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Nguyen THM, Carreira PE, Sanchez-Luque FJ, Schauer SN, Fagg AC, Richardson SR, Davies CM, Jesuadian JS, Kempen MJHC, Troskie RL, James C, Beaven EA, Wallis TP, Coward JIG, Chetty NP, Crandon AJ, Venter DJ, Armes JE, Perrin LC, Hooper JD, Ewing AD, Upton KR, Faulkner GJ. L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution. Cell Rep 2019; 23:3730-3740. [PMID: 29949758 DOI: 10.1016/j.celrep.2018.05.090] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 01/04/2018] [Accepted: 05/26/2018] [Indexed: 01/07/2023] Open
Abstract
LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity.
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Affiliation(s)
- Thu H M Nguyen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Pfizer-University of Granada-Andalusian Government Centre for Genomics and Oncological Research, PT Ciencias de la Salud, Granada 18016, Spain
| | - Stephanie N Schauer
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Allister C Fagg
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | | | - J Samuel Jesuadian
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Marie-Jeanne H C Kempen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Robin-Lee Troskie
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Cini James
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | | | | | - Jermaine I G Coward
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Naven P Chetty
- Mater Health Services, South Brisbane, QLD 4101, Australia
| | | | - Deon J Venter
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Jane E Armes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Mater Health Services, South Brisbane, QLD 4101, Australia
| | - Lewis C Perrin
- Mater Health Services, South Brisbane, QLD 4101, Australia
| | - John D Hooper
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Kyle R Upton
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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Cook C, Petrucelli L. Genetic Convergence Brings Clarity to the Enigmatic Red Line in ALS. Neuron 2019; 101:1057-1069. [PMID: 30897357 DOI: 10.1016/j.neuron.2019.02.032] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 02/07/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is an aggressive neurodegenerative disorder that orchestrates an attack on the motor nervous system that is unrelenting. Recent discoveries into the pathogenic consequences of repeat expansions in C9ORF72, which are the most common genetic cause of ALS, combined with the identification of new genetic mutations are providing novel insight into the underlying mechanism(s) that cause ALS. In particular, the myriad of functions linked to ALS-associated genes have collectively implicated four main pathways in disease pathogenesis, including RNA metabolism and translational biology; protein quality control; cytoskeletal integrity and trafficking; and mitochondrial function and transport. Through the identification of common disease mechanisms on which multiple ALS genes converge, key targets for potential therapeutic intervention are highlighted.
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Affiliation(s)
- Casey Cook
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA
| | - Leonard Petrucelli
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Neurobiology of Disease Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Jacksonville, FL, USA.
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53
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McKerrow W, Fenyö D. L1EM: a tool for accurate locus specific LINE-1 RNA quantification. Bioinformatics 2019; 36:1167-1173. [PMID: 31584629 PMCID: PMC8215917 DOI: 10.1093/bioinformatics/btz724] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/31/2019] [Accepted: 09/25/2019] [Indexed: 01/31/2023] Open
Abstract
MOTIVATION LINE-1 elements are retrotransposons that are capable of copying their sequence to new genomic loci. LINE-1 derepression is associated with a number of disease states, and has the potential to cause significant cellular damage. Because LINE-1 elements are repetitive, it is difficult to quantify LINE-1 RNA at specific loci and to separate transcripts with protein coding capability from other sources of LINE-1 RNA. RESULTS We provide a tool, L1EM that uses the expectation maximization algorithm to quantify LINE-1 RNA at each genomic locus, separating transcripts that are capable of generating retrotransposition from those that are not. We show the accuracy of L1EM on simulated data and against long read sequencing from HEK cells. AVAILABILITY AND IMPLEMENTATION L1EM is written in python. The source code along with the necessary annotations are available at https://github.com/FenyoLab/L1EM and distributed under GPLv3. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - David Fenyö
- To whom correspondence should be addressed. or
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54
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Saleh A, Macia A, Muotri AR. Transposable Elements, Inflammation, and Neurological Disease. Front Neurol 2019; 10:894. [PMID: 31481926 PMCID: PMC6710400 DOI: 10.3389/fneur.2019.00894] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 08/02/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable Elements (TE) are mobile DNA elements that can replicate and insert themselves into different locations within the host genome. Their propensity to self-propagate has a myriad of consequences and yet their biological significance is not well-understood. Indeed, retrotransposons have evaded evolutionary attempts at repression and may contribute to somatic mosaicism. Retrotransposons are emerging as potent regulatory elements within the human genome. In the diseased state, there is mounting evidence that endogenous retroelements play a role in etiopathogenesis of inflammatory diseases, with a disposition for both autoimmune and neurological disorders. We postulate that active mobile genetic elements contribute more to human disease pathogenesis than previously thought.
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Affiliation(s)
- Aurian Saleh
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
| | - Angela Macia
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
| | - Alysson R Muotri
- Department of Pediatrics, Rady Children's Hospital San Diego, University of California, San Diego, San Diego, CA, United States
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55
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Sanchez-Luque FJ, Kempen MJHC, Gerdes P, Vargas-Landin DB, Richardson SR, Troskie RL, Jesuadian JS, Cheetham SW, Carreira PE, Salvador-Palomeque C, García-Cañadas M, Muñoz-Lopez M, Sanchez L, Lundberg M, Macia A, Heras SR, Brennan PM, Lister R, Garcia-Perez JL, Ewing AD, Faulkner GJ. LINE-1 Evasion of Epigenetic Repression in Humans. Mol Cell 2019; 75:590-604.e12. [PMID: 31230816 DOI: 10.1016/j.molcel.2019.05.024] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 04/08/2019] [Accepted: 05/15/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic silencing defends against LINE-1 (L1) retrotransposition in mammalian cells. However, the mechanisms that repress young L1 families and how L1 escapes to cause somatic genome mosaicism in the brain remain unclear. Here we report that a conserved Yin Yang 1 (YY1) transcription factor binding site mediates L1 promoter DNA methylation in pluripotent and differentiated cells. By analyzing 24 hippocampal neurons with three distinct single-cell genomic approaches, we characterized and validated a somatic L1 insertion bearing a 3' transduction. The source (donor) L1 for this insertion was slightly 5' truncated, lacked the YY1 binding site, and was highly mobile when tested in vitro. Locus-specific bisulfite sequencing revealed that the donor L1 and other young L1s with mutated YY1 binding sites were hypomethylated in embryonic stem cells, during neurodifferentiation, and in liver and brain tissue. These results explain how L1 can evade repression and retrotranspose in the human body.
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Affiliation(s)
- Francisco J Sanchez-Luque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain.
| | - Marie-Jeanne H C Kempen
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Dulce B Vargas-Landin
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Sandra R Richardson
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Robin-Lee Troskie
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - J Samuel Jesuadian
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Seth W Cheetham
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Carmen Salvador-Palomeque
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Marta García-Cañadas
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Martin Muñoz-Lopez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Laura Sanchez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain
| | - Mischa Lundberg
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Sara R Heras
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Paul M Brennan
- Edinburgh Cancer Research Centre, Western General Hospital, Edinburgh, EH4 2XR, UK
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, the University of Western Australia, Perth, WA 6009, Australia; Harry Perkins Institute of Medical Research, Perth, WA 6009, Australia
| | - Jose L Garcia-Perez
- GENYO Centre for Genomics and Oncological Research, Pfizer University of Granada, Andalusian Regional Government, Avda Ilustración, 114, PTS Granada 18016, Spain; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Adam D Ewing
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD 4102, Australia; Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia.
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56
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Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp 2019. [PMID: 31157783 DOI: 10.3791/59771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Long INterspersed Elements-1 (LINEs/L1s) are repetitive elements that can copy and randomly insert in the genome resulting in genomic instability and mutagenesis. Understanding the expression patterns of L1 loci at the individual level will lend to the understanding of the biology of this mutagenic element. This autonomous element makes up a significant portion of the human genome with over 500,000 copies, though 99% are truncated and defective. However, their abundance and dominant number of defective copies make it challenging to identify authentically expressed L1s from L1-related sequences expressed as part of other genes. It is also challenging to identify which specific L1 locus is expressed due to the repetitive nature of the elements. Overcoming these challenges, we present an RNA-Seq bioinformatic approach to identify L1 expression at the locus specific level. In summary, we collect cytoplasmic RNA, select for polyadenylated transcripts, and utilize strand-specific RNA-Seq analyses to uniquely map reads to L1 loci in the human reference genome. We visually curate each L1 locus with uniquely mapped reads to confirm transcription from its own promoter and adjust mapped transcript reads to account for mappability of each individual L1 locus. This approach was applied to a prostate tumor cell line, DU145, to demonstrate the ability of this protocol to detect expression from a small number of the full-length L1 elements.
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Affiliation(s)
| | | | | | - Melody Baddoo
- Tulane Cancer Center, Tulane University; Department of Pathology, Tulane University
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane University; Department of Structural and Cellular Biology, Tulane University
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University; Department of Epidemiology, Tulane University;
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Chen C, Wang W, Wang X, Shen D, Wang S, Wang Y, Gao B, Wimmers K, Mao J, Li K, Song C. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mob DNA 2019; 10:19. [PMID: 31080521 PMCID: PMC6501411 DOI: 10.1186/s13100-019-0161-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/11/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Retrotransposons are the major determinants of genome sizes and they have shaped both genes and genomes in mammalian organisms, but their overall activity, diversity, and evolution dynamics, particularly their impact on protein coding and lncRNA genes in pigs remain largely unknown. RESULTS In the present study, we performed de novo detection of retrotransposons in pigs by using multiple pipelines, four distinct families of pig-specific L1 s classified into 51 distinct subfamilies and representing four evolution models and three expansion waves of pig-specific SINEs represented by three distinct families were identified. ERVs were classified into 18 families and found two most "modern" subfamilies in the pig genome. The transposition activity of pig L1 was verified by experiment, the sense and antisense promoter activities of young L1 5'UTRs and ERV LTRs and expression profiles of young retrotransposons in multiple tissues and cell lines were also validated. Furthermore, retrotransposons had an extensive impact on lncRNA and protein coding genes at both the genomic and transcriptomic levels. Most protein coding and lncRNA (> 80%) genes contained retrotransposon insertions, and about half of protein coding genes (44.30%) and one-fourth (24.13%) of lncRNA genes contained the youngest retrotransposon insertions. Nearly half of protein coding genes (43.78%) could generate chimeric transcripts with retrotransposons. Significant distribution bias of retrotransposon composition, location, and orientation in lncRNA and protein coding genes, and their transcripts, were observed. CONCLUSIONS In the current study, we characterized the classification and evolution profile of retrotransposons in pigs, experimentally proved the transposition activity of the young pig L1 subfamily, characterized the sense and antisense expression profiles and promoter activities of young retrotransposons, and investigated their impact on lncRNA and protein coding genes by defining the mobilome landscapes at the genomic and transcriptomic levels. These findings help provide a better understanding of retrotransposon evolution in mammal and their impact on the genome and transcriptome.
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Affiliation(s)
- Cai Chen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wei Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaoyan Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Bo Gao
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Jiude Mao
- Life Science Center, University of Missouri, Columbia, MO 65211 USA
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengyi Song
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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58
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Jiang JC, Upton KR. Human transposons are an abundant supply of transcription factor binding sites and promoter activities in breast cancer cell lines. Mob DNA 2019; 10:16. [PMID: 31061680 PMCID: PMC6486989 DOI: 10.1186/s13100-019-0158-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/01/2019] [Indexed: 12/22/2022] Open
Abstract
Background Transposable elements (TE) are commonly regarded as “junk DNA” with no apparent regulatory roles in the human genome. However, a growing body of evidence demonstrates that some TEs exhibit regulatory activities in a range of biological pathways and diseases, with notable examples in bile metabolism and innate immunity. TEs are typically suppressed by epigenetic modifications in healthy somatic tissues, which prevents both undesirable effects of insertional mutagenesis, and also unwanted gene activation. Interestingly, TEs are widely reported to be dysregulated in epithelial cancers, and while much attention has been paid to their effects on genome instability, relatively little has been reported on their effects on gene regulation. Here, we investigated the contribution of TEs to the transcriptional regulation in breast cancer cell lines. Results We found that a subset of TE subfamilies were enriched in oncogenic transcription factor binding sites and also harboured histone marks associated with active transcription, raising the possibility of these subfamilies playing a broad role in breast cancer transcriptional regulation. To directly assess promoter activity in triple negative breast cancer cell lines, we identified four breast cancer-associated genes with putative TE-derived promoters. TE deletion confirmed a contribution to promoter activity in all cases, and for two examples the promoter activity was almost completely contained within the TE. Conclusions Our findings demonstrate that TEs provide abundant oncogenic transcription factor binding sites in breast cancer and that individual TEs contain substantial promoter activity. Our findings provide further evidence for transcriptional regulation of human genes through TE exaptation by demonstrating the regulatory potential of TEs in multiple breast cancer cell lines. Electronic supplementary material The online version of this article (10.1186/s13100-019-0158-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiayue-Clara Jiang
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
| | - Kyle R Upton
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072 Australia
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59
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Fung L, Guzman H, Sevrioukov E, Idica A, Park E, Bochnakian A, Daugaard I, Jury D, Mortazavi A, Zisoulis DG, Pedersen IM. miR-128 Restriction of LINE-1 (L1) Retrotransposition Is Dependent on Targeting hnRNPA1 mRNA. Int J Mol Sci 2019; 20:E1955. [PMID: 31010097 PMCID: PMC6515209 DOI: 10.3390/ijms20081955] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/15/2019] [Accepted: 04/19/2019] [Indexed: 12/25/2022] Open
Abstract
The majority of the human genome is made of transposable elements, giving rise to interspaced repeats, including Long INterspersed Element-1s (LINE-1s or L1s). L1s are active human transposable elements involved in genomic diversity and evolution; however, they can also contribute to genomic instability and diseases. L1s require host factors to complete their life cycles, whereas the host has evolved numerous mechanisms to restrict L1-induced mutagenesis. Restriction mechanisms in somatic cells include methylation of the L1 promoter, anti-viral factors and RNA-mediated processes such as small RNAs. microRNAs (miRNAs or miRs) are small non-coding RNAs that post-transcriptionally repress multiple target genes often found in the same cellular pathways. We have recently established that miR-128 functions as a novel restriction factor inhibiting L1 mobilization in somatic cells. We have further demonstrated that miR-128 functions through a dual mechanism; by directly targeting L1 RNA for degradation and indirectly by inhibiting a cellular co-factor which L1 is dependent on to transpose to new genomic locations (TNPO1). Here, we add another piece to the puzzle of the enigmatic L1 lifecycle. We show that miR-128 also inhibits another key cellular factor, hnRNPA1 (heterogeneous nuclear ribonucleoprotein A1), by significantly reducing mRNA and protein levels through direct interaction with the coding sequence (CDS) of hnRNPA1 mRNA. In addition, we demonstrate that repression of hnRNPA1 using hnRNPA1-shRNA significantly decreases de novo L1 retro-transposition and that induced hnRNPA1 expression enhances L1 mobilization. Furthermore, we establish that hnRNPA1 is a functional target of miR-128. Finally, we determine that induced hnRNPA1 expression in miR-128-overexpressing cells can partly rescue the miR-128-induced repression of L1's ability to transpose to different genomic locations. Thus, we have identified an additional mechanism by which miR-128 represses L1 retro-transposition and mediates genomic stability.
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Affiliation(s)
- Lianna Fung
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Herlinda Guzman
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Evgueni Sevrioukov
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Adam Idica
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Eddie Park
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.
| | - Aurore Bochnakian
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Iben Daugaard
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Douglas Jury
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA.
| | - Dimitrios G Zisoulis
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
| | - Irene M Pedersen
- Department of Molecular Biology and Biochemistry, Francisco J. AyalaSchool of Biological Sciences, University of California, Irvine, CA 92697, USA.
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Zhou M, Smith AD. Subtype classification and functional annotation of L1Md retrotransposon promoters. Mob DNA 2019; 10:14. [PMID: 31007728 PMCID: PMC6454616 DOI: 10.1186/s13100-019-0156-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/28/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND L1Md retrotransposons are the most abundant and active transposable elements in the mouse genome. The promoters of many L1Md retrotransposons are composed of tandem repeats called monomers. The number of monomers varies between retrotransposon copies, thus making it difficult to annotate L1Md promoters. Duplication of monomers contributes to the maintenance of L1Md promoters during truncation-prone retrotranspositions, but the associated mechanism remains unclear. Since the current classification of monomers is based on limited data, a comprehensive monomer annotation is needed for supporting functional studies of L1Md promoters genome-wide. RESULTS We developed a pipeline for de novo monomer detection and classification. Identified monomers are further classified into subtypes based on their sequence profiles. We applied this pipeline to genome assemblies of various rodent species. A major monomer subtype of the lab mouse was also found in other Mus species, implying that such subtype has emerged in the common ancestor of involved species. We also characterized the positioning pattern of monomer subtypes within individual promoters. Our analyses indicate that the subtype composition of an L1Md promoter can be used to infer its transcriptional activity during male germ cell development. CONCLUSIONS We identified subtypes for all monomer types using comprehensive data, greatly expanding the spectrum of monomer variants. The analysis of monomer subtype positioning provides evidence supporting both previously proposed models of L1Md promoter expansion. The transcription silencing of L1Md promoters differs between promoter types, which supports a model involving distinct suppressive pathways rather than a universal mechanism for retrotransposon repression in gametogenesis.
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Affiliation(s)
- Meng Zhou
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, USA
| | - Andrew D. Smith
- Molecular and Computational Biology Section, Division of Biological Sciences, University of Southern California, Los Angeles, USA
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Bodea GO, McKelvey EGZ, Faulkner GJ. Retrotransposon-induced mosaicism in the neural genome. Open Biol 2019; 8:rsob.180074. [PMID: 30021882 PMCID: PMC6070720 DOI: 10.1098/rsob.180074] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Gabriela O Bodea
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eleanor G Z McKelvey
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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62
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Dynamic Methylation of an L1 Transduction Family during Reprogramming and Neurodifferentiation. Mol Cell Biol 2019; 39:MCB.00499-18. [PMID: 30692270 PMCID: PMC6425141 DOI: 10.1128/mcb.00499-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/11/2019] [Indexed: 01/28/2023] Open
Abstract
The retrotransposon LINE-1 (L1) is a significant source of endogenous mutagenesis in humans. In each individual genome, a few retrotransposition-competent L1s (RC-L1s) can generate new heritable L1 insertions in the early embryo, primordial germ line, and germ cells. L1 retrotransposition can also occur in the neuronal lineage and cause somatic mosaicism. Although DNA methylation mediates L1 promoter repression, the temporal pattern of methylation applied to individual RC-L1s during neurogenesis is unclear. Here, we identified a de novo L1 insertion in a human induced pluripotent stem cell (hiPSC) line via retrotransposon capture sequencing (RC-seq). The L1 insertion was full-length and carried 5' and 3' transductions. The corresponding donor RC-L1 was part of a large and recently active L1 transduction family and was highly mobile in a cultured-cell L1 retrotransposition reporter assay. Notably, we observed distinct and dynamic DNA methylation profiles for the de novo L1 and members of its extended transduction family during neuronal differentiation. These experiments reveal how a de novo L1 insertion in a pluripotent stem cell is rapidly recognized and repressed, albeit incompletely, by the host genome during neurodifferentiation, while retaining potential for further retrotransposition.
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63
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Schumann GG, Fuchs NV, Tristán-Ramos P, Sebe A, Ivics Z, Heras SR. The impact of transposable element activity on therapeutically relevant human stem cells. Mob DNA 2019; 10:9. [PMID: 30899334 PMCID: PMC6408843 DOI: 10.1186/s13100-019-0151-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.
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Affiliation(s)
- Gerald G Schumann
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Nina V Fuchs
- 2Host-Pathogen Interactions, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Pablo Tristán-Ramos
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Attila Sebe
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Zoltán Ivics
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Sara R Heras
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
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64
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Teo YV, Capri M, Morsiani C, Pizza G, Faria AMC, Franceschi C, Neretti N. Cell-free DNA as a biomarker of aging. Aging Cell 2019; 18:e12890. [PMID: 30575273 PMCID: PMC6351822 DOI: 10.1111/acel.12890] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 10/12/2018] [Accepted: 11/10/2018] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA (cfDNA) is present in the circulating plasma and other body fluids and is known to originate mainly from apoptotic cells. Here, we provide the first in vivo evidence of global and local chromatin changes in human aging by analyzing cfDNA from the blood of individuals of different age groups. Our results show that nucleosome signals inferred from cfDNA are consistent with the redistribution of heterochromatin observed in cellular senescence and aging in other model systems. In addition, we detected a relative cfDNA loss at several genomic locations, such as transcription start and termination sites, 5'UTR of L1HS retrotransposons and dimeric AluY elements with age. Our results also revealed age and deteriorating health status correlate with increased enrichment of signals from cells in different tissues. In conclusion, our results show that the sequencing of circulating cfDNA from human blood plasma can be used as a noninvasive methodology to study age-associated changes to the epigenome in vivo.
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Affiliation(s)
- Yee Voan Teo
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Miriam Capri
- CIG Interdepartmental Centre "Galvani", University of Bologna, Bologna, Italy
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Cristina Morsiani
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
| | - Grazia Pizza
- DIMES-Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology & Metabolism, Department of Medicine, Imperial College London, London, UK
| | - Ana Maria Caetano Faria
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
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65
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Abstract
Transposable elements (TEs) are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in molecular functions that influence genomic plasticity and gene expression regulation. With the advent of next-generation sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. In this chapter, the Authors comprehensively summarize the state-of the-art of TE research in animal models and humans supporting a framework in which TEs play a functional role in mechanisms affecting a variety of behaviors, including neurodevelopmental, neuropsychiatric, and neurodegenerative disorders. Finally, the Authors discuss recent therapeutic applications raised from the increasing experimental evidence on TE functional mechanisms.
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Affiliation(s)
- G Guffanti
- McLean Hospital - Harvard Medical School, Belmont, MA, USA.
| | - A Bartlett
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
| | - P DeCrescenzo
- McLean Hospital - Harvard Medical School, Belmont, MA, USA
| | - F Macciardi
- Department of Psychiatry and Human Behavior, University of California, Irvine, Irvine, CA, USA
| | - R Hunter
- Department of Psychology, University of Massachusetts, Boston, Boston, MA, USA
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66
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Pereira GC, Sanchez L, Schaughency PM, Rubio-Roldán A, Choi JA, Planet E, Batra R, Turelli P, Trono D, Ostrow LW, Ravits J, Kazazian HH, Wheelan SJ, Heras SR, Mayer J, García-Pérez JL, Goodier JL. Properties of LINE-1 proteins and repeat element expression in the context of amyotrophic lateral sclerosis. Mob DNA 2018; 9:35. [PMID: 30564290 PMCID: PMC6295051 DOI: 10.1186/s13100-018-0138-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease involving loss of motor neurons and having no known cure and uncertain etiology. Several studies have drawn connections between altered retrotransposon expression and ALS. Certain features of the LINE-1 (L1) retrotransposon-encoded ORF1 protein (ORF1p) are analogous to those of neurodegeneration-associated RNA-binding proteins, including formation of cytoplasmic aggregates. In this study we explore these features and consider possible links between L1 expression and ALS. RESULTS We first considered factors that modulate aggregation and subcellular distribution of LINE-1 ORF1p, including nuclear localization. Changes to some ORF1p amino acid residues alter both retrotransposition efficiency and protein aggregation dynamics, and we found that one such polymorphism is present in endogenous L1s abundant in the human genome. We failed, however, to identify CRM1-mediated nuclear export signals in ORF1p nor strict involvement of cell cycle in endogenous ORF1p nuclear localization in human 2102Ep germline teratocarcinoma cells. Some proteins linked with ALS bind and colocalize with L1 ORF1p ribonucleoprotein particles in cytoplasmic RNA granules. Increased expression of several ALS-associated proteins, including TAR DNA Binding Protein (TDP-43), strongly limits cell culture retrotransposition, while some disease-related mutations modify these effects. Using quantitative reverse transcription PCR (RT-qPCR) of ALS tissues and reanalysis of publicly available RNA-Seq datasets, we asked if changes in expression of retrotransposons are associated with ALS. We found minimal altered expression in sporadic ALS tissues but confirmed a previous report of differential expression of many repeat subfamilies in C9orf72 gene-mutated ALS patients. CONCLUSIONS Here we extended understanding of the subcellular localization dynamics of the aggregation-prone LINE-1 ORF1p RNA-binding protein. However, we failed to find compelling evidence for misregulation of LINE-1 retrotransposons in sporadic ALS nor a clear effect of ALS-associated TDP-43 protein on L1 expression. In sum, our study reveals that the interplay of active retrotransposons and the molecular features of ALS are more complex than anticipated. Thus, the potential consequences of altered retrotransposon activity for ALS and other neurodegenerative disorders are worthy of continued investigation.
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Affiliation(s)
- Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Paul M. Schaughency
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Alejandro Rubio-Roldán
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jungbin A. Choi
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Priscilla Turelli
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Lyle W. Ostrow
- Neuromuscular Division, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, University of California at San Diego, San Diego, California USA
| | - Haig H. Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sarah J. Wheelan
- Oncology Center-Cancer Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Jens Mayer
- Department of Human Genetics, Medical Faculty, University of Saarland, Homburg/Saar, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland USA
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67
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Kerachian MA, Kerachian M. Long interspersed nucleotide element-1 (LINE-1) methylation in colorectal cancer. Clin Chim Acta 2018; 488:209-214. [PMID: 30445031 DOI: 10.1016/j.cca.2018.11.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) represents a group of molecularly heterogeneous diseases characterized by genetic and epigenetic alterations. Long interspersed nuclear elements (LINEs) are a form of retrotransposable element found in many eukaryotic genomes. These LINEs, when active, can mobilize in the cell and steadily cause genomic rearrangement. Active LINE reorganization is a source of endogenous mutagenesis and polymorphism in the cell that brings about individual genomic variation. In normal somatic cells, these elements are heavily methylated and thus mostly suppressed, in turn, preventing their potential for bringing about genomic instability. When LINEs are inadequately controlled, they can play a role in the pathogenesis of several genetic diseases, such as cancer. In tumor cells, LINE hypomethylation can reactivate the mobilization of these elements and is associated with both an advanced stage and a poor prognosis. In this article, we summarize the current knowledge surrounding LINE methylation, its correlation to CRC and its application as a diagnostic, prognostic and predictive biomarker in colon cancer.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran; Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Matin Kerachian
- Faculty of Medicine, McGill University, Montreal, Canada; Research Institute at McGill University Health Center, Montreal, Canada
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68
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Regulating gene expression in animals through RNA endonucleolytic cleavage. Heliyon 2018; 4:e00908. [PMID: 30426105 PMCID: PMC6223193 DOI: 10.1016/j.heliyon.2018.e00908] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 12/22/2022] Open
Abstract
The expression of any gene must be precisely controlled for appropriate function. This expression can be controlled at various levels. This includes epigenetic regulation through DNA methylation or histone modifications. At the posttranscriptional level, regulation can be via alternative splicing or controlling messenger RNA (mRNA) stability. RNA cleavage is one way to control mRNA stability. For example, microRNA (miRNA)-induced mRNA cleavage has long been recognised in plants. RNA cleavage also appears to be widespread in other kingdoms of life, and it is now clear that mRNA cleavage plays critical functions in animals. Although miRNA-induced mRNA cleavage can occur in animals, it is not a widespread mechanism. Instead, mRNA cleavage can be induced by a range of other mechanisms, including by endogenous short inhibitory RNAs (endo-siRNAs), as well as the Ribonuclease III (RNase III) enzymes Drosha and Dicer. In addition, RNA cleavage induced by endo-siRNAs and PIWI-interacting RNAs (piRNAs) is important for genome defence against transposons. Moreover, several RNase has been identified as important antiviral mediators. In this review, we will discuss these various RNA endonucleolytic cleavage mechanisms utilised by animals to regulate the expression of genes and as a defence against retrotransposons and viral infection.
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69
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Inhibition of LINE-1 Retrotransposition by Capsaicin. Int J Mol Sci 2018; 19:ijms19103243. [PMID: 30347711 PMCID: PMC6214084 DOI: 10.3390/ijms19103243] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/13/2018] [Accepted: 10/16/2018] [Indexed: 12/18/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is a non-long terminal repeat (LTR) retrotransposon that constitutes approximately 17% of the human genome. Since approximately 100 copies are still competent for retrotransposition to other genomic loci, dysregulated retrotransposition of L1 is considered to be a major risk factor of endogenous mutagenesis in humans. Thus, it is important to find drugs to regulate this process. Although various chemicals are reportedly capable of affecting L1 retrotransposition, it is poorly understood whether phytochemicals modulate L1 retrotransposition. Here, we screened a library of compounds that were derived from phytochemicals for reverse transcriptase (RT) inhibition with an in vitro RT assay. We identified capsaicin as a novel RT inhibitor that also suppressed L1 retrotransposition. The inhibitory effect of capsaicin on L1 retrotransposition was mediated neither through its receptor, nor through its modulation of the L1 promoter and/or antisense promoter activity, excluding the possibility that capsaicin indirectly affected L1 retrotransposition. Collectively, capsaicin suppressed L1 retrotransposition most likely by inhibiting the RT activity of L1 ORF2p, which is the L1-encoded RT responsible for L1 retrotransposition. Given that L1-mediated mutagenesis can cause tumorigenesis, our findings suggest the potential of capsaicin for suppressing cancer development.
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70
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Miglio U, Berrino E, Panero M, Ferrero G, Coscujuela Tarrero L, Miano V, Dell'Aglio C, Sarotto I, Annaratone L, Marchiò C, Comoglio PM, De Bortoli M, Pasini B, Venesio T, Sapino A. The expression of LINE1-MET chimeric transcript identifies a subgroup of aggressive breast cancers. Int J Cancer 2018; 143:2838-2848. [PMID: 30144023 DOI: 10.1002/ijc.31831] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 07/17/2018] [Accepted: 08/15/2018] [Indexed: 01/03/2023]
Abstract
Demethylation of the long interspersed nuclear element (LINE-1; L1) antisense promoter can result in transcription of neighboring sequences as for the L1-MET transcript produced by the L1 placed in the second intron of MET. To define the role of L1-MET, we investigated the sequence and the transcription of L1-MET in vitro models and heterogeneous breast cancers, previously reported to show other L1-derived transcripts. L1-MET expressing cell lines were initially identified in silico and investigated for L1-MET promoter methylation, cDNA sequence and cell fraction mRNA. The transcriptional level of L1-MET and MET were then evaluated in breast specimens, including 9 cancer cell lines, 41 carcinomas of different subtypes, and 11 normal tissues. In addition to a L1-MET transcript ending at MET exon 21, six novel L1-MET splice variants were identified. Normal breast tissues were negative for the L1-MET expression, whereas the triple-negative breast cancer (TNBC) and the high-grade carcinomas were enriched with the L1-MET mRNA (p = 0.005 and p = 0.018, respectively). In cancer cells and tissues the L1-MET expression was associated with its promoter hypomethylation (ρ = -0.8 and -0.9, respectively). No correlation was found between L1-MET and MET mRNA although L1-MET expressing tumors with higher L1-MET/MET ratio were negative for the MET protein expression (p = 0.006). Besides providing the first identification and detailed description of L1-MET in breast cancer, we clearly demonstrate that higher levels of this transcript specifically recognize a subset of more aggressive carcinomas, mainly TNBC. We suggest the possible evaluation of L1-MET in the challenging diagnosis of early TNBCs.
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Affiliation(s)
- Umberto Miglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Enrico Berrino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Mara Panero
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy.,Department of Computer Science, University of Turin, Turin, Italy
| | | | - Valentina Miano
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Carmine Dell'Aglio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Ivana Sarotto
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Laura Annaratone
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Caterina Marchiò
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
| | - Paolo M Comoglio
- Molecular Therapeutics and Exploratory Research Laboratory, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Michele De Bortoli
- Department of Clinical and Biological Sciences, University of Turin, Orbassano, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Tiziana Venesio
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Anna Sapino
- Unit of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Turin, Turin, Italy
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71
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Line-1: Implications in the etiology of cancer, clinical applications, and pharmacologic targets. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 778:51-60. [DOI: 10.1016/j.mrrev.2018.09.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/15/2018] [Accepted: 09/17/2018] [Indexed: 11/21/2022]
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72
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Guichard E, Peona V, Malagoli Tagliazucchi G, Abitante L, Jagoda E, Musella M, Ricci M, Rubio-Roldán A, Sarno S, Luiselli D, Pettener D, Taccioli C, Pagani L, Garcia-Perez JL, Boattini A. Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans. Mob DNA 2018; 9:28. [PMID: 30147753 PMCID: PMC6094920 DOI: 10.1186/s13100-018-0133-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 08/07/2018] [Indexed: 12/31/2022] Open
Abstract
Background Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage. Results We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection. Conclusions Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage. Electronic supplementary material The online version of this article (10.1186/s13100-018-0133-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Etienne Guichard
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Valentina Peona
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy.,2Department of Evolutionary Biology (EBC), Uppsala University, SE-752 36 Uppsala, Sweden
| | | | - Lucia Abitante
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Evelyn Jagoda
- 4Human Evolutionary Biology, Harvard University, Cambridge, MA 02138 USA
| | - Margherita Musella
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Marco Ricci
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Alejandro Rubio-Roldán
- 5GENYO - Pfizer - Universidad de Granada - Junta de Andalucía Centre for Genomics and Oncological Research, PTS Granada, 18007 Granada, Spain
| | - Stefania Sarno
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Donata Luiselli
- 6Department of Cultural Heritage, University of Bologna, Ravenna Campus, 48121 Ravenna, Italy
| | - Davide Pettener
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
| | - Cristian Taccioli
- 7Department of Animal Medicine, Production and Health, University of Padova, 35020 Legnaro, Pd Italy
| | - Luca Pagani
- 8Department of Biology, University of Padova, 35131 Padova, Italy.,9Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Jose Luis Garcia-Perez
- 5GENYO - Pfizer - Universidad de Granada - Junta de Andalucía Centre for Genomics and Oncological Research, PTS Granada, 18007 Granada, Spain.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU UK
| | - Alessio Boattini
- 1Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126 Bologna, Italy
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73
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Mayer J, Harz C, Sanchez L, Pereira GC, Maldener E, Heras SR, Ostrow LW, Ravits J, Batra R, Meese E, García-Pérez JL, Goodier JL. Transcriptional profiling of HERV-K(HML-2) in amyotrophic lateral sclerosis and potential implications for expression of HML-2 proteins. Mol Neurodegener 2018; 13:39. [PMID: 30068350 PMCID: PMC6091006 DOI: 10.1186/s13024-018-0275-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder. About 90% of ALS cases are without a known genetic cause. The human endogenous retrovirus multi-copy HERV-K(HML-2) group was recently reported to potentially contribute to neurodegeneration and disease pathogenesis in ALS because of transcriptional upregulation and toxic effects of HML-2 Envelope (Env) protein. Env and other proteins are encoded by some transcriptionally active HML-2 loci. However, more detailed information is required regarding which HML-2 loci are transcribed in ALS, which of their proteins are expressed, and differences between the disease and non-disease states. METHODS For brain and spinal cord tissue samples from ALS patients and controls, we identified transcribed HML-2 loci by generating and mapping HML-2-specific cDNA sequences. We predicted expression of HML-2 env gene-derived proteins based on the observed cDNA sequences. Furthermore, we determined overall HML-2 transcript levels by RT-qPCR and investigated presence of HML-2 Env protein in ALS and control tissue samples by Western blotting. RESULTS We identified 24 different transcribed HML-2 loci. Some of those loci are transcribed at relatively high levels. However, significant differences in HML-2 loci transcriptional activities were not seen when comparing ALS and controls. Likewise, overall HML-2 transcript levels, as determined by RT-qPCR, were not significantly different between ALS and controls. Indeed, we were unable to detect full-length HML-2 Env protein in ALS and control tissue samples despite reasonable sensitivity. Rather our analyses suggest that a number of HML-2 protein variants other than full-length Env may potentially be expressed in ALS patients. CONCLUSIONS Our results expand and refine recent publications on HERV-K(HML-2) and ALS. Some of our results are in conflict with recent findings and call for further specific analyses. Our profiling of HML-2 transcription in ALS opens up the possibility that HML-2 proteins other than canonical full-length Env may have to be considered when studying the role of HML-2 in ALS disease.
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Affiliation(s)
- Jens Mayer
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Christian Harz
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Laura Sanchez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Gavin C. Pereira
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Esther Maldener
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Sara R. Heras
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Lyle W. Ostrow
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 28217 USA
| | - John Ravits
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Ranjan Batra
- Department of Neurosciences, School of Medicine, UCSD, San Diego, CA USA
| | - Eckart Meese
- Department of Human Genetics, University of Saarland, Homburg, Germany
| | - Jose Luis García-Pérez
- GENYO. Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - John L. Goodier
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
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74
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Faulkner GJ, Billon V. L1 retrotransposition in the soma: a field jumping ahead. Mob DNA 2018; 9:22. [PMID: 30002735 PMCID: PMC6035798 DOI: 10.1186/s13100-018-0128-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.
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Affiliation(s)
- Geoffrey J. Faulkner
- Mater Research Institute – University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 61 Avenue du Président Wilson, 94230 Cachan, France
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75
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Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A 2018; 115:E5526-E5535. [PMID: 29802231 PMCID: PMC6004460 DOI: 10.1073/pnas.1722565115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs' interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors.
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76
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Li C, Lenhard B, Luscombe NM. Integrated analysis sheds light on evolutionary trajectories of young transcription start sites in the human genome. Genome Res 2018; 28:676-688. [PMID: 29618487 PMCID: PMC5932608 DOI: 10.1101/gr.231449.117] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/21/2018] [Indexed: 01/06/2023]
Abstract
Understanding the molecular mechanisms and evolution of the gene regulatory system remains a major challenge in biology. Transcription start sites (TSSs) are especially interesting because they are central to initiating gene expression. Previous studies revealed widespread transcription initiation and fast turnover of TSSs in mammalian genomes. Yet, how new TSSs originate and how they evolve over time remain poorly understood. To address these questions, we analyzed ∼200,000 human TSSs by integrating evolutionary (inter- and intra-species) and functional genomic data, particularly focusing on evolutionarily young TSSs that emerged in the primate lineage. TSSs were grouped according to their evolutionary age using sequence alignment information as a proxy. Comparisons of young and old TSSs revealed that (1) new TSSs emerge through a combination of intrinsic factors, like the sequence properties of transposable elements and tandem repeats, and extrinsic factors such as their proximity to existing regulatory modules; (2) new TSSs undergo rapid evolution that reduces the inherent instability of repeat sequences associated with a high propensity of TSS emergence; and (3) once established, the transcriptional competence of surviving TSSs is gradually enhanced, with evolutionary changes subject to temporal (fewer regulatory changes in younger TSSs) and spatial constraints (fewer regulatory changes in more isolated TSSs). These findings advance our understanding of how regulatory innovations arise in the genome throughout evolution and highlight the genomic robustness and evolvability in these processes.
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Affiliation(s)
- Cai Li
- The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Boris Lenhard
- Computational Regulatory Genomics, MRC London Institute of Medical Sciences, London W12 0NN, United Kingdom.,Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London W12 0NN, United Kingdom.,Sars International Centre for Marine Molecular Biology, University of Bergen, N-5008 Bergen, Norway
| | - Nicholas M Luscombe
- The Francis Crick Institute, London NW1 1AT, United Kingdom.,UCL Genetics Institute, University College London, London WC1E 6BT, United Kingdom.,Okinawa Institute of Science & Technology Graduate University, Okinawa, 904-0495, Japan
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77
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Spliced integrated retrotransposed element (SpIRE) formation in the human genome. PLoS Biol 2018; 16:e2003067. [PMID: 29505568 PMCID: PMC5860796 DOI: 10.1371/journal.pbio.2003067] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 03/20/2018] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Human Long interspersed element-1 (L1) retrotransposons contain an internal RNA polymerase II promoter within their 5′ untranslated region (UTR) and encode two proteins, (ORF1p and ORF2p) required for their mobilization (i.e., retrotransposition). The evolutionary success of L1 relies on the continuous retrotransposition of full-length L1 mRNAs. Previous studies identified functional splice donor (SD), splice acceptor (SA), and polyadenylation sequences in L1 mRNA and provided evidence that a small number of spliced L1 mRNAs retrotransposed in the human genome. Here, we demonstrate that the retrotransposition of intra-5′UTR or 5′UTR/ORF1 spliced L1 mRNAs leads to the generation of spliced integrated retrotransposed elements (SpIREs). We identified a new intra-5′UTR SpIRE that is ten times more abundant than previously identified SpIREs. Functional analyses demonstrated that both intra-5′UTR and 5′UTR/ORF1 SpIREs lack Cis-acting transcription factor binding sites and exhibit reduced promoter activity. The 5′UTR/ORF1 SpIREs also produce nonfunctional ORF1p variants. Finally, we demonstrate that sequence changes within the L1 5′UTR over evolutionary time, which permitted L1 to evade the repressive effects of a host protein, can lead to the generation of new L1 splicing events, which, upon retrotransposition, generates a new SpIRE subfamily. We conclude that splicing inhibits L1 retrotransposition, SpIREs generally represent evolutionary “dead-ends” in the L1 retrotransposition process, mutations within the L1 5′UTR alter L1 splicing dynamics, and that retrotransposition of the resultant spliced transcripts can generate interindividual genomic variation. Long interspersed element-1 (L1) sequences comprise about 17% of the human genome reference sequence. The average human genome contains about 100 active L1s that mobilize throughout the genome by a “copy and paste” process termed retrotransposition. Active L1s encode two proteins (ORF1p and ORF2p). ORF1p and ORF2p preferentially bind to their encoding RNA, forming a ribonucleoprotein particle (RNP). During retrotransposition, the L1 RNP translocates to the nucleus, where the ORF2p endonuclease makes a single-strand nick in target site DNA that exposes a 3′ hydroxyl group in genomic DNA. The 3′ hydroxyl group then is used as a primer by the ORF2p reverse transcriptase to copy the L1 RNA into cDNA, leading to the integration of an L1 copy at a new genomic location. The evolutionary success of L1 requires the faithful retrotransposition of full-length L1 mRNAs; thus, it was surprising to find that a small number of L1 retrotransposition events are derived from spliced L1 mRNAs. By using genetic, biochemical, and computational approaches, we demonstrate that spliced L1 mRNAs can undergo an initial round of retrotransposition, leading to the generation of spliced integrated retrotransposed elements (SpIREs). SpIREs represent about 2% of previously annotated full-length primate-specific L1s in the human genome reference sequence. However, because splicing leads to intra-L1 deletions that remove critical sequences required for L1 expression, SpIREs generally cannot undergo subsequent rounds of retrotransposition and can be considered “dead on arrival” insertions. Our data further highlight how genetic conflict between L1 and its host has influenced L1 expression, L1 retrotransposition, and L1 splicing dynamics over evolutionary time.
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78
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Orecchini E, Frassinelli L, Galardi S, Ciafrè SA, Michienzi A. Post-transcriptional regulation of LINE-1 retrotransposition by AID/APOBEC and ADAR deaminases. Chromosome Res 2018; 26:45-59. [PMID: 29396793 DOI: 10.1007/s10577-018-9572-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/07/2018] [Indexed: 02/05/2023]
Abstract
Long interspersed element-1 (LINE-1 or L1) retrotransposons represent the only functional family of autonomous transposable elements in humans and formed 17% of our genome. Even though most of the human L1 sequences are inactive, a limited number of copies per individual retain the ability to mobilize by a process termed retrotransposition. The ongoing L1 retrotransposition may result in insertional mutagenesis that could lead to negative consequences such as genetic disease and cancer. For this reason, cells have evolved several mechanisms of defense to restrict L1 activity. Among them, a critical role for cellular deaminases [activation-induced deaminase (AID)/apolipoprotein B mRNA-editing catalytic polypeptide-like (APOBEC) and adenosine deaminases that act on RNA (ADAR) enzymes] has emerged. The majority of the AID/APOBEC family of proteins are responsible for the deamination of cytosine to uracil (C-to-U editing) within DNA and RNA targets. The ADARs convert adenosine bases to inosines (A-to-I editing) within double-stranded RNA (dsRNA) targets. This review will discuss the current understanding of the regulation of LINE-1 retrotransposition mediated by these enzymes.
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Affiliation(s)
- Elisa Orecchini
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Loredana Frassinelli
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Galardi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Silvia Anna Ciafrè
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy
| | - Alessandro Michienzi
- Department of Biomedicine and Prevention, University of Rome "Tor Vergata", Rome, Italy.
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79
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Jung J, Lee S, Cho HS, Park K, Ryu JW, Jung M, Kim J, Kim H, Kim DS. Bioinformatic analysis of regulation of natural antisense transcripts by transposable elements in human mRNA. Genomics 2018; 111:159-166. [PMID: 29366860 DOI: 10.1016/j.ygeno.2018.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 12/19/2022]
Abstract
Non-coding RNA is no longer considered to be "junk" DNA, based on evidence uncovered in recent decades. In particular, the important role played by natural antisense transcripts (NATs) in regulating the expression of genes is receiving increasing attention. However, the regulatory mechanisms of NATs remain incompletely understood. It is well-known that the insertion of transposable elements (TEs) can affect gene transcription. Using a bioinformatics approach, we identified NATs using human mRNA sequences from the UCSC Genome Browser Database. Our in silico analysis identified 1079 NATs and 700 sense-antisense gene pairs. We identified 179 NATs that showed evidence of having been affected by TEs during cellular gene expression. These findings may provide an understanding of the complex regulation mechanisms of NATs. If our understanding of NATs as modulators of gene expression is further enhanced, we can develop ways to control gene expression.
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Affiliation(s)
- Jaeeun Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Sugi Lee
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Hyun-Soo Cho
- Department of Stem Cell Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Kunhyang Park
- Department of Core Facility Management Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jea-Woon Ryu
- Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Minah Jung
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Jeongkil Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - HyeRan Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Plant Systems Engineering Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Dae-Soo Kim
- Department of Bioinformatics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, Republic of Korea; Department of Rare Disease Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea.
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80
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Boissinot S, Sookdeo A. The Evolution of LINE-1 in Vertebrates. Genome Biol Evol 2018; 8:3485-3507. [PMID: 28175298 PMCID: PMC5381506 DOI: 10.1093/gbe/evw247] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2016] [Indexed: 12/21/2022] Open
Abstract
The abundance and diversity of the LINE-1 (L1) retrotransposon differ greatly among vertebrates. Mammalian genomes contain hundreds of thousands L1s that have accumulated since the origin of mammals. A single group of very similar elements is active at a time in mammals, thus a single lineage of active families has evolved in this group. In contrast, non-mammalian genomes (fish, amphibians, reptiles) harbor a large diversity of concurrently transposing families, which are all represented by very small number of recently inserted copies. Why the pattern of diversity and abundance of L1 is so different among vertebrates remains unknown. To address this issue, we performed a detailed analysis of the evolution of active L1 in 14 mammals and in 3 non-mammalian vertebrate model species. We examined the evolution of base composition and codon bias, the general structure, and the evolution of the different domains of L1 (5′UTR, ORF1, ORF2, 3′UTR). L1s differ substantially in length, base composition, and structure among vertebrates. The most variation is found in the 5′UTR, which is longer in amniotes, and in the ORF1, which tend to evolve faster in mammals. The highly divergent L1 families of lizard, frog, and fish share species-specific features suggesting that they are subjected to the same functional constraints imposed by their host. The relative conservation of the 5′UTR and ORF1 in non-mammalian vertebrates suggests that the repression of transposition by the host does not act in a sequence-specific manner and did not result in an arms race, as is observed in mammals.
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81
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Soares ML, Edwards CA, Dearden FL, Ferrón SR, Curran S, Corish JA, Rancourt RC, Allen SE, Charalambous M, Ferguson-Smith MA, Rens W, Adams DJ, Ferguson-Smith AC. Targeted deletion of a 170-kb cluster of LINE-1 repeats and implications for regional control. Genome Res 2018; 28:gr.221366.117. [PMID: 29367313 PMCID: PMC5848613 DOI: 10.1101/gr.221366.117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 01/10/2018] [Indexed: 12/31/2022]
Abstract
Approximately half the mammalian genome is composed of repetitive sequences, and accumulating evidence suggests that some may have an impact on genome function. Here, we characterized a large array class of repeats of long-interspersed elements (LINE-1). Although widely distributed in mammals, locations of such arrays are species specific. Using targeted deletion, we asked whether a 170-kb LINE-1 array located at a mouse imprinted domain might function as a modulator of local transcriptional control. The LINE-1 array is lamina associated in differentiated ES cells consistent with its AT-richness, and although imprinting occurs both proximally and distally to the array, active LINE-1 transcripts within the tract are biallelically expressed. Upon deletion of the array, no perturbation of imprinting was observed, and abnormal phenotypes were not detected in maternal or paternal heterozygous or homozygous mutant mice. The array does not shield nonimprinted genes in the vicinity from local imprinting control. Reduced neural expression of protein-coding genes observed upon paternal transmission of the deletion is likely due to the removal of a brain-specific enhancer embedded within the LINE array. Our findings suggest that presence of a 170-kb LINE-1 array reflects the tolerance of the site for repeat insertion rather than an important genomic function in normal development.
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Affiliation(s)
- Miguel L Soares
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
- Departamento de Biomedicina, Unidade de Biologia Experimental, Faculdade de Medicina da Universidade do Porto, Porto; and i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-319 Porto, Portugal
| | - Carol A Edwards
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Frances L Dearden
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sacri R Ferrón
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Scott Curran
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Jennifer A Corish
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Rebecca C Rancourt
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Sarah E Allen
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | - Marika Charalambous
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom
| | | | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom
| | - David J Adams
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
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82
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Chishima T, Iwakiri J, Hamada M. Identification of Transposable Elements Contributing to Tissue-Specific Expression of Long Non-Coding RNAs. Genes (Basel) 2018; 9:E23. [PMID: 29315213 PMCID: PMC5793176 DOI: 10.3390/genes9010023] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 12/24/2017] [Accepted: 12/28/2017] [Indexed: 12/05/2022] Open
Abstract
It has been recently suggested that transposable elements (TEs) are re-used as functional elements of long non-coding RNAs (lncRNAs). This is supported by some examples such as the human endogenous retrovirus subfamily H (HERVH) elements contained within lncRNAs and expressed specifically in human embryonic stem cells (hESCs), as required to maintain hESC identity. There are at least two unanswered questions about all lncRNAs. How many TEs are re-used within lncRNAs? Are there any other TEs that affect tissue specificity of lncRNA expression? To answer these questions, we comprehensively identify TEs that are significantly related to tissue-specific expression levels of lncRNAs. We downloaded lncRNA expression data corresponding to normal human tissue from the Expression Atlas and transformed the data into tissue specificity estimates. Then, Fisher's exact tests were performed to verify whether the presence or absence of TE-derived sequences influences the tissue specificity of lncRNA expression. Many TE-tissue pairs associated with tissue-specific expression of lncRNAs were detected, indicating that multiple TE families can be re-used as functional domains or regulatory sequences of lncRNAs. In particular, we found that the antisense promoter region of L1PA2, a LINE-1 subfamily, appears to act as a promoter for lncRNAs with placenta-specific expression.
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Affiliation(s)
- Takafumi Chishima
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 63-520, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.
| | - Junichi Iwakiri
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, 277-8562 Chiba, Japan.
| | - Michiaki Hamada
- Department of Electrical Engineering and Bioscience, Faculty of Science and Engineering, Waseda University, 55N-06-10, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), 63-520, 3-4-1, Okubo Shinjuku-ku, Tokyo 169-8555, Japan.
- Artificial Intelligence Research Center (AIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-3-26, Aomi, Koto-ku, Tokyo 135-0064, Japan.
- Institute for Medical-oriented Structural Biology, Waseda University, 2-2, Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Graduate School of Medicine, Nippon Medical School, 1-1-5, Sendagi, Bunkyo-ku, Tokyo 113-8602, Japan.
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83
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Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. eLife 2018; 7:30058. [PMID: 29309036 PMCID: PMC5821460 DOI: 10.7554/elife.30058] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/04/2018] [Indexed: 01/12/2023] Open
Abstract
LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition. Only two percent of our genetic material or genome are occupied by genes, while between 60-70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repetitive sequences evolved from genetic elements called transposons. Transposons are often referred to as ‘jumping genes’, as they can randomly move within the genome and thereby create dangerous mutations that may lead to cancer or other genetic diseases. LINE-1 is the only remaining active transposon in humans, and it expands by copying and pasting itself to new locations via a process called 'retrotransposition'. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences. Previous research has shown that LINE-1 can form complexes with a series of proteins, including the two encoded by LINE-1 RNA itself: ORF1p and ORF2p. The LINE-1 complexes can enter the nucleus of the cell and insert a new copy of LINE-1 into the genome. However, until now it was not known how they do this. To investigate this further, Mita et al. used human cancer cells grown in the lab and tracked LINE-1 during the different stages of the cell cycle. The results showed that LINE-1 enters the nucleus as the cell starts to divide and the membrane of the nucleus breaks down. The LINE-1 complexes are then retained in the nucleus while the membrane of the nucleus reforms. Later, as the cell duplicates its genetic material, LINE-1 starts to copy and paste itself. Mita et al., together with another group of researchers, also found that during this process, only LINE-1 RNA and ORF2p were found in the nucleus. This shows that the cell cycle dictates both where the LINE-1 complexes gather and when LINE-1 is active. A next step will be to further investigate how the ‘copy and paste’ mechanisms of LINE-1 and the two LINE-1 proteins are regulated during the cell cycle. In future, this may help to identify LINE-1’s role in processes like aging or in diseases such as cancer.
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Affiliation(s)
- Paolo Mita
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Aleksandra Wudzinska
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Xiaoji Sun
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Joshua Andrade
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - Shruti Nayak
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - David J Kahler
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - John LaCava
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Beatrix Ueberheide
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Proteomics laboratory, NYU Langone Health, New York, United States
| | - Chi Y Yun
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - David Fenyö
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Jef D Boeke
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
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84
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Suarez NA, Macia A, Muotri AR. LINE-1 retrotransposons in healthy and diseased human brain. Dev Neurobiol 2017; 78:434-455. [PMID: 29239145 DOI: 10.1002/dneu.22567] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is a transposable element with the ability to self-mobilize throughout the human genome. The L1 elements found in the human brain is hypothesized to date back 56 million years ago and has survived evolution, currently accounting for 17% of the human genome. L1 retrotransposition has been theorized to contribute to somatic mosaicism. This review focuses on the presence of L1 in the healthy and diseased human brain, such as in autism spectrum disorders. Throughout this exploration, we will discuss the impact L1 has on neurological disorders that can occur throughout the human lifetime. With this, we hope to better understand the complex role of L1 in the human brain development and its implications to human cognition. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 434-455, 2018.
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Affiliation(s)
- Nicole A Suarez
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
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85
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Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells. PLoS Genet 2017; 13:e1007051. [PMID: 29028794 PMCID: PMC5656329 DOI: 10.1371/journal.pgen.1007051] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 10/25/2017] [Accepted: 10/03/2017] [Indexed: 12/15/2022] Open
Abstract
LINE-1 (L1) retrotransposons can mobilize (retrotranspose) within the human genome, and mutagenic de novo L1 insertions can lead to human diseases, including cancers. As a result, cells are actively engaged in preventing L1 retrotransposition. This work reveals that the human Condensin II complex restricts L1 retrotransposition in both non-transformed and transformed cell lines through inhibition of L1 transcription and translation. Condensin II subunits, CAP-D3 and CAP-H2, interact with members of the Gamma-Interferon Activated Inhibitor of Translation (GAIT) complex including the glutamyl-prolyl-tRNA synthetase (EPRS), the ribosomal protein L13a, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and NS1 associated protein 1 (NSAP1). GAIT has been shown to inhibit translation of mRNAs encoding inflammatory proteins in myeloid cells by preventing the binding of the translation initiation complex, in response to Interferon gamma (IFN-γ). Excitingly, our data show that Condensin II promotes complexation of GAIT subunits. Furthermore, RNA-Immunoprecipitation experiments in epithelial cells demonstrate that Condensin II and GAIT subunits associate with L1 RNA in a co-dependent manner, independent of IFN-γ. These findings suggest that cooperation between the Condensin II and GAIT complexes may facilitate a novel mechanism of L1 repression, thus contributing to the maintenance of genome stability in somatic cells.
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86
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Idica A, Sevrioukov EA, Zisoulis DG, Hamdorf M, Daugaard I, Kadandale P, Pedersen IM. MicroRNA miR-128 represses LINE-1 (L1) retrotransposition by down-regulating the nuclear import factor TNPO1. J Biol Chem 2017; 292:20494-20508. [PMID: 28974576 DOI: 10.1074/jbc.m117.807677] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/20/2017] [Indexed: 01/04/2023] Open
Abstract
Repetitive elements, including LINE-1 (L1), comprise approximately half of the human genome. These elements can potentially destabilize the genome by initiating their own replication and reintegration into new sites (retrotransposition). In somatic cells, transcription of L1 elements is repressed by distinct molecular mechanisms, including DNA methylation and histone modifications, to repress transcription. Under conditions of hypomethylation (e.g. in tumor cells), a window of opportunity for L1 derepression arises, and additional restriction mechanisms become crucial. We recently demonstrated that the microRNA miR-128 represses L1 activity by directly binding to L1 ORF2 RNA. In this study, we tested whether miR-128 can also control L1 activity by repressing cellular proteins important for L1 retrotransposition. We found that miR-128 targets the 3' UTR of nuclear import factor transportin 1 (TNPO1) mRNA. Manipulation of miR-128 and TNPO1 levels demonstrated that induction or depletion of TNPO1 affects L1 retrotransposition and nuclear import of an L1-ribonucleoprotein complex (using L1-encoded ORF1p as a proxy for L1-ribonucleoprotein complexes). Moreover, TNPO1 overexpression partially reversed the repressive effect of miR-128 on L1 retrotransposition. Our study represents the first description of a protein factor involved in nuclear import of the L1 element and demonstrates that miR-128 controls L1 activity in somatic cells through two independent mechanisms: direct binding to L1 RNA and regulation of a cellular factor necessary for L1 nuclear import and retrotransposition.
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Affiliation(s)
- Adam Idica
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Evgueni A Sevrioukov
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Dimitrios G Zisoulis
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Matthias Hamdorf
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Iben Daugaard
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Pavan Kadandale
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
| | - Irene M Pedersen
- From the Department of Molecular Biology and Biochemistry, Francisco J. Ayala School of Biological Sciences, University of California, Irvine, California 92697
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87
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Sokolowski M, Chynces M, deHaro D, Christian CM, Belancio VP. Truncated ORF1 proteins can suppress LINE-1 retrotransposition in trans. Nucleic Acids Res 2017; 45:5294-5308. [PMID: 28431148 PMCID: PMC5605252 DOI: 10.1093/nar/gkx211] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/12/2017] [Indexed: 01/15/2023] Open
Abstract
Long interspersed element 1 (L1) is an autonomous non-LTR retroelement that is active in mammalian genomes. Although retrotranspositionally incompetent and functional L1 loci are present in the same genomes, it remains unknown whether non-functional L1s have any trans effect on mobilization of active elements. Using bioinformatic analysis, we identified over a thousand of human L1 loci containing at least one stop codon in their ORF1 sequence. RNAseq analysis confirmed that many of these loci are expressed. We demonstrate that introduction of equivalent stop codons in the full-length human L1 sequence leads to the expression of truncated ORF1 proteins. When supplied in trans some truncated human ORF1 proteins suppress human L1 retrotransposition. This effect requires the N-terminus and coiled-coil domain (C-C) as mutations within the ORF1p C-C domain abolish the suppressive effect of truncated proteins on L1 retrotransposition. We demonstrate that the expression levels and length of truncated ORF1 proteins influence their ability to suppress L1 retrotransposition. Taken together these findings suggest that L1 retrotransposition may be influenced by coexpression of defective L1 loci and that these L1 loci may reduce accumulation of de novo L1 integration events.
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Affiliation(s)
- Mark Sokolowski
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - May Chynces
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Dawn deHaro
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Claiborne M Christian
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Department of Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA 70112, USA
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88
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L1 Mosaicism in Mammals: Extent, Effects, and Evolution. Trends Genet 2017; 33:802-816. [PMID: 28797643 DOI: 10.1016/j.tig.2017.07.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 06/30/2017] [Accepted: 07/14/2017] [Indexed: 10/19/2022]
Abstract
The retrotransposon LINE-1 (long interspersed element 1, L1) is a transposable element that has extensively colonized the mammalian germline. L1 retrotransposition can also occur in somatic cells, causing genomic mosaicism, as well as in cancer. However, the extent of L1-driven mosaicism arising during ontogenesis is unclear. We discuss here recent experimental data which, at a minimum, fully substantiate L1 mosaicism in early embryonic development and neural cells, including post-mitotic neurons. We also consider the possible biological impact of somatic L1 insertions in neurons, the existence of donor L1s that are highly active ('hot') in specific spatiotemporal niches, and the evolutionary selection of donor L1s driving neuronal mosaicism.
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89
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Vafadar-Isfahani N, Parr C, McMillan LE, Sanner J, Yeo Z, Saddington S, Peacock O, Cruickshanks HA, Meehan RR, Lund JN, Tufarelli C. Decoupling of DNA methylation and activity of intergenic LINE-1 promoters in colorectal cancer. Epigenetics 2017; 12:465-475. [PMID: 28300471 PMCID: PMC5501206 DOI: 10.1080/15592294.2017.1300729] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/17/2017] [Accepted: 02/23/2017] [Indexed: 01/02/2023] Open
Abstract
Hypomethylation of LINE-1 repeats in cancer has been proposed as the main mechanism behind their activation; this assumption, however, was based on findings from early studies that were biased toward young and transpositionally active elements. Here, we investigate the relationship between methylation of 2 intergenic, transpositionally inactive LINE-1 elements and expression of the LINE-1 chimeric transcript (LCT) 13 and LCT14 driven by their antisense promoters (L1-ASP). Our data from DNA modification, expression, and 5'RACE analyses suggest that colorectal cancer methylation in the regions analyzed is not always associated with LCT repression. Consistent with this, in HCT116 colorectal cancer cells lacking DNA methyltransferases DNMT1 or DNMT3B, LCT13 expression decreases, while cells lacking both DNMTs or treated with the DNMT inhibitor 5-azacytidine (5-aza) show no change in LCT13 expression. Interestingly, levels of the H4K20me3 histone modification are inversely associated with LCT13 and LCT14 expression. Moreover, at these LINE-1s, H4K20me3 levels rather than DNA methylation seem to be good predictor of their sensitivity to 5-aza treatment. Therefore, by studying individual LINE-1 promoters we have shown that in some cases these promoters can be active without losing methylation; in addition, we provide evidence that other factors (e.g., H4K20me3 levels) play prominent roles in their regulation.
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Affiliation(s)
| | - Christina Parr
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Lara E. McMillan
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Juliane Sanner
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Zhao Yeo
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Stephen Saddington
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Oliver Peacock
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | | | - Richard R. Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan N. Lund
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
| | - Cristina Tufarelli
- School of Medicine, Royal Derby Hospital, University of Nottingham, Derby, UK
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90
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Marchant TW, Johnson EJ, McTeir L, Johnson CI, Gow A, Liuti T, Kuehn D, Svenson K, Bermingham ML, Drögemüller M, Nussbaumer M, Davey MG, Argyle DJ, Powell RM, Guilherme S, Lang J, Ter Haar G, Leeb T, Schwarz T, Mellanby RJ, Clements DN, Schoenebeck JJ. Canine Brachycephaly Is Associated with a Retrotransposon-Mediated Missplicing of SMOC2. Curr Biol 2017; 27:1573-1584.e6. [PMID: 28552356 PMCID: PMC5462623 DOI: 10.1016/j.cub.2017.04.057] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/14/2017] [Accepted: 04/27/2017] [Indexed: 12/30/2022]
Abstract
In morphological terms, “form” is used to describe an object’s shape and size. In dogs, facial form is stunningly diverse. Facial retrusion, the proximodistal shortening of the snout and widening of the hard palate is common to brachycephalic dogs and is a welfare concern, as the incidence of respiratory distress and ocular trauma observed in this class of dogs is highly correlated with their skull form. Progress to identify the molecular underpinnings of facial retrusion is limited to association of a missense mutation in BMP3 among small brachycephalic dogs. Here, we used morphometrics of skull isosurfaces derived from 374 pedigree and mixed-breed dogs to dissect the genetics of skull form. Through deconvolution of facial forms, we identified quantitative trait loci that are responsible for canine facial shapes and sizes. Our novel insights include recognition that the FGF4 retrogene insertion, previously associated with appendicular chondrodysplasia, also reduces neurocranium size. Focusing on facial shape, we resolved a quantitative trait locus on canine chromosome 1 to a 188-kb critical interval that encompasses SMOC2. An intronic, transposable element within SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts, and drastically reduces SMOC2 gene expression in brachycephalic dogs. SMOC2 disruption affects the facial skeleton in a dose-dependent manner. The size effects of the associated SMOC2 haplotype are profound, accounting for 36% of facial length variation in the dogs we tested. Our data bring new focus to SMOC2 by highlighting its clinical implications in both human and veterinary medicine. A population-based genetics study of dogs that required diagnostic imaging Resolution of a QTL associated with face length reduction (brachycephaly) Association of brachycephaly with a retrotransposon that disrupts SMOC2 splicing The SMOC2 locus explains up to 36% of face length variation in dogs
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Affiliation(s)
- Thomas W Marchant
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Edward J Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Lynn McTeir
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Craig I Johnson
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Adam Gow
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tiziana Liuti
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dana Kuehn
- Friendship Hospital for Animals, Washington, DC 20016, USA
| | | | - Mairead L Bermingham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Marc Nussbaumer
- Naturhistorisches Museum, Bernastrasse 15, 3005 Bern, Switzerland
| | - Megan G Davey
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - David J Argyle
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Roger M Powell
- Powell Torrance Diagnostic Services, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Sérgio Guilherme
- Davies Veterinary Specialists, Manor Farm Business Park, Higham Gobion, Hertfordshire SG5 3HR, UK
| | - Johann Lang
- Division of Clinical Radiology, Department of Clinical Veterinary Medicine, University of Bern, 3001 Bern, Switzerland
| | - Gert Ter Haar
- Department of Clinical Sciences and Services, Royal Veterinary College, Hertfordshire AL9 7TA, UK
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Tobias Schwarz
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Richard J Mellanby
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Dylan N Clements
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Jeffrey J Schoenebeck
- Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK.
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91
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LINE-1 methylation level and prognosis in pancreas cancer: pyrosequencing technology and literature review. Surg Today 2017; 47:1450-1459. [DOI: 10.1007/s00595-017-1539-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 04/04/2017] [Indexed: 12/18/2022]
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92
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Kannan M, Li J, Fritz SE, Husarek KE, Sanford JC, Sullivan TL, Tiwary PK, An W, Boeke JD, Symer DE. Dynamic silencing of somatic L1 retrotransposon insertions reflects the developmental and cellular contexts of their genomic integration. Mob DNA 2017; 8:8. [PMID: 28491150 PMCID: PMC5424313 DOI: 10.1186/s13100-017-0091-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 05/03/2017] [Indexed: 02/15/2023] Open
Abstract
Background The ongoing mobilization of mammalian transposable elements (TEs) contributes to natural genetic variation. To survey the epigenetic control and expression of reporter genes inserted by L1 retrotransposition in diverse cellular and genomic contexts, we engineered highly sensitive, real-time L1 retrotransposon reporter constructs. Results Here we describe different patterns of expression and epigenetic controls of newly inserted sequences retrotransposed by L1 in various somatic cells and tissues including cultured human cancer cells, mouse embryonic stem cells, and tissues of pseudofounder transgenic mice and their progeny. In cancer cell lines, the newly inserted sequences typically underwent rapid transcriptional gene silencing, but they lacked cytosine methylation even after many cell divisions. L1 reporter expression was reversible and oscillated frequently. Silenced or variegated reporter expression was strongly and uniformly reactivated by treatment with inhibitors of histone deacetylation, revealing the mechanism for their silencing. By contrast, de novo integrants retrotransposed by L1 in pluripotent mouse embryonic stem (ES) cells underwent rapid silencing by dense cytosine methylation. Similarly, de novo cytosine methylation also was identified at new integrants when studied in several distinct somatic tissues of adult founder mice. Pre-existing L1 elements in cultured human cancer cells were stably silenced by dense cytosine methylation, whereas their transcription modestly increased when cytosine methylation was experimentally reduced in cells lacking DNA methyltransferases DNMT1 and DNMT3b. As a control, reporter genes mobilized by piggyBac (PB), a DNA transposon, revealed relatively stable and robust expression without apparent silencing in both cultured cancer cells and ES cells. Conclusions We hypothesize that the de novo methylation marks at newly inserted sequences retrotransposed by L1 in early pre-implantation development are maintained or re-established in adult somatic tissues. By contrast, histone deacetylation reversibly silences L1 reporter insertions that had mobilized at later timepoints in somatic development and differentiation, e.g., in cancer cell lines. We conclude that the cellular contexts of L1 retrotransposition can determine expression or silencing of newly integrated sequences. We propose a model whereby reporter expression from somatic TE insertions reflects the timing, molecular mechanism, epigenetic controls and the genomic, cellular and developmental contexts of their integration. Electronic supplementary material The online version of this article (doi:10.1186/s13100-017-0091-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Manoj Kannan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Pilani, 333031 Rajasthan India.,Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Birla Institute of Technology and Science, Pilani, Dubai campus, Dubai, United Arab Emirates
| | - Jingfeng Li
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Department of Internal Medicine, The Ohio State University, Columbus, OH USA
| | - Sarah E Fritz
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kathryn E Husarek
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Aventiv Research, Inc., Columbus, OH USA
| | - Jonathan C Sanford
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH USA.,Present Address: Drug Safety Research and Development, Pfizer, Inc., Groton, CT USA
| | - Teresa L Sullivan
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - Pawan Kumar Tiwary
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Present Address: Biocon, Bangalore, India
| | - Wenfeng An
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Department of Pharmaceutical Sciences, South Dakota State University, Brookings, SD USA
| | - Jef D Boeke
- Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present Address: Institute for Systems Genetics, New York University Langone Medical Center, New York, NY USA
| | - David E Symer
- Laboratory of Immunobiology, Mouse Cancer Genetics Program and Basic Research Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA.,Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, and Department of Biomedical Informatics, The Ohio State University, Columbus, OH USA.,Human Cancer Genetics Program, Department of Cancer Biology and Genetics, and Department of Biomedical Informatics, The Ohio State University, Tzagournis Research Facility, Room 440, 420 West 12th Ave, Columbus, OH 43210 USA
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93
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Protein-Coding Genes' Retrocopies and Their Functions. Viruses 2017; 9:v9040080. [PMID: 28406439 PMCID: PMC5408686 DOI: 10.3390/v9040080] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/07/2017] [Accepted: 04/11/2017] [Indexed: 12/11/2022] Open
Abstract
Transposable elements, often considered to be not important for survival, significantly contribute to the evolution of transcriptomes, promoters, and proteomes. Reverse transcriptase, encoded by some transposable elements, can be used in trans to produce a DNA copy of any RNA molecule in the cell. The retrotransposition of protein-coding genes requires the presence of reverse transcriptase, which could be delivered by either non-long terminal repeat (non-LTR) or LTR transposons. The majority of these copies are in a state of “relaxed” selection and remain “dormant” because they are lacking regulatory regions; however, many become functional. In the course of evolution, they may undergo subfunctionalization, neofunctionalization, or replace their progenitors. Functional retrocopies (retrogenes) can encode proteins, novel or similar to those encoded by their progenitors, can be used as alternative exons or create chimeric transcripts, and can also be involved in transcriptional interference and participate in the epigenetic regulation of parental gene expression. They can also act in trans as natural antisense transcripts, microRNA (miRNA) sponges, or a source of various small RNAs. Moreover, many retrocopies of protein-coding genes are linked to human diseases, especially various types of cancer.
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94
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Papin C, Ibrahim A, Gras SL, Velt A, Stoll I, Jost B, Menoni H, Bronner C, Dimitrov S, Hamiche A. Combinatorial DNA methylation codes at repetitive elements. Genome Res 2017; 27:934-946. [PMID: 28348165 PMCID: PMC5453327 DOI: 10.1101/gr.213983.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/21/2017] [Indexed: 12/30/2022]
Abstract
DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC, and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionarily conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m, and L1Md-LINEs. DNA methylation controls the expression of these retroelements, which are clustered at specific locations in the mouse genome. We show that TDG is implicated in the regulation of their unique DNA methylation/oxidation signatures and their dynamics. Our data suggest the existence of a novel epigenetic code for the most recently acquired evolutionarily conserved repeats that could play a major role in cell differentiation.
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Affiliation(s)
- Christophe Papin
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Abdulkhaleg Ibrahim
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Stéphanie Le Gras
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Amandine Velt
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Isabelle Stoll
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Bernard Jost
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Hervé Menoni
- Institut Albert Bonniot, Université de Grenoble Alpes /INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Christian Bronner
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- Institut Albert Bonniot, Université de Grenoble Alpes /INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
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95
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Qamra A, Xing M, Padmanabhan N, Kwok JJT, Zhang S, Xu C, Leong YS, Lee Lim AP, Tang Q, Ooi WF, Suling Lin J, Nandi T, Yao X, Ong X, Lee M, Tay ST, Keng ATL, Gondo Santoso E, Ng CCY, Ng A, Jusakul A, Smoot D, Ashktorab H, Rha SY, Yeoh KG, Peng Yong W, Chow PK, Chan WH, Ong HS, Soo KC, Kim KM, Wong WK, Rozen SG, Teh BT, Kappei D, Lee J, Connolly J, Tan P. Epigenomic Promoter Alterations Amplify Gene Isoform and Immunogenic Diversity in Gastric Adenocarcinoma. Cancer Discov 2017; 7:630-651. [DOI: 10.1158/2159-8290.cd-16-1022] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/27/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023]
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96
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Casa V, Runfola V, Micheloni S, Aziz A, Dilworth FJ, Gabellini D. Polycomb repressive complex 1 provides a molecular explanation for repeat copy number dependency in FSHD muscular dystrophy. Hum Mol Genet 2017; 26:753-767. [PMID: 28040729 PMCID: PMC5409123 DOI: 10.1093/hmg/ddw426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 12/15/2016] [Indexed: 11/13/2022] Open
Abstract
Repression of repetitive elements is crucial to preserve genome integrity and has been traditionally ascribed to constitutive heterochromatin pathways. FacioScapuloHumeral Muscular Dystrophy (FSHD), one of the most common myopathies, is characterized by a complex interplay of genetic and epigenetic events. The main FSHD form is linked to a reduced copy number of the D4Z4 macrosatellite repeat on 4q35, causing loss of silencing and aberrant expression of the D4Z4-embedded DUX4 gene leading to disease. By an unknown mechanism, D4Z4 copy-number correlates with FSHD phenotype. Here we show that the DUX4 proximal promoter (DUX4p) is sufficient to nucleate the enrichment of both constitutive and facultative heterochromatin components and to mediate a copy-number dependent gene silencing. We found that both the CpG/GC dense DNA content and the repetitive nature of DUX4p arrays are important for their repressive ability. We showed that DUX4p mediates a copy number-dependent Polycomb Repressive Complex 1 (PRC1) recruitment, which is responsible for the copy-number dependent gene repression. Overall, we directly link genetic and epigenetic defects in FSHD by proposing a novel molecular explanation for the copy number-dependency in FSHD pathogenesis, and offer insight into the molecular functions of repeats in chromatin regulation.
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Affiliation(s)
- Valentina Casa
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Università Vita-Salute San Raffaele, Milan 20132, Italy
| | - Valeria Runfola
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Stefano Micheloni
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Arif Aziz
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - F Jeffrey Dilworth
- The Sprott Center for Stem Cell Research, Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, ON K1Y 4E9, Canada
| | - Davide Gabellini
- Gene Expression and Muscular Dystrophy Unit, Division of Regenerative Medicine, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy.,Dulbecco Telethon Institute, Milan 20132, Italy
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97
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Bodak M, Cirera-Salinas D, Yu J, Ngondo RP, Ciaudo C. Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells. FEBS Open Bio 2017; 7:204-220. [PMID: 28174687 PMCID: PMC5292673 DOI: 10.1002/2211-5463.12174] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/18/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022] Open
Abstract
A gene regulation network orchestrates processes ensuring the maintenance of cellular identity and genome integrity. Small RNAs generated by the RNAse III DICER have emerged as central players in this network. Moreover, deletion of Dicer in mice leads to early embryonic lethality. To better understand the underlying mechanisms leading to this phenotype, we generated Dicer‐deficient mouse embryonic stem cells (mESCs). Their detailed characterization revealed an impaired differentiation potential, and incapacity to exit from the pluripotency state. We also observed a strong accumulation of LINE‐1 (L1s) transcripts, which was translated at protein level and led to an increased L1s retrotransposition. Our findings reveal Dicer as a new essential player that sustains mESCs self‐renewal and genome integrity by controlling L1s regulation.
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Affiliation(s)
- Maxime Bodak
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland; Life Science Zurich Graduate School Molecular Life Science Program University of Zurich Switzerland
| | - Daniel Cirera-Salinas
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
| | - Jian Yu
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland; Life Science Zurich Graduate School Molecular and Translational Biomedicine Program University of Zurich Switzerland
| | - Richard P Ngondo
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
| | - Constance Ciaudo
- Department of Biology RNAi and Genome Integrity IMHS Swiss Federal Institute of Technology Zurich Zurich Switzerland
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98
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Tumor LINE-1 Methylation Level in Association with Survival of Patients with Stage II Colon Cancer. Int J Mol Sci 2016; 18:ijms18010036. [PMID: 28035987 PMCID: PMC5297671 DOI: 10.3390/ijms18010036] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 12/20/2022] Open
Abstract
Genome-wide DNA hypomethylation is associated with a worse prognosis in early-stage colorectal cancer. To measure genome-wide DNA methylation levels, long interspersed nucleotide element (LINE-1) repeats are used as a surrogate marker. Cohort studies on the clinical impact of genome-wide DNA methylation level in patients with only early-stage colon cancer, are currently lacking. This study aimed to investigate the prognostic value of LINE-1 methylation in a stage II colon cancer cohort (n = 164). Manual needle microdissection of tumor areas was performed on formalin-fixed paraffin-embedded tumor tissue sections followed by DNA extraction. Bisulfite converted DNA was used to assess tumor LINE-1 methylation level by qPCR. Patients with LINE-1 hypomethylated tumors had a significantly worse overall survival compared to patients with a higher level of LINE-1 tumor DNA methylation (HR 1.68, 95% CI 1.03–2.75; p = 0.04). This effect was more prominent in patients aged over 65 years (HR 2.00, 95% CI 1.13–3.52; p = 0.02), although the test for age interaction was not significant. No significant effect on recurrence-free survival was observed. Based on these results, tumor LINE-1 hypomethylation is associated with a worse overall survival in stage II colon cancer. Whether the origin of this causation is cancer-specific or age-related can be debated.
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99
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Radion E, Ryazansky S, Akulenko N, Rozovsky Y, Kwon D, Morgunova V, Olovnikov I, Kalmykova A. Telomeric Retrotransposon HeT-A Contains a Bidirectional Promoter that Initiates Divergent Transcription of piRNA Precursors in Drosophila Germline. J Mol Biol 2016; 429:3280-3289. [PMID: 27939293 DOI: 10.1016/j.jmb.2016.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 11/18/2016] [Accepted: 12/01/2016] [Indexed: 11/30/2022]
Abstract
PIWI-interacting RNAs (piRNAs) provide the silencing of transposable elements in the germline. Drosophila telomeres are maintained by transpositions of specialized telomeric retroelements. piRNAs generated from sense and antisense transcripts of telomeric elements provide telomere length control in the germline. Previously, we have found that antisense transcription of the major telomeric retroelement HeT-A is initiated upstream of the HeT-A sense transcription start site. Here, we performed a deletion analysis of the HeT-A promoter and show that common regulatory elements are shared by sense and antisense promoters of HeT-A. Therefore, the HeT-A promoter is a bidirectional promoter capable of processive sense and antisense transcription. Ovarian small RNA data show that a solo HeT-A promoter within an euchromatic transgene initiates the divergent transcription of transgenic reporter genes and subsequent processing of these transcripts into piRNAs. These events lead to the formation of a divergent unistrand piRNA cluster at solo HeT-A promoters, in contrast to endogenous telomeres that represent strong dual-strand piRNA clusters. Solo HeT-A promoters are not immunoprecipitated with heterochromatin protein 1 (HP1) homolog Rhino, a marker of the dual-strand piRNA clusters, but are associated with HP1 itself, which provides piRNA-mediated transcriptional repression of the reporter genes. Unlike endogenous dual-strand piRNA clusters, the solo HeT-A promoter does not produce overlapping transcripts. In a telomeric context, however, bidirectional promoters of tandem HeT-A repeats provide a read-through transcription of both genomic strands, followed by Rhi binding. These data indicate that Drosophila telomeres share properties of unistrand and dual-strand piRNA clusters.
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Affiliation(s)
- Elizaveta Radion
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Sergei Ryazansky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Natalia Akulenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Yakov Rozovsky
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Dmitry Kwon
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Valeriya Morgunova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Ivan Olovnikov
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Alla Kalmykova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia.
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100
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Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK. URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells. J Biol Chem 2016; 291:25516-25528. [PMID: 27780869 PMCID: PMC5207251 DOI: 10.1074/jbc.m116.741660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells.
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Affiliation(s)
- Paolo Mita
- From the Institute of Systems Genetics and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jeffrey N Savas
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Erica M Briggs
- the Departments of Biochemistry and Molecular Pharmacology
| | - Susan Ha
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Veena Gnanakkan
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - John R Yates
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Diane M Robins
- the Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Gregory David
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jef D Boeke
- From the Institute of Systems Genetics and
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Michael J Garabedian
- Urology, and
- Microbiology at New York University School of Medicine, New York, New York 10016
| | - Susan K Logan
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
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