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Kohlrausch FB, Wang F, McKerrow W, Grivainis M, Fenyo D, Keefe DL. Mapping of long interspersed element-1 (L1) insertions by TIPseq provides information about sub chromosomal genetic variation in human embryos. J Assist Reprod Genet 2024:10.1007/s10815-024-03176-9. [PMID: 38951360 DOI: 10.1007/s10815-024-03176-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
PURPOSE Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
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Affiliation(s)
- Fabiana B Kohlrausch
- Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA.
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - Mark Grivainis
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David Fenyo
- Institute for Systems Genetics, New York University, New York, NY, 10016, USA
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University, New York, NY, 10016, USA
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2
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Lanciano S, Philippe C, Sarkar A, Pratella D, Domrane C, Doucet AJ, van Essen D, Saccani S, Ferry L, Defossez PA, Cristofari G. Locus-level L1 DNA methylation profiling reveals the epigenetic and transcriptional interplay between L1s and their integration sites. CELL GENOMICS 2024; 4:100498. [PMID: 38309261 PMCID: PMC10879037 DOI: 10.1016/j.xgen.2024.100498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/20/2023] [Accepted: 01/09/2024] [Indexed: 02/05/2024]
Abstract
Long interspersed element 1 (L1) retrotransposons are implicated in human disease and evolution. Their global activity is repressed by DNA methylation, but deciphering the regulation of individual copies has been challenging. Here, we combine short- and long-read sequencing to unveil L1 methylation heterogeneity across cell types, families, and individual loci and elucidate key principles involved. We find that the youngest primate L1 families are specifically hypomethylated in pluripotent stem cells and the placenta but not in most tumors. Locally, intronic L1 methylation is intimately associated with gene transcription. Conversely, the L1 methylation state can propagate to the proximal region up to 300 bp. This phenomenon is accompanied by the binding of specific transcription factors, which drive the expression of L1 and chimeric transcripts. Finally, L1 hypomethylation alone is typically insufficient to trigger L1 expression due to redundant silencing pathways. Our results illuminate the epigenetic and transcriptional interplay between retrotransposons and their host genome.
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Affiliation(s)
- Sophie Lanciano
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Claude Philippe
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Arpita Sarkar
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - David Pratella
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Cécilia Domrane
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Aurélien J Doucet
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Dominic van Essen
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Simona Saccani
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France
| | - Laure Ferry
- University Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | - Gael Cristofari
- University Cote d'Azur, INSERM, CNRS, Institute for Research on Cancer and Aging of Nice (IRCAN), Nice, France.
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3
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Yang L, Metzger GA, Padilla Del Valle R, Delgadillo Rubalcaba D, McLaughlin RN. Evolutionary insights from profiling LINE-1 activity at allelic resolution in a single human genome. EMBO J 2024; 43:112-131. [PMID: 38177314 PMCID: PMC10883270 DOI: 10.1038/s44318-023-00007-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/18/2023] [Accepted: 11/10/2023] [Indexed: 01/06/2024] Open
Abstract
Transposable elements have created the majority of the sequence in many genomes. In mammals, LINE-1 retrotransposons have been expanding for more than 100 million years as distinct, consecutive lineages; however, the drivers of this recurrent lineage emergence and disappearance are unknown. Most human genome assemblies provide a record of this ancient evolution, but fail to resolve ongoing LINE-1 retrotranspositions. Utilizing the human CHM1 long-read-based haploid assembly, we identified and cloned all full-length, intact LINE-1s, and found 29 LINE-1s with measurable in vitro retrotransposition activity. Among individuals, these LINE-1s varied in their presence, their allelic sequences, and their activity. We found that recently retrotransposed LINE-1s tend to be active in vitro and polymorphic in the population relative to more ancient LINE-1s. However, some rare allelic forms of old LINE-1s retain activity, suggesting older lineages can persist longer than expected. Finally, in LINE-1s with in vitro activity and in vivo fitness, we identified mutations that may have increased replication in ancient genomes and may prove promising candidates for mechanistic investigations of the drivers of LINE-1 evolution and which LINE-1 sequences contribute to human disease.
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Affiliation(s)
- Lei Yang
- Pacific Northwest Research Institute, Seattle, WA, USA
| | | | - Ricky Padilla Del Valle
- Pacific Northwest Research Institute, Seattle, WA, USA
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA
| | | | - Richard N McLaughlin
- Pacific Northwest Research Institute, Seattle, WA, USA.
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA, USA.
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4
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Baba Y, Yasuda N, Bundo M, Nakachi Y, Ueda J, Ishimoto T, Iwatsuki M, Miyamoto Y, Yoshida N, Oshiumi H, Iwamoto K, Baba H. LINE-1 hypomethylation, increased retrotransposition and tumor-specific insertion in upper gastrointestinal cancer. Cancer Sci 2024; 115:247-256. [PMID: 38013627 PMCID: PMC10823286 DOI: 10.1111/cas.16007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
The long interspersed nuclear element-1 (LINE-1) retrotransposons are a major family of mobile genetic elements, comprising approximately 17% of the human genome. The methylation state of LINE-1 is often used as an indicator of global DNA methylation levels and it regulates the retrotransposition and somatic insertion of the genetic element. We have previously reported the significant relationship between LINE-1 hypomethylation and poor prognosis in upper gastrointestinal (GI) cancers. However, the causal relationships between LINE-1 hypomethylation, retrotransposition, and tumor-specific insertion in upper GI cancers remain unknown. We used bisulfite-pyrosequencing and quantitative real-time PCR to verify LINE-1 methylation and copy number in tissue samples of 101 patients with esophageal and 103 patients with gastric cancer. Furthermore, we analyzed the LINE-1 retrotransposition profile with an originally developed L1Hs-seq. In tumor samples, LINE-1 methylation levels were significantly lower than non-tumor controls, while LINE-1 copy numbers were markedly increased. As such, there was a significant inverse correlation between the LINE-1 methylation level and copy number in tumor tissues, with lower LINE-1 methylation levels corresponding to higher LINE-1 copy numbers. Of particular importance is that somatic LINE-1 insertions were more numerous in tumor than normal tissues. Furthermore, we observed that LINE-1 was inserted evenly across all chromosomes, and most often within genomic regions associated with tumor-suppressive genes. LINE-1 hypomethylation in upper GI cancers is related to increased LINE-1 retrotransposition and tumor-specific insertion events, which may collectively contribute to the acquisition of aggressive tumor features through the inactivation of tumor-suppressive genes.
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Affiliation(s)
- Yoshifumi Baba
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
- Department of Next‐Generation Surgical Therapy DevelopmentKumamoto University HospitalKumamotoJapan
| | - Noriko Yasuda
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yutaka Nakachi
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Junko Ueda
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Takatsugu Ishimoto
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Masaaki Iwatsuki
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Yuji Miyamoto
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Naoya Yoshida
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
| | - Hiroyuki Oshiumi
- Department of Immunology, Graduate School of Medical Sciences, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical ScienceKumamoto UniversityKumamotoJapan
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5
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Lee AS, Ayers LJ, Kosicki M, Chan WM, Fozo LN, Pratt BM, Collins TE, Zhao B, Rose MF, Sanchis-Juan A, Fu JM, Wong I, Zhao X, Tenney AP, Lee C, Laricchia KM, Barry BJ, Bradford VR, Lek M, MacArthur DG, Lee EA, Talkowski ME, Brand H, Pennacchio LA, Engle EC. A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.22.23300468. [PMID: 38234731 PMCID: PMC10793524 DOI: 10.1101/2023.12.22.23300468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Unsolved Mendelian cases often lack obvious pathogenic coding variants, suggesting potential non-coding etiologies. Here, we present a single cell multi-omic framework integrating embryonic mouse chromatin accessibility, histone modification, and gene expression assays to discover cranial motor neuron (cMN) cis-regulatory elements and subsequently nominate candidate non-coding variants in the congenital cranial dysinnervation disorders (CCDDs), a set of Mendelian disorders altering cMN development. We generated single cell epigenomic profiles for ~86,000 cMNs and related cell types, identifying ~250,000 accessible regulatory elements with cognate gene predictions for ~145,000 putative enhancers. Seventy-five percent of elements (44 of 59) validated in an in vivo transgenic reporter assay, demonstrating that single cell accessibility is a strong predictor of enhancer activity. Applying our cMN atlas to 899 whole genome sequences from 270 genetically unsolved CCDD pedigrees, we achieved significant reduction in our variant search space and nominated candidate variants predicted to regulate known CCDD disease genes MAFB, PHOX2A, CHN1, and EBF3 - as well as new candidates in recurrently mutated enhancers through peak- and gene-centric allelic aggregation. This work provides novel non-coding variant discoveries of relevance to CCDDs and a generalizable framework for nominating non-coding variants of potentially high functional impact in other Mendelian disorders.
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Affiliation(s)
- Arthur S Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Lauren J Ayers
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Michael Kosicki
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Wai-Man Chan
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Lydia N Fozo
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Brandon M Pratt
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Thomas E Collins
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Boxun Zhao
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Matthew F Rose
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Pathology, Boston Children's Hospital, Boston, MA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA
| | - Alba Sanchis-Juan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Jack M Fu
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Isaac Wong
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Alan P Tenney
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cassia Lee
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Harvard College, Cambridge, MA
| | - Kristen M Laricchia
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Brenda J Barry
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
| | - Victoria R Bradford
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
| | - Monkol Lek
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Daniel G MacArthur
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Centre for Population Genomics, Garvan Institute of Medical Research and UNSW Sydney, Sydney, NSW, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | - Eunjung Alice Lee
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Michael E Talkowski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Harrison Brand
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA
| | - Len A Pennacchio
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA
| | - Elizabeth C Engle
- Department of Neurology, Boston Children's Hospital and Harvard Medical School, Boston, MA
- Kirby Neurobiology Center, Boston Children's Hospital, Boston, MA
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Chevy Chase, MD
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
- Medical Genetics Training Program, Harvard Medical School, Boston, MA
- Department of Ophthalmology, Boston Children's Hospital and Harvard Medical School, Boston, MA
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6
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Boeke JD, Burns KH, Chiappinelli KB, Classon M, Coffin JM, DeCarvalho DD, Dukes JD, Greenbaum B, Kassiotis G, Knutson SK, Levine AJ, Nath A, Papa S, Rios D, Sedivy J, Ting DT. Proceedings of the inaugural Dark Genome Symposium: November 2022. Mob DNA 2023; 14:18. [PMID: 37990347 PMCID: PMC10664479 DOI: 10.1186/s13100-023-00306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/08/2023] [Indexed: 11/23/2023] Open
Abstract
In November 2022 the first Dark Genome Symposium was held in Boston, USA. The meeting was hosted by Rome Therapeutics and Enara Bio, two biotechnology companies working on translating our growing understanding of this vast genetic landscape into therapies for human disease. The spirit and ambition of the meeting was one of shared knowledge, looking to strengthen the network of researchers engaged in the field. The meeting opened with a welcome from Rosana Kapeller and Kevin Pojasek followed by a first session of field defining talks from key academics in the space. A series of panels, bringing together academia and industry views, were then convened covering a wide range of pertinent topics. Finally, Richard Young and David Ting gave their views on the future direction and promise for patient impact inherent in the growing understanding of the Dark Genome.
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Affiliation(s)
- Jef D Boeke
- Institute for Systems Genetics, NYU Langone Health, New York, NY, 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, 10016, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Marie Classon
- Pfizer Centre for Therapeutic Innovation, San Diego, USA
| | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, 02111, USA
| | - Daniel D DeCarvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Joseph D Dukes
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK
| | - Benjamin Greenbaum
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Sarah K Knutson
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Avindra Nath
- Section for Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Sophie Papa
- Enara Bio Limited, Magdalen Centre, 1 Robert Robinson Avenue, The Oxford Science Park, Oxford, OX4 4GA, UK.
- School of Cancer and Pharmaceutical Sciences, Faculty of Life Sciences and Medicine, King's College London, London, UK.
| | - Daniel Rios
- Rome Therapeutics, 201 Brookline Avenue, Suite 1001, Boston, MA, USA
| | - John Sedivy
- Center on the Biology of Aging, Brown University, Providence, RI, USA
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - David T Ting
- Department of Medical Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
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7
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Alkailani MI, Gibbings D. The Regulation and Immune Signature of Retrotransposons in Cancer. Cancers (Basel) 2023; 15:4340. [PMID: 37686616 PMCID: PMC10486412 DOI: 10.3390/cancers15174340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Advances in sequencing technologies and the bioinformatic analysis of big data facilitate the study of jumping genes' activity in the human genome in cancer from a broad perspective. Retrotransposons, which move from one genomic site to another by a copy-and-paste mechanism, are regulated by various molecular pathways that may be disrupted during tumorigenesis. Active retrotransposons can stimulate type I IFN responses. Although accumulated evidence suggests that retrotransposons can induce inflammation, the research investigating the exact mechanism of triggering these responses is ongoing. Understanding these mechanisms could improve the therapeutic management of cancer through the use of retrotransposon-induced inflammation as a tool to instigate immune responses to tumors.
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Affiliation(s)
- Maisa I. Alkailani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha P.O. Box 34110, Qatar
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada;
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8
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Abstract
By silencing L1 retrotransposons, DNA methylation protects mammalian genomes from potent endogenous mutagens. However, some loci can escape this repressive mechanism and become active, particularly in carcinomas. Alterations of L1 DNA methylation can also locally influence gene expression. Comprehensive measurement of L1 DNA methylation at the locus level remains challenging. Here, we present bs-ATLAS-seq, a genome-wide approach to locate full-length L1 elements in the human genome, and assess their methylation levels at single-base and single-locus resolutions. This strategy targets the youngest, and only retrotransposition-competent family, L1HS, but also detects a significant fraction of older elements (L1PA2 to L1PA8). Bs-ATLAS-seq evaluates methylation at the first 15 CpGs of L1 5' UTR, which corresponds to the first half of the sense promoter. It relies on random fragmentation of the genomic DNA, adapter ligation, bisulfite treatment and suppression PCR, and ends by asymmetrical paired-end sequencing. A dedicated pipeline provides the location of L1 elements and their methylation status, including for non-reference loci, as well as their single-molecule DNA profiles.
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9
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Bundo M, Iwamoto K. A Method for Detection of Somatic LINE-1 Insertions at the Single-Cell Level from Postmortem Human Brain. Methods Mol Biol 2023; 2577:147-159. [PMID: 36173571 DOI: 10.1007/978-1-0716-2724-2_10] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Long Interspersed Element-1 (LINE-1, L1) is a retrotransposon that has the ability to amplify its copy in the genome autonomously. L1Hs is a human-specific active subtype of L1 reported to amplify its copy in neural progenitor cells causing genomic mosaicism. This chapter describes a new method named NECO-seq (Novel Elements Concentrated-sequence) to identify the genomic locus of L1Hs insertions at the single-cell level. This protocol contains the steps of (1) preparation of neuronal cell nuclei from a postmortem human brain, (2) whole genome amplification from single neural nuclei (snWGA), (3) single nucleotide polymorphisms (SNPs) genotyping for quality control of snWGA products, (4) library preparation for next-generation sequencing to enrich the genomic locus of L1Hs insertions, and (5) bioinformatic analysis to detect novel somatic L1Hs insertions. This method can detect approximately 97% of L1Hs originally existing in reference human genome and approximately 10-20 newly inserted L1Hs copies in a neuronal cell of a postmortem human brain.
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Affiliation(s)
- Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan.
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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10
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Lee H, Min JW, Mun S, Han K. Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101583. [PMID: 36295018 PMCID: PMC9605557 DOI: 10.3390/life12101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the "cut and paste" mechanism, retrotransposons mobilize via the "copy and paste" method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Correspondence: (S.M.); (K.H.)
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- HuNbiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Correspondence: (S.M.); (K.H.)
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11
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Creamer KM, Larsen EC, Lawrence JB. ZNF146/OZF and ZNF507 target LINE-1 sequences. G3 (BETHESDA, MD.) 2022; 12:jkac002. [PMID: 35100360 PMCID: PMC8896011 DOI: 10.1093/g3journal/jkac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Repetitive sequences including transposable elements and transposon-derived fragments account for nearly half of the human genome. While transposition-competent transposable elements must be repressed to maintain genomic stability, mutated and fragmented transposable elements comprising the bulk of repetitive sequences can also contribute to regulation of host gene expression and broader genome organization. Here, we analyzed published ChIP-seq data sets to identify proteins broadly enriched on transposable elements in the human genome. We show 2 of the proteins identified, C2H2 zinc finger-containing proteins ZNF146 (also known as OZF) and ZNF507, are targeted to distinct sites within LINE-1 ORF2 at thousands of locations in the genome. ZNF146 binding sites are found at old and young LINE-1 elements. In contrast, ZNF507 preferentially binds at young LINE-1 sequences correlated to sequence changes in LINE-1 elements at ZNF507's binding site. To gain further insight into ZNF146 and ZNF507 function, we disrupt their expression in HEK293 cells using CRISPR/Cas9 and perform RNA sequencing, finding modest gene expression changes in cells where ZNF507 has been disrupted. We further identify a physical interaction between ZNF507 and PRMT5, suggesting ZNF507 may target arginine methylation activity to LINE-1 sequences.
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Affiliation(s)
- Kevin M Creamer
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Eric C Larsen
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Jeanne B Lawrence
- Department of Neurology and Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA
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12
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Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T, He S. Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res 2022; 50:2493-2508. [PMID: 35212372 PMCID: PMC8934628 DOI: 10.1093/nar/gkac128] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.
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Affiliation(s)
- Yiwei Niu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiheng Tang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Kang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Peze-Heidsieck E, Bonnifet T, Znaidi R, Ravel-Godreuil C, Massiani-Beaudoin O, Joshi RL, Fuchs J. Retrotransposons as a Source of DNA Damage in Neurodegeneration. Front Aging Neurosci 2022; 13:786897. [PMID: 35058771 PMCID: PMC8764243 DOI: 10.3389/fnagi.2021.786897] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
The etiology of aging-associated neurodegenerative diseases (NDs), such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), still remains elusive and no curative treatment is available. Age is the major risk factor for PD and AD, but the molecular link between aging and neurodegeneration is not fully understood. Aging is defined by several hallmarks, some of which partially overlap with pathways implicated in NDs. Recent evidence suggests that aging-associated epigenetic alterations can lead to the derepression of the LINE-1 (Long Interspersed Element-1) family of transposable elements (TEs) and that this derepression might have important implications in the pathogenesis of NDs. Almost half of the human DNA is composed of repetitive sequences derived from TEs and TE mobility participated in shaping the mammalian genomes during evolution. Although most TEs are mutated and no longer mobile, more than 100 LINE-1 elements have retained their full coding potential in humans and are thus retrotransposition competent. Uncontrolled activation of TEs has now been reported in various models of neurodegeneration and in diseased human brain tissues. We will discuss in this review the potential contribution of LINE-1 elements in inducing DNA damage and genomic instability, which are emerging pathological features in NDs. TEs might represent an important molecular link between aging and neurodegeneration, and a potential target for urgently needed novel therapeutic disease-modifying interventions.
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Affiliation(s)
- Eugenie Peze-Heidsieck
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Tom Bonnifet
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rania Znaidi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rajiv L Joshi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
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14
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Merkerova MD, Krejcik Z. Transposable elements and Piwi‑interacting RNAs in hemato‑oncology with a focus on myelodysplastic syndrome (Review). Int J Oncol 2021; 59:105. [PMID: 34779490 DOI: 10.3892/ijo.2021.5285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/12/2021] [Indexed: 11/06/2022] Open
Abstract
Our current understanding of hematopoietic stem cell differentiation and the abnormalities that lead to leukemogenesis originates from the accumulation of knowledge regarding protein‑coding genes. However, the possible impact of transposable element (TE) mobilization and the expression of P‑element‑induced WImpy testis‑interacting RNAs (piRNAs) on leukemogenesis has been beyond the scope of scientific interest to date. The expression profiles of these molecules and their importance for human health have only been characterized recently due to the rapid progress of high‑throughput sequencing technology development. In the present review, current knowledge on the expression profile and function of TEs and piRNAs was summarized, with specific focus on their reported involvement in leukemogenesis and pathogenesis of myelodysplastic syndrome.
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Affiliation(s)
| | - Zdenek Krejcik
- Institute of Hematology and Blood Transfusion, 128 20 Prague, Czech Republic
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15
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Gorbunova V, Seluanov A, Mita P, McKerrow W, Fenyö D, Boeke JD, Linker SB, Gage FH, Kreiling JA, Petrashen AP, Woodham TA, Taylor JR, Helfand SL, Sedivy JM. The role of retrotransposable elements in ageing and age-associated diseases. Nature 2021; 596:43-53. [PMID: 34349292 PMCID: PMC8600649 DOI: 10.1038/s41586-021-03542-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 04/13/2021] [Indexed: 02/06/2023]
Abstract
The genomes of virtually all organisms contain repetitive sequences that are generated by the activity of transposable elements (transposons). Transposons are mobile genetic elements that can move from one genomic location to another; in this process, they amplify and increase their presence in genomes, sometimes to very high copy numbers. In this Review we discuss new evidence and ideas that the activity of retrotransposons, a major subgroup of transposons overall, influences and even promotes the process of ageing and age-related diseases in complex metazoan organisms, including humans. Retrotransposons have been coevolving with their host genomes since the dawn of life. This relationship has been largely competitive, and transposons have earned epithets such as 'junk DNA' and 'molecular parasites'. Much of our knowledge of the evolution of retrotransposons reflects their activity in the germline and is evident from genome sequence data. Recent research has provided a wealth of information on the activity of retrotransposons in somatic tissues during an individual lifespan, the molecular mechanisms that underlie this activity, and the manner in which these processes intersect with our own physiology, health and well-being.
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Affiliation(s)
- Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, New York 14627, USA
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, New York 14627, USA
| | - Paolo Mita
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - David Fenyö
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics, and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, New York 10016, USA.,Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn 11201, NY, USA
| | - Sara B. Linker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Jill A. Kreiling
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Anna P. Petrashen
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Trenton A. Woodham
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Jackson R. Taylor
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Stephen L. Helfand
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - John M. Sedivy
- Center on the Biology of Aging, and Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA.,Corresponding author
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16
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Doyle GA, Reiner BC, Crist RC, Rao AM, Ojeah NS, Arauco-Shapiro G, Levinson RN, Shah LD, Sperling MR, Ferraro TN, Buono RJ, Berrettini WH. Investigation of long interspersed element-1 retrotransposons as potential risk factors for idiopathic temporal lobe epilepsy. Epilepsia 2021; 62:1329-1342. [PMID: 33826137 DOI: 10.1111/epi.16897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 11/29/2022]
Abstract
OBJECTIVE To determine if long interspersed element-1 (L1) retrotransposons convey risk for idiopathic temporal lobe epilepsy (TLE). METHODS Surgically resected temporal cortex from individuals with TLE (N = 33) and postmortem temporal cortex from individuals with no known neurological disease (N = 33) were analyzed for L1 content by Restriction Enzyme Based Enriched L1Hs sequencing (REBELseq). Expression of three KCNIP4 splice variants was assessed by droplet digital PCR (ddPCR). Protein ANalysis THrough Evolutionary Relationships (PANTHER) was used to determine ontologies and pathways for lists of genes harboring L1 insertions. RESULTS We identified novel L1 insertions specific to individuals with TLE, and others specific to controls. Although there were no statistically significant differences between cases and controls in the numbers of known and novel L1 insertions, PANTHER analyses of intragenic L1 insertions showed statistically significant enrichments for epilepsy-relevant gene ontologies in both cases and controls. Gene ontologies "neuron projection development" and "calcium ion transmembrane transport" were among those found only in individuals with TLE. We confirmed novel L1 insertions in several genes associated with seizures/epilepsy, including a de novo somatic L1 retrotransposition in KCNIP4 that occurred after neural crest formation in one patient. However, ddPCR results suggest this de novo L1 did not alter KCNIP4 mRNA expression. SIGNIFICANCE Given current data from this small cohort, we conclude that L1 elements, either rare heritable germline insertions or de novo somatic retrotranspositions, may contribute only minimally to overall genetic risk for idiopathic TLE. We suggest that further studies in additional patients and additional brain regions are warranted.
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Affiliation(s)
- Glenn A Doyle
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin C Reiner
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Richard C Crist
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Aditya M Rao
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nkechi S Ojeah
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Lincoln University of School of Natural Sciences and Mathematics, Lincoln University, Lincoln, PA, USA
| | - Gabriella Arauco-Shapiro
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Rachel N Levinson
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lokesh D Shah
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Michael R Sperling
- Department of Neurology, Comprehensive Epilepsy Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Thomas N Ferraro
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.,Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Russell J Buono
- Department of Neurology, Comprehensive Epilepsy Center, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Biomedical Sciences, Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Wade H Berrettini
- Department of Psychiatry, Center for Neurobiology and Behavior, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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17
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Alkailani M, Palidwor G, Poulin A, Mohan R, Pepin D, Vanderhyden B, Gibbings D. A genome-wide strategy to identify causes and consequences of retrotransposon expression finds activation by BRCA1 in ovarian cancer. NAR Cancer 2021; 3:zcaa040. [PMID: 33447827 PMCID: PMC7787265 DOI: 10.1093/narcan/zcaa040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 11/20/2020] [Accepted: 11/30/2020] [Indexed: 12/03/2022] Open
Abstract
It is challenging to identify the causes and consequences of retrotransposon expression in human disease due to the hundreds of active genomic copies and their poor conservation across species. We profiled genomic insertions of retrotransposons in ovarian cancer. In addition, in ovarian and breast cancer we analyzed RNAs exhibiting Bayesian correlation with retrotransposon RNA to identify causes and consequences of retrotransposon expression. This strategy finds divergent inflammatory responses associated with retrotransposon expression in ovarian and breast cancer and identifies new factors inducing expression of endogenous retrotransposons including anti-viral responses and the common tumor suppressor BRCA1. In cell lines, mouse ovarian epithelial cells and patient-derived tumor spheroids, BRCA1 promotes accumulation of retrotransposon RNA. BRCA1 promotes transcription of active families of retrotransposons and their insertion into the genome. Intriguingly, elevated retrotransposon expression predicts survival in ovarian cancer patients. Retrotransposons are part of a complex regulatory network in ovarian cancer including BRCA1 that contributes to patient survival. The described strategy can be used to identify the regulators and impacts of retrotransposons in various contexts of biology and disease in humans.
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Affiliation(s)
- Maisa Alkailani
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Gareth Palidwor
- Ottawa Institute for Systems Biology, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
- Bioinformatics, Ottawa Hospital Research Institute, Ottawa, Ontario, K1H 8L6, Canada
| | - Ariane Poulin
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
| | - Raghav Mohan
- Pediatrics Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 021145, USA
| | - David Pepin
- Pediatrics Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA 021145, USA
- Department of Surgery, Harvard Medical School, Boston, MA 021156, USA
| | - Barbara Vanderhyden
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Ontario, K1H 8L6, Canada
| | - Derrick Gibbings
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, K1H 8M5, Canada
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18
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Komkov AY, Urazbakhtin SZ, Saliutina MV, Komech EA, Shelygin YA, Nugmanov GA, Shubin VP, Smirnova AO, Bobrov MY, Tsukanov AS, Snezhkina AV, Kudryavtseva AV, Lebedev YB, Mamedov IZ. SeqURE - a new copy-capture based method for sequencing of unknown Retroposition events. Mob DNA 2020; 11:33. [PMID: 33317630 PMCID: PMC7734759 DOI: 10.1186/s13100-020-00228-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 12/01/2020] [Indexed: 11/24/2022] Open
Abstract
Background Retroelements (REs) occupy a significant part of all eukaryotic genomes including humans. The majority of retroelements in the human genome are inactive and unable to retrotranspose. Dozens of active copies are repressed in most normal tissues by various cellular mechanisms. These copies can become active in normal germline and brain tissues or in cancer, leading to new retroposition events. The consequences of such events and their role in normal cell functioning and carcinogenesis are not yet fully understood. If new insertions occur in a small portion of cells they can be found only with the use of specific methods based on RE enrichment and high-throughput sequencing. The downside of the high sensitivity of such methods is the presence of various artifacts imitating real insertions, which in many cases cannot be validated due to lack of the initial template DNA. For this reason, adequate assessment of rare (< 1%) subclonal cancer specific RE insertions is complicated. Results Here we describe a new copy-capture technique which we implemented in a method called SeqURE for Sequencing Unknown of Retroposition Events that allows for efficient and reliable identification of new genomic RE insertions. The method is based on the capture of copies of target molecules (copy-capture), selective amplification and sequencing of genomic regions adjacent to active RE insertions from both sides. Importantly, the template genomic DNA remains intact and can be used for validation experiments. In addition, we applied a novel system for testing method sensitivity and precisely showed the ability of the developed method to reliably detect insertions present in 1 out of 100 cells and a substantial portion of insertions present in 1 out of 1000 cells. Using advantages of the method we showed the absence of somatic Alu insertions in colorectal cancer samples bearing tumor-specific L1HS insertions. Conclusions This study presents the first description and implementation of the copy-capture technique and provides the first methodological basis for the quantitative assessment of RE insertions present in a small portion of cells. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-020-00228-6.
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Affiliation(s)
- Alexander Y Komkov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.
| | | | - Maria V Saliutina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | | | - Yuri A Shelygin
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | - Gaiaz A Nugmanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Vitaliy P Shubin
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | | | - Mikhail Y Bobrov
- V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia
| | - Alexey S Tsukanov
- Ryzhikh National Medical Research Centre for Coloproctology of the Ministry of Health of Russia, Moscow, Russia
| | - Anastasia V Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna V Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Yuri B Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Ilgar Z Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia. .,Dmitry Rogachev National Medical and Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia. .,V.I. Kulakov National Medical Research Center for Obstetrics, Gynecology and Perinatology, Moscow, Russia. .,Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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19
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The tumor suppressor microRNA let-7 inhibits human LINE-1 retrotransposition. Nat Commun 2020; 11:5712. [PMID: 33177501 PMCID: PMC7658363 DOI: 10.1038/s41467-020-19430-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/03/2020] [Indexed: 12/13/2022] Open
Abstract
Nearly half of the human genome is made of transposable elements (TEs) whose activity continues to impact its structure and function. Among them, Long INterspersed Element class 1 (LINE-1 or L1) elements are the only autonomously active TEs in humans. L1s are expressed and mobilized in different cancers, generating mutagenic insertions that could affect tumor malignancy. Tumor suppressor microRNAs are ∼22nt RNAs that post-transcriptionally regulate oncogene expression and are frequently downregulated in cancer. Here we explore whether they also influence L1 mobilization. We show that downregulation of let-7 correlates with accumulation of L1 insertions in human lung cancer. Furthermore, we demonstrate that let-7 binds to the L1 mRNA and impairs the translation of the second L1-encoded protein, ORF2p, reducing its mobilization. Overall, our data reveals that let-7, one of the most relevant microRNAs, maintains somatic genome integrity by restricting L1 retrotransposition. Human Long INterspersed Element class 1 (LINE-1) elements are expressed and mobilized in many types of cancer, contributing to malignancy. Here the authors show that the tumor suppressor microRNA let-7 targets the LINE-1 mRNA and reduces LINE-1 mobilization.
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20
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Lanciano S, Cristofari G. Measuring and interpreting transposable element expression. Nat Rev Genet 2020; 21:721-736. [PMID: 32576954 DOI: 10.1038/s41576-020-0251-y] [Citation(s) in RCA: 164] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) are insertional mutagens that contribute greatly to the plasticity of eukaryotic genomes, influencing the evolution and adaptation of species as well as physiology or disease in individuals. Measuring TE expression helps to understand not only when and where TE mobilization can occur but also how this process alters gene expression, chromatin accessibility or cellular signalling pathways. Although genome-wide gene expression assays such as RNA sequencing include transposon-derived transcripts, most computational analytical tools discard or misinterpret TE-derived reads. Emerging approaches are improving the identification of expressed TE loci and helping to discriminate TE transcripts that permit TE mobilization from chimeric gene-TE transcripts or pervasive transcription. Here we review the main challenges associated with the detection of TE expression, including mappability, insertional and internal sequence polymorphisms, and the diversity of the TE transcriptional landscape, as well as the different experimental and computational strategies to solve them.
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21
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Yu H, Zhao S, Ness S, Kang H, Sheng Q, Samuels DC, Oyebamiji O, Zhao YY, Guo Y. Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats. PLoS Comput Biol 2020; 16:e1007968. [PMID: 32511223 PMCID: PMC7302867 DOI: 10.1371/journal.pcbi.1007968] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/18/2020] [Accepted: 05/19/2020] [Indexed: 11/19/2022] Open
Abstract
Very short tandem repeats bear substantial genetic, evolutional, and pathological significance in genome analyses. Here, we compiled a census of tandem mono-nucleotide/di-nucleotide/tri-nucleotide repeats (MNRs/DNRs/TNRs) in GRCh38, which we term "polytracts" in general. Of the human genome, 144.4 million nucleotides (4.7%) are occupied by polytracts, and 0.47 million single nucleotides are identified as polytract hinges, i.e., break-points of tandem polytracts. Preliminary exploration of the census suggested polytract hinge sites and boundaries of AAC polytracts may bear a higher mapping error rate than other polytract regions. Further, we revealed landscapes of polytract enrichment with respect to nearly a hundred genomic features. We found MNRs, DNRs, and TNRs displayed noticeable difference in terms of locational enrichment for miscellaneous genomic features, especially RNA editing events. Non-canonical and C-to-U RNA-editing events are enriched inside and/or adjacent to MNRs, while all categories of RNA-editing events are under-represented in DNRs. A-to-I RNA-editing events are generally under-represented in polytracts. The selective enrichment of non-canonical RNA-editing events within MNR adjacency provides a negative evidence against their authenticity. To enable similar locational enrichment analyses in relation to polytracts, we developed a software Polytrap which can handle 11 reference genomes. Additionally, we compiled polytracts of four model organisms into a Track Hub which can be integrated into USCS Genome Browser as an official track for convenient visualization of polytracts.
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Affiliation(s)
- Hui Yu
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail: (HY); (YG)
| | - Shilin Zhao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Scott Ness
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Huining Kang
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - David C. Samuels
- Deptartment of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Olufunmilola Oyebamiji
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Ying-yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, School of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yan Guo
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail: (HY); (YG)
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22
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McKerrow W, Tang Z, Steranka JP, Payer LM, Boeke JD, Keefe D, Fenyö D, Burns KH, Liu C. Human transposon insertion profiling by sequencing (TIPseq) to map LINE-1 insertions in single cells. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190335. [PMID: 32075555 PMCID: PMC7061987 DOI: 10.1098/rstb.2019.0335] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Long interspersed element-1 (LINE-1, L1) sequences, which comprise about 17% of human genome, are the product of one of the most active types of mobile DNAs in modern humans. LINE-1 insertion alleles can cause inherited and de novo genetic diseases, and LINE-1-encoded proteins are highly expressed in some cancers. Genome-wide LINE-1 mapping in single cells could be useful for defining somatic and germline retrotransposition rates, and for enabling studies to characterize tumour heterogeneity, relate insertions to transcriptional and epigenetic effects at the cellular level, or describe cellular phylogenies in development. Our laboratories have reported a genome-wide LINE-1 insertion site mapping method for bulk DNA, named transposon insertion profiling by sequencing (TIPseq). There have been significant barriers applying LINE-1 mapping to single cells, owing to the chimeric artefacts and features of repetitive sequences. Here, we optimize a modified TIPseq protocol and show its utility for LINE-1 mapping in single lymphoblastoid cells. Results from single-cell TIPseq experiments compare well to known LINE-1 insertions found by whole-genome sequencing and TIPseq on bulk DNA. Among the several approaches we tested, whole-genome amplification by multiple displacement amplification followed by restriction enzyme digestion, vectorette ligation and LINE-1-targeted PCR had the best assay performance. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Wilson McKerrow
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Zuojian Tang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - David Keefe
- Department of Obstetrics and Gynecology, New York University Langone School of Medicine, 462 First Avenue, New York, NY 10016, USA.,Department of Cell Biology, New York University Langone School of Medicine, 462 First Avenue, New York, NY 10016, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,High Throughput (HiT) Biology Center, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 401N Broadway, Baltimore, MD 21231, USA
| | - Chunhong Liu
- Department of Pathology, Johns Hopkins University School of Medicine, 733N Broadway, Baltimore, MD 21205, USA
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23
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Lou C, Goodier JL, Qiang R. A potential new mechanism for pregnancy loss: considering the role of LINE-1 retrotransposons in early spontaneous miscarriage. Reprod Biol Endocrinol 2020; 18:6. [PMID: 31964400 PMCID: PMC6971995 DOI: 10.1186/s12958-020-0564-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
LINE1 retrotransposons are mobile DNA elements that copy and paste themselves into new sites in the genome. To ensure their evolutionary success, heritable new LINE-1 insertions accumulate in cells that can transmit genetic information to the next generation (i.e., germ cells and embryonic stem cells). It is our hypothesis that LINE1 retrotransposons, insertional mutagens that affect expression of genes, may be causal agents of early miscarriage in humans. The cell has evolved various defenses restricting retrotransposition-caused mutation, but these are occasionally relaxed in certain somatic cell types, including those of the early embryo. We predict that reduced suppression of L1s in germ cells or early-stage embryos may lead to excessive genome mutation by retrotransposon insertion, or to the induction of an inflammatory response or apoptosis due to increased expression of L1-derived nucleic acids and proteins, and so disrupt gene function important for embryogenesis. If correct, a novel threat to normal human development is revealed, and reverse transcriptase therapy could be one future strategy for controlling this cause of embryonic damage in patients with recurrent miscarriages.
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Affiliation(s)
- Chao Lou
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
| | - John L. Goodier
- 0000 0001 2171 9311grid.21107.35McKusick-Nathans Deartment of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Rong Qiang
- Department of Genetics, Northwest Women’s and Children’s Hospital, 1616 Yanxiang Road, Xi’an, Shaanxi Province People’s Republic of China
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24
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Yang WR, Ardeljan D, Pacyna CN, Payer LM, Burns KH. SQuIRE reveals locus-specific regulation of interspersed repeat expression. Nucleic Acids Res 2019; 47:e27. [PMID: 30624635 PMCID: PMC6411935 DOI: 10.1093/nar/gky1301] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/18/2018] [Accepted: 01/03/2019] [Indexed: 12/13/2022] Open
Abstract
Transposable elements (TEs) are interspersed repeat sequences that make up much of the human genome. Their expression has been implicated in development and disease. However, TE-derived RNA-seq reads are difficult to quantify. Past approaches have excluded these reads or aggregated RNA expression to subfamilies shared by similar TE copies, sacrificing quantitative accuracy or the genomic context necessary to understand the basis of TE transcription. As a result, the effects of TEs on gene expression and associated phenotypes are not well understood. Here, we present Software for Quantifying Interspersed Repeat Expression (SQuIRE), the first RNA-seq analysis pipeline that provides a quantitative and locus-specific picture of TE expression (https://github.com/wyang17/SQuIRE). SQuIRE is an accurate and user-friendly tool that can be used for a variety of species. We applied SQuIRE to RNA-seq from normal mouse tissues and a Drosophila model of amyotrophic lateral sclerosis. In both model organisms, we recapitulated previously reported TE subfamily expression levels and revealed locus-specific TE expression. We also identified differences in TE transcription patterns relating to transcript type, gene expression and RNA splicing that would be lost with other approaches using subfamily-level analyses. Altogether, our findings illustrate the importance of studying TE transcription with locus-level resolution.
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Affiliation(s)
- Wan R Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Clarissa N Pacyna
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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25
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Cajuso T, Sulo P, Tanskanen T, Katainen R, Taira A, Hänninen UA, Kondelin J, Forsström L, Välimäki N, Aavikko M, Kaasinen E, Ristimäki A, Koskensalo S, Lepistö A, Renkonen-Sinisalo L, Seppälä T, Kuopio T, Böhm J, Mecklin JP, Kilpivaara O, Pitkänen E, Palin K, Aaltonen LA. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. Nat Commun 2019; 10:4022. [PMID: 31492840 PMCID: PMC6731219 DOI: 10.1038/s41467-019-11770-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 07/31/2019] [Indexed: 12/20/2022] Open
Abstract
Genomic instability pathways in colorectal cancer (CRC) have been extensively studied, but the role of retrotransposition in colorectal carcinogenesis remains poorly understood. Although retrotransposons are usually repressed, they become active in several human cancers, in particular those of the gastrointestinal tract. Here we characterize retrotransposon insertions in 202 colorectal tumor whole genomes and investigate their associations with molecular and clinical characteristics. We find highly variable retrotransposon activity among tumors and identify recurrent insertions in 15 known cancer genes. In approximately 1% of the cases we identify insertions in APC, likely to be tumor-initiating events. Insertions are positively associated with the CpG island methylator phenotype and the genomic fraction of allelic imbalance. Clinically, high number of insertions is independently associated with poor disease-specific survival. Retrotransposons are usually dormant in healthy tissue, but become activated during malignancy. Here, in colorectal cancer, Cajuso et al. show that retrotransposon activity associates with clinical features of the disease.
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Affiliation(s)
- Tatiana Cajuso
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Päivi Sulo
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Tomas Tanskanen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Aurora Taira
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Ulrika A Hänninen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Johanna Kondelin
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Linda Forsström
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Niko Välimäki
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Mervi Aavikko
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Eevi Kaasinen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Pathology, HUSLAB, University of Helsinki and Helsinki University Hospital, (Haartmaninkatu 3), FI-00290, Helsinki, Finland
| | - Selja Koskensalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital, University of Helsinki, (Haartmaninkatu 4), FI-00290, Helsinki, Finland
| | - Anna Lepistö
- Department of Gastrointestinal Surgery, Helsinki University Hospital, University of Helsinki, (Haartmaninkatu 4), FI-00290, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital, University of Helsinki, (Haartmaninkatu 4), FI-00290, Helsinki, Finland
| | - Toni Seppälä
- Department of Gastrointestinal Surgery, Helsinki University Hospital, University of Helsinki, (Haartmaninkatu 4), FI-00290, Helsinki, Finland
| | - Teijo Kuopio
- Biological and Environmental Science, University of Jyväskylä, PO Box 35, (Seminaarinkatu 15), FI-40014, Jyväskylä, Finland.,Department of Pathology, Central Finland Health Care District, (Keskussairaalantie 19), FI-40620 Jyväskylä, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, (Keskussairaalantie 19), FI-40620 Jyväskylä, Finland
| | - Jukka-Pekka Mecklin
- Department of Surgery, Jyväskylä Central Hospital, (Keskussairaalantie 19), FI-40620, Jyväskylä, Finland.,Department of Health Sciences, Faculty of Sport and Health Sciences, University of Jyväskylä, PO Box 35, (Seminaarinkatu 15), FI-40014, Jyväskylä, Finland
| | - Outi Kilpivaara
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Esa Pitkänen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Kimmo Palin
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland
| | - Lauri A Aaltonen
- Applied Tumor Genomics Research Program, Faculty of Medicine University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland. .,Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Biomedicum Helsinki, PO Box 63, (Haartmaninkatu 8), FI-00014, Helsinki, Finland.
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26
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Somatic LINE-1 retrotransposition in cortical neurons and non-brain tissues of Rett patients and healthy individuals. PLoS Genet 2019; 15:e1008043. [PMID: 30973874 PMCID: PMC6478352 DOI: 10.1371/journal.pgen.1008043] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 04/23/2019] [Accepted: 02/21/2019] [Indexed: 11/19/2022] Open
Abstract
Mounting evidence supports that LINE-1 (L1) retrotransposition can occur postzygotically in healthy and diseased human tissues, contributing to genomic mosaicism in the brain and other somatic tissues of an individual. However, the genomic distribution of somatic human-specific LINE-1 (L1Hs) insertions and their potential impact on carrier cells remain unclear. Here, using a PCR-based targeted bulk sequencing approach, we profiled 9,181 somatic insertions from 20 postmortem tissues from five Rett patients and their matched healthy controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues. In Rett patients, somatic insertions were significantly depleted in exons—mainly contributed by long genes—than healthy controls, implying that cells carrying MECP2 mutations might be defenseless against a second exonic L1Hs insertion. We observed a significant increase of somatic L1Hs insertions in the brain compared with non-brain tissues from the same individual. Compared to germline insertions, somatic insertions were less sense-depleted to transcripts, indicating that they underwent weaker selective pressure on the orientation of insertion. Our observations demonstrate that somatic L1Hs insertions contribute to genomic diversity and MeCP2 dysfunction alters their genomic patterns in Rett patients. Human-specific LINE-1 (L1Hs) is the most active autonomous retrotransposon family in the human genome. Mounting evidence supports that L1Hs retrotransposition occurs postzygotically in the human brain cells, contributing to neuronal genomic diversity, but the extent of L1Hs-driven mosaicism in the brain is debated. In this study, we profiled genome-wide L1Hs insertions among 20 postmortem tissues from Rett patients and matched controls. We identified and validated somatic L1Hs insertions in both cortical neurons and non-brain tissues, with a higher jumping activity in the brain. We further found that MeCP2 dysfunction might alter the genomic pattern of somatic L1Hs in Rett patients.
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27
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Sultana T, van Essen D, Siol O, Bailly-Bechet M, Philippe C, Zine El Aabidine A, Pioger L, Nigumann P, Saccani S, Andrau JC, Gilbert N, Cristofari G. The Landscape of L1 Retrotransposons in the Human Genome Is Shaped by Pre-insertion Sequence Biases and Post-insertion Selection. Mol Cell 2019; 74:555-570.e7. [PMID: 30956044 DOI: 10.1016/j.molcel.2019.02.036] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 01/10/2023]
Abstract
L1 retrotransposons are transposable elements and major contributors of genetic variation in humans. Where L1 integrates into the genome can directly impact human evolution and disease. Here, we experimentally induced L1 retrotransposition in cells and mapped integration sites at nucleotide resolution. At local scales, L1 integration is mostly restricted by genome sequence biases and the specificity of the L1 machinery. At regional scales, L1 shows a broad capacity for integration into all chromatin states, in contrast to other known mobile genetic elements. However, integration is influenced by the replication timing of target regions, suggesting a link to host DNA replication. The distribution of new L1 integrations differs from those of preexisting L1 copies, which are significantly reshaped by natural selection. Our findings reveal that the L1 machinery has evolved to efficiently target all genomic regions and underline a predominant role for post-integrative processes on the distribution of endogenous L1 elements.
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Affiliation(s)
- Tania Sultana
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | | | - Oliver Siol
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France
| | | | | | - Amal Zine El Aabidine
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Léo Pioger
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Pilvi Nigumann
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | - Simona Saccani
- Université Côte d'Azur, Inserm, CNRS, IRCAN, Nice, France
| | - Jean-Christophe Andrau
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS, Montpellier, France
| | - Nicolas Gilbert
- Institut de Génétique Humaine, University of Montpellier, CNRS, Montpellier, France; Institut de Médecine Régénératrice et de Biothérapie, Inserm U1183, CHU Montpellier, Montpellier, France
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28
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Abstract
BACKGROUND Numerous different types of variations can occur in DNA and have diverse effects and consequences. The Variation Ontology (VariO) was developed for systematic descriptions of variations and their effects at DNA, RNA and protein levels. RESULTS VariO use and terms for DNA variations are described in depth. VariO provides systematic names for variation types and detailed descriptions for changes in DNA function, structure and properties. The principles of VariO are presented along with examples from published articles or databases, most often in relation to human diseases. VariO terms describe local DNA changes, chromosome number and structure variants, chromatin alterations, as well as genomic changes, whether of genetic or non-genetic origin. CONCLUSIONS DNA variation systematics facilitates unambiguous descriptions of variations and their effects and further reuse and integration of data from different sources by both human and computers.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184, Lund, Sweden.
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29
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Xiang Y, Yan K, Zheng Q, Ke H, Cheng J, Xiong W, Shi X, Wei L, Zhao M, Yang F, Wang P, Lu X, Fu L, Lu X, Li F. Histone Demethylase KDM4B Promotes DNA Damage by Activating Long Interspersed Nuclear Element-1. Cancer Res 2018; 79:86-98. [PMID: 30459150 DOI: 10.1158/0008-5472.can-18-1310] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 10/02/2018] [Accepted: 10/30/2018] [Indexed: 11/16/2022]
Abstract
The histone demethylase KDM4B is frequently overexpressed in various cancer types, and previous studies have indicated that the primary oncogenic function of KDM4B is its ability to demethylate H3K9me3 in different tumors, resulting in altered gene expression and genome instability. A genome-wide analysis to evaluate the effect of KDM4B on the global or local H3K9me3 level has not been performed. In this study, we assess whole-genome H3K9me3 distribution in cancer cells and find that H3K9me3 is largely enriched in long interspersed nuclear element-1 (LINE-1). A significant proportion of KDM4B-dependent H3K9me3 was located in evolutionarily young LINE-1 elements, which likely retain retrotransposition activity. Ectopic expression of KDM4B promoted LINE-1 expression, while depletion of KDM4B reduced it. Furthermore, KDM4B overexpression enhanced LINE-1 retrotransposition efficacy, copy number, and associated DNA damage, presumably via the histone demethylase activity of KDM4B. Breast cancer cell lines expressing high levels of KDM4B also exhibited increased LINE-1 expression and copy number compared with other cell lines. Pharmacologic inhibition of KDM4B significantly reduced LINE-1 expression and DNA damage in breast cancer cells with excessive KDM4B. Our study not only identifies KDM4B as a novel regulator of LINE-1, but it also suggests an unexpected oncogenic role for KDM4B overexpression in tumorigenesis, providing clues for the development of new cancer prevention strategies and therapies. SIGNIFICANCE: The histone demethylase KDM4B promotes tumorigenesis by inducing retrotransposition and DNA damage.
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Affiliation(s)
- Ying Xiang
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Kai Yan
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qian Zheng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, China
| | - Haiqiang Ke
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Jie Cheng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China.,Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, Hubei, China
| | - Wenjun Xiong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Xin Shi
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lei Wei
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Min Zhao
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Fei Yang
- Department of Cell Biology and Genetics, Yangtze University, Jingzhou, Hubei, China
| | - Ping Wang
- Department of Oncology, Huanggang Central Hospital, Huanggang, Hubei, China
| | - Xing Lu
- Key Laboratory of Freshwater Biodiversity Conservation and Utilization of Ministry of Agriculture, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China
| | - Li Fu
- Guangdong Key Laboratory of Genome Stability and Human Disease Prevention, Department of Pharmacology and Shenzhen University International Cancer Center, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xuemei Lu
- Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Feng Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, China.
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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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Abstract
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.
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Affiliation(s)
- Kathleen H Burns
- Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
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33
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Transposable elements in cancer. NATURE REVIEWS. CANCER 2017. [PMID: 28642606 DOI: 10.1038/nrc.2017.35+[doi]] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.
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Nozu K, Iijima K, Igarashi T, Yamada S, Kralovicova J, Nozu Y, Yamamura T, Minamikawa S, Morioka I, Ninchoji T, Kaito H, Nakanishi K, Vorechovsky I. A birth of bipartite exon by intragenic deletion. Mol Genet Genomic Med 2017; 5:287-294. [PMID: 28546999 PMCID: PMC5441408 DOI: 10.1002/mgg3.277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 01/03/2017] [Accepted: 01/06/2017] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome. The deletion encompassed exons 38 through 41 and activated a cryptic 3' and 5' splice site that were derived from intron 37 and intron 41, respectively. The deletion breakpoint was in the middle of the new exon, with considerable complementarity between the two exonic parts, potentially bringing the cryptic 3' and 5' splice site into proximity. The 3' splice site, polypyrimidine tract and the branch site of the new exon were derived from an inactive, 5' truncated LINE-1 retrotransposon. This ancient LINE-1 copy sustained a series of mutations that created the highly conserved AG dinucleotide at the 3' splice site early in primate development. The exon was fully included in mature transcripts and introduced a stop codon in the shortened COL4A5 mRNA, illustrating pitfalls of inferring disease severity from DNA mutation alone. CONCLUSION These results expand the repertoire of mutational mechanisms that alter RNA processing in genetic disease and illustrate the extraordinary versatility of transposed elements in shaping the new exon-intron structure and the phenotypic variability.
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Affiliation(s)
- Kandai Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Kazumoto Iijima
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Toru Igarashi
- Department of PediatricsNippon Medical School HospitalTokyoJapan
| | - Shiro Yamada
- Department of PediatricsTokai University Oiso HospitalOisoJapan.,Division of Human GeneticsNational Institute of GeneticsMishimaJapan
| | | | - Yoshimi Nozu
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Tomohiko Yamamura
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Shogo Minamikawa
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Ichiro Morioka
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Takeshi Ninchoji
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Hiroshi Kaito
- Department of PediatricsKobe University Graduate School of MedicineKobeJapan
| | - Koichi Nakanishi
- Department of PediatricsWakayama Medical UniversityWakayamaJapan
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Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proc Natl Acad Sci U S A 2017; 114:E733-E740. [PMID: 28096347 DOI: 10.1073/pnas.1619797114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning-based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in high-grade ovarian serous carcinoma.
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36
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Doucet TT, Kazazian HH. Long Interspersed Element Sequencing (L1-Seq): A Method to Identify Somatic LINE-1 Insertions in the Human Genome. Methods Mol Biol 2016; 1400:79-93. [PMID: 26895047 DOI: 10.1007/978-1-4939-3372-3_5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
L1-seq is a high-throughput sequencing technique which is utilized to identify novel L1 insertions in genomic DNA samples of interest. Using special diagnostic nucleotides unique to the youngest and most active L1 sequence, we can amplify new somatic insertions. This technique has helped to establish the number of L1 insertions present in the general population as well as the variation among individuals with regard to their complement of active L1 elements. More recently, this technique has been employed to assess the level of retrotransposition occurring in various diseases such as cancer. These efforts try to establish a connection between the process of retrotransposition and disease development and/or progression.
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Affiliation(s)
- Tara T Doucet
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Haig H Kazazian
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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37
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Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH. Somatic retrotransposition is infrequent in glioblastomas. Mob DNA 2016; 7:22. [PMID: 27843500 PMCID: PMC5105304 DOI: 10.1186/s13100-016-0077-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/13/2016] [Indexed: 11/10/2022] Open
Abstract
Background Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals. Results We found and PCR validated one somatically acquired tumor-specific insertion in a case of secondary GBM. No LINE-1 insertions present in primary GBM oncosphere cultures were missing from corresponding blood samples. However, several copies of the element (11) were found in genomic DNA from blood and not in the oncosphere cultures. SNP 6.0 microarray analysis revealed deletions or loss of heterozygosity in the tumor genomes over the intervals corresponding to these LINE-1 insertions. Conclusions These findings indicate that LINE-1 retrotransposon can act as an infrequent insertional mutagen in secondary GBM, but that retrotransposition is uncommon in these central nervous system tumors as compared to other neoplasias. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0077-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pragathi Achanta
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Zuojian Tang
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: Yale University, New Haven, CT USA
| | - Reema Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Sisi Ma
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA
| | - Mark Grivainis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Cheng Ran Lisa Huang
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: L.E.K. Consulting, Boston, MA USA
| | - Anna M Schneider
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: BioNTech AG, Mainz, Germany
| | - Gary L Gallia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Gregory J Riggins
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alfredo Quinones-Hinojosa
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present address: Mayo Clinic, Jacksonville, FL USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
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38
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Zampella JG, Rodić N, Yang WR, Huang CRL, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mob DNA 2016; 7:20. [PMID: 27807467 PMCID: PMC5087121 DOI: 10.1186/s13100-016-0078-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
Background The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. Method We used Transposon Insertion Profiling by microarray (TIP-chip) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. We focused this discovery effort on annotated Cancer Gene Index loci. Results We catalogued a total of 749 and 2,100 loci corresponding to candidate LINE-1 and Alu insertion sites, respectively. As expected, these numbers encompass previously known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. We also conducted association analyses relating individual insertions to a variety of cellular phenotypes. Conclusions These data provide a resource for investigators with interests in specific cancer gene loci or mobile element insertion effects more broadly. Our data underscore that significant genetic variation in cancer genomes is owed to LINE-1 and Alu retrotransposons. Our findings also indicate that as large numbers of cancer genomes become available, it will be possible to associate individual transposable element insertion variants with molecular and phenotypic features of these malignancies. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0078-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John G Zampella
- Department of Dermatology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Cheng Ran Lisa Huang
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Jane Welch
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Veena P Gnanakkan
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Toby C Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Jef D Boeke
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; Present address: Institute for Systems Genetics, NYU Langone University School of Medicine, New York, NY 10016 USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
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Penzkofer T, Jäger M, Figlerowicz M, Badge R, Mundlos S, Robinson PN, Zemojtel T. L1Base 2: more retrotransposition-active LINE-1s, more mammalian genomes. Nucleic Acids Res 2016; 45:D68-D73. [PMID: 27924012 PMCID: PMC5210629 DOI: 10.1093/nar/gkw925] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 09/28/2016] [Accepted: 10/05/2016] [Indexed: 12/28/2022] Open
Abstract
LINE-1 (L1) insertions comprise as much as 17% of the human genome sequence, and similar proportions have been recorded for other mammalian species. Given the established role of L1 retrotransposons in shaping mammalian genomes, it becomes an important task to track and annotate the sources of this activity: full length elements, able to encode the cis and trans acting components of the retrotransposition machinery. The L1Base database (http://l1base.charite.de) contains annotated full-length sequences of LINE-1 transposons including putatively active L1s. For the new version of L1Base, a LINE-1 annotation tool, L1Xplorer, has been used to mine potentially active L1 retrotransposons from the reference genome sequences of 17 mammals. The current release of the human genome, GRCh38, contains 146 putatively active L1 elements or full length intact L1 elements (FLIs). The newest versions of the mouse, GRCm38 and the rat, Rnor_6.0, genomes contain 2811 and 492 FLIs, respectively. Most likely reflecting the current level of completeness of the genome project, the latest reference sequence of the common chimpanzee genome, PT 2.19, only contains 19 FLIs. Of note, the current assemblies of the dog, CF 3.1 and the sheep, OA 3.1, genomes contain 264 and 598 FLIs, respectively. Further developments in the new version of L1Base include an updated website with implementation of modern web server technologies. including a more responsive design for an improved user experience, as well as the addition of data sharing capabilities for L1Xplorer annotation.
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Affiliation(s)
- Tobias Penzkofer
- Department of Radiology, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marten Jäger
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
| | - Richard Badge
- Department of Genetics, University of Leicester, Leicester, LE1 7RH, UK
| | - Stefan Mundlos
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany
| | - Peter N Robinson
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany.,The Jackson Laboratory for Genomic medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Tomasz Zemojtel
- Institut für Medizinische Genetik und Humangenetik, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany .,Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60-569 Poznan, Poland
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Guffanti G, Gaudi S, Klengel T, Fallon JH, Mangalam H, Madduri R, Rodriguez A, DeCrescenzo P, Glovienka E, Sobell J, Klengel C, Pato M, Ressler KJ, Pato C, Macciardi F. LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family. Am J Med Genet B Neuropsychiatr Genet 2016; 171:534-45. [PMID: 26990047 DOI: 10.1002/ajmg.b.32437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
Recent studies show that human-specific LINE1s (L1HS) play a key role in the development of the central nervous system (CNS) and its disorders, and that their transpositions within the human genome are more common than previously thought. Many polymorphic L1HS, that is, present or absent across individuals, are not annotated in the current release of the genome and are customarily termed "non-reference L1s." We developed an analytical workflow to identify L1 polymorphic insertions with next-generation sequencing (NGS) using data from a family in which SZ segregates. Our workflow exploits two independent algorithms to detect non-reference L1 insertions, performs local de novo alignment of the regions harboring predicted L1 insertions and resolves the L1 subfamily designation from the de novo assembled sequence. We found 110 non-reference L1 polymorphic loci exhibiting Mendelian inheritance, the vast majority of which are already reported in dbRIP and/or euL1db, thus, confirming their status as non-reference L1 polymorphic insertions. Four previously undetected L1 polymorphic loci were confirmed by PCR amplification and direct sequencing of the insert. A large fraction of our non-reference L1s is located within the open reading frame of protein-coding genes that belong to pathways already implicated in the pathogenesis of schizophrenia. The finding of these polymorphic variants among SZ offsprings is intriguing and suggestive of putative pathogenic role. Our data show the utility of NGS to uncover L1 polymorphic insertions, a neglected type of genetic variants with the potential to influence the risk to develop schizophrenia like SNVs and CNVs. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Simona Gaudi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian National Institute of Health, Rome, Italy
| | - Torsten Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - James H Fallon
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Harry Mangalam
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Ravi Madduri
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Alex Rodriguez
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Paula DeCrescenzo
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Emily Glovienka
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Janet Sobell
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Claudia Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Michele Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Carlos Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California.,Center for Autism Research and Treatment (CART), University of California, Irvine, California.,Center for Epigenetics and Metabolism, University of California, Irvine, California
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Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 2016; 5. [PMID: 27016617 PMCID: PMC4866827 DOI: 10.7554/elife.13926] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI:http://dx.doi.org/10.7554/eLife.13926.001 Retrotransposons, also known as jumping genes, have invaded the genomes of most living organisms. These fragments of DNA have the ability to move or copy themselves from one location of a chromosome to another. Depending on where they insert themselves, retrotransposons can modify the sequence of nearby genes, which can alter or even abolish their activity. Although these genetic modifications have contributed significantly to the evolution of different species, retrotransposons can also have detrimental effects; for example, by causing new cases of genetic diseases. Adult human cells have a number of mechanisms that work to keep the activity of retrotransposons at a very low level. However, in many types of cancers retrotransposons escape these defense mechanisms and ‘jump’ actively. This is thought to contribute to the development and spread of cancerous tumors. To understand how jumping genes are mobilized, a fundamental question must be answered: is the high jumping gene activity observed in some cell types a result of activating many copies of the retrotransposons, or only a few of them? This question has been difficult to address because there are more than one hundred copies of retrotransposons that could potentially move in humans, many of which have not even been referenced in the human genome map. Furthermore, each copy is almost identical to another one, making it difficult to discriminate between them. Philippe et al. have now developed an approach that can map where individual retrotransposons are located in the genome of normal and cancerous cells and measure how active these jumping genes are. This revealed that only a very restricted number of them are active in any given cell type. Moreover, different subsets of jumping genes are active in different cell types, and their locations in the genome often do not overlap. Thus, whether jumping genes are activated depends on the cell type and their position in the genome. These results are in contrast to the prevalent view that retrotransposons are activated in a more widespread manner across the genome, at least in cancerous cells. Overall, Philippe et al.’s findings pave the way towards characterizing the chromosome regions in which retrotransposons are frequently activated and understanding how they contribute to cancer and other diseases. DOI:http://dx.doi.org/10.7554/eLife.13926.002
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Affiliation(s)
- Claude Philippe
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dulce B Vargas-Landin
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure, Paris, France
| | - Aurélien J Doucet
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dominic van Essen
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Jorge Vera-Otarola
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Monika Kuciak
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | | | - Pilvi Nigumann
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Gaël Cristofari
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
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42
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Pizarro JG, Cristofari G. Post-Transcriptional Control of LINE-1 Retrotransposition by Cellular Host Factors in Somatic Cells. Front Cell Dev Biol 2016; 4:14. [PMID: 27014690 PMCID: PMC4782638 DOI: 10.3389/fcell.2016.00014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 02/18/2016] [Indexed: 12/13/2022] Open
Abstract
Long INterspersed Element-1 (LINE-1 or L1) retrotransposons form the only autonomously active family of transposable elements in humans. They are expressed and mobile in the germline, in embryonic stem cells and in the early embryo, but are silenced in most somatic tissues. Consistently, they play an important role in individual genome variations through insertional mutagenesis and sequence transduction, which occasionally lead to novel genetic diseases. In addition, they are reactivated in nearly half of the human epithelial cancers, contributing to tumor genome dynamics. The L1 element codes for two proteins, ORF1p and ORF2p, which are essential for its mobility. ORF1p is an RNA-binding protein with nucleic acid chaperone activity and ORF2p possesses endonuclease and reverse transcriptase activities. These proteins and the L1 RNA assemble into a ribonucleoprotein particle (L1 RNP), considered as the core of the retrotransposition machinery. The L1 RNP mediates the synthesis of new L1 copies upon cleavage of the target DNA and reverse transcription of the L1 RNA at the target site. The L1 element takes benefit of cellular host factors to complete its life cycle, however several cellular pathways also limit the cellular accumulation of L1 RNPs and their deleterious activities. Here, we review the known cellular host factors and pathways that regulate positively or negatively L1 retrotransposition at post-transcriptional level, in particular by interacting with the L1 machinery or L1 replication intermediates; and how they contribute to control L1 activity in somatic cells.
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Affiliation(s)
- Javier G Pizarro
- Institute for Research on Cancer and Aging of Nice (IRCAN), Faculty of Medicine, CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis Nice, France
| | - Gaël Cristofari
- Institute for Research on Cancer and Aging of Nice (IRCAN), Faculty of Medicine, CNRS UMR7284, INSERM U1081, University of Nice Sophia Antipolis Nice, France
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43
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Klawitter S, Fuchs NV, Upton KR, Muñoz-Lopez M, Shukla R, Wang J, Garcia-Cañadas M, Lopez-Ruiz C, Gerhardt DJ, Sebe A, Grabundzija I, Merkert S, Gerdes P, Pulgarin JA, Bock A, Held U, Witthuhn A, Haase A, Sarkadi B, Löwer J, Wolvetang EJ, Martin U, Ivics Z, Izsvák Z, Garcia-Perez JL, Faulkner GJ, Schumann GG. Reprogramming triggers endogenous L1 and Alu retrotransposition in human induced pluripotent stem cells. Nat Commun 2016; 7:10286. [PMID: 26743714 PMCID: PMC4729875 DOI: 10.1038/ncomms10286] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 11/26/2015] [Indexed: 02/08/2023] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) are capable of unlimited proliferation and can differentiate in vitro to generate derivatives of the three primary germ layers. Genetic and epigenetic abnormalities have been reported by Wissing and colleagues to occur during hiPSC derivation, including mobilization of engineered LINE-1 (L1) retrotransposons. However, incidence and functional impact of endogenous retrotransposition in hiPSCs are yet to be established. Here we apply retrotransposon capture sequencing to eight hiPSC lines and three human embryonic stem cell (hESC) lines, revealing endogenous L1, Alu and SINE-VNTR-Alu (SVA) mobilization during reprogramming and pluripotent stem cell cultivation. Surprisingly, 4/7 de novo L1 insertions are full length and 6/11 retrotransposition events occurred in protein-coding genes expressed in pluripotent stem cells. We further demonstrate that an intronic L1 insertion in the CADPS2 gene is acquired during hiPSC cultivation and disrupts CADPS2 expression. These experiments elucidate endogenous retrotransposition, and its potential consequences, in hiPSCs and hESCs. Genetic and epigenetic abnormalities have been found to result from reprogramming of differentiated cells into human induced pluripotent stem cells (hiPSCs). Here, Klawitter et al. identify endogenous L1, Alu and SVA mobilization during reprogramming, highlighting the risk of insertional mutagens in hiPSCs.
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Affiliation(s)
- Sabine Klawitter
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Nina V Fuchs
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany.,Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Kyle R Upton
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Martin Muñoz-Lopez
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Ruchi Shukla
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Marta Garcia-Cañadas
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Cesar Lopez-Ruiz
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Daniel J Gerhardt
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - Attila Sebe
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | | | - Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Patricia Gerdes
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia
| | - J Andres Pulgarin
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Anja Bock
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Ulrike Held
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Anett Witthuhn
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Balázs Sarkadi
- Department of Biophysics and Radiation Biology, Semmelweis University, H-1094 Budapest, Hungary
| | - Johannes Löwer
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Ernst J Wolvetang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplantation, and Vascular Surgery; REBIRTH, Cluster of Excellence, Hannover Medical School, D-30625 Hannover, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine, D-13125 Berlin, Germany
| | - Jose L Garcia-Perez
- Department of Human DNA Variability, Pfizer/University of Granada and Andalusian Regional Government Center for Genomics and Oncology (GENYO), PTS Granada, 18016 Granada, Spain
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, Brisbane, Queensland 4102, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, D-63225 Langen, Germany
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44
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Rahbari R, Badge RM. Combining Amplification Typing of L1 Active Subfamilies (ATLAS) with High-Throughput Sequencing. Methods Mol Biol 2016; 1400:95-106. [PMID: 26895048 DOI: 10.1007/978-1-4939-3372-3_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
With the advent of new generations of high-throughput sequencing technologies, the catalog of human genome variants created by retrotransposon activity is expanding rapidly. However, despite these advances in describing L1 diversity and the fact that L1 must retrotranspose in the germline or prior to germline partitioning to be evolutionarily successful, direct assessment of de novo L1 retrotransposition in the germline or early embryogenesis has not been achieved for endogenous L1 elements. A direct study of de novo L1 retrotransposition into susceptible loci within sperm DNA (Freeman et al., Hum Mutat 32(8):978-988, 2011) suggested that the rate of L1 retrotransposition in the germline is much lower than previously estimated (<1 in 400 individuals versus 1 in 9 individuals (Kazazian, Nat Genet 22(2):130, 1999). Based on these revised estimates of the L1 retrotransposition rate, we modified the ATLAS L1 display technique (Badge et al., Am J Hum Genet 72(4):823-838, 2003) to investigate de novo L1 retrotransposition in human genomes. In this chapter, we describe how we combined a high-coverage ATLAS variant with high-throughput sequencing, achieving 11-25× sequence depth per single amplicon, to study L1 retrotransposition in whole genome amplified (WGA) DNAs.
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Affiliation(s)
- Raheleh Rahbari
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Richard M Badge
- Department of Genetics, University of Leicester, Leicester, UK
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45
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Ewing AD. Transposable element detection from whole genome sequence data. Mob DNA 2015; 6:24. [PMID: 26719777 PMCID: PMC4696183 DOI: 10.1186/s13100-015-0055-3] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/21/2015] [Indexed: 11/25/2022] Open
Abstract
The number of software tools available for detecting transposable element insertions from whole genome sequence data has been increasing steadily throughout the last ~5 years. Some of these methods have unique features suiting them for particular use cases, but in general they follow one or more of a common set of approaches. Here, detection and filtering approaches are reviewed in the light of transposable element biology and the current state of whole genome sequencing. We demonstrate that the current state-of-the-art methods still do not produce highly concordant results and provide resources to assist future development in transposable element detection methods.
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Affiliation(s)
- Adam D Ewing
- Mater Research Institute - University of Queensland, 37 Kent St Level 4, Woolloongabba, QLD 4102 Australia
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46
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Paterson AL, Weaver JMJ, Eldridge MD, Tavaré S, Fitzgerald RC, Edwards PAW. Mobile element insertions are frequent in oesophageal adenocarcinomas and can mislead paired-end sequencing analysis. BMC Genomics 2015; 16:473. [PMID: 26159513 PMCID: PMC4498532 DOI: 10.1186/s12864-015-1685-z] [Citation(s) in RCA: 20] [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: 11/10/2014] [Accepted: 06/05/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mobile elements are active in the human genome, both in the germline and cancers, where they can mutate driver genes. RESULTS While analysing whole genome paired-end sequencing of oesophageal adenocarcinomas to find genomic rearrangements, we identified three ways in which new mobile element insertions appear in the data, resembling translocation or insertion junctions: inserts where unique sequence has been transduced by an L1 (Long interspersed element 1) mobile element; novel inserts that are confidently, but often incorrectly, mapped by alignment software to L1s or polyA tracts in the reference sequence; and a combination of these two ways, where different sequences within one insert are mapped to different loci. We identified nine unique sequences that were transduced by neighbouring L1s, both L1s in the reference genome and L1s not present in the reference. Many of the resulting inserts were small fragments that include little or no recognisable mobile element sequence. We found 6 loci in the reference genome to which sequence reads from inserts were frequently mapped, probably erroneously, by alignment software: these were either L1 sequence or particularly long polyA runs. Inserts identified from such apparent rearrangement junctions averaged 16 inserts/tumour, range 0-153 insertions in 43 tumours. However, many inserts would not be detected by mapping the sequences to the reference genome, because they do not include sufficient mappable sequence. To estimate total somatic inserts we searched for polyA sequences that were not present in the matched normal or other normals from the same tumour batch, and were not associated with known polymorphisms. Samples of these candidate inserts were verified by sequencing across them or manual inspection of surrounding reads: at least 85 % were somatic and resembled L1-mediated events, most including L1Hs sequence. Approximately 100 such inserts were detected per tumour on average (range zero to approximately 700). CONCLUSIONS Somatic mobile elements insertions are abundant in these tumours, with over 75 % of cases having a number of novel inserts detected. The inserts create a variety of problems for the interpretation of paired-end sequencing data.
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Affiliation(s)
- Anna L Paterson
- Department of Pathology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK.
- Department of Pathology, Addenbrookes Hospital, Cambridge, UK.
| | - Jamie M J Weaver
- Department of Pathology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK.
| | - Matthew D Eldridge
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Simon Tavaré
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK.
| | - Paul A W Edwards
- Department of Pathology, University of Cambridge, Hutchison-MRC Research Centre, Cambridge, UK.
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47
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Miousse IR, Chalbot MCG, Lumen A, Ferguson A, Kavouras IG, Koturbash I. Response of transposable elements to environmental stressors. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2015; 765:19-39. [PMID: 26281766 PMCID: PMC4544780 DOI: 10.1016/j.mrrev.2015.05.003] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 12/21/2022]
Abstract
Transposable elements (TEs) comprise a group of repetitive sequences that bring positive, negative, as well as neutral effects to the host organism. Earlier considered as "junk DNA," TEs are now well-accepted driving forces of evolution and critical regulators of the expression of genetic information. Their activity is regulated by epigenetic mechanisms, including methylation of DNA and histone modifications. The loss of epigenetic control over TEs, exhibited as loss of DNA methylation and decondensation of the chromatin structure, may result in TEs reactivation, initiation of their insertional mutagenesis (retrotransposition) and has been reported in numerous human diseases, including cancer. Accumulating evidence suggests that these alterations are not the simple consequences of the disease, but often may drive the pathogenesis, as they can be detected early during disease development. Knowledge derived from the in vitro, in vivo, and epidemiological studies, clearly demonstrates that exposure to ubiquitous environmental stressors, many of which are carcinogens or suspected carcinogens, are capable of causing alterations in methylation and expression of TEs and initiate retrotransposition events. Evidence summarized in this review suggests that TEs are the sensitive endpoints for detection of effects caused by such environmental stressors, as ionizing radiation (terrestrial, space, and UV-radiation), air pollution (including particulate matter [PM]-derived and gaseous), persistent organic pollutants, and metals. Furthermore, the significance of these effects is characterized by their early appearance, persistence and presence in both, target organs and peripheral blood. Altogether, these findings suggest that TEs may potentially be introduced into safety and risk assessment and serve as biomarkers of exposure to environmental stressors. Furthermore, TEs also show significant potential to become invaluable surrogate biomarkers in clinic and possible targets for therapeutic modalities for disease treatment and prevention.
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Affiliation(s)
- Isabelle R Miousse
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Marie-Cecile G Chalbot
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Annie Lumen
- Division of Biochemical Toxicology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR 72079, USA.
| | - Alesia Ferguson
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Ilias G Kavouras
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
| | - Igor Koturbash
- Department of Environmental and Occupational Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
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48
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Hayano T, Yamada S, Hosomichi K, Nakaoka H, Yoshihara K, Adachi S, Kashima K, Tanaka K, Enomoto T, Inoue I. Identification of novel exonic mobile element insertions in epithelial ovarian cancers. Hum Genome Var 2015; 2:15030. [PMID: 27081539 PMCID: PMC4785551 DOI: 10.1038/hgv.2015.30] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 11/09/2022] Open
Abstract
Mobile elements comprise about half of the human genome. Three active mobile element families (L1, Alu, and SVA) possibly cause diseases such as cancer. We conducted mobile element insertion (MEI) profiling of 44 epithelial ovarian cancers using exome-sequencing data. We identified a total of 106 MEIs using the Mobster program, 8 of which were novel exonic MEIs.
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Affiliation(s)
- Takahide Hayano
- Division of Human Genetics, National Institute of Genetics , Mishima, Japan
| | - Shiro Yamada
- Division of Human Genetics, National Institute of Genetics , Mishima, Japan
| | | | - Hirofumi Nakaoka
- Division of Human Genetics, National Institute of Genetics , Mishima, Japan
| | - Kosuke Yoshihara
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences , Niigata, Japan
| | - Sosuke Adachi
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences , Niigata, Japan
| | - Katsunori Kashima
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences , Niigata, Japan
| | - Kenichi Tanaka
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan; Niigata Medical Center Hospital, Niigata, Japan
| | - Takayuki Enomoto
- Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences , Niigata, Japan
| | - Ituro Inoue
- Division of Human Genetics, National Institute of Genetics , Mishima, Japan
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