1
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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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2
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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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3
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Mendez-Dorantes C, Burns KH. LINE-1 retrotransposition and its deregulation in cancers: implications for therapeutic opportunities. Genes Dev 2023; 37:948-967. [PMID: 38092519 PMCID: PMC10760644 DOI: 10.1101/gad.351051.123] [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] [Indexed: 12/28/2023]
Abstract
Long interspersed element 1 (LINE-1) is the only protein-coding transposon that is active in humans. LINE-1 propagates in the genome using RNA intermediates via retrotransposition. This activity has resulted in LINE-1 sequences occupying approximately one-fifth of our genome. Although most copies of LINE-1 are immobile, ∼100 copies are retrotransposition-competent. Retrotransposition is normally limited via epigenetic silencing, DNA repair, and other host defense mechanisms. In contrast, LINE-1 overexpression and retrotransposition are hallmarks of cancers. Here, we review mechanisms of LINE-1 regulation and how LINE-1 may promote genetic heterogeneity in tumors. Finally, we discuss therapeutic strategies to exploit LINE-1 biology in cancers.
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Affiliation(s)
- Carlos Mendez-Dorantes
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
| | - Kathleen H Burns
- Department of Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA;
- Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
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4
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Shin W, Mun S, Han K. Human Endogenous Retrovirus-K (HML-2)-Related Genetic Variation: Human Genome Diversity and Disease. Genes (Basel) 2023; 14:2150. [PMID: 38136972 PMCID: PMC10742618 DOI: 10.3390/genes14122150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/23/2023] [Accepted: 11/26/2023] [Indexed: 12/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise a significant portion of the human genome, making up roughly 8%, a notable comparison to the 2-3% represented by coding sequences. Numerous studies have underscored the critical role and importance of HERVs, highlighting their diverse and extensive influence on the evolution of the human genome and establishing their complex correlation with various diseases. Among HERVs, the HERV-K (HML-2) subfamily has recently attracted significant attention, integrating into the human genome after the divergence between humans and chimpanzees. Its insertion in the human genome has received considerable attention due to its structural and functional characteristics and the time of insertion. Originating from ancient exogenous retroviruses, these elements succeeded in infecting germ cells, enabling vertical transmission and existing as proviruses within the genome. Remarkably, these sequences have retained the capacity to form complete viral sequences, exhibiting activity in transcription and translation. The HERV-K (HML-2) subfamily is the subject of active debate about its potential positive or negative effects on human genome evolution and various pathologies. This review summarizes the variation, regulation, and diseases in human genome evolution arising from the influence of HERV-K (HML-2).
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Affiliation(s)
- Wonseok Shin
- NGS Clinical Laboratory, Division of Cancer Research, Dankook University Hospital, Cheonan 31116, Republic of Korea;
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
| | - Seyoung Mun
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyudong Han
- Smart Animal Bio Institute, Dankook University, Cheonan 31116, Republic of Korea;
- Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Republic of Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Republic of Korea
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Republic of Korea
- R&D Center, HuNBiome Co., Ltd., Seoul 08507, Republic of Korea
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5
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Erenpreisa J, Vainshelbaum NM, Lazovska M, Karklins R, Salmina K, Zayakin P, Rumnieks F, Inashkina I, Pjanova D, Erenpreiss J. The Price of Human Evolution: Cancer-Testis Antigens, the Decline in Male Fertility and the Increase in Cancer. Int J Mol Sci 2023; 24:11660. [PMID: 37511419 PMCID: PMC10380301 DOI: 10.3390/ijms241411660] [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: 06/08/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
The increasing frequency of general and particularly male cancer coupled with the reduction in male fertility seen worldwide motivated us to seek a potential evolutionary link between these two phenomena, concerning the reproductive transcriptional modules observed in cancer and the expression of cancer-testis antigens (CTA). The phylostratigraphy analysis of the human genome allowed us to link the early evolutionary origin of cancer via the reproductive life cycles of the unicellulars and early multicellulars, potentially driving soma-germ transition, female meiosis, and the parthenogenesis of polyploid giant cancer cells (PGCCs), with the expansion of the CTA multi-families, very late during their evolution. CTA adaptation was aided by retrovirus domestication in the unstable genomes of mammals, for protecting male fertility in stress conditions, particularly that of humans, as compensation for the energy consumption of a large complex brain which also exploited retrotransposition. We found that the early and late evolutionary branches of human cancer are united by the immunity-proto-placental network, which evolved in the Cambrian and shares stress regulators with the finely-tuned sex determination system. We further propose that social stress and endocrine disruption caused by environmental pollution with organic materials, which alter sex determination in male foetuses and further spermatogenesis in adults, bias the development of PGCC-parthenogenetic cancer by default.
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Affiliation(s)
| | | | - Marija Lazovska
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Roberts Karklins
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Kristine Salmina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Pawel Zayakin
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Felikss Rumnieks
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
| | - Dace Pjanova
- Latvian Biomedical Research and Study Centre, Ratsupites 1-1k, LV-1067 Riga, Latvia
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
| | - Juris Erenpreiss
- Molecular Genetics Scientific Laboratory, Riga Stradins University, Dzirciema 16, LV-1007 Riga, Latvia
- Clinic iVF-Riga, Zala 1, LV-1010 Riga, Latvia
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6
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Du Q, Stow EC, LaCoste D, Freeman B, Baddoo M, Shareef A, Miller KM, Belancio VP. A novel role of TRIM28 B box domain in L1 retrotransposition and ORF2p-mediated cDNA synthesis. Nucleic Acids Res 2023; 51:4429-4450. [PMID: 37070200 PMCID: PMC10201437 DOI: 10.1093/nar/gkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 03/22/2023] [Accepted: 03/25/2023] [Indexed: 04/19/2023] Open
Abstract
The long interspersed element 1 (LINE-1 or L1) integration is affected by many cellular factors through various mechanisms. Some of these factors are required for L1 amplification, while others either suppress or enhance specific steps during L1 propagation. Previously, TRIM28 has been identified to suppress transposable elements, including L1 expression via its canonical role in chromatin remodeling. Here, we report that TRIM28 through its B box domain increases L1 retrotransposition and facilitates shorter cDNA and L1 insert generation in cultured cells. Consistent with the latter, we observe that tumor specific L1 inserts are shorter in endometrial, ovarian, and prostate tumors with higher TRIM28 mRNA expression than in those with lower TRIM28 expression. We determine that three amino acids in the B box domain that are involved in TRIM28 multimerization are critical for its effect on both L1 retrotransposition and cDNA synthesis. We provide evidence that B boxes from the other two members in the Class VI TRIM proteins, TRIM24 and TRIM33, also increase L1 retrotransposition. Our findings could lead to a better understanding of the host/L1 evolutionary arms race in the germline and their interplay during tumorigenesis.
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Affiliation(s)
- Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Dawn LaCoste
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Benjamin Freeman
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Afzaal M Shareef
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
| | - Kyle M Miller
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 100 E 24th Street, Austin, TX 78712, USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans 70112, USA
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7
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Son JH, Do H, Han J. Intragenic L1 Insertion: One Possibility of Brain Disorder. Life (Basel) 2022; 12:life12091425. [PMID: 36143463 PMCID: PMC9505610 DOI: 10.3390/life12091425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/29/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Long interspersed nuclear element 1 (LINE1, L1) is a retrotransposon comprising ~17% of the human genome. A subset of L1s maintains the potential to mobilize and alter the genomic landscape, consequently contributing to the change in genome integrity and gene expression. L1 retrotransposition occurs in the human brain regardless of disease status. However, in the brain of patients with various brain diseases, the expression level and copy number of L1 are significantly increased. In this review, we briefly introduce the methodologies applied to measure L1 mobility and identify genomic loci where new insertion of L1 occurs in the brain. Then, we present a list of genes disrupted by L1 transposition in the genome of patients with brain disorders. Finally, we discuss the association between genes disrupted by L1 and relative brain disorders.
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Affiliation(s)
- Ji-Hoon Son
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Hyunsu Do
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jinju Han
- Graduate School of Medical Science and Engineering, Korea Advanced Institute for Science and Technology (KAIST), Daejeon 34141, Korea
- BioMedical Research Center, KAIST, Daejeon 34141, Korea
- Correspondence:
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8
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Stow EC, Baddoo M, LaRosa AJ, LaCoste D, Deininger P, Belancio V. SCIFER: approach for analysis of LINE-1 mRNA expression in single cells at a single locus resolution. Mob DNA 2022; 13:21. [PMID: 36028901 PMCID: PMC9413895 DOI: 10.1186/s13100-022-00276-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 08/09/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Endogenous expression of L1 mRNA is the first step in an L1-initiated mutagenesis event. However, the contribution of individual cell types to patterns of organ-specific L1 mRNA expression remains poorly understood, especially at single-locus resolution. We introduce a method to quantify expression of mobile elements at the single-locus resolution in scRNA-Seq datasets called Single Cell Implementation to Find Expressed Retrotransposons (SCIFER). SCIFER aligns scRNA-Seq reads uniquely to the genome and extracts alignments from single cells by cell-specific barcodes. In contrast to the alignment performed using default parameters, this alignment strategy increases accuracy of L1 locus identification by retaining only reads that are uniquely mapped to individual L1 loci. L1 loci expressed in single cells are unambiguously identified using a list of L1 loci manually validated to be expressed in bulk RNA-Seq datasets generated from the same cell line or organ. RESULTS Validation of SCIFER using MCF7 cells determined technical parameters needed for optimal detection of L1 expression in single cells. We show that unsupervised analysis of L1 expression in single cells exponentially inflates both the levels of L1 expression and the number of expressed L1 loci. Application of SCIFER to analysis of scRNA-Seq datasets generated from mouse and human testes identified that mouse Round Spermatids and human Spermatogonia, Spermatocytes, and Round Spermatids express the highest levels of L1 mRNA. Our analysis also determined that similar to mice, human testes from unrelated individuals share as much as 80% of expressed L1 loci. Additionally, SCIFER determined that individual mouse cells co-express different L1 sub-families and different families of transposable elements, experimentally validating their co-existence in the same cell. CONCLUSIONS SCIFER detects mRNA expression of individual L1 loci in single cells. It is compatible with scRNA-Seq datasets prepared using traditional sequencing methods. Validated using a human cancer cell line, SCIFER analysis of mouse and human testes identified key cell types supporting L1 expression in these species. This will further our understanding of differences and similarities in endogenous L1 mRNA expression patterns in mice and humans.
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Affiliation(s)
- Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112, USA
| | - Alexis J LaRosa
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112, USA
| | - Dawn LaCoste
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA
| | - Victoria Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA, 70112, USA.
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, 70112, USA.
- Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA, 70112, USA.
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9
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Genomic Organization of Microsatellites and LINE-1-like Retrotransposons: Evolutionary Implications for Ctenomys minutus (Rodentia: Ctenomyidae) Cytotypes. Animals (Basel) 2022; 12:ani12162091. [PMID: 36009681 PMCID: PMC9405301 DOI: 10.3390/ani12162091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/28/2022] [Accepted: 08/13/2022] [Indexed: 12/05/2022] Open
Abstract
Simple Summary In animals, several species contain substantial chromosomal and genomic variation among their populations, but as to what could have driven such diversification is still a puzzle for most cases. Here, we used molecular cytogenetic analysis to expose the main genomic elements involved in the population variation observed in the Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae), which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoint regions (EBRs) and highlight their direct impact in promoting chromosomal rearrangements. Abstract The Neotropical underground rodents of the genus Ctenomys (Rodentia: Ctenomyidae) comprise about 65 species, which harbor the most significant chromosomal variation among mammals (2n = 10 to 2n = 70). Among them, C. minutus stands out with 45 different cytotypes already identified, among which, seven parental ones, named A to G, are parapatrically distributed in the coastal plains of Southern Brazil. Looking for possible causes that led to such extensive karyotype diversification, we performed chromosomal mapping of different repetitive DNAs, including microsatellites and long interspersed element-1 (LINE-1) retrotransposons in the seven parental cytotypes. Although microsatellites were found mainly in the centromeric and telomeric regions of the chromosomes, different patterns occur for each cytotype, thus revealing specific features. Likewise, the LINE-1-like retrotransposons also showed a differential distribution for each cytotype, which may be linked to stochastic loss of LINE-1 in some populations. Here, microsatellite motifs (A)30, (C)30, (CA)15, (CAC)10, (CAG)10, (CGG)10, (GA)15, and (GAG)10 could be mapped to fusion of chromosomes 20/17, fission and inversion in the short arm of chromosome 2, fusion of chromosomes 23/19, and different combinations of centric and tandem fusions of chromosomes 22/24/16. These data provide evidence for a correlation between repetitive genomic content and localization of evolutionary breakpoints and highlight their direct impact in promoting chromosomal rearrangements.
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10
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Stekelenburg C, Blouin JL, Santoni F, Zaghloul N, O'Hare EA, Dusaulcy R, Maechler P, Schwitzgebel VM. Loss of Nexmif results in the expression of phenotypic variability and loss of genomic integrity. Sci Rep 2022; 12:13815. [PMID: 35970867 PMCID: PMC9378738 DOI: 10.1038/s41598-022-17845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 08/02/2022] [Indexed: 11/17/2022] Open
Abstract
We identified two NEXMIF variants in two unrelated individuals with non-autoimmune diabetes and autistic traits, and investigated the expression of Nexmif in mouse and human pancreas and its function in pancreatic beta cells in vitro and in vivo. In insulin-secreting INS-1E cells, Nexmif expression increased strongly in response to oxidative stress. CRISPR Cas9-generated Nexmif knockout mice exhibited a reduced number of proliferating beta cells in pancreatic islets. RNA sequencing of pancreatic islets showed that the downregulated genes in Nexmif mutant islets are involved in stress response and the deposition of epigenetic marks. They include H3f3b, encoding histone H3.3, which is associated with the regulation of beta-cell proliferation and maintains genomic integrity by silencing transposable elements, particularly LINE1 elements. LINE1 activity has been associated with autism and neurodevelopmental disorders in which patients share characteristics with NEXMIF patients, and can cause genomic instability and genetic variation through retrotransposition. Nexmif knockout mice exhibited various other phenotypes. Mortality and phenotypic abnormalities increased in each generation in both Nexmif mutant and non-mutant littermates. In Nexmif mutant mice, LINE1 element expression was upregulated in the pancreas, brain, and testis, possibly inducing genomic instability in Nexmif mutant mice and causing phenotypic variability in their progeny.
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Affiliation(s)
- Caroline Stekelenburg
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Blouin
- Department of Genetic Medicine and Laboratory, University Hospitals of Geneva, 1211, Geneva, Switzerland.,Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Federico Santoni
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland
| | - Norann Zaghloul
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Elisabeth A O'Hare
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, USA
| | - Rodolphe Dusaulcy
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland.,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Pierre Maechler
- Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.,Department of Cell Physiology and Metabolism, University of Geneva Medical Center, 1206, Geneva, Switzerland
| | - Valerie M Schwitzgebel
- Pediatric Endocrine and Diabetes Unit, Division of Development and Growth, Department of Pediatrics, Gynecology and Obstetrics, University Hospitals of Geneva, Children's University Hospital, 6, Rue Willy Donze, 1205, Geneva, Switzerland. .,Faculty Diabetes Center, Faculty of Medicine, University of Geneva, Geneva, Switzerland.
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11
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A retrotransposon storm marks clinical phenoconversion to late-onset Alzheimer's disease. GeroScience 2022; 44:1525-1550. [PMID: 35585302 PMCID: PMC9213607 DOI: 10.1007/s11357-022-00580-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/26/2022] [Indexed: 12/03/2022] Open
Abstract
Recent reports have suggested that the reactivation of otherwise transcriptionally silent transposable elements (TEs) might induce brain degeneration, either by dysregulating the expression of genes and pathways implicated in cognitive decline and dementia or through the induction of immune-mediated neuroinflammation resulting in the elimination of neural and glial cells. In the work we present here, we test the hypothesis that differentially expressed TEs in blood could be used as biomarkers of cognitive decline and development of AD. To this aim, we used a sample of aging subjects (age > 70) that developed late-onset Alzheimer’s disease (LOAD) over a relatively short period of time (12–48 months), for which blood was available before and after their phenoconversion, and a group of cognitive stable subjects as controls. We applied our developed and validated customized pipeline that allows the identification, characterization, and quantification of the differentially expressed (DE) TEs before and after the onset of manifest LOAD, through analyses of RNA-Seq data. We compared the level of DE TEs within more than 600,000 TE-mapping RNA transcripts from 25 individuals, whose specimens we obtained before and after their phenotypic conversion (phenoconversion) to LOAD, and discovered that 1790 TE transcripts showed significant expression differences between these two timepoints (logFC ± 1.5, logCMP > 5.3, nominal p value < 0.01). These DE transcripts mapped both over- and under-expressed TE elements. Occurring before the clinical phenoconversion, this TE storm features significant increases in DE transcripts of LINEs, LTRs, and SVAs, while those for SINEs are significantly depleted. These dysregulations end with signs of manifest LOAD. This set of highly DE transcripts generates a TE transcriptional profile that accurately discriminates the before and after phenoconversion states of these subjects. Our findings suggest that a storm of DE TEs occurs before phenoconversion from normal cognition to manifest LOAD in risk individuals compared to controls, and may provide useful blood-based biomarkers for heralding such a clinical transition, also suggesting that TEs can indeed participate in the complex process of neurodegeneration.
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12
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Pinter TB, Ervin CS, Deb A, Penner-Hahn JE, Pecoraro VL. Cu(I) Binding to Designed Proteins Reveals a Putative Copper Binding Site of the Human Line1 Retrotransposon Protein ORF1p. Inorg Chem 2022; 61:5084-5091. [PMID: 35286080 PMCID: PMC10754372 DOI: 10.1021/acs.inorgchem.2c00057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Long interspersed nuclear elements-1 (L1) are autonomous retrotransposons that encode two proteins in different open reading frames (ORF1 and ORF2). The ORF1p, which may be an RNA binding and chaperone protein, contains a three-stranded coiled coil (3SCC) domain that facilitates the formation of the biologically active homotrimer. This 3SCC domain is composed of seven amino acid (heptad) repeats as found in native and designed peptides and a stammer that modifies the helical structure. Cysteine residues occur at three hydrophobic positions (2 a and 1 d sites) within this domain. We recently showed that the cysteine layers in ORF1p and model de novo designed peptides bind the toxic metalloid lead(II) with high affinities, a feature that had not been previously recognized. However, there is little understanding of how essential metal ions might interact with this metal binding domain. We have, therefore, investigated the copper(I) binding properties of analogous de novo designed 3SCCs that contain cysteine layers within the hydrophobic core. The results from UV-visible and X-ray absorption spectroscopy show that these designed peptides bind Cu(I) with high affinity in a pH-dependent manner. At pH 9, monomeric trigonal planar Cu(I)S3 centers are formed with 1 equiv of metal, while dinuclear centers form with a second equivalent of metal. At physiologic pH conditions, the dinuclear center forms cooperatively. These data suggest that ORF1p is capable of binding two copper ions to its tris(cysteine) layers. This has major implications for ORF1p coiled coil domain stability and dynamics, ultimately potentially impacting the resulting biological activity.
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Affiliation(s)
- Tyler B.J. Pinter
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Catherine S. Ervin
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- These authors contributed equally to this work
| | - Aniruddha Deb
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - James E. Penner-Hahn
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent L. Pecoraro
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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13
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Chuang NT, Gardner EJ, Terry DM, Crabtree J, Mahurkar AA, Rivell GL, Hong CC, Perry JA, Devine SE. Mutagenesis of human genomes by endogenous mobile elements on a population scale. Genome Res 2021; 31:2225-2235. [PMID: 34772701 PMCID: PMC8647825 DOI: 10.1101/gr.275323.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/16/2021] [Indexed: 01/22/2023]
Abstract
Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of these MEIs on human genomes. However, these projects also have presented major challenges with respect to the scalability and computational costs associated with performing MEI discovery on tens or even hundreds of thousands of samples. To meet these challenges, we have developed a more efficient and scalable version of our mobile element locator tool (MELT) called CloudMELT. We then used MELT and CloudMELT to perform MEI discovery in 57,919 human genomes and exomes, leading to the discovery of 104,350 nonredundant MEIs. We leveraged this collection (1) to examine potentially active L1 source elements that drive the mobilization of new Alu, L1, and SVA MEIs in humans; (2) to examine the population distributions and subfamilies of these MEIs; and (3) to examine the mutagenesis of GENCODE genes, ENCODE-annotated features, and disease genes by these MEIs. Our study provides new insights on the L1 source elements that drive MEI mutagenesis and brings forth a better understanding of how this mutagenesis impacts human genomes.
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Affiliation(s)
- Nelson T Chuang
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Division of Gastroenterology, Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Eugene J Gardner
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Diane M Terry
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Jonathan Crabtree
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Anup A Mahurkar
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Guillermo L Rivell
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
| | - Scott E Devine
- Graduate Program in Molecular Medicine, University of Maryland, Baltimore, Baltimore, Maryland 21201, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA
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14
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Wehbi SS, Zu Dohna H. A comparative analysis of L1 retrotransposition activities in human genomes suggests an ongoing increase in L1 number despite an evolutionary trend towards lower activity. Mob DNA 2021; 12:26. [PMID: 34782009 PMCID: PMC8594186 DOI: 10.1186/s13100-021-00255-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Background LINE-1 (Long Interspersed Nuclear Elements, L1) retrotransposons are the only autonomously active transposable elements in the human genome. The evolution of L1 retrotransposition rates and its implications for L1 dynamics are poorly understood. Retrotransposition rates are commonly measured in cell culture-based assays, but it is unclear how well these measurements provide insight into L1 population dynamics. This study applied comparative methods to estimate parameters for the evolution of retrotransposition rates, and infer L1 dynamics from these estimates. Results Our results show that the rates at which new L1s emerge in the human population correlate positively to cell-culture based retrotransposition activities, that there is an evolutionary trend towards lower retrotransposition activity, and that this evolutionary trend is not sufficient to counter-balance the increase in active L1s resulting from continuing retrotransposition. Conclusions Together, these findings support a model of the population-level L1 retrotransposition dynamics that is consistent with prior expectations and indicate the remaining gaps in the understanding of L1 dynamics in human genomes.
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Affiliation(s)
- Sawsan Sami Wehbi
- Department of Biology, American University of Beirut, Beirut, Lebanon
| | - Heinrich Zu Dohna
- Department of Biology, American University of Beirut, Beirut, Lebanon.
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15
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Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements. BIOLOGY 2021; 10:biology10090896. [PMID: 34571773 PMCID: PMC8465862 DOI: 10.3390/biology10090896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 11/22/2022]
Abstract
Simple Summary Transposable elements (TEs) are DNA sequences that are, or were, able to move (transpose) within the genome of a single cell. They were first discovered by Barbara McClintock while working on maize, and they make up a large fraction of the genome. Transpositions can result in mutations and they can alter the genome size. Cells regulate the activity of TEs using a variety of mechanisms, such as chemical modifications of DNA and small RNAs. Machine learning (ML) is an interdisciplinary subject that studies computer algorithms that can improve through experience and by the use of data. ML has been successfully applied to a variety of problems in bioinformatics and has exhibited favorable precision and speed. Here, we provide a systematic and guided review on the ML and bioinformatic methods and tools that are used for the analysis of the regulation of TEs. Abstract Transposable elements (TEs, or mobile genetic elements, MGEs) are ubiquitous genetic elements that make up a substantial proportion of the genome of many species. The recent growing interest in understanding the evolution and function of TEs has revealed that TEs play a dual role in genome evolution, development, disease, and drug resistance. Cells regulate TE expression against uncontrolled activity that can lead to developmental defects and disease, using multiple strategies, such as DNA chemical modification, small RNA (sRNA) silencing, chromatin modification, as well as sequence-specific repressors. Advancements in bioinformatics and machine learning approaches are increasingly contributing to the analysis of the regulation mechanisms. A plethora of tools and machine learning approaches have been developed for prediction, annotation, and expression profiling of sRNAs, for methylation analysis of TEs, as well as for genome-wide methylation analysis through bisulfite sequencing data. In this review, we provide a guided overview of the bioinformatic and machine learning state of the art of fields closely associated with TE regulation and function.
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16
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Hermant C, Torres-Padilla ME. TFs for TEs: the transcription factor repertoire of mammalian transposable elements. Genes Dev 2021; 35:22-39. [PMID: 33397727 PMCID: PMC7778262 DOI: 10.1101/gad.344473.120] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Hermant and Torres-Padilla summarize and discuss the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific transposable element families or subfamilies. Transposable elements (TEs) are genetic elements capable of changing position within the genome. Although their mobilization can constitute a threat to genome integrity, nearly half of modern mammalian genomes are composed of remnants of TE insertions. The first critical step for a successful transposition cycle is the generation of a full-length transcript. TEs have evolved cis-regulatory elements enabling them to recruit host-encoded factors driving their own, selfish transcription. TEs are generally transcriptionally silenced in somatic cells, and the mechanisms underlying their repression have been extensively studied. However, during germline formation, preimplantation development, and tumorigenesis, specific TE families are highly expressed. Understanding the molecular players at stake in these contexts is of utmost importance to establish the mechanisms regulating TEs, as well as the importance of their transcription to the biology of the host. Here, we review the transcription factors known to be involved in the sequence-specific recognition and transcriptional activation of specific TE families or subfamilies. We discuss the diversity of TE regulatory elements within mammalian genomes and highlight the importance of TE mobilization in the dispersal of transcription factor-binding sites over the course of evolution.
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Affiliation(s)
- Clara Hermant
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany.,Faculty of Biology, Ludwig-Maximilians Universität München, D-82152 Planegg-Martinsried, Germany
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17
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Watkins WS, Feusier JE, Thomas J, Goubert C, Mallick S, Jorde LB. The Simons Genome Diversity Project: A Global Analysis of Mobile Element Diversity. Genome Biol Evol 2021; 12:779-794. [PMID: 32359137 PMCID: PMC7290288 DOI: 10.1093/gbe/evaa086] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2020] [Indexed: 12/30/2022] Open
Abstract
Ongoing retrotransposition of Alu, LINE-1, and SINE–VNTR–Alu elements generates diversity and variation among human populations. Previous analyses investigating the population genetics of mobile element insertions (MEIs) have been limited by population ascertainment bias or by relatively small numbers of populations and low sequencing coverage. Here, we use 296 individuals representing 142 global populations from the Simons Genome Diversity Project (SGDP) to discover and characterize MEI diversity from deeply sequenced whole-genome data. We report 5,742 MEIs not originally reported by the 1000 Genomes Project and show that high sampling diversity leads to a 4- to 7-fold increase in MEI discovery rates over the original 1000 Genomes Project data. As a result of negative selection, nonreference polymorphic MEIs are underrepresented within genes, and MEIs within genes are often found in the transcriptional orientation opposite that of the gene. Globally, 80% of Alu subfamilies predate the expansion of modern humans from Africa. Polymorphic MEIs show heterozygosity gradients that decrease from Africa to Eurasia to the Americas, and the number of MEIs found uniquely in a single individual are also distributed in this general pattern. The maximum fraction of MEI diversity partitioned among the seven major SGDP population groups (FST) is 7.4%, similar to, but slightly lower than, previous estimates and likely attributable to the diverse sampling strategy of the SGDP. Finally, we utilize these MEIs to extrapolate the primary Native American shared ancestry component to back to Asia and provide new evidence from genome-wide identical-by-descent genetic markers that add additional support for a southeastern Siberian origin for most Native Americans.
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Affiliation(s)
| | | | - Jainy Thomas
- Department of Human Genetics, University of Utah
| | - Clement Goubert
- Department of Molecular Biology and Genetics, Cornell University
| | - Swapon Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah
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18
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Stow EC, Kaul T, deHaro DL, Dem MR, Beletsky AG, Morales ME, Du Q, LaRosa AJ, Yang H, Smither E, Baddoo M, Ungerleider N, Deininger P, Belancio VP. Organ-, sex- and age-dependent patterns of endogenous L1 mRNA expression at a single locus resolution. Nucleic Acids Res 2021; 49:5813-5831. [PMID: 34023901 PMCID: PMC8191783 DOI: 10.1093/nar/gkab369] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/21/2021] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
Expression of L1 mRNA, the first step in the L1 copy-and-paste amplification cycle, is a prerequisite for L1-associated genomic instability. We used a reported stringent bioinformatics method to parse L1 mRNA transcripts and measure the level of L1 mRNA expressed in mouse and rat organs at a locus-specific resolution. This analysis determined that mRNA expression of L1 loci in rodents exhibits striking organ specificity with less than 0.8% of loci shared between organs of the same organism. This organ specificity in L1 mRNA expression is preserved in male and female mice and across age groups. We discovered notable differences in L1 mRNA expression between sexes with only 5% of expressed L1 loci shared between male and female mice. Moreover, we report that the levels of total L1 mRNA expression and the number and spectrum of expressed L1 loci fluctuate with age as independent variables, demonstrating different patterns in different organs and sexes. Overall, our comparisons between organs and sexes and across ages ranging from 2 to 22 months establish previously unforeseen dynamic changes in L1 mRNA expression in vivo. These findings establish the beginning of an atlas of endogenous L1 mRNA expression across a broad range of biological variables that will guide future studies.
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Affiliation(s)
- Emily C Stow
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Tiffany Kaul
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Dawn L deHaro
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Madeleine R Dem
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Anna G Beletsky
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Maria E Morales
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Qianhui Du
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Alexis J LaRosa
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Hanlin Yang
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Emily Smither
- Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA
| | - Prescott Deininger
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane School of Public Health and Tropical Medicine, New Orleans, LA 70112 USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane Health Sciences Center, 1700 Tulane Ave, New Orleans, LA 70112, USA.,Department of Structural and Cellular Biology, Tulane School of Medicine, 1430 Tulane Ave, New Orleans, LA 70112 USA
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19
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McDonald TL, Zhou W, Castro CP, Mumm C, Switzenberg JA, Mills RE, Boyle AP. Cas9 targeted enrichment of mobile elements using nanopore sequencing. Nat Commun 2021; 12:3586. [PMID: 34117247 PMCID: PMC8196195 DOI: 10.1038/s41467-021-23918-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/25/2021] [Indexed: 02/05/2023] Open
Abstract
Mobile element insertions (MEIs) are repetitive genomic sequences that contribute to genetic variation and can lead to genetic disorders. Targeted and whole-genome approaches using short-read sequencing have been developed to identify reference and non-reference MEIs; however, the read length hampers detection of these elements in complex genomic regions. Here, we pair Cas9-targeted nanopore sequencing with computational methodologies to capture active MEIs in human genomes. We demonstrate parallel enrichment for distinct classes of MEIs, averaging 44% of reads on-targeted signals and exhibiting a 13.4-54x enrichment over whole-genome approaches. We show an individual flow cell can recover most MEIs (97% L1Hs, 93% AluYb, 51% AluYa, 99% SVA_F, and 65% SVA_E). We identify seventeen non-reference MEIs in GM12878 overlooked by modern, long-read analysis pipelines, primarily in repetitive genomic regions. This work introduces the utility of nanopore sequencing for MEI enrichment and lays the foundation for rapid discovery of elusive, repetitive genetic elements.
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Affiliation(s)
- Torrin L McDonald
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Christopher P Castro
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Camille Mumm
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Jessica A Switzenberg
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Ryan E Mills
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
| | - Alan P Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.
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20
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Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Mol Biol Evol 2021; 37:3576-3600. [PMID: 32722770 DOI: 10.1093/molbev/msaa194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.
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Affiliation(s)
- Di Chen
- Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA.,Department of Operations and Decision Systems, Université Laval, Québec, Canada
| | - Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA.,EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.,The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA
| | - Kateryna D Makova
- The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
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21
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Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science 2021; 372:eabf7117. [PMID: 33632895 PMCID: PMC8026704 DOI: 10.1126/science.abf7117] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Long-read and strand-specific sequencing technologies together facilitate the de novo assembly of high-quality haplotype-resolved human genomes without parent-child trio data. We present 64 assembled haplotypes from 32 diverse human genomes. These highly contiguous haplotype assemblies (average minimum contig length needed to cover 50% of the genome: 26 million base pairs) integrate all forms of genetic variation, even across complex loci. We identified 107,590 structural variants (SVs), of which 68% were not discovered with short-read sequencing, and 278 SV hotspots (spanning megabases of gene-rich sequence). We characterized 130 of the most active mobile element source elements and found that 63% of all SVs arise through homology-mediated mechanisms. This resource enables reliable graph-based genotyping from short reads of up to 50,340 SVs, resulting in the identification of 1526 expression quantitative trait loci as well as SV candidates for adaptive selection within the human population.
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Affiliation(s)
- Peter Ebert
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Bernardo Rodriguez-Martin
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Marc Jan Bonder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Jana Ebler
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Rebecca Serra Mari
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Feyza Yilmaz
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Xuefang Zhao
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA 92121, USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jiadong Lin
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yu Chen
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Jingwen Ren
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Martin Santamarina
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Wolfram Höps
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Hufsah Ashraf
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - Nelson T Chuang
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Susan Fairley
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | | | | | | | | | | | - Tsung-Yu Lu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Mark J P Chaisson
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Junjie Chen
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Chong Li
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Aaron M Wenger
- Pacific Biosciences of California, Menlo Park, CA 94025, USA
| | - Maryam Ghareghani
- Max Planck Institute for Informatics, Saarland Informatics Campus E1.4, 66123 Saarbrücken, Germany
- Saarbrücken Graduate School of Computer Science, Saarland University, Saarland Informatics Campus E1.3, 66123 Saarbrücken, Germany
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA
| | - Benjamin Raeder
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Patrick Hasenfeld
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Allison A Regier
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Haley J Abel
- Department of Medicine, Washington University, St. Louis, MO 63108, USA
| | - Ira M Hall
- Department of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mark B Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, BASS 432 and 437, 266 Whitney Avenue, New Haven, CT 06520, USA
| | - Jose M C Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Department of Zoology, Genetics, and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Zepeng Mu
- Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Yang I Li
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xinghua Shi
- Department of Computer and Information Sciences, Temple University, Philadelphia, PA 19122, USA
| | | | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Zechen Chong
- Department of Genetics and Informatics Institute, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Ashley D Sanders
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | | | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Department of Neurology, Harvard Medical School, Boston, MA 02114, USA
- Program in Medical and Population Genetics and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
- Department of Human Genetics, University of Michigan, 1241 E. Catherine Street, Ann Arbor, MI 48109, USA
| | - Scott E Devine
- Institute for Genome Sciences, University of Maryland School of Medicine, 670 W Baltimore Street, Baltimore, MD 21201, USA
| | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA.
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
- Department of Graduate Studies-Life Sciences, Ewha Womans University, Ewhayeodae-gil, Seodaemun-gu, Seoul 120-750, South Korea
| | - Jan O Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Meyerhofstraße 1, 69117 Heidelberg, Germany.
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Tobias Marschall
- Heinrich Heine University, Medical Faculty, Institute for Medical Biometry and Bioinformatics, Moorenstraße 20, 40225 Düsseldorf, Germany.
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, 3720 15th Avenue NE, Seattle, WA 98195-5065, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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22
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Reiner BC, Doyle GA, Weller AE, Levinson RN, Rao AM, Davila Perea E, Namoglu E, Pigeon A, Arauco-Shapiro G, Weickert CS, Turecki G, Crist RC, Berrettini WH. Inherited L1 Retrotransposon Insertions Associated With Risk for Schizophrenia and Bipolar Disorder. SCHIZOPHRENIA BULLETIN OPEN 2021; 2:sgab031. [PMID: 34901866 PMCID: PMC8650070 DOI: 10.1093/schizbullopen/sgab031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Studies of the genetic heritability of schizophrenia and bipolar disorder examining single nucleotide polymorphisms (SNPs) and copy number variations have failed to explain a large portion of the genetic liability, resulting in substantial missing heritability. Long interspersed element 1 (L1) retrotransposons are a type of inherited polymorphic variant that may be associated with risk for schizophrenia and bipolar disorder. We performed REBELseq, a genome wide assay for L1 sequences, on DNA from male and female persons with schizophrenia and controls (n = 63 each) to identify inherited L1 insertions and validated priority insertions. L1 insertions of interest were genotyped in DNA from a replication cohort of persons with schizophrenia, bipolar disorder, and controls (n = 2268 each) to examine differences in carrier frequencies. We identified an inherited L1 insertion in ARHGAP24 and a quadallelic SNP (rs74169643) inside an L1 insertion in SNTG2 that are associated with risk for developing schizophrenia and bipolar disorder (all odds ratios ~1.2). Pathway analysis identified 15 gene ontologies that were differentially affected by L1 burden, including multiple ontologies related to glutamatergic signaling and immune function, which have been previously associated with schizophrenia. These findings provide further evidence supporting the role of inherited repetitive genetic elements in the heritability of psychiatric disorders.
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Affiliation(s)
- Benjamin C Reiner
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Glenn A Doyle
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Weller
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rachel N Levinson
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditya M Rao
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Emilie Davila Perea
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Esin Namoglu
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Alicia Pigeon
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Gabriella Arauco-Shapiro
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cyndi Shannon Weickert
- Schizophrenia Research Laboratory, Neuroscience Research Australia & School of Psychiatry, Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
- Department of Neuroscience & Physiology, Upstate Medical University, Syracuse, NY, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, McGill University, Montreal, Canada
| | - Richard C Crist
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Wade H Berrettini
- Molecular and Neural Basis of Psychiatric Disease Section, Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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23
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Ahmadi A, De Toma I, Vilor-Tejedor N, Eftekhariyan Ghamsari MR, Sadeghi I. Transposable elements in brain health and disease. Ageing Res Rev 2020; 64:101153. [PMID: 32977057 DOI: 10.1016/j.arr.2020.101153] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 07/22/2020] [Accepted: 08/19/2020] [Indexed: 12/17/2022]
Abstract
Transposable elements (TEs) occupy a large fraction of the human genome but only a small proportion of these elements are still active today. Recent works have suggested that TEs are expressed and active in the brain, challenging the dogma that neuronal genomes are static and revealing that they are susceptible to somatic genomic alterations. These new findings have major implications for understanding the neuroplasticity of the brain, which could hypothetically have a role in behavior and cognition, and contribute to vulnerability to disease. As active TEs could induce genetic diversity and mutagenesis, their influences on human brain development and diseases are of great interest. In this review, we will focus on the active TEs in the human genome and discuss in detail their impacts on human brain development. Furthermore, the association between TEs and brain-related diseases is discussed.
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24
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Yamamoto S, Ding N, Matsumoto SI, Hirabayashi H. Highly specific, quantitative polymerase chain reaction probe for the quantification of human cells in cynomolgus monkeys. Drug Metab Pharmacokinet 2020; 36:100359. [PMID: 33348238 DOI: 10.1016/j.dmpk.2020.09.004] [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: 04/21/2020] [Revised: 09/17/2020] [Accepted: 09/23/2020] [Indexed: 10/23/2022]
Abstract
Quantification of human cells may be performed using quantitative polymerase chain reaction (qPCR). In preclinical studies, the human Alu sequence is widely used as biomarker for human DNA. However, because the Alu gene is shared by primates, its use is limited to non-primate studies. The biodistribution of human cells in primates is also necessary for translational studies. Therefore, we aimed to design a novel, human-specific primer/probe that enables the quantification of human cells in primates and other animal models. A novel primer/probe set was successfully designed based on highly repetitive LINE1 sequences. qPCR efficiency (94.95-99.21%) and linearity of calibration curves (r2 = 0.996-0.999) were confirmed in tissue homogenates of cynomolgus monkey. The lower limit of detection was 10 cells per 15-mg tissue sample, a sensitivity that is equivalent to existing Alu primers/probes. The set was also effective in other animal models such as mice, rabbits, pigs, and common marmosets. To our knowledge, this is the first study describing the successful design of a human-specific qPCR primer/probe for human cell quantification in various animals, including non-human primates, using LINE1 sequence. The excellent selectivity, sensitivity, and versatility of the LINE1 primers/probes make it a promising quantification tool in preclinical biodistribution studies.
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Affiliation(s)
- Syunsuke Yamamoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Ning Ding
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Shin-Ichi Matsumoto
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
| | - Hideki Hirabayashi
- Drug Metabolism and Pharmacokinetics Research Laboratories, Research, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa, Japan.
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25
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Furano AV, Jones CE, Periwal V, Callahan KE, Walser JC, Cook PR. Cryptic genetic variation enhances primate L1 retrotransposon survival by enlarging the functional coiled coil sequence space of ORF1p. PLoS Genet 2020; 16:e1008991. [PMID: 32797042 PMCID: PMC7449397 DOI: 10.1371/journal.pgen.1008991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 08/26/2020] [Accepted: 07/13/2020] [Indexed: 11/18/2022] Open
Abstract
Accounting for continual evolution of deleterious L1 retrotransposon families, which can contain hundreds to thousands of members remains a major issue in mammalian biology. L1 activity generated upwards of 40% of some mammalian genomes, including humans where they remain active, causing genetic defects and rearrangements. L1 encodes a coiled coil-containing protein that is essential for retrotransposition, and the emergence of novel primate L1 families has been correlated with episodes of extensive amino acid substitutions in the coiled coil. These results were interpreted as an adaptive response to maintain L1 activity, however its mechanism remained unknown. Although an adventitious mutation can inactivate coiled coil function, its effect could be buffered by epistatic interactions within the coiled coil, made more likely if the family contains a diverse set of coiled coil sequences-collectively referred to as the coiled coil sequence space. Amino acid substitutions that do not affect coiled coil function (i.e., its phenotype) could be "hidden" from (not subject to) purifying selection. The accumulation of such substitutions, often referred to as cryptic genetic variation, has been documented in various proteins. Here we report that this phenomenon was in effect during the latest episode of primate coiled coil evolution, which occurred 30-10 MYA during the emergence of primate L1Pa7-L1Pa3 families. First, we experimentally demonstrated that while coiled coil function (measured by retrotransposition) can be eliminated by single epistatic mutations, it nonetheless can also withstand extensive amino acid substitutions. Second, principal component and cluster analysis showed that the coiled coil sequence space of each of the L1Pa7-3 families was notably increased by the presence of distinct, coexisting coiled coil sequences. Thus, sampling related networks of functional sequences rather than traversing discrete adaptive states characterized the persistence L1 activity during this evolutionary event.
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Affiliation(s)
- Anthony V. Furano
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
| | - Charlie E. Jones
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vipul Periwal
- Laboratory of Biological Modeling, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathryn E. Callahan
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Jean-Claude Walser
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Pamela R. Cook
- Laboratory of Cellular and Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland, United States of America
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26
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Burns KH. Our Conflict with Transposable Elements and Its Implications for Human Disease. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 15:51-70. [PMID: 31977294 DOI: 10.1146/annurev-pathmechdis-012419-032633] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Our genome is a historic record of successive invasions of mobile genetic elements. Like other eukaryotes, we have evolved mechanisms to limit their propagation and minimize the functional impact of new insertions. Although these mechanisms are vitally important, they are imperfect, and a handful of retroelement families remain active in modern humans. This review introduces the intrinsic functions of transposons, the tactics employed in their restraint, and the relevance of this conflict to human pathology. The most straightforward examples of disease-causing transposable elements are germline insertions that disrupt a gene and result in a monogenic disease allele. More enigmatic are the abnormal patterns of transposable element expression in disease states. Changes in transposon regulation and cellular responses to their expression have implicated these sequences in diseases as diverse as cancer, autoimmunity, and neurodegeneration. Distinguishing their epiphenomenal from their pathogenic effects may provide wholly new perspectives on our understanding of disease.
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Affiliation(s)
- Kathleen H Burns
- Department of Pathology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
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27
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Restriction Enzyme Based Enriched L1Hs Sequencing (REBELseq): A Scalable Technique for Detection of Ta Subfamily L1Hs in the Human Genome. G3-GENES GENOMES GENETICS 2020; 10:1647-1655. [PMID: 32132168 PMCID: PMC7202019 DOI: 10.1534/g3.119.400613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Long interspersed element-1 retrotransposons (LINE-1 or L1) are ∼6 kb mobile DNA elements implicated in the origins of many Mendelian and complex diseases. The actively retrotransposing L1s are mostly limited to the L1 human specific (L1Hs) transcriptional active (Ta) subfamily. In this manuscript, we present REBELseq as a method for the construction of Ta subfamily L1Hs-enriched next-generation sequencing libraries and bioinformatic identification. REBELseq was performed on DNA isolated from NeuN+ neuronal nuclei from postmortem brain samples of 177 individuals and empirically-driven bioinformatic and experimental cutoffs were established. Putative L1Hs insertions passing bioinformatics cutoffs were experimentally validated. REBELseq reliably identified both known and novel Ta subfamily L1Hs insertions distributed throughout the genome. Differences in the proportion of individuals possessing a given reference or non-reference retrotransposon insertion were identified. We conclude that REBELseq is an unbiased, whole genome approach to the amplification and detection of Ta subfamily L1Hs retrotransposons.
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28
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O'Neill K, Brocks D, Hammell MG. Mobile genomics: tools and techniques for tackling transposons. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190345. [PMID: 32075565 PMCID: PMC7061981 DOI: 10.1098/rstb.2019.0345] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/20/2019] [Indexed: 12/22/2022] Open
Abstract
Next-generation sequencing approaches have fundamentally changed the types of questions that can be asked about gene function and regulation. With the goal of approaching truly genome-wide quantifications of all the interaction partners and downstream effects of particular genes, these quantitative assays have allowed for an unprecedented level of detail in exploring biological interactions. However, many challenges remain in our ability to accurately describe and quantify the interactions that take place in those hard to reach and extremely repetitive regions of our genome comprised mostly of transposable elements (TEs). Tools dedicated to TE-derived sequences have lagged behind, making the inclusion of these sequences in genome-wide analyses difficult. Recent improvements, both computational and experimental, allow for the better inclusion of TE sequences in genomic assays and a renewed appreciation for the importance of TE biology. This review will discuss the recent improvements that have been made in the computational analysis of TE-derived sequences as well as the areas where such analysis still proves difficult. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
- Kathryn O'Neill
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - David Brocks
- Department of Computer Science and Applied Mathematics, The Weizmann Institute of Science, Rehovot, Israel
| | - Molly Gale Hammell
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
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29
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Zhou W, Emery SB, Flasch DA, Wang Y, Kwan KY, Kidd JM, Moran JV, Mills RE. Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology. Nucleic Acids Res 2020; 48:1146-1163. [PMID: 31853540 PMCID: PMC7026601 DOI: 10.1093/nar/gkz1173] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/14/2019] [Accepted: 12/05/2019] [Indexed: 11/13/2022] Open
Abstract
Long Interspersed Element-1 (LINE-1) retrotransposition contributes to inter- and intra-individual genetic variation and occasionally can lead to human genetic disorders. Various strategies have been developed to identify human-specific LINE-1 (L1Hs) insertions from short-read whole genome sequencing (WGS) data; however, they have limitations in detecting insertions in complex repetitive genomic regions. Here, we developed a computational tool (PALMER) and used it to identify 203 non-reference L1Hs insertions in the NA12878 benchmark genome. Using PacBio long-read sequencing data, we identified L1Hs insertions that were absent in previous short-read studies (90/203). Approximately 81% (73/90) of the L1Hs insertions reside within endogenous LINE-1 sequences in the reference assembly and the analysis of unique breakpoint junction sequences revealed 63% (57/90) of these L1Hs insertions could be genotyped in 1000 Genomes Project sequences. Moreover, we observed that amplification biases encountered in single-cell WGS experiments led to a wide variation in L1Hs insertion detection rates between four individual NA12878 cells; under-amplification limited detection to 32% (65/203) of insertions, whereas over-amplification increased false positive calls. In sum, these data indicate that L1Hs insertions are often missed using standard short-read sequencing approaches and long-read sequencing approaches can significantly improve the detection of L1Hs insertions present in individual genomes.
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Affiliation(s)
- Weichen Zhou
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA
| | - Sarah B Emery
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Diane A Flasch
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Yifan Wang
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - Kenneth Y Kwan
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Molecular and Behavioral Neuroscience Institute, University of Michigan Medical School, 109 Zina Pitcher Place, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA.,Department of Internal Medicine, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Ryan E Mills
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, 100 Washtenaw Avenue, Ann Arbor, MI 48109, USA.,Department of Human Genetics, University of Michigan Medical School, 1241 East Catherine Street, Ann Arbor, MI 48109, USA
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30
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Iwasaki WM, Kijima TE, Innan H. Population Genetics and Molecular Evolution of DNA Sequences in Transposable Elements. II. Accumulation of Variation and Evolution of a New Subfamily. Mol Biol Evol 2020; 37:355-364. [PMID: 31580443 DOI: 10.1093/molbev/msz220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.
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Affiliation(s)
- Watal M Iwasaki
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - T E Kijima
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
| | - Hideki Innan
- SOKENDAI, The Graduate University for Advanced Studies, Hayama, Kanagawa, Japan
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Ardeljan D, Wang X, Oghbaie M, Taylor MS, Husband D, Deshpande V, Steranka JP, Gorbounov M, Yang WR, Sie B, Larman HB, Jiang H, Molloy KR, Altukhov I, Li Z, McKerrow W, Fenyö D, Burns KH, LaCava J. LINE-1 ORF2p expression is nearly imperceptible in human cancers. Mob DNA 2019; 11:1. [PMID: 31892958 PMCID: PMC6937734 DOI: 10.1186/s13100-019-0191-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 11/22/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. RESULTS We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. CONCLUSIONS Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth.
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Affiliation(s)
- Daniel Ardeljan
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Xuya Wang
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Martin S. Taylor
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - David Husband
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114 USA
| | - Jared P. Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Brandon Sie
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - H. Benjamin Larman
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
| | - Kelly R. Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065 USA
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701 Russia
| | - Zhi Li
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Wilson McKerrow
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - David Fenyö
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016 USA
| | - Kathleen H. Burns
- McKusick Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065 USA
- European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen, 9713 AV The Netherlands
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32
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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: 91] [Impact Index Per Article: 18.2] [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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33
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Sexton CE, Han MV. Paired-end mappability of transposable elements in the human genome. Mob DNA 2019; 10:29. [PMID: 31320939 PMCID: PMC6617613 DOI: 10.1186/s13100-019-0172-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/02/2019] [Indexed: 01/02/2023] Open
Abstract
Though transposable elements make up around half of the human genome, the repetitive nature of their sequences makes it difficult to accurately align conventional sequencing reads. However, in light of new advances in sequencing technology, such as increased read length and paired-end libraries, these repetitive regions are now becoming easier to align to. This study investigates the mappability of transposable elements with 50 bp, 76 bp and 100 bp paired-end read libraries. With respect to those read lengths and allowing for 3 mismatches during alignment, over 68, 85, and 88% of all transposable elements in the RepeatMasker database are uniquely mappable, suggesting that accurate locus-specific mapping of older transposable elements is well within reach.
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Affiliation(s)
- Corinne E Sexton
- 1School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA.,Nevada Institute of Personalized Medicine, Las Vegas, NV 89154 USA
| | - Mira V Han
- 1School of Life Sciences, University of Nevada, Las Vegas, NV 89154 USA.,Nevada Institute of Personalized Medicine, Las Vegas, NV 89154 USA
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34
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Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp 2019. [PMID: 31157783 DOI: 10.3791/59771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Long INterspersed Elements-1 (LINEs/L1s) are repetitive elements that can copy and randomly insert in the genome resulting in genomic instability and mutagenesis. Understanding the expression patterns of L1 loci at the individual level will lend to the understanding of the biology of this mutagenic element. This autonomous element makes up a significant portion of the human genome with over 500,000 copies, though 99% are truncated and defective. However, their abundance and dominant number of defective copies make it challenging to identify authentically expressed L1s from L1-related sequences expressed as part of other genes. It is also challenging to identify which specific L1 locus is expressed due to the repetitive nature of the elements. Overcoming these challenges, we present an RNA-Seq bioinformatic approach to identify L1 expression at the locus specific level. In summary, we collect cytoplasmic RNA, select for polyadenylated transcripts, and utilize strand-specific RNA-Seq analyses to uniquely map reads to L1 loci in the human reference genome. We visually curate each L1 locus with uniquely mapped reads to confirm transcription from its own promoter and adjust mapped transcript reads to account for mappability of each individual L1 locus. This approach was applied to a prostate tumor cell line, DU145, to demonstrate the ability of this protocol to detect expression from a small number of the full-length L1 elements.
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Affiliation(s)
| | | | | | - Melody Baddoo
- Tulane Cancer Center, Tulane University; Department of Pathology, Tulane University
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane University; Department of Structural and Cellular Biology, Tulane University
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University; Department of Epidemiology, Tulane University;
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35
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Blumenstiel JP. Birth, School, Work, Death, and Resurrection: The Life Stages and Dynamics of Transposable Element Proliferation. Genes (Basel) 2019; 10:genes10050336. [PMID: 31058854 PMCID: PMC6562965 DOI: 10.3390/genes10050336] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/18/2022] Open
Abstract
Transposable elements (TEs) can be maintained in sexually reproducing species even if they are harmful. However, the evolutionary strategies that TEs employ during proliferation can modulate their impact. In this review, I outline the different life stages of a TE lineage, from birth to proliferation to extinction. Through their interactions with the host, TEs can exploit diverse strategies that range from long-term coexistence to recurrent movement across species boundaries by horizontal transfer. TEs can also engage in a poorly understood phenomenon of TE resurrection, where TE lineages can apparently go extinct, only to proliferate again. By determining how this is possible, we may obtain new insights into the evolutionary dynamics of TEs and how they shape the genomes of their hosts.
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Affiliation(s)
- Justin P Blumenstiel
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66049, USA.
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36
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A comprehensive analysis of chimpanzee (Pan troglodytes)-specific LINE-1 retrotransposons. Gene 2019; 693:46-51. [DOI: 10.1016/j.gene.2019.01.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/08/2019] [Accepted: 01/22/2019] [Indexed: 01/08/2023]
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37
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Bodea GO, McKelvey EGZ, Faulkner GJ. Retrotransposon-induced mosaicism in the neural genome. Open Biol 2019; 8:rsob.180074. [PMID: 30021882 PMCID: PMC6070720 DOI: 10.1098/rsob.180074] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/21/2018] [Indexed: 12/18/2022] Open
Abstract
Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
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Affiliation(s)
- Gabriela O Bodea
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eleanor G Z McKelvey
- Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, TRI Building, Brisbane, Queensland 4102, Australia .,Queensland Brain Institute, University of Queensland, Brisbane, Queensland 4072, Australia
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38
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Shin W, Mun S, Kim J, Lee W, Park DG, Choi S, Lee TY, Cha S, Han K. Novel Discovery of LINE-1 in a Korean Individual by a Target Enrichment Method. Mol Cells 2019; 42:87-95. [PMID: 30699287 PMCID: PMC6354063 DOI: 10.14348/molcells.2018.0351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/10/2018] [Accepted: 10/26/2018] [Indexed: 11/27/2022] Open
Abstract
Long interspersed element-1 (LINE-1 or L1) is an autonomous retrotransposon, which is capable of inserting into a new region of genome. Previous studies have reported that these elements lead to genomic variations and altered functions by affecting gene expression and genetic networks. Mounting evidence strongly indicates that genetic diseases or various cancers can occur as a result of retrotransposition events that involve L1s. Therefore, the development of methodologies to study the structural variations and interpersonal insertion polymorphisms by L1 element-associated changes in an individual genome is invaluable. In this study, we applied a systematic approach to identify human-specific L1s (i.e., L1Hs) through the bioinformatics analysis of high-throughput next-generation sequencing data. We identified 525 candidates that could be inferred to carry non-reference L1Hs in a Korean individual genome (KPGP9). Among them, we randomly selected 40 candidates and validated that approximately 92.5% of non-reference L1Hs were inserted into a KPGP9 genome. In addition, unlike conventional methods, our relatively simple and expedited approach was highly reproducible in confirming the L1 insertions. Taken together, our findings strongly support that the identification of non-reference L1Hs by our novel target enrichment method demonstrates its future application to genomic variation studies on the risk of cancer and genetic disorders.
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Affiliation(s)
- Wonseok Shin
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Seyoung Mun
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Junse Kim
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Wooseok Lee
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
| | - Dong-Guk Park
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Seungkyu Choi
- Department of Pathology, Dankook University College of Medicine, Cheonan 31116,
Korea
| | - Tae Yoon Lee
- Department of Technology Education and Department of Biomedical Engineering, Chungnam National University, Daejeon 34134,
Korea
| | - Seunghee Cha
- Department of Oral and Maxillofacial Diagnostic Sciences, University of Florida College of Dentistry, Gainesville, FL 32610,
USA
| | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan 31116,
Korea
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39
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Bronkhorst AJ, Wentzel JF, Ungerer V, Peters DL, Aucamp J, de Villiers EP, Holdenrieder S, Pretorius PJ. Sequence analysis of cell-free DNA derived from cultured human bone osteosarcoma (143B) cells. Tumour Biol 2018; 40:1010428318801190. [PMID: 30261820 DOI: 10.1177/1010428318801190] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The true importance of cell-free DNA in human biology, together with the potential scale of its clinical utility, is tarnished by a lack of understanding of its composition and origin. In investigating the cell-free DNA present in the growth medium of cultured 143B cells, we previously demonstrated that the majority of cell-free DNA is neither a product of apoptosis nor necrosis. In the present study, we investigated the composition and origin of this cell-free DNA population using next-generation sequencing. We found that the cell-free DNA comprises mainly of repetitive DNA, including α-satellite DNA, mini satellites, and transposons that are currently active or exhibit the capacity to become reactivated. A significant portion of these cell-free DNA fragments originates from specific chromosomes, especially chromosomes 1 and 9. In healthy adult somatic cells, the centromeric and pericentromeric regions of these chromosomes are normally densely methylated. However, in many cancer types, these regions are preferentially hypomethylated. This can lead to double-stranded DNA breaks or it can directly impair the formation of proper kinetochore structures. This type of chromosomal instability is a precursor to the formation of nuclear anomalies, including lagging chromosomes and anaphase bridges. DNA fragments derived from these structures can recruit their own nuclear envelope and form secondary nuclear structures known as micronuclei, which can localize to the nuclear periphery and bud out from the membrane. We postulate that the majority of cell-free DNA present in the growth medium of cultured 143B cells originates from these micronuclei.
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Affiliation(s)
- Abel Jacobus Bronkhorst
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Johannes F Wentzel
- 2 Centre of Excellence for Nutrition (CEN), North-West University, Potchefstroom, South Africa
| | - Vida Ungerer
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Dimetrie L Peters
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
| | - Janine Aucamp
- 4 Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, South Africa
| | | | - Stefan Holdenrieder
- 1 Institute for Laboratory Medicine, German Heart Centre, Technical University Munich, Munich, Germany
| | - Piet J Pretorius
- 3 Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, South Africa
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40
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Whongsiri P, Pimratana C, Wijitsettakul U, Jindatip D, Sanpavat A, Schulz WA, Hoffmann MJ, Goering W, Boonla C. LINE-1 ORF1 Protein Is Up-regulated by Reactive Oxygen Species and Associated with Bladder Urothelial Carcinoma Progression. Cancer Genomics Proteomics 2018; 15:143-151. [PMID: 29496693 DOI: 10.21873/cgp.20072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/23/2018] [Accepted: 02/01/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND/AIM Reactivation of long interspersed nuclear element-1 (LINE-1) and oxidative stress are suggested to have oncogenic potential to drive tumorigenesis and cancer progression. We previously demonstrated that reactive oxygen species (ROS) caused hypomethylation of LINE-1 elements in bladder cancer cells. In this study, we investigated the expression of LINE-1-encoded protein (ORF1p) and oxidative stress marker 4-hydroxynonenal (4-HNE) in human bladder cancer tissues, as well as induction of ORF1p expression by ROS in bladder cancer cell lines. MATERIALS AND METHODS Thirty-six cancerous and 15 non-cancerous adjacent tissues were immunohistochemically stained for ORF1p and 4-HNE. ORF1p expression and cell migration were determined in bladder cancer cells exposed to H2O2 Results: ORF1p and 4-HNE expression was higher in cancerous than non-cancerous tissues. Elevated ORF1p expression was associated with increased 4-HNE expression and with advanced tumors. H2O2 provoked oxidative stress and up-regulated ORF1p expression in VM-CUB-1 compared to the untreated control, and to a lesser degree in TCCSUP. H2O2 exposure enhanced cell migration in UM-UC-3, TCCSUP and VM-CUB-1. CONCLUSION Elevated ORF1p expression is associated with tumor progression. ROS experimentally induce ORF1p expression and promote migration in bladder cancer cells.
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Affiliation(s)
- Patcharawalai Whongsiri
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | | | | | - Depicha Jindatip
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Anapat Sanpavat
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wolfgang A Schulz
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Michèle J Hoffmann
- Department of Urology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Wolfgang Goering
- Department of Pathology, Medical Faculty, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany
| | - Chanchai Boonla
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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41
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Tangsuwansri C, Saeliw T, Thongkorn S, Chonchaiya W, Suphapeetiporn K, Mutirangura A, Tencomnao T, Hu VW, Sarachana T. Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PLoS One 2018; 13:e0201071. [PMID: 30036398 PMCID: PMC6056057 DOI: 10.1371/journal.pone.0201071] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/06/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The exact cause and mechanisms underlying the pathobiology of autism spectrum disorder (ASD) remain unclear. Dysregulation of long interspersed element-1 (LINE-1) has been reported in the brains of ASD-like mutant mice and ASD brain tissues. However, the role and methylation of LINE-1 in individuals with ASD remain unclear. In this study, we aimed to investigate whether LINE-1 insertion is associated with differentially expressed genes (DEGs) and to assess LINE-1 methylation in ASD. METHODS To identify DEGs associated with LINE-1 in ASD, we reanalyzed previously published transcriptome profiles and overlapped them with the list of LINE-1-containing genes from the TranspoGene database. An Ingenuity Pathway Analysis (IPA) of DEGs associated with LINE-1 insertion was conducted. DNA methylation of LINE-1 was assessed via combined bisulfite restriction analysis (COBRA) of lymphoblastoid cell lines from ASD individuals and unaffected individuals, and the methylation levels were correlated with the expression levels of LINE-1 and two LINE-1-inserted DEGs, C1orf27 and ARMC8. RESULTS We found that LINE-1 insertion was significantly associated with DEGs in ASD. The IPA showed that LINE-1-inserted DEGs were associated with ASD-related mechanisms, including sex hormone receptor signaling and axon guidance signaling. Moreover, we observed that the LINE-1 methylation level was significantly reduced in lymphoblastoid cell lines from ASD individuals with severe language impairment and was inversely correlated with the transcript level. The methylation level of LINE-1 was also correlated with the expression of the LINE-1-inserted DEG C1orf27 but not ARMC8. CONCLUSIONS In ASD individuals with severe language impairment, LINE-1 methylation was reduced and correlated with the expression levels of LINE-1 and the LINE-1-inserted DEG C1orf27. Our findings highlight the association of LINE-1 with DEGs in ASD blood samples and warrant further investigation. The molecular mechanisms of LINE-1 and the effects of its methylation in ASD pathobiology deserve further study.
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Affiliation(s)
- Chayanin Tangsuwansri
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Thanit Saeliw
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Surangrat Thongkorn
- M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Weerasak Chonchaiya
- Division of Growth and Development and Maximizing Thai Children’s Developmental Potential Research Unit, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie Wailin Hu
- Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC, United States of America
| | - Tewarit Sarachana
- Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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42
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Turnbull MG, Douville RN. Related Endogenous Retrovirus-K Elements Harbor Distinct Protease Active Site Motifs. Front Microbiol 2018; 9:1577. [PMID: 30072963 PMCID: PMC6058741 DOI: 10.3389/fmicb.2018.01577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 02/06/2023] Open
Abstract
Background: Endogenous retrovirus-K is a group of related genomic elements descending from retroviral infections in human ancestors. HML2 is the clade of these viruses which contains the most intact provirus copies. These elements can be transcribed and translated in healthy and diseased tissues, and some of them produce active retroviral enzymes, such as protease. Retroviral gene products, including protease, contribute to illness in exogenous retroviral infections. There are ongoing efforts to test anti-retroviral regimens against endogenous retroviruses. Herein, we examine the potential activity and diversity of human endogenous retrovirus-K proteases, and their potential for impact on immunity and human disease. Results: Sequences similar to the endogenous retrovirus-K HML2 protease and reverse transcriptase were identified in the human genome, classified by phylogenetic inference and compared to Repbase reference sequences. The topologies of trees inferred from protease and reverse transcriptase sequences were similar and agreed with the classification using reference sequences. Surprisingly, only 62/480 protease sequences identified by BLAST were classified as HML2; the remainder were classified as other HML groups, with the majority (216) classified as HML3. Variation in functionally significant protease motifs was explored, and two major active site variants were identified – the DTGAD variant is common in all groups, but the DTGVD motif appears limited to HML3, HML5, and HML6. Furthermore, distinct RNA expression patterns of protease variants are seen in disease states, such as amyotrophic lateral sclerosis, breast cancer, and prostate cancer. Conclusion: Transcribed ERVK proteases exhibit a diversity which could impact immunity and inhibitor-based treatments, and these facets should be considered when designing therapeutic regimens.
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Affiliation(s)
| | - Renée N Douville
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada.,Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
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43
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Faulkner GJ, Billon V. L1 retrotransposition in the soma: a field jumping ahead. Mob DNA 2018; 9:22. [PMID: 30002735 PMCID: PMC6035798 DOI: 10.1186/s13100-018-0128-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 06/27/2018] [Indexed: 12/13/2022] Open
Abstract
Retrotransposons are transposable elements (TEs) capable of "jumping" in germ, embryonic and tumor cells and, as is now clearly established, in the neuronal lineage. Mosaic TE insertions form part of a broader landscape of somatic genome variation and hold significant potential to generate phenotypic diversity, in the brain and elsewhere. At present, the LINE-1 (L1) retrotransposon family appears to be the most active autonomous TE in most mammals, based on experimental data obtained from disease-causing L1 mutations, engineered L1 reporter systems tested in cultured cells and transgenic rodents, and single-cell genomic analyses. However, the biological consequences of almost all somatic L1 insertions identified thus far remain unknown. In this review, we briefly summarize the current state-of-the-art in the field, including estimates of L1 retrotransposition rate in neurons. We bring forward the hypothesis that an extensive subset of retrotransposition-competent L1s may be de-repressed and mobile in the soma but largely inactive in the germline. We discuss recent reports of non-canonical L1-associated sequence variants in the brain and propose that the elevated L1 DNA content reported in several neurological disorders may predominantly comprise accumulated, unintegrated L1 nucleic acids, rather than somatic L1 insertions. Finally, we consider the main objectives and obstacles going forward in elucidating the biological impact of somatic retrotransposition.
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Affiliation(s)
- Geoffrey J. Faulkner
- Mater Research Institute – University of Queensland, TRI Building, Woolloongabba, QLD 4102 Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072 Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
| | - Victor Billon
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072 Australia
- Biology Department, École Normale Supérieure Paris-Saclay, 61 Avenue du Président Wilson, 94230 Cachan, France
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44
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Bojang P, Ramos KS. Epigenetic reactivation of LINE-1 retrotransposon disrupts NuRD corepressor functions and induces oncogenic transformation in human bronchial epithelial cells. Mol Oncol 2018; 12:1342-1357. [PMID: 29845737 PMCID: PMC6068357 DOI: 10.1002/1878-0261.12329] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/01/2018] [Accepted: 05/01/2018] [Indexed: 01/16/2023] Open
Abstract
Long interspersed nuclear element‐1 (LINE‐1 or L1) reactivation is linked to poor prognosis in non‐small‐cell lung carcinoma (NSCLC), but the molecular bases of this response remain largely unknown. In this report, we show that challenge of human bronchial epithelial cells (HBECs) with the lung carcinogen, benzo(a)pyrene (BaP), shifted the L1 promoter from a heterochromatic to euchromatic state through disassembly of the nucleosomal and remodeling deacetylase (NuRD) complex. Carcinogen challenge was also associated with partial displacement of constituent proteins from the nuclear to the cytoplasmic compartment. Disruption of NuRD corepression by genetic ablation or carcinogen treatment correlated with accumulation of L1 mRNA and proteins. Mi2β bound directly to the L1 promoter to effect retroelement silencing, and this response required the DNA‐ and ATPase‐binding domains of Mi2β. Sustained expression of L1 in HBECs was tumorigenic in a human–SCID mouse xenograft model, giving rise to tumors that regressed over time. Together, these results show that functional modulation of the NuRD constituent proteins is a critical molecular event in the activation of L1 retrotransposon. L1 expression creates a microenvironment in HBECs that is conducive to neoplasia and malignant transformation.
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Affiliation(s)
- Pasano Bojang
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kenneth S Ramos
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, University of Arizona College of Medicine, Tucson, AZ, USA.,Center for Applied Genetics and Genomic Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
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45
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Transcription factor profiling reveals molecular choreography and key regulators of human retrotransposon expression. Proc Natl Acad Sci U S A 2018; 115:E5526-E5535. [PMID: 29802231 PMCID: PMC6004460 DOI: 10.1073/pnas.1722565115] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) represent a substantial fraction of many eukaryotic genomes, and transcriptional regulation of these factors is important to determine TE activities in human cells. However, due to the repetitive nature of TEs, identifying transcription factor (TF)-binding sites from ChIP-sequencing (ChIP-seq) datasets is challenging. Current algorithms are focused on subtle differences between TE copies and thus bias the analysis to relatively old and inactive TEs. Here we describe an approach termed "MapRRCon" (mapping repeat reads to a consensus) which allows us to identify proteins binding to TE DNA sequences by mapping ChIP-seq reads to the TE consensus sequence after whole-genome alignment. Although this method does not assign binding sites to individual insertions in the genome, it provides a landscape of interacting TFs by capturing factors that bind to TEs under various conditions. We applied this method to screen TFs' interaction with L1 in human cells/tissues using ENCODE ChIP-seq datasets and identified 178 of the 512 TFs tested as bound to L1 in at least one biological condition with most of them (138) localized to the promoter. Among these L1-binding factors, we focused on Myc and CTCF, as they play important roles in cancer progression and 3D chromatin structure formation. Furthermore, we explored the transcriptomes of The Cancer Genome Atlas breast and ovarian tumor samples in which a consistent anti-/correlation between L1 and Myc/CTCF expression was observed, suggesting that these two factors may play roles in regulating L1 transcription during the development of such tumors.
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46
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Yu Q, Zhang W, Zhang X, Zeng Y, Wang Y, Wang Y, Xu L, Huang X, Li N, Zhou X, Lu J, Guo X, Li G, Hou Y, Liu S, Li B. Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection. Gigascience 2018; 6:1-11. [PMID: 28938719 PMCID: PMC5603766 DOI: 10.1093/gigascience/gix066] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Active retrotransposons play important roles during evolution and continue to shape our genomes today, especially in genetic polymorphisms underlying a diverse set of diseases. However, studies of human retrotransposon insertion polymorphisms (RIPs) based on whole-genome deep sequencing at the population level have not been sufficiently undertaken, despite the obvious need for a thorough characterization of RIPs in the general population. Herein, we present a novel and efficient computational tool called Specific Insertions Detector (SID) for the detection of non-reference RIPs. We demonstrate that SID is suitable for high-depth whole-genome sequencing data using paired-end reads obtained from simulated and real datasets. We construct a comprehensive RIP database using a large population of 90 Han Chinese individuals with a mean ×68 depth per individual. In total, we identify 9342 recent RIPs, and 8433 of these RIPs are novel compared with dbRIP, including 5826 Alu, 2169 long interspersed nuclear element 1 (L1), 383 SVA, and 55 long terminal repeats. Among the 9342 RIPs, 4828 were located in gene regions and 5 were located in protein-coding regions. We demonstrate that RIPs can, in principle, be an informative resource to perform population evolution and phylogenetic analyses. Taking the demographic effects into account, we identify a weak negative selection on SVA and L1 but an approximately neutral selection for Alu elements based on the frequency spectrum of RIPs. SID is a powerful open-source program for the detection of non-reference RIPs. We built a non-reference RIP dataset that greatly enhanced the diversity of RIPs detected in the general population, and it should be invaluable to researchers interested in many aspects of human evolution, genetics, and disease. As a proof of concept, we demonstrate that the RIPs can be used as biomarkers in a similar way as single nucleotide polymorphisms.
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Affiliation(s)
- Qichao Yu
- BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Wei Zhang
- BGI Education Center, UCAS: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaolong Zhang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yongli Zeng
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yeming Wang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Yanhui Wang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Liqin Xu
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaoyun Huang
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Nannan Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xinlan Zhou
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Jie Lu
- BGI College: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Xiaosen Guo
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Guibo Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen: Nørregade 10, Copenhagen 1165, Denmark
| | - Yong Hou
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,Department of Biology, University of Copenhagen: Nørregade 10, Copenhagen 1165, Denmark
| | - Shiping Liu
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,School of Biology and Biological Engineering, SCUT: Postdoctoral Apartment Building, South China University of Technology, Wushan RD., TianHe District, Guangzhou, 510640, China
| | - Bo Li
- BGI-Shenzhen: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.,BGI-Forensics: Building 11, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
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47
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Schauer SN, Carreira PE, Shukla R, Gerhardt DJ, Gerdes P, Sanchez-Luque FJ, Nicoli P, Kindlova M, Ghisletti S, Santos AD, Rapoud D, Samuel D, Faivre J, Ewing AD, Richardson SR, Faulkner GJ. L1 retrotransposition is a common feature of mammalian hepatocarcinogenesis. Genome Res 2018; 28:639-653. [PMID: 29643204 PMCID: PMC5932605 DOI: 10.1101/gr.226993.117] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/26/2018] [Indexed: 12/15/2022]
Abstract
The retrotransposon Long Interspersed Element 1 (LINE-1 or L1) is a continuing source of germline and somatic mutagenesis in mammals. Deregulated L1 activity is a hallmark of cancer, and L1 mutagenesis has been described in numerous human malignancies. We previously employed retrotransposon capture sequencing (RC-seq) to analyze hepatocellular carcinoma (HCC) samples from patients infected with hepatitis B or hepatitis C virus and identified L1 variants responsible for activating oncogenic pathways. Here, we have applied RC-seq and whole-genome sequencing (WGS) to an Abcb4 (Mdr2)-/- mouse model of hepatic carcinogenesis and demonstrated for the first time that L1 mobilization occurs in murine tumors. In 12 HCC nodules obtained from 10 animals, we validated four somatic L1 insertions by PCR and capillary sequencing, including TF subfamily elements, and one GF subfamily example. One of the TF insertions carried a 3' transduction, allowing us to identify its donor L1 and to demonstrate that this full-length TF element retained retrotransposition capacity in cultured cancer cells. Using RC-seq, we also identified eight tumor-specific L1 insertions from 25 HCC patients with a history of alcohol abuse. Finally, we used RC-seq and WGS to identify three tumor-specific L1 insertions among 10 intra-hepatic cholangiocarcinoma (ICC) patients, including one insertion traced to a donor L1 on Chromosome 22 known to be highly active in other cancers. This study reveals L1 mobilization as a common feature of hepatocarcinogenesis in mammals, demonstrating that the phenomenon is not restricted to human viral HCC etiologies and is encountered in murine liver tumors.
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Affiliation(s)
- Stephanie N Schauer
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Patricia E Carreira
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Ruchi Shukla
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Daniel J Gerhardt
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Invenra, Incorporated, Madison, Wisconsin 53719, USA
| | - Patricia Gerdes
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Francisco J Sanchez-Luque
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research: Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Paola Nicoli
- Department of Experimental Oncology, European Institute of Oncology, 20146 Milan, Italy
| | - Michaela Kindlova
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | | | - Alexandre Dos Santos
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Delphine Rapoud
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Didier Samuel
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
| | - Jamila Faivre
- INSERM, U1193, Paul-Brousse University Hospital, Hepatobiliary Centre, Villejuif 94800, France
- Université Paris-Sud, Faculté de Médecine, Villejuif 94800, France
- Assistance Publique-Hôpitaux de Paris (AP-HP), Pôle de Biologie Médicale, Paul-Brousse University Hospital, Villejuif 94800, France
| | - Adam D Ewing
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Sandra R Richardson
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
| | - Geoffrey J Faulkner
- Mater Research Institute-University of Queensland, Woolloongabba, QLD 4102, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD 4072, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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48
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Xue AT, Ruggiero RP, Hickerson MJ, Boissinot S. Differential Effect of Selection against LINE Retrotransposons among Vertebrates Inferred from Whole-Genome Data and Demographic Modeling. Genome Biol Evol 2018; 10:1265-1281. [PMID: 29688421 PMCID: PMC5963298 DOI: 10.1093/gbe/evy083] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2018] [Indexed: 12/30/2022] Open
Abstract
Variation in LINE composition is one of the major determinants for the substantial size and structural differences among vertebrate genomes. In particular, the larger genomes of mammals are characterized by hundreds of thousands of copies from a single LINE clade, L1, whereas nonmammalian vertebrates possess a much greater diversity of LINEs, yet with orders of magnitude less in copy number. It has been proposed that such variation in copy number among vertebrates is due to differential effect of LINE insertions on host fitness. To investigate LINE selection, we deployed a framework of demographic modeling, coalescent simulations, and probabilistic inference against population-level whole-genome data sets for four model species: one population each of threespine stickleback, green anole, and house mouse, as well as three human populations. Specifically, we inferred a null demographic background utilizing SNP data, which was then exploited to simulate a putative null distribution of summary statistics that was compared with LINE data. Subsequently, we applied the inferred null demographic model with an additional exponential size change parameter, coupled with model selection, to test for neutrality as well as estimate the strength of either negative or positive selection. We found a robust signal for purifying selection in anole and mouse, but a lack of clear evidence for selection in stickleback and human. Overall, we demonstrated LINE insertion dynamics that are not in accordance to a mammalian versus nonmammalian dichotomy, and instead the degree of existing LINE activity together with host-specific demographic history may be the main determinants of LINE abundance.
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Affiliation(s)
- Alexander T Xue
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York
- Human Genetics Institute of New Jersey and Department of Genetics, Rutgers University, Piscataway
| | - Robert P Ruggiero
- New York University Abu Dhabi, Saadiyat Island Campus, United Arab Emirates
| | - Michael J Hickerson
- Department of Biology: Subprogram in Ecology, Evolutionary Biology, and Behavior, City College and Graduate Center of City University of New York
- Division of Invertebrate Zoology, American Museum of Natural History, New York, New York
| | - Stéphane Boissinot
- New York University Abu Dhabi, Saadiyat Island Campus, United Arab Emirates
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49
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Naufer MN, Furano AV, Williams MC. Protein-nucleic acid interactions of LINE-1 ORF1p. Semin Cell Dev Biol 2018; 86:140-149. [PMID: 29596909 PMCID: PMC6428221 DOI: 10.1016/j.semcdb.2018.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 11/03/2022]
Abstract
Long interspersed nuclear element 1 (LINE-1 or L1) is the dominant retrotransposon in mammalian genomes. L1 encodes two proteins ORF1p and ORF2p that are required for retrotransposition. ORF2p functions as the replicase. ORF1p is a coiled coil-mediated trimeric, high affinity RNA binding protein that packages its full- length coding transcript into an ORF2p-containing ribonucleoprotein (RNP) complex, the retrotransposition intermediate. ORF1p also is a nucleic acid chaperone that presumably facilitates the proposed nucleic acid remodeling steps involved in retrotransposition. Although detailed mechanistic understanding of ORF1p function in this process is lacking, recent studies showed that the rate at which ORF1p can form stable nucleic acid-bound oligomers in vitro is positively correlated with formation of an active L1 RNP as assayed in vivo using a cell culture-based retrotransposition assay. This rate was sensitive to minor amino acid changes in the coiled coil domain, which had no effect on nucleic acid chaperone activity. Additional studies linking the complex nucleic acid binding properties to the conformational changes of the protein are needed to understand how ORF1p facilitates retrotransposition.
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Affiliation(s)
- M Nabuan Naufer
- Northeastern University, Department of Physics, Boston, MA 02115, USA
| | - Anthony V Furano
- The Laboratory of Molecular and Cellular Biology, NIDDK, NIH, Bethesda, MD 20892, USA
| | - Mark C Williams
- Northeastern University, Department of Physics, Boston, MA 02115, USA.
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50
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Sookdeo A, Hepp CM, Boissinot S. Contrasted patterns of evolution of the LINE-1 retrotransposon in perissodactyls: the history of a LINE-1 extinction. Mob DNA 2018; 9:12. [PMID: 29610583 PMCID: PMC5872511 DOI: 10.1186/s13100-018-0117-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/22/2018] [Indexed: 12/30/2022] Open
Abstract
Background LINE-1 (L1) is the dominant autonomously replicating non-LTR retrotransposon in mammals. Although our knowledge of L1 evolution across the tree of life has considerably improved in recent years, what we know of L1 evolution in mammals is biased and comes mostly from studies in primates (mostly human) and rodents (mostly mouse). It is unclear if patterns of evolution that are shared between those two groups apply to other mammalian orders. Here we performed a detailed study on the evolution of L1 in perissodactyls by making use of the complete genome of the domestic horse and of the white rhinoceros. This mammalian order offers an excellent model to study the extinction of L1 since the rhinoceros is one of the few mammalian species to have lost active L1. Results We found that multiple L1 lineages, carrying different 5’UTRs, have been simultaneously active during the evolution of perissodactyls. We also found that L1 has continuously amplified and diversified in horse. In rhinoceros, L1 was very prolific early on. Two successful families were simultaneously active until ~20my ago but became extinct suddenly at exactly the same time. Conclusions The general pattern of L1 evolution in perissodactyls is very similar to what was previously described in mouse and human, suggesting some commonalities in the way mammalian genomes interact with L1. We confirmed the extinction of L1 in rhinoceros and we discuss several possible mechanisms. Electronic supplementary material The online version of this article (10.1186/s13100-018-0117-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Akash Sookdeo
- 1Department of Biology, New York University, New York, NY USA
| | - Crystal M Hepp
- 2School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ USA
| | - Stéphane Boissinot
- 3New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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