. MOPDII is the most common and well described form of MPD. The classic features of the MPD group are severe pre- and postnatal growth retardation, with marked microcephaly. In addition to these features, individuals with MOPDII have characteristic facies, skeletal dysplasia, abnormal dentition, and an increased risk for cerebrovascular disease and insulin resistance. Biallelic loss-of-function mutations in the pericentrin gene cause MOPDII, which is inherited in an autosomal recessive manner.
Collapse
Affiliation(s)
- Michael B. Bober
- 0000 0001 2166 5843grid.265008.9Stanley Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA USA
- 0000 0004 0458 9676grid.239281.3A. I. DuPont Hospital for Children, 1600 Rockland-Road, Wilmington, DE 19803 USA
| | - Andrew P. Jackson
- 0000 0004 1936 7988grid.4305.2MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| |
Collapse
|
10
|
Common variants on 17q25 and gene-gene interactions conferring risk of schizophrenia in Han Chinese population and regulating gene expressions in human brain. Mol Psychiatry 2016; 21:1244-50. [PMID: 26728569 DOI: 10.1038/mp.2015.204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 10/11/2015] [Accepted: 11/05/2015] [Indexed: 11/09/2022]
Abstract
Recently, two genome-wide association studies (GWASs) of schizophrenia (SCZ) in Han Chinese identified several susceptibility loci. Replication efforts aiming to validate the GWAS findings were made and focused on the top hits. We conducted a more extensive follow-up study in an independent sample of 1471 cases and 1528 matched controls to verify 26 genetic variants by including nine top single-nucleotide polymorphisms (SNPs) that reached genome-wide significance and 17 promising SNPs nominated in the initial discovery phase. rs8073471 in an intron of tubulin-folding cofactor D (TBCD) obtained nominal significance (P<0.01) in single SNP analysis. Logistic regression identified significant interaction between rs3744165 (5'-untranslated region variant of exon 2 of zinc finger protein 750 (ZNF750), and in an intron of TBCD) and rs8073471 (Deviance test P-value=2.77 × 10(-34)). Both SNPs are located at 17q25, an interesting region that has been implicated in SCZ. By using the Genotype-Tissue Expression (GTEx) data set, we implemented an expression quantitative trait loci epistasis analysis to explore the association between the genotype combinations of the two SNPs and gene expression levels in 13 areas of human central nervous system. We observed that rs3744165 × rs8073471 interaction modulated the expression profile of TEAD3 (P=1.87 × 10(-8)), SH3TC2 (P=2.00 × 10(-8)), KCNK9 (P=5.20 × 10(-7)) and PPDPF (P=1.13 × 10(-6)) in postmortem cortex tissue; EFNA1 (P=7.26 × 10(-9)), RNU4ATAC (P=2.32 × 10(-8)) and NUPL2 (P=6.79 × 10(-8)) in cerebellum tissue. To the best of our knowledge, our study is the first one that links TBCD and ZNF750 mutations to SCZ susceptibility and to the transcript levels in human brain tissues. Further efforts are needed to understand the role of those variants in the pathogenesis of SCZ.
Collapse
|
11
|
Putoux A, Alqahtani A, Pinson L, Paulussen ADC, Michel J, Besson A, Mazoyer S, Borg I, Nampoothiri S, Vasiljevic A, Uwineza A, Boggio D, Champion F, de Die-Smulders CE, Gardeitchik T, van Putten WK, Perez MJ, Musizzano Y, Razavi F, Drunat S, Verloes A, Hennekam R, Guibaud L, Alix E, Sanlaville D, Lesca G, Edery P. Refining the phenotypical and mutational spectrum of Taybi-Linder syndrome. Clin Genet 2016; 90:550-555. [PMID: 27040866 DOI: 10.1111/cge.12781] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 03/19/2016] [Accepted: 03/21/2016] [Indexed: 02/04/2023]
Abstract
Taybi-Linder syndrome (TALS, OMIM 210710) is a rare autosomal recessive disorder belonging to the group of microcephalic osteodysplastic primordial dwarfisms (MOPD). This syndrome is characterized by short stature, skeletal anomalies, severe microcephaly with brain malformations and facial dysmorphism, and is caused by mutations in RNU4ATAC. RNU4ATAC is transcribed into a non-coding small nuclear RNA which is a critical component of the minor spliceosome. We report here four foetuses and four unrelated patients with RNU4ATAC mutations. We provide antenatal descriptions of this rare syndrome including unusual features found in two twin foetuses with compound heterozygosity for two rare mutations who presented with mild intrauterine growth retardation and atypical dysmorphic facial features. We also carried out a literature review of the patients described up to now with RNU4ATAC mutations, affected either with TALS or Roifman syndrome, a recently described allelic disorder.
Collapse
Affiliation(s)
- A Putoux
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - A Alqahtani
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - L Pinson
- Département de Génétique Médicale, Centre Hospitalier Universitaire, Montpellier, France
| | - A D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands.,School for Oncology & Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - J Michel
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - A Besson
- Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - S Mazoyer
- Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - I Borg
- Department of Pathology, University of Malta, Medical Genetics Unit, Mater Dei Hospital, Malta
| | - S Nampoothiri
- Department of Paediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, India
| | - A Vasiljevic
- Centre de Pathologie et Neuropathologie Est, Hospices Civils de Lyon, Lyon, France
| | - A Uwineza
- Centre for Medical Genetics, College of Medicine and Health Sciences, University of Rwanda, Huye, Rwanda
| | - D Boggio
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - F Champion
- Service de Gynécologie-Obstétrique, Hospices Civils de Lyon, Lyon, France
| | - C E de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Centre, Maastricht, the Netherlands.,School for Oncology & Developmental Biology (GROW), Maastricht University Medical Centre, Maastricht, the Netherlands
| | - T Gardeitchik
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - W K van Putten
- Paediatric Intensive Care Unit, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - M J Perez
- Département de Génétique Médicale, Unité de fœtopathologie, Centre Hospitalier Universitaire, Montpellier, France
| | - Y Musizzano
- Département de Pathologie Tissulaire et Cellulaire des tumeurs, Pôle Biologie Pathologie, Centre Hospitalier Universitaire, Montpellier, France
| | - F Razavi
- Département de Génétique Histologie-Embryologie-Cytogénétique, Hôpital Necker-Enfant Malade, Paris, France
| | - S Drunat
- Department of Genetics, APHP-Robert DEBRE University Hospital, and Paris-Diderot University, Paris, France
| | - A Verloes
- Department of Genetics, APHP-Robert DEBRE University Hospital, and Paris-Diderot University, Paris, France
| | - R Hennekam
- Department of Paediatrics, Academic Medical Centre, University of Amsterdam, Amsterdam, the Netherlands
| | - L Guibaud
- Département d'Imagerie Pédiatrique et Fœtale, Centre Pluridisciplinaire de Diagnostic Prénatal, Hôpital Femme Mère Enfant, Lyon-Bron, France
| | - E Alix
- Service de Génétique, Hospices Civils de Lyon, Lyon, France
| | - D Sanlaville
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - G Lesca
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| | - P Edery
- Service de Génétique, Hospices Civils de Lyon, Lyon, France.,Centre de Recherche en Neurosciences de Lyon, INSERM U1028, UMR CNRS 5292, Université Claude Bernard Lyon 1, Lyon, France
| |
Collapse
|
12
|
Abstract
The human transcriptome is composed of a vast RNA population that undergoes further diversification by splicing. Detecting specific splice sites in this large sequence pool is the responsibility of the major and minor spliceosomes in collaboration with numerous splicing factors. This complexity makes splicing susceptible to sequence polymorphisms and deleterious mutations. Indeed, RNA mis-splicing underlies a growing number of human diseases with substantial societal consequences. Here, we provide an overview of RNA splicing mechanisms followed by a discussion of disease-associated errors, with an emphasis on recently described mutations that have provided new insights into splicing regulation. We also discuss emerging strategies for splicing-modulating therapy.
Collapse
Affiliation(s)
- Marina M Scotti
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
| | - Maurice S Swanson
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, Florida 32610-3610 USA
| |
Collapse
|
13
|
Merico D, Roifman M, Braunschweig U, Yuen RKC, Alexandrova R, Bates A, Reid B, Nalpathamkalam T, Wang Z, Thiruvahindrapuram B, Gray P, Kakakios A, Peake J, Hogarth S, Manson D, Buncic R, Pereira SL, Herbrick JA, Blencowe BJ, Roifman CM, Scherer SW. Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing. Nat Commun 2015; 6:8718. [PMID: 26522830 PMCID: PMC4667643 DOI: 10.1038/ncomms9718] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/25/2015] [Indexed: 11/09/2022] Open
Abstract
Roifman Syndrome is a rare congenital disorder characterized by growth retardation, cognitive delay, spondyloepiphyseal dysplasia and antibody deficiency. Here we utilize whole-genome sequencing of Roifman Syndrome patients to reveal compound heterozygous rare variants that disrupt highly conserved positions of the RNU4ATAC small nuclear RNA gene, a minor spliceosome component that is essential for minor intron splicing. Targeted sequencing confirms allele segregation in six cases from four unrelated families. RNU4ATAC rare variants have been recently reported to cause microcephalic osteodysplastic primordial dwarfism, type I (MOPD1), whose phenotype is distinct from Roifman Syndrome. Strikingly, all six of the Roifman Syndrome cases have one variant that overlaps MOPD1-implicated structural elements, while the other variant overlaps a highly conserved structural element not previously implicated in disease. RNA-seq analysis confirms extensive and specific defects of minor intron splicing. Available allele frequency data suggest that recessive genetic disorders caused by RNU4ATAC rare variants may be more prevalent than previously reported. Roifman Syndrome is a rare disorder whose disease manifestations include growth retardation, spondyloepiphyseal dysplasia and immunodeficiency. Here, the authors use whole-genome sequencing to discover that rare compound heterozygous variants disrupting the small nuclear RNA gene RNU4ATAC cause Roifman Syndrome.
Collapse
Affiliation(s)
- Daniele Merico
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8.,The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, Toronto, Ontario, Canada M5G 1Z5.,Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada M5G 1X8
| | | | - Ryan K C Yuen
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Roumiana Alexandrova
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Andrea Bates
- Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Brenda Reid
- Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Thomas Nalpathamkalam
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Zhuozhi Wang
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Paul Gray
- Department of Immunology and Infectious Diseases, Sydney Children's Hospital, Sydney, New South Wales 2031, Australia
| | - Alyson Kakakios
- Department of Allergy and Immunology, The Children's Hospital at Westmead, Westmead, New South Wales 2145, Australia
| | - Jane Peake
- Queensland Paediatric Immunology and Allergy Service, The Lady Cilento Children's Hospital, South Brisbane, Queensland 4101, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland 4006, Australia
| | - Stephanie Hogarth
- Queensland Paediatric Immunology and Allergy Service, The Lady Cilento Children's Hospital, South Brisbane, Queensland 4101, Australia.,School of Medicine, University of Queensland, Brisbane, Queensland 4006, Australia
| | - David Manson
- Department of Diagnostic Imaging, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Raymond Buncic
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Sergio L Pereira
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Jo-Anne Herbrick
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada M5S 3E1.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8
| | - Chaim M Roifman
- Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada M5G 1X8.,Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 1X8
| | - Stephen W Scherer
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada M5G 0A4.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada M5S 1A8.,McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada M5G 0A4.,Centre of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah 21589, Kingdom of Saudi Arabia
| |
Collapse
|
14
|
Sam C, Li FF, Liu SL. Inherited neurovascular diseases affecting cerebral blood vessels and smooth muscle. Metab Brain Dis 2015; 30:1105-16. [PMID: 25893882 DOI: 10.1007/s11011-015-9668-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 04/01/2015] [Indexed: 12/15/2022]
Abstract
Neurovascular diseases are among the leading causes of mortality and permanent disability due to stroke, aneurysm, and other cardiovascular complications. Cerebral autosomal-dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) and Marfan syndrome are two neurovascular disorders that affect smooth muscle cells through accumulation of granule and osmiophilic materials and defective elastic fiber formations respectively. Moyamoya disease, hereditary hemorrhagic telangiectasia (HHT), microcephalic osteodysplastic primordial dwarfism type II (MOPD II), and Fabry's disease are disorders that affect the endothelium cells of blood vessels through occlusion or abnormal development. While much research has been done on mapping out mutations in these diseases, the exact mechanisms are still largely unknown. This paper briefly introduces the pathogenesis, genetics, clinical symptoms, and current methods of treatment of the diseases in the hope that it can help us better understand the mechanism of these diseases and work on ways to develop better diagnosis and treatment.
Collapse
Affiliation(s)
- Christine Sam
- Genomics Research Center (One of the State-Province Key Laboratory of Biopharmaceutical Engineering, China), Harbin, China
| | | | | |
Collapse
|
15
|
Abdel-Salam GMH, Emam BA, Khalil YM, Abdel-Hamid MS. Long-term survival in microcephalic osteodysplastic primordial dwarfism type I: Evaluation of an 18-year-old male with g.55G>A homozygous mutation in RNU4ATAC. Am J Med Genet A 2015; 170A:277-82. [PMID: 26419500 DOI: 10.1002/ajmg.a.37409] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/16/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Ghada M H Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Bayoumi A Emam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Yasmin M Khalil
- Department of Orodental Genetics, Orodental Research Division, National Research Centre, Cairo, Egypt
| | - Mohamed S Abdel-Hamid
- Department of Medical Molecular Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| |
Collapse
|
16
|
Primordial dwarfism: overview of clinical and genetic aspects. Mol Genet Genomics 2015; 291:1-15. [PMID: 26323792 DOI: 10.1007/s00438-015-1110-y] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 08/21/2015] [Indexed: 01/16/2023]
Abstract
Primordial dwarfism is a group of genetic disorders which include Seckel Syndrome, Silver-Russell Syndrome, Microcephalic Osteodysplastic Primordial Dwarfism types I/III, II and Meier-Gorlin Syndrome. This genetic disorder group is characterized by intra-uterine growth retardation and post-natal growth abnormalities which occur as a result of disorganized molecular and genomic changes in embryonic stage and, thus, it represents a unique area to study growth and developmental abnormalities. Lot of research has been carried out on different aspects; however, a consolidated review that discusses an overall spectrum of this disorder is not accessible. Recent research in this area points toward important molecular and cellular mechanisms in human body that regulate the complexity of growth process. Studies have emerged that have clearly associated with a number of abnormal chromosomal, genetic and epigenetic alterations that can predispose an embryo to develop PD-associated developmental defects. Finding and associating such fundamental changes to its subtypes will help in re-examination of alleged functions at both cellular and developmental levels and thus reveal the intrinsic mechanism that leads to a balanced growth. Although such findings have unraveled a subtle understanding of growth process, we further require active research in terms of identification of reliable biomarkers for different subtypes as an immediate requirement for clinical utilization. It is hoped that further study will advance the understanding of basic mechanisms regulating growth relevant to human health. Therefore, this review has been written with an aim to present an overview of chromosomal, molecular and epigenetic modifications reported to be associated with different subtypes of this heterogenous disorder. Further, latest findings with respect to clinical and molecular genetics research have been summarized to aid the medical fraternity in their clinical utility, for diagnosing disorders where there are overlapping physical attributes and simultaneously inform about the latest developments in PD biology.
Collapse
|
17
|
Kilic E, Yigit G, Utine GE, Wollnik B, Mihci E, Nur BG, Boduroglu K. A novel mutation in RNU4ATAC in a patient with microcephalic osteodysplastic primordial dwarfism type I. Am J Med Genet A 2015; 167A:919-21. [PMID: 25735804 DOI: 10.1002/ajmg.a.36955] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/21/2014] [Indexed: 11/11/2022]
Affiliation(s)
- Esra Kilic
- Faculty of Medicine, Division of Pediatric Genetics, Hacettepe University, Ankara, Turkey
| | | | | | | | | | | | | |
Collapse
|
18
|
Jafarifar F, Dietrich RC, Hiznay JM, Padgett RA. Biochemical defects in minor spliceosome function in the developmental disorder MOPD I. RNA (NEW YORK, N.Y.) 2014; 20:1078-89. [PMID: 24865609 PMCID: PMC4114687 DOI: 10.1261/rna.045187.114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Biallelic mutations of the human RNU4ATAC gene, which codes for the minor spliceosomal U4atac snRNA, cause the developmental disorder, MOPD I/TALS. To date, nine separate mutations in RNU4ATAC have been identified in MOPD I patients. Evidence suggests that all of these mutations lead to abrogation of U4atac snRNA function and impaired minor intron splicing. However, the molecular basis of these effects is unknown. Here, we use a variety of in vitro and in vivo assays to address this question. We find that only one mutation, 124G>A, leads to significantly reduced expression of U4atac snRNA, whereas four mutations, 30G>A, 50G>A, 50G>C and 51G>A, show impaired binding of essential protein components of the U4atac/U6atac di-snRNP in vitro and in vivo. Analysis of MOPD I patient fibroblasts and iPS cells homozygous for the most common mutation, 51G>A, shows reduced levels of the U4atac/U6atac.U5 tri-snRNP complex as determined by glycerol gradient sedimentation and immunoprecipitation. In this report, we establish a mechanistic basis for MOPD I disease and show that the inefficient splicing of genes containing U12-dependent introns in patient cells is due to defects in minor tri-snRNP formation, and the MOPD I-associated RNU4ATAC mutations can affect multiple facets of minor snRNA function.
Collapse
|
19
|
Minor class splicing shapes the zebrafish transcriptome during development. Proc Natl Acad Sci U S A 2014; 111:3062-7. [PMID: 24516132 DOI: 10.1073/pnas.1305536111] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Minor class or U12-type splicing is a highly conserved process required to remove a minute fraction of introns from human pre-mRNAs. Defects in this splicing pathway have recently been linked to human disease, including a severe developmental disorder encompassing brain and skeletal abnormalities known as Taybi-Linder syndrome or microcephalic osteodysplastic primordial dwarfism 1, and a hereditary intestinal polyposis condition, Peutz-Jeghers syndrome. Although a key mechanism for regulating gene expression, the impact of impaired U12-type splicing on the transcriptome is unknown. Here, we describe a unique zebrafish mutant, caliban (clbn), with arrested development of the digestive organs caused by an ethylnitrosourea-induced recessive lethal point mutation in the rnpc3 [RNA-binding region (RNP1, RRM) containing 3] gene. rnpc3 encodes the zebrafish ortholog of human RNPC3, also known as the U11/U12 di-snRNP 65-kDa protein, a unique component of the U12-type spliceosome. The biochemical impact of the mutation in clbn is the formation of aberrant U11- and U12-containing small nuclear ribonucleoproteins that impair the efficiency of U12-type splicing. Using RNA sequencing and microarrays, we show that multiple genes involved in various steps of mRNA processing, including transcription, splicing, and nuclear export are disrupted in clbn, either through intron retention or differential gene expression. Thus, clbn provides a useful and specific model of aberrant U12-type splicing in vivo. Analysis of its transcriptome reveals efficient mRNA processing as a critical process for the growth and proliferation of cells during vertebrate development.
Collapse
|
20
|
Rogler LE, Kosmyna B, Moskowitz D, Bebawee R, Rahimzadeh J, Kutchko K, Laederach A, Notarangelo LD, Giliani S, Bouhassira E, Frenette P, Roy-Chowdhury J, Rogler CE. Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. Hum Mol Genet 2013; 23:368-82. [PMID: 24009312 DOI: 10.1093/hmg/ddt427] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Post-transcriptional processing of some long non-coding RNAs (lncRNAs) reveals that they are a source of miRNAs. We show that the 268-nt non-coding RNA component of mitochondrial RNA processing endoribonuclease, (RNase MRP), is the source of at least two short (∼20 nt) RNAs designated RMRP-S1 and RMRP-S2, which function as miRNAs. Point mutations in RNase MRP cause human cartilage-hair hypoplasia (CHH), and several disease-causing mutations map to RMRP-S1 and -S2. SHAPE chemical probing identified two alternative secondary structures altered by disease mutations. RMRP-S1 and -S2 are significantly reduced in two fibroblast cell lines and a B-cell line derived from CHH patients. Tests of gene regulatory activity of RMRP-S1 and -S2 identified over 900 genes that were significantly regulated, of which over 75% were down-regulated, and 90% contained target sites with seed complements of RMRP-S1 and -S2 predominantly in their 3' UTRs. Pathway analysis identified regulated genes that function in skeletal development, hair development and hematopoietic cell differentiation including PTCH2 and SOX4 among others, linked to major CHH phenotypes. Also, genes associated with alternative RNA splicing, cell proliferation and differentiation were highly targeted. Therefore, alterations RMRP-S1 and -S2, caused by point mutations in RMRP, are strongly implicated in the molecular mechanism of CHH.
Collapse
|
21
|
Younis I, Dittmar K, Wang W, Foley SW, Berg MG, Hu KY, Wei Z, Wan L, Dreyfuss G. Minor introns are embedded molecular switches regulated by highly unstable U6atac snRNA. eLife 2013; 2:e00780. [PMID: 23908766 PMCID: PMC3728624 DOI: 10.7554/elife.00780] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/27/2013] [Indexed: 11/13/2022] Open
Abstract
Eukaryotes have two types of spliceosomes, comprised of either major (U1, U2, U4, U5, U6) or minor (U11, U12, U4atac, U6atac; <1%) snRNPs. The high conservation of minor introns, typically one amidst many major introns in several hundred genes, despite their poor splicing, has been a long-standing enigma. Here, we discovered that the low abundance minor spliceosome's catalytic snRNP, U6atac, is strikingly unstable (t½<2 hr). We show that U6atac level depends on both RNA polymerases II and III and can be rapidly increased by cell stress-activated kinase p38MAPK, which stabilizes it, enhancing mRNA expression of hundreds of minor intron-containing genes that are otherwise suppressed by limiting U6atac. Furthermore, p38MAPK-dependent U6atac modulation can control minor intron-containing tumor suppressor PTEN expression and cytokine production. We propose that minor introns are embedded molecular switches regulated by U6atac abundance, providing a novel post-transcriptional gene expression mechanism and a rationale for the minor spliceosome's evolutionary conservation. DOI:http://dx.doi.org/10.7554/eLife.00780.001.
Collapse
Affiliation(s)
- Ihab Younis
- Department of Biochemistry and Biophysics , Howard Hughes Medical Institute, University of Pennsylvania School of Medicine , Philadelphia , United States
| | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Abdel-Salam GM, Abdel-Hamid MS, Hassan NA, Issa MY, Effat L, Ismail S, Aglan MS, Zaki MS. Further delineation of the clinical spectrum inRNU4ATACrelated microcephalic osteodysplastic primordial dwarfism type I. Am J Med Genet A 2013; 161A:1875-81. [DOI: 10.1002/ajmg.a.36009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 04/08/2013] [Indexed: 11/11/2022]
Affiliation(s)
- Ghada M.H. Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Mohamed S. Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Nihal A. Hassan
- Ophthalmology Department, Faculty of Medicine; Cairo University; Cairo; Egypt
| | - Mahmoud Y. Issa
- Clinical Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Laila Effat
- Medical Molecular Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Samira Ismail
- Clinical Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Mona S. Aglan
- Clinical Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| | - Maha S. Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division; National Research Centre; Cairo; Egypt
| |
Collapse
|
23
|
Abdel-Salam GMH, Abdel-Hamid MS, Saleem SN, Ahmed MKH, Issa M, Effat LK, Kayed HF, Zaki MS, Gaber KR. Profound microcephaly, primordial dwarfism with developmental brain malformations: a new syndrome. Am J Med Genet A 2012; 158A:1823-31. [PMID: 22786707 DOI: 10.1002/ajmg.a.35480] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 04/23/2012] [Indexed: 11/09/2022]
Abstract
We describe two sibs with a lethal form of profound congenital microcephaly, intrauterine and postnatal growth retardation, subtle skeletal changes, and poorly developed brain. The sibs had striking absent cranial vault with sloping of the forehead, large beaked nose, relatively large ears, and mandibular micro-retrognathia. Brain magnetic resonance imaging (MRI) revealed extremely simplified gyral pattern, large interhemispheric cyst and agenesis of corpus callosum, abnormally shaped hippocampus, and proportionately affected cerebellum and brainstem. In addition, fundus examination showed foveal hypoplasia with optic nerve atrophy. No abnormalities of the internal organs were found. This profound form of microcephaly was identified at 17 weeks gestation by ultrasound and fetal brain MRI helped in characterizing the developmental brain malformations in the second sib. Molecular analysis excluded mutations in potentially related genes such as RNU4ATAC, SLC25A19, and ASPM. These clinical and imaging findings are unlike that of any recognized severe forms of microcephaly which is believed to be a new microcephalic primordial dwarfism (MPD) with developmental brain malformations with most probably autosomal recessive inheritance based on consanguinity and similarly affected male and female sibs.
Collapse
Affiliation(s)
- Ghada M H Abdel-Salam
- Division of Human Genetics and Genome Research, Department of Clinical Genetics, National Research Centre, Cairo, Egypt.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Abdel-Salam GMH, Abdel-Hamid MS, Issa M, Magdy A, El-Kotoury A, Amr K. Expanding the phenotypic and mutational spectrum in microcephalic osteodysplastic primordial dwarfism type I. Am J Med Genet A 2012; 158A:1455-61. [PMID: 22581640 DOI: 10.1002/ajmg.a.35356] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 02/02/2012] [Indexed: 11/09/2022]
Abstract
Mutations in the RNU4ATAC gene cause microcephalic osteodysplastic primordial dwarfism type I. It encodes U4atac, a small nuclear RNA that is a component of the minor spliceosome. Six distinct mutations in 30 patients diagnosed as microcephalic osteodysplastic primordial dwarfism type I have been described. We report on three additional patients from two unrelated families presenting with a milder phenotype of microcephalic osteodysplastic primordial dwarfism type I and metopic synostosis. Patient 1 had two novel heterozygous mutations in the 3' prime stem-loop, g.66G > C and g.124G > A while Patients 2 and 3 had a homozygous mutation g.55G > A in the 5' prime stem-loop. Although they manifested the known spectrum of clinical features of microcephalic osteodysplastic primordial dwarfism type I, they lacked evidence of severe developmental delay and neurological symptoms. These findings expand the mutational and phenotypic spectrum of this syndrome.
Collapse
Affiliation(s)
- Ghada M H Abdel-Salam
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt.
| | | | | | | | | | | |
Collapse
|