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Barington M, Bak M, Kjartansdóttir KR, Hansen TVO, Birkedal U, Østergaard E, Hove HB. Novel Alu insertion in the ZEB2 gene causing Mowat-Wilson syndrome. Am J Med Genet A 2024:e63581. [PMID: 38600862 DOI: 10.1002/ajmg.a.63581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/06/2024] [Accepted: 02/21/2024] [Indexed: 04/12/2024]
Abstract
Alu elements are short, interspersed elements located throughout the genome, playing a role in human diversity, and occasionally causing genetic diseases. Here, we report a novel Alu insertion causing Mowat-Wilson syndrome, a rare neurodevelopmental disorder, in an 8-year-old boy displaying the typical clinical features for Mowat-Wilson syndrome. The variant was not initially detected in genome sequencing data, but through deep phenotyping, which pointed to only one plausible candidate gene, manual inspection of genome sequencing alignment data enabled us to identify a de novo heterozygous Alu insertion in exon 8 of the ZEB2 gene. Nanopore long-read sequencing confirmed the Alu insertion, leading to the formation of a premature stop codon and likely haploinsufficiency of ZEB2. This underscores the importance of deep phenotyping and mobile element insertion analysis in uncovering genetic causes of monogenic disorders as these elements might be overlooked in standard next-generation sequencing protocols.
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Affiliation(s)
- Maria Barington
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
| | - Elsebet Østergaard
- Department of Clinical Genetics, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Hanne Buciek Hove
- Center for Rare Diseases, Department of Paediatrics and Adolescent Medicine, Copenhagen University Hospital, Copenhagen, Denmark
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Jelsig AM, Rønlund K, Gede LB, Frederiksen JH, Karstensen JG, Birkedal U, van Overeem Hansen T. Identification of a novel pathogenic deep intronic variant in PTEN resulting in pseudoexon inclusion in a patient with juvenile polyps. J Hum Genet 2023; 68:721-724. [PMID: 37336910 DOI: 10.1038/s10038-023-01174-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 06/21/2023]
Abstract
Colorectal, hamartomatous juvenile polyps occur as part of different hereditary syndromes, including Juvenile polyposis syndrome and PTEN-hamartoma tumour syndrome. However, based on clinical manifestations alone, it is difficult to differentiate between the syndromes, and genetic analysis with an NGS-panel is often used to aid diagnostics. We report a 59-year-old male with colorectal juvenile polyps, who had been referred to genetic testing but had normal genetic analysis. He did not fulfil the clinical criteria of PTEN- hamartoma tumour syndrome, but the clinical criteria of Juvenile polyposis syndrome. With Whole Genome Sequencing we detected a novel intronic variant of unknown significance in PTEN (NC_000010.11:g.89687361 A > G(chr10, hg19), NM_000314.8:c.209 + 2047 A > G). RNA analysis classified the variant as likely pathogenic as it results in a pseudoexon inclusion introducing a frameshift and a premature stop codon. The patient was then diagnosed with PTEN-hamartoma Tumour syndrome. To our knowledge this is the first report of a variant resulting in pseudoexon inclusion in PTEN.
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Affiliation(s)
- Anne Marie Jelsig
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark.
| | - Karina Rønlund
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle Hospital, Vejle, Denmark
| | - Lene Bjerring Gede
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Jane Hübertz Frederiksen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - John Gásdal Karstensen
- Danish Polyposis Registry, Gastrounit, Copenhagen University Hospital - Amager and Hvidovre, Hvidovre, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Byrjalsen A, Stoltze U, Mehrjouy M, Frederiksen JH, Bak M, Birkedal U, Hasle H, Gerdes A, Schmiegelow K, Wadt K, Hansen TVO. The effect of a single SMARCA4 exon deletion on RNA splicing: Implications for variant classification. Mol Genet Genomic Med 2023; 11:e2232. [PMID: 37430472 PMCID: PMC10568377 DOI: 10.1002/mgg3.2232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 03/10/2023] [Accepted: 06/18/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Exon deletions are generally considered pathogenic, particularly when they are located out of frame. Here, we describe a pediatric, female patient presenting with hypercalcemia and a small cell carcinoma of the ovary, hypercalcemic type, and carrying a germline de novo SMARCA4 exon 14 deletion. METHODS The SMARCA4 deletion was identified by whole genome sequencing, and the effect on the RNA level was examined by gel- and capillary electrophoresis and nanopore sequencing. RESULTS The deletion was in silico predicted to be truncating, but RNA analysis revealed two major transcripts with deletion of exon 14 alone or exon 14 through 15, where the latter was located in-frame. Because the patient's phenotype matched that of other patients with pathogenic germline variants in SMARCA4, the deletion was classified as likely pathogenic. CONCLUSION We propose to include RNA analysis in classification of single-exon deletions, especially if located outside of known functional domains, as this can identify any disparate effects on the RNA and DNA level, which may have implications for variant classification using the American College of Medical Genetics and Genomics guidelines.
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Affiliation(s)
- Anna Byrjalsen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Ulrik Stoltze
- Department of Pediatrics and Adolescent Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Mana Mehrjouy
- Department of Pediatrics and Adolescent Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | | | - Mads Bak
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Ulf Birkedal
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Henrik Hasle
- Department of PediatricsAarhus University HospitalAarhus NDenmark
| | - Anne‐Marie Gerdes
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Karin Wadt
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, RigshospitaletCopenhagen University HospitalCopenhagenDenmark
- Department of Clinical Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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Barington M, Dunø M, Birkedal U, Vissing J, Born AP, Krag T, Hansen TVO, Østergaard E. Homozygous splice variant (c.1741-6G>A) of the COL6A1 gene in three patients with Ullrich congenital muscular dystrophy. Neuromuscul Disord 2023; 33:539-545. [PMID: 37315421 DOI: 10.1016/j.nmd.2023.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]
Abstract
The three major collagen VI genes: COL6A1, COL6A2, and COL6A3 encode microfibrillar components of extracellular matrices in multiple tissues including muscles and tendons. Pathogenic variants in the collagen VI genes cause collagen VI-related dystrophies representing a continuum of conditions from Bethlem myopathy at the milder end to Ullrich congenital muscular dystrophy at the more severe end. Here we describe a pathogenic variant in the COL6A1 gene (NM_001848.3; c.1741-6G>A) found in homozygosity in three patients with Ullrich congenital muscular dystrophy. The patients suffered from severe muscle impairment characterised by proximal weakness, distal hyperlaxity, joint contractures, wheelchair-dependency, and use of nocturnal non-invasive ventilation. The pathogenicity was verified by RNA analyses showing that the variant induced aberrant splicing leading to a frameshift and loss of function. The analyses were in line with immunocytochemistry studies of patient-derived skin fibroblasts and muscle tissue demonstrating impaired secretion of collagen VI into the extracellular matrix. Thereby, we add the variant c.1741-6G>A to the list of pathogenic, recessive, splice variants in COL6A1 causing Ullrich congenital muscular dystrophy. The variant is listed in ClinVar as of "uncertain significance" and "likely benign" and may presumably have been overlooked in other patients.
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Affiliation(s)
- Maria Barington
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark.
| | - Morten Dunø
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - John Vissing
- Copenhagen Neuromuscular Center, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Alfred Peter Born
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas Krag
- Copenhagen Neuromuscular Center, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Elsebet Østergaard
- Department of Genetics, Rigshospitalet, Blegdamsvej 9, 2100 Copenhagen, Denmark; Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen, Denmark
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Rasmussen A, Hildonen M, Vissing J, Duno M, Tümer Z, Birkedal U. High Resolution Analysis of DMPK Hypermethylation and Repeat Interruptions in Myotonic Dystrophy Type 1. Genes (Basel) 2022; 13:genes13060970. [PMID: 35741732 PMCID: PMC9222588 DOI: 10.3390/genes13060970] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/19/2022] [Accepted: 05/26/2022] [Indexed: 02/05/2023] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a multisystemic neuromuscular disorder caused by the expansion of a CTG repeat in the 3′-UTR of DMPK, which is transcribed to a toxic gain-of-function RNA that affects splicing of a range of genes. The expanded repeat is unstable in both germline and somatic cells. The variable age at disease onset and severity of symptoms have been linked to the inherited CTG repeat length, non-CTG interruptions, and methylation levels flanking the repeat. In general, the genetic biomarkers are investigated separately with specific methods, making it tedious to obtain an overall characterisation of the repeat for a given individual. In the present study, we employed Oxford nanopore sequencing in a pilot study to simultaneously determine the repeat lengths, investigate the presence and nature of repeat interruptions, and quantify methylation levels in the regions flanking the CTG-repeats in four patients with DM1. We determined the repeat lengths, and in three patients, we observed interruptions which were not detected using repeat-primed PCR. Interruptions may thus be more common than previously anticipated and should be investigated in larger cohorts. Allele-specific analyses enabled characterisation of aberrant methylation levels specific to the expanded allele, which greatly increased the sensitivity and resolved cases where the methylation levels were ambiguous.
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Affiliation(s)
- Astrid Rasmussen
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark; (A.R.); (M.H.); (U.B.)
| | - Mathis Hildonen
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark; (A.R.); (M.H.); (U.B.)
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of Neurology, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark;
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Morten Duno
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2100 Copenhagen, Denmark;
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark; (A.R.); (M.H.); (U.B.)
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Correspondence:
| | - Ulf Birkedal
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, 2600 Glostrup, Denmark; (A.R.); (M.H.); (U.B.)
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Birkedal U, Beckert B, Wilson DN, Nielsen H. The 23S Ribosomal RNA From Pyrococcus furiosus Is Circularly Permuted. Front Microbiol 2020; 11:582022. [PMID: 33362734 PMCID: PMC7758197 DOI: 10.3389/fmicb.2020.582022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022] Open
Abstract
Synthesis and assembly of ribosomal components are fundamental cellular processes and generally well-conserved within the main groups of organisms. Yet, provocative variations to the general schemes exist. We have discovered an unusual processing pathway of pre-rRNA in extreme thermophilic archaea exemplified by Pyrococcus furiosus. The large subunit (LSU) rRNA is produced as a circularly permuted form through circularization followed by excision of Helix 98. As a consequence, the terminal domain VII that comprise the binding site for the signal recognition particle is appended to the 5´ end of the LSU rRNA that instead terminates in Domain VI carrying the Sarcin-Ricin Loop, the primary interaction site with the translational GTPases. To our knowledge, this is the first example of a true post-transcriptional circular permutation of a main functional molecule and the first example of rRNA fragmentation in archaea.
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Affiliation(s)
- Ulf Birkedal
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Bertrand Beckert
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, Hamburg, Germany
| | - Daniel N Wilson
- Institut für Biochemie und Molekularbiologie, Universität Hamburg, Hamburg, Germany
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark.,Genomics Group, Nord University, Bodø, Norway
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Seistrup KH, Rose S, Birkedal U, Nielsen H, Huber H, Douthwaite S. Bypassing rRNA methylation by RsmA/Dim1during ribosome maturation in the hyperthermophilic archaeon Nanoarchaeum equitans. Nucleic Acids Res 2017; 45:2007-2015. [PMID: 28204608 PMCID: PMC5389701 DOI: 10.1093/nar/gkw839] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 09/10/2016] [Indexed: 12/16/2022] Open
Abstract
In all free-living organisms a late-stage checkpoint in the biogenesis of the small ribosomal subunit involves rRNA modification by an RsmA/Dim1 methyltransferase. The hyperthermophilic archaeon Nanoarchaeum equitans, whose existence is confined to the surface of a second archaeon, Ignicoccus hospitalis, lacks an RsmA/Dim1 homolog. We demonstrate here that the I. hospitalis host possesses the homolog Igni_1059, which dimethylates the N6-positions of two invariant adenosines within helix 45 of 16S rRNA in a manner identical to other RsmA/Dim1 enzymes. However, Igni_1059 is not transferred from I. hospitalis to N. equitans across their fused cell membrane structures and the corresponding nucleotides in N. equitans 16S rRNA remain unmethylated. An alternative mechanism for ribosomal subunit maturation in N. equitans is suggested by sRNA interactions that span the redundant RsmA/Dim1 site to introduce 2΄-O-ribose methylations within helices 44 and 45 of the rRNA.
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Affiliation(s)
- Kenneth H. Seistrup
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Simon Rose
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ulf Birkedal
- Department of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Henrik Nielsen
- Department of Cellular & Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | - Harald Huber
- Lehrstuhl für Mikrobiologie und Archaeenzentrum Universität Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Stephen Douthwaite
- Department of Biochemistry & Molecular Biology, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Abstract
RiboMeth-seq is a sequencing-based method for mapping and quantitation of one of the most abundant RNA modifications, ribose methylation. It is based on a simple chemical principle, namely the several orders of magnitude difference in nucleophilicity of a 2'-OH and a 2'-O-Me. Thus, the method combines alkaline fragmentation and a specialized library construction protocol based on 5'-OH and 2',3' cyclic phosphate ends to prepare RNA for sequencing. The read-ends of library fragments are used for mapping with nucleotide resolution and calculation of the fraction of molecules methylated at the 2'-O-Me sites.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Ulf Birkedal
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, The Panum Institute, University of Copenhagen, 3 Blegdamsvej, 18.2.22, DK-2200N, Copenhagen, Denmark.
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9
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Krogh N, Jansson MD, Häfner SJ, Tehler D, Birkedal U, Christensen-Dalsgaard M, Lund AH, Nielsen H. Profiling of 2'-O-Me in human rRNA reveals a subset of fractionally modified positions and provides evidence for ribosome heterogeneity. Nucleic Acids Res 2016; 44:7884-95. [PMID: 27257078 PMCID: PMC5027482 DOI: 10.1093/nar/gkw482] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/19/2016] [Indexed: 01/05/2023] Open
Abstract
Ribose methylation is one of the two most abundant modifications in human ribosomal RNA and is believed to be important for ribosome biogenesis, mRNA selectivity and translational fidelity. We have applied RiboMeth-seq to rRNA from HeLa cells for ribosome-wide, quantitative mapping of 2'-O-Me sites and obtained a comprehensive set of 106 sites, including two novel sites, and with plausible box C/D guide RNAs assigned to all but three sites. We find approximately two-thirds of the sites to be fully methylated and the remainder to be fractionally modified in support of ribosome heterogeneity at the level of RNA modifications. A comparison to HCT116 cells reveals similar 2'-O-Me profiles with distinct differences at several sites. This study constitutes the first comprehensive mapping of 2'-O-Me sites in human rRNA using a high throughput sequencing approach. It establishes the existence of a core of constitutively methylated positions and a subset of variable, potentially regulatory positions, and paves the way for experimental analyses of the role of variations in rRNA methylation under different physiological or pathological settings.
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Affiliation(s)
- Nicolai Krogh
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
| | - Martin D Jansson
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Sophia J Häfner
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Disa Tehler
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Ulf Birkedal
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
| | | | - Anders H Lund
- Biotech Research and Innovation Centre, University of Copenhagen, DK-2200N, Denmark
| | - Henrik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200N, Denmark
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Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angew Chem Int Ed Engl 2014; 54:451-5. [PMID: 25417815 DOI: 10.1002/anie.201408362] [Citation(s) in RCA: 125] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Indexed: 11/07/2022]
Abstract
Ribose methylations are the most abundant chemical modifications of ribosomal RNA and are critical for ribosome assembly and fidelity of translation. Many aspects of ribose methylations have been difficult to study due to lack of efficient mapping methods. Here, we present a sequencing-based method (RiboMeth-seq) and its application to yeast ribosomes, presently the best-studied eukaryotic model system. We demonstrate detection of the known as well as new modifications, reveal partial modifications and unexpected communication between modification events, and determine the order of modification at several sites during ribosome biogenesis. Surprisingly, the method also provides information on a subset of other modifications. Hence, RiboMeth-seq enables a detailed evaluation of the importance of RNA modifications in the cells most sophisticated molecular machine. RiboMeth-seq can be adapted to other RNA classes, for example, mRNA, to reveal new biology involving RNA modifications.
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Affiliation(s)
- Ulf Birkedal
- Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen N (Denmark)
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Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of Ribose Methylations in RNA by High-Throughput Sequencing. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408362] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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