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Ansell BRE, Thomas SN, Bonelli R, Munro JE, Freytag S, Bahlo M. A survey of RNA editing at single-cell resolution links interneurons to schizophrenia and autism. RNA 2021; 27:1482-1496. [PMID: 34535545 PMCID: PMC8594476 DOI: 10.1261/rna.078804.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 09/12/2021] [Indexed: 06/13/2023]
Abstract
Conversion of adenosine to inosine in RNA by ADAR enzymes, termed "RNA editing," is essential for healthy brain development. Editing is dysregulated in neuropsychiatric diseases, but has not yet been investigated at scale at the level of individual neurons. We quantified RNA editing sites in nuclear transcriptomes of 3055 neurons from six cortical regions of a neurotypical female donor, and found 41,930 sites present in at least ten nuclei. Most sites were located within Alu repeats in introns or 3' UTRs, and approximately 80% were cataloged in public RNA editing databases. We identified 9285 putative novel editing sites, 29% of which were also detectable in unrelated donors. Intersection with results from bulk RNA-seq studies provided cell-type and spatial context for 1730 sites that are differentially edited in schizophrenic brain donors, and 910 such sites in autistic donors. Autism-related genes were also enriched with editing sites predicted to modify RNA structure. Inhibitory neurons showed higher overall transcriptome editing than excitatory neurons, and the highest editing rates were observed in the frontal cortex. We used generalized linear models to identify differentially edited sites and genes between cell types. Twenty nine genes were preferentially edited in excitatory neurons, and 43 genes were edited more heavily in inhibitory neurons, including RBFOX1, its target genes, and genes in the autism-associated Prader-Willi locus (15q11). The abundance of SNORD115/116 genes from locus 15q11 was positively associated with editing activity across the transcriptome. We contend that insufficient editing of autism-related genes in inhibitory neurons may contribute to the specific perturbation of those cells in autism.
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Affiliation(s)
- Brendan Robert E Ansell
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Simon N Thomas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Roberto Bonelli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Jacob E Munro
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia
| | - Saskia Freytag
- Molecular Medicine Division, Harry Perkins Institute of Medical Research, Nedlands 6009, Western Australia, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville 3052, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville 3052, Victoria, Australia
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Vocke CD, Ricketts CJ, Schmidt LS, Ball MW, Middelton LA, Zbar B, Linehan WM. Comprehensive characterization of Alu-mediated breakpoints in germline VHL gene deletions and rearrangements in patients from 71 VHL families. Hum Mutat 2021; 42:520-529. [PMID: 33675279 PMCID: PMC8068631 DOI: 10.1002/humu.24194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 11/03/2020] [Revised: 02/04/2021] [Accepted: 02/11/2021] [Indexed: 12/31/2022]
Abstract
Von Hippel‐Lindau (VHL) is a hereditary multisystem disorder caused by germline alterations in the VHL gene. VHL patients are at risk for benign as well as malignant lesions in multiple organs including kidney, adrenal, pancreas, the central nervous system, retina, endolymphatic sac of the ear, epididymis, and broad ligament. An estimated 30%–35% of all families with VHL inherit a germline deletion of one, two, or all three exons. In this study, we have extensively characterized germline deletions identified in patients from 71 VHL families managed at the National Cancer Institute, including 59 partial (PD) and 12 complete VHL deletions (CD). Deletions that ranged in size from 1.09 to 355 kb. Fifty‐eight deletions (55 PD and 3 CD) have been mapped to the exact breakpoints. Ninety‐five percent (55 of 58) of mapped deletions involve Alu repeats at both breakpoints. Several novel classes of deletions were identified in this cohort, including two cases that have complex rearrangements involving both deletion and inversion, two cases with inserted extra Alu‐like sequences, six cases that involve breakpoints in Alu repeats situated in opposite orientations, and a “hotspot” PD of Exon 3 observed in 12 families that involves the same pair of Alu repeats.
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Affiliation(s)
- Cathy D Vocke
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program and Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Mark W Ball
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Lindsay A Middelton
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Clinical Research Directorate, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Berton Zbar
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Tatosyan KA, Zinevich LS, Demin DE, Schwartz AM. [Functional Characteristics of Long Noncoding RNAs Containing Sequences of Mobile Genetic Elements]. Mol Biol (Mosk) 2020; 54:718-724. [PMID: 33009786 DOI: 10.31857/s0026898420050109] [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: 04/21/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Long nonconding RNAs (lncRNAs) perform a variety of functions: they are involved in chromatin organization, regulation of gene expression at the transcriptional and post-transcriptional levels, and regulation of activity and stability of some proteins. The majority of known lncRNAs contain sequences of mobile genetic elements (MGEs) in a sense or antisense orientation. According to several studies, MGE may serve as functional modules responsible for interactions between the lncRNA and certain proteins, DNA regions, or other RNAs. The available data make it possible to describe groups of lncRNAs that possess common structural features and contain certain MGEs and to predict the characteristics of new lncRNAs. The review summarizes the data on the role that MGE sequences play in lncRNA functions.
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Affiliation(s)
- K A Tatosyan
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - L S Zinevich
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D E Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow oblast, 141701 Russia
| | - A M Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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Abstract
One of the distinctive features of the primate genome is the Alu element, a repetitive short interspersed element, over a million highly similar copies of which account for >10% of the genome. A direct consequence of this feature is that primates' transcriptome is highly enriched in long stable dsRNA structures, the preferred target of adenosine deaminases acting on RNAs (ADARs), which are the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, there are few essential editing sites conserved across mammals that have maintained their editing level despite the radical change in ADAR target landscape. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which might have contributed to the accelerated evolution of the primates.
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Affiliation(s)
- Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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Witt N, Rodger G, Vandesompele J, Benes V, Zumla A, Rook GA, Huggett JF. An assessment of air as a source of DNA contamination encountered when performing PCR. J Biomol Tech 2009; 20:236-240. [PMID: 19949694 PMCID: PMC2777341] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Sensitive molecular methods, such as the PCR, can detect low-level contamination, and careful technique is required to reduce the impact of contaminants. Yet, some assays that are designed to detect high copy-number target sequences appear to be impossible to perform without contamination, and frequently, personnel or laboratory environment are held responsible as the source. This complicates diagnostic and research analysis when using molecular methods. To investigate the air specifically as a source of contamination, which might occur during PCR setup, we exposed tubes of water to the air of a laboratory and clean hood for up to 24 h. To increase the chances of contamination, we also investigated a busy open-plan office in the same way. All of the experiments showed the presence of human and rodent DNA contamination. However, there was no accumulation of the contamination in any of the environments investigated, suggesting that the air was not the source of contamination. Even the air from a busy open-plan office was a poor source of contamination for all of the DNA sequences investigated (human, bacterial, fungal, and rodent). This demonstrates that the personnel and immediate laboratory environment are not necessarily to blame for the observed contamination.
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Affiliation(s)
- Nina Witt
- Centre for Infectious Diseases and International Health, Windeyer Institute for Medical Sciences, University College London, London W1T 4JF, United Kingdom
| | - Gillian Rodger
- Centre for Infectious Diseases and International Health, Windeyer Institute for Medical Sciences, University College London, London W1T 4JF, United Kingdom
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; and
| | - Vladimir Benes
- European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg, Germany
| | - Alimuddin Zumla
- Centre for Infectious Diseases and International Health, Windeyer Institute for Medical Sciences, University College London, London W1T 4JF, United Kingdom
| | - Graham A. Rook
- Centre for Infectious Diseases and International Health, Windeyer Institute for Medical Sciences, University College London, London W1T 4JF, United Kingdom
| | - Jim F. Huggett
- Centre for Infectious Diseases and International Health, Windeyer Institute for Medical Sciences, University College London, London W1T 4JF, United Kingdom
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