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Trost H, Lopezcolorado FW, Merkell A, Stark JM. Functions of PMS2 and MLH1 important for regulation of divergent repeat-mediated deletions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.05.606388. [PMID: 39149360 PMCID: PMC11326157 DOI: 10.1101/2024.08.05.606388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Repeat-mediated deletions (RMDs) are a type of deletion rearrangement that utilizes two repetitive elements to bridge a DNA double-strand break (DSB) that leads to loss of the intervening sequence and one of the repeats. Sequence divergence between repeats causes RMD suppression and indeed this divergence must be resolved in the RMD products. The mismatch repair factor, MLH1, was shown to be critical for both RMD suppression and a polarity of sequence divergence resolution in RMDs. Here, we sought to study the interrelationship between these two aspects of RMD regulation (i.e., RMD suppression and polar divergence resolution), by examining several mutants of MLH1 and its binding partner PMS2. To begin with, we show that PMS2 is also critical for both RMD suppression and polar resolution of sequence divergence in RMD products. Then, with six mutants of the MLH1-PMS2 heterodimer, we found several different patterns: three mutants showed defects in both functions, one mutant showed loss of RMD suppression but not polar divergence resolution, whereas another mutant showed the opposite, and finally one mutant showed loss of RMD suppression but had a complex effect on polar divergence resolution. These findings indicate that RMD suppression vs. polar resolution of sequence divergence are distinct functions of MLH1-PMS2. HIGHLIGHTS MLH1-PMS2 suppresses divergent repeat-mediated deletions (RMDs).MLH1-PMS2 promotes polar resolution of sequence divergence.Several mutants of MLH1-PMS2 affect both aspects of RMDs.Some MLH1-PMS2 mutants affect only one aspect of RMDs.Suppression of RMDs vs. polar resolution of divergence appear distinct.
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Vongprommool A, Mutirangura A, Pavasant P, Subbalekha K. Alu methylation level, morphological, and senescence changes during in vitro aging of human dental pulp stem cells. Tissue Cell 2024; 90:102512. [PMID: 39126831 DOI: 10.1016/j.tice.2024.102512] [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: 02/02/2024] [Revised: 07/23/2024] [Accepted: 07/31/2024] [Indexed: 08/12/2024]
Abstract
INTRODUCTION Human dental pulp stem cells (DPSCs) are pivotal in tissue engineering and cell-based therapies due to their significant differentiation potential and accessibility. A major challenge in in vitro cell expansion is their replicative senescence, which impacts their regeneration and differentiation capabilities. While genetic factors influence these processes, epigenetic regulations such as Alu methylation also play crucial roles. Changes in Alu methylation have been associated with human aging and age-related diseases, contributing to cellular dysfunction and stem cell senescence. Despite this, the implications of Alu methylation alterations in stem cell senescence remain underexplored. This study focuses on examining Alu methylation during the replicative senescence of DPSCs. METHODS The methylation status of Alu elements in serially passaged, long-term cultured human DPSCs was assessed using combined bisulfite restriction analysis. Morphological changes and indicators of replicative senescence were also evaluated. DPSCs were divided into three passage groups for analysis: early, middle, and late. Methylation levels across these groups were compared to identify trends correlating with passage number. RESULTS Significant morphological changes and markers of replicative senescence were observed predominantly in the late-passage DPSCs. These cells exhibited notably lower levels of Alu methylation and higher proportions of hypomethylated Alu CpG sites compared to those in early passages. CONCLUSION The study confirmed that alterations in Alu methylation are evident in the replicative senescence of human DPSCs, suggesting that epigenetic modifications could influence the aging process of these cells and potentially impact their therapeutic efficacy.
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Affiliation(s)
- Atitaya Vongprommool
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand (Oral and Maxillofacial Surgery Department, 1st Building, 34 Henri-Dunant Rd., Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Pattayapatana Building, Henri Dunant Road, Pathumwan, Bangkok 10330, Thailand
| | - Prasit Pavasant
- Mineralized Tissue Research Unit, Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, (Preclinic Building, 34 Henri-Dunant Rd., Wangmai, Pathumwan, Bangkok 10330, Thailand
| | - Keskanya Subbalekha
- Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Chulalongkorn University, Bangkok, Thailand (Oral and Maxillofacial Surgery Department, 1st Building, 34 Henri-Dunant Rd., Wangmai, Pathumwan, Bangkok 10330, Thailand.
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Cinar M, Martinez-Medina L, Puvvula P, Arakelyan A, Vardarajan B, Anthony N, Nagaraju G, Park D, Feng L, Sheff F, Mosunjac M, Saxe D, Flygare S, Alese O, Kaufman J, Lonial S, Sarmiento J, Lossos I, Vertino P, Lopez J, El-Rayes B, Bernal-Mizrachi L. Transposon DNA sequences facilitate the tissue-specific gene transfer of circulating tumor DNA between human cells. Nucleic Acids Res 2024; 52:7539-7555. [PMID: 38783375 PMCID: PMC11260451 DOI: 10.1093/nar/gkae427] [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: 05/06/2023] [Revised: 05/01/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024] Open
Abstract
The exchange of genes between cells is known to play an important physiological and pathological role in many organisms. We show that circulating tumor DNA (ctDNA) facilitates cell-specific gene transfer between human cancer cells and explain part of the mechanisms behind this phenomenon. As ctDNA migrates into the nucleus, genetic information is transferred. Cell targeting and ctDNA integration require ERVL, SINE or LINE DNA sequences. Chemically manufactured AluSp and MER11C sequences replicated multiple myeloma (MM) ctDNA cell targeting and integration. Additionally, we found that ctDNA may alter the treatment response of MM and pancreatic cancer models. This study shows that retrotransposon DNA sequences promote cancer gene transfer. However, because cell-free DNA has been detected in physiological and other pathological conditions, our findings have a broader impact than just cancer. Furthermore, the discovery that transposon DNA sequences mediate tissue-specific targeting will open up a new avenue for the delivery of genes and therapies.
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Affiliation(s)
- Munevver Cinar
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | | | | | - Arsen Arakelyan
- Bioinformatics group, Institute of Molecular Biology NAS RA, Yerevan, Armenia
| | | | - Neil Anthony
- Integrated Cellular Imaging Core, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Ganji P Nagaraju
- Division of hematology and oncology, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dongkyoo Park
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Lei Feng
- Kodikaz Therapeutic Solutions, Inc, New York, NY, USA
| | - Faith Sheff
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Marina Mosunjac
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Debra Saxe
- Pathology and Laboratory Medicine, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Steven Flygare
- Department of Computational Biology/ Genetics, The University of Utah, Salt Lake City, UT, USA
| | - Olatunji B Alese
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Jonathan L Kaufman
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Juan M Sarmiento
- Department of Surgery, Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Izidore S Lossos
- Department of Medicine, Division of Hematology-Oncology and Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Paula M Vertino
- Department of Biomedical Genetics and the Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY, USA
| | - Jose A Lopez
- Bloodworks Northwest Research Institute, Division of Hematology, University of Washington School of Medicine, Seattle, WA, USA
| | - Bassel El-Rayes
- Division of hematology and oncology, O’Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Leon Bernal-Mizrachi
- Department of Hematology and Medical Oncology, Winship Cancer Institute of Emory University, Atlanta, GA, USA
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4
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone P, Sanchez L, Kitzman J, Kidd J, Garcia-Perez J, Moran J. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. Nucleic Acids Res 2024; 52:7761-7779. [PMID: 38850156 PMCID: PMC11260458 DOI: 10.1093/nar/gkae448] [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: 02/16/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/10/2024] Open
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1) ORF2-encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 (Alu-permissive) strains, but not in HeLa-JVM or HeLa-H1 (Alu-nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA-derived SINEs and tRNA-derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR-Alu (SVA) element, and an L1 ORF1-containing mRNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu-permissive and Alu-nonpermissive HeLa strains, suggesting that 7SL- and tRNA-derived SINEs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1-containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu-permissive and Alu-nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu-nonpermissive HeLa strains.
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Affiliation(s)
- John B Moldovan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C Kopera
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Liu
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marta Garcia-Canadas
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | | | - Paola E Leone
- Genetics and Genomics Laboratory, SOLCA Hospital, Quito, Ecuador
| | - Laura Sanchez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - Jacob O Kitzman
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jose Luis Garcia-Perez
- Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada 18016, Spain
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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Morales-Vicente DA, Tahira AC, Woellner-Santos D, Amaral MS, Berzoti-Coelho MG, Verjovski-Almeida S. The Human Developing Cerebral Cortex Is Characterized by an Elevated De Novo Expression of Long Noncoding RNAs in Excitatory Neurons. Mol Biol Evol 2024; 41:msae123. [PMID: 38913688 PMCID: PMC11221658 DOI: 10.1093/molbev/msae123] [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: 11/23/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/26/2024] Open
Abstract
The outstanding human cognitive capacities are computed in the cerebral cortex, a mammalian-specific brain region and the place of massive biological innovation. Long noncoding RNAs have emerged as gene regulatory elements with higher evolutionary turnover than mRNAs. The many long noncoding RNAs identified in neural tissues make them candidates for molecular sources of cerebral cortex evolution and disease. Here, we characterized the genomic and cellular shifts that occurred during the evolution of the long noncoding RNA repertoire expressed in the developing cerebral cortex and explored putative roles for these long noncoding RNAs in the evolution of the human brain. Using transcriptomics and comparative genomics, we comprehensively annotated the cortical transcriptomes of humans, rhesus macaques, mice, and chickens and classified human cortical long noncoding RNAs into evolutionary groups as a function of their predicted minimal ages. Long noncoding RNA evolutionary groups showed differences in expression levels, splicing efficiencies, transposable element contents, genomic distributions, and transcription factor binding to their promoters. Furthermore, older long noncoding RNAs showed preferential expression in germinative zones, outer radial glial cells, and cortical inhibitory (GABAergic) neurons. In comparison, younger long noncoding RNAs showed preferential expression in cortical excitatory (glutamatergic) neurons, were enriched in primate and human-specific gene co-expression modules, and were dysregulated in neurodevelopmental disorders. These results suggest different evolutionary routes for older and younger cortical long noncoding RNAs, highlighting old long noncoding RNAs as a possible source of molecular evolution of conserved developmental programs; conversely, we propose that the de novo expression of primate- and human-specific young long noncoding RNAs is a putative source of molecular evolution and dysfunction of cortical excitatory neurons, warranting further investigation.
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Affiliation(s)
- David A Morales-Vicente
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Daisy Woellner-Santos
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Murilo S Amaral
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
| | - Maria G Berzoti-Coelho
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Laboratório de Ciclo Celular, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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6
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [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: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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7
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Moldovan JB, Kopera HC, Liu Y, Garcia-Canadas M, Catalina P, Leone PE, Sanchez L, Kitzman JO, Kidd JM, Garcia-Perez JL, Moran JV. Variable patterns of retrotransposition in different HeLa strains provide mechanistic insights into SINE RNA mobilization processes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592410. [PMID: 38746229 PMCID: PMC11092746 DOI: 10.1101/2024.05.03.592410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Alu elements are non-autonomous Short INterspersed Elements (SINEs) derived from the 7SL RNA gene that are present at over one million copies in human genomic DNA. Alu mobilizes by a mechanism known as retrotransposition, which requires the Long INterspersed Element-1 (LINE-1 or L1) ORF2 -encoded protein (ORF2p). Here, we demonstrate that HeLa strains differ in their capacity to support Alu retrotransposition. Human Alu elements retrotranspose efficiently in HeLa-HA and HeLa-CCL2 ( Alu -permissive) strains, but not in HeLa-JVM or HeLa-H1 ( Alu -nonpermissive) strains. A similar pattern of retrotransposition was observed for other 7SL RNA -derived SINEs and tRNA -derived SINEs. In contrast, mammalian LINE-1s, a zebrafish LINE, a human SINE-VNTR - Alu ( SVA ) element, and an L1 ORF1 -containing messenger RNA can retrotranspose in all four HeLa strains. Using an in vitro reverse transcriptase-based assay, we show that Alu RNAs associate with ORF2p and are converted into cDNAs in both Alu -permissive and Alu -nonpermissive HeLa strains, suggesting that 7SL - and tRNA -derived SINE RNAs use strategies to 'hijack' L1 ORF2p that are distinct from those used by SVA elements and ORF1 -containing mRNAs. These data further suggest ORF2p associates with the Alu RNA poly(A) tract in both Alu -permissive and Alu -nonpermissive HeLa strains, but that Alu retrotransposition is blocked after this critical step in Alu -nonpermissive HeLa strains.
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8
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Le Breton A, Bettencourt MP, Gendrel AV. Navigating the brain and aging: exploring the impact of transposable elements from health to disease. Front Cell Dev Biol 2024; 12:1357576. [PMID: 38476259 PMCID: PMC10927736 DOI: 10.3389/fcell.2024.1357576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/08/2024] [Indexed: 03/14/2024] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that constitute on average 45% of mammalian genomes. Their presence and activity in genomes represent a major source of genetic variability. While this is an important driver of genome evolution, TEs can also have deleterious effects on their hosts. A growing number of studies have focused on the role of TEs in the brain, both in physiological and pathological contexts. In the brain, their activity is believed to be important for neuronal plasticity. In neurological and age-related disorders, aberrant activity of TEs may contribute to disease etiology, although this remains unclear. After providing a comprehensive overview of transposable elements and their interactions with the host, this review summarizes the current understanding of TE activity within the brain, during the aging process, and in the context of neurological and age-related conditions.
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Affiliation(s)
| | | | - Anne-Valerie Gendrel
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
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9
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Matsushima W, Planet E, Trono D. Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants. CELL GENOMICS 2024; 4:100497. [PMID: 38295789 PMCID: PMC10879028 DOI: 10.1016/j.xgen.2024.100497] [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: 04/26/2023] [Revised: 08/09/2023] [Accepted: 01/06/2024] [Indexed: 02/17/2024]
Abstract
Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual species, which limits its scope to relatively intact TE sequences. Here, we report a novel approach to uncover previously unannotated degenerate TEs (degTEs) by probing multiple ancestral genomes reconstructed from hundreds of species. We applied this method to the human genome and achieved a 10.8% increase in coverage over the most recent annotation. Further, we discovered that degTEs contribute to various cis-regulatory elements and transcription factor binding sites, including those of a known TE-controlling family, the KRAB zinc-finger proteins. We also report unannotated chimeric transcripts between degTEs and human genes expressed in embryos. This study provides a novel methodology and a freely available resource that will facilitate the investigation of TE co-option events on a full scale.
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Affiliation(s)
- Wayo Matsushima
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
| | - Evarist Planet
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Didier Trono
- School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Fukuda K. The role of transposable elements in human evolution and methods for their functional analysis: current status and future perspectives. Genes Genet Syst 2024; 98:289-304. [PMID: 37866889 DOI: 10.1266/ggs.23-00140] [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] [Indexed: 10/24/2023] Open
Abstract
Transposable elements (TEs) are mobile DNA sequences that can insert themselves into various locations within the genome, causing mutations that may provide advantages or disadvantages to individuals and species. The insertion of TEs can result in genetic variation that may affect a wide range of human traits including genetic disorders. Understanding the role of TEs in human biology is crucial for both evolutionary and medical research. This review discusses the involvement of TEs in human traits and disease susceptibility, as well as methods for functional analysis of TEs.
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Affiliation(s)
- Kei Fukuda
- Integrative Genomics Unit, The University of Melbourne
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11
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Wijngaard R, Demidov G, O'Gorman L, Corominas-Galbany J, Yaldiz B, Steyaert W, de Boer E, Vissers LELM, Kamsteeg EJ, Pfundt R, Swinkels H, den Ouden A, Te Paske IBAW, de Voer RM, Faivre L, Denommé-Pichon AS, Duffourd Y, Vitobello A, Chevarin M, Straub V, Töpf A, van der Kooi AJ, Magrinelli F, Rocca C, Hanna MG, Vandrovcova J, Ossowski S, Laurie S, Gilissen C. Mobile element insertions in rare diseases: a comparative benchmark and reanalysis of 60,000 exome samples. Eur J Hum Genet 2024; 32:200-208. [PMID: 37853102 PMCID: PMC10853235 DOI: 10.1038/s41431-023-01478-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 08/29/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
Mobile element insertions (MEIs) are a known cause of genetic disease but have been underexplored due to technical limitations of genetic testing methods. Various bioinformatic tools have been developed to identify MEIs in Next Generation Sequencing data. However, most tools have been developed specifically for genome sequencing (GS) data rather than exome sequencing (ES) data, which remains more widely used for routine diagnostic testing. In this study, we benchmarked six MEI detection tools (ERVcaller, MELT, Mobster, SCRAMble, TEMP2 and xTea) on ES data and on GS data from publicly available genomic samples (HG002, NA12878). For all the tools we evaluated sensitivity and precision of different filtering strategies. Results show that there were substantial differences in tool performance between ES and GS data. MELT performed best with ES data and its combination with SCRAMble increased substantially the detection rate of MEIs. By applying both tools to 10,890 ES samples from Solve-RD and 52,624 samples from Radboudumc we were able to diagnose 10 patients who had remained undiagnosed by conventional ES analysis until now. Our study shows that MELT and SCRAMble can be used reliably to identify clinically relevant MEIs in ES data. This may lead to an additional diagnosis for 1 in 3000 to 4000 patients in routine clinical ES.
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Affiliation(s)
- Robin Wijngaard
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - German Demidov
- Universitätsklinikum Tübingen - Institut für Medizinische Genetik und angewandte Genomik, Tübingen, Germany
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Burcu Yaldiz
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Wouter Steyaert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Hilde Swinkels
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Amber den Ouden
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Iris B A W Te Paske
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Richarda M de Voer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Laurence Faivre
- Centre de Référence Maladies Rares "Anomalies du développement et syndromes malformatifs", Centre de Génétique, FHU-TRANSLAD et Institut GIMI, CHU Dijon Bourgogne, Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231-Inserm, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
- Laboratoire de Génétique chromosomique et moléculaire, UF6254 Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Yannis Duffourd
- UMR1231-Inserm, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
- Laboratoire de Génétique chromosomique et moléculaire, UF6254 Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Antonio Vitobello
- UMR1231-Inserm, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
- Laboratoire de Génétique chromosomique et moléculaire, UF6254 Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Martin Chevarin
- UMR1231-Inserm, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, Dijon, France
- Laboratoire de Génétique chromosomique et moléculaire, UF6254 Innovation en diagnostic génomique des maladies rares, Centre Hospitalier Universitaire de Dijon, Dijon, France
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Anneke J van der Kooi
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam Neuroscience, Amsterdam, The Netherlands
| | - Francesca Magrinelli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Clarissa Rocca
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- Clinical Pharmacology, William Harvey Research Institute, School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Jana Vandrovcova
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Stephan Ossowski
- Universitätsklinikum Tübingen - Institut für Medizinische Genetik und angewandte Genomik, Tübingen, Germany
| | - Steven Laurie
- Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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12
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Mandal AK. Recent insights into crosstalk between genetic parasites and their host genome. Brief Funct Genomics 2024; 23:15-23. [PMID: 36307128 PMCID: PMC10799329 DOI: 10.1093/bfgp/elac032] [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: 08/04/2022] [Revised: 09/14/2022] [Accepted: 09/21/2022] [Indexed: 01/21/2024] Open
Abstract
The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.
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Affiliation(s)
- Amit K Mandal
- Corresponding author: A.K. Mandal, Nuffield Department of Surgical Sciences (NDS), University of Oxford, Old Road Campus Research building (ORCRB), Oxford OX3 7DQ, UK. Tel: +44 (0)1865 617123; Fax: +44 (0)1865 768876; E-mail:
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13
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Ow MC, Hall SE. Inheritance of Stress Responses via Small Non-Coding RNAs in Invertebrates and Mammals. EPIGENOMES 2023; 8:1. [PMID: 38534792 DOI: 10.3390/epigenomes8010001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 03/28/2024] Open
Abstract
While reports on the generational inheritance of a parental response to stress have been widely reported in animals, the molecular mechanisms behind this phenomenon have only recently emerged. The booming interest in epigenetic inheritance has been facilitated in part by the discovery that small non-coding RNAs are one of its principal conduits. Discovered 30 years ago in the Caenorhabditis elegans nematode, these small molecules have since cemented their critical roles in regulating virtually all aspects of eukaryotic development. Here, we provide an overview on the current understanding of epigenetic inheritance in animals, including mice and C. elegans, as it pertains to stresses such as temperature, nutritional, and pathogenic encounters. We focus on C. elegans to address the mechanistic complexity of how small RNAs target their cohort mRNAs to effect gene expression and how they govern the propagation or termination of generational perdurance in epigenetic inheritance. Presently, while a great amount has been learned regarding the heritability of gene expression states, many more questions remain unanswered and warrant further investigation.
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Affiliation(s)
- Maria C Ow
- Department of Biology, Syracuse University, Syracuse, NY 13210, USA
| | - Sarah E Hall
- Department of Biology and Program in Neuroscience, Syracuse University, Syracuse, NY 13210, USA
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14
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Wang Y. Algorithms for the Uniqueness of the Longest Common Subsequence. J Bioinform Comput Biol 2023; 21:2350027. [PMID: 38212873 DOI: 10.1142/s0219720023500270] [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] [Indexed: 01/13/2024]
Abstract
Given several number sequences, determining the longest common subsequence is a classical problem in computer science. This problem has applications in bioinformatics, especially determining transposable genes. Nevertheless, related works only consider how to find one longest common subsequence. In this paper, we consider how to determine the uniqueness of the longest common subsequence. If there are multiple longest common subsequences, we also determine which number appears in all/some/none of the longest common subsequences. We focus on four scenarios: (1) linear sequences without duplicated numbers; (2) circular sequences without duplicated numbers; (3) linear sequences with duplicated numbers; (4) circular sequences with duplicated numbers. We develop corresponding algorithms and apply them to gene sequencing data.
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Affiliation(s)
- Yue Wang
- Department of Computational Medicine, University of California, Los Angeles, California, USA
- Irving Institute for Cancer Dynamics and Department of Statistics, Columbia University, New York, New York, USA
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15
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Gao D, Fox-Fogle E. Identification of transcriptionally active transposons in Barley. BMC Genom Data 2023; 24:64. [PMID: 37925398 PMCID: PMC10625261 DOI: 10.1186/s12863-023-01170-1] [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: 08/07/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND The genomes of many major crops including barley (Hordeum vulgare) consist of numerous transposons. Despite their important roles in crop genome evolution and morphological variations, most of these elements are silent or truncated and unable to be mobile in host genomes. Thus far, only a very limited number of active transposons were identified in plants. RESULTS We analyzed the barley full-length cDNA (FLcDNA) sequences and detected 71 unique FLcDNAs exhibiting significant sequence similarity to the extant transposase proteins. These FLcDNAs were then used to search against the genome of a malting barley cultivar 'Morex', seven new intact transposons were identified. Sequence alignments indicated that six intact transposons contained the entire FLcDNAs whereas another one served as 3' untranslated region (3' UTR) of a barley gene. Our reverse transcription-PCR (RT-PCR) experiment further confirmed the expression of these six transposons and revealed their differential expression. We conducted genome-wide transposon comparisons and detected polymorphisms of three transposon families between the genomes of 'Morex' and other three genotypes including the wild barley (Hordeum spontaneum, B1K-04-12) and two cultivated barley varieties, 'Golden Promise' and 'Lasa Goumang'. Lastly, we screened the transcripts of all annotated barley genes and found that some transposons may serve as the coding regions (CDSs) or UTRs of barley genes. CONCLUSION We identified six newly expressed transposons in the barley genome and revealed the recent mobility of three transposon families. Our efforts provide a valuable resource for understanding the effects of transposons on barley genome evolution and for developing novel molecular tools for barley genetic improvement and other research.
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Affiliation(s)
- Dongying Gao
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA.
| | - Emma Fox-Fogle
- Small Grains and Potato Germplasm Research Unit, USDA-ARS, Aberdeen, ID, 83210, USA
- National Agricultural Statistical Service, USDA, Olympia, WA, 98501, USA
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16
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Devine SE. Emerging Opportunities to Study Mobile Element Insertions and Their Source Elements in an Expanding Universe of Sequenced Human Genomes. Genes (Basel) 2023; 14:1923. [PMID: 37895272 PMCID: PMC10606232 DOI: 10.3390/genes14101923] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 09/29/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Three mobile element classes, namely Alu, LINE-1 (L1), and SVA elements, remain actively mobile in human genomes and continue to produce new mobile element insertions (MEIs). Historically, MEIs have been discovered and studied using several methods, including: (1) Southern blots, (2) PCR (including PCR display), and (3) the detection of MEI copies from young subfamilies. We are now entering a new phase of MEI discovery where these methods are being replaced by whole genome sequencing and bioinformatics analysis to discover novel MEIs. We expect that the universe of sequenced human genomes will continue to expand rapidly over the next several years, both with short-read and long-read technologies. These resources will provide unprecedented opportunities to discover MEIs and study their impact on human traits and diseases. They also will allow the MEI community to discover and study the source elements that produce these new MEIs, which will facilitate our ability to study source element regulation in various tissue contexts and disease states. This, in turn, will allow us to better understand MEI mutagenesis in humans and the impact of this mutagenesis on human biology.
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Affiliation(s)
- Scott E Devine
- Institute for Genome Sciences, Department of Medicine, and Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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17
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Frost B. Alzheimer's disease and related tauopathies: disorders of disrupted neuronal identity. Trends Neurosci 2023; 46:797-813. [PMID: 37591720 PMCID: PMC10528597 DOI: 10.1016/j.tins.2023.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/20/2023] [Accepted: 07/24/2023] [Indexed: 08/19/2023]
Abstract
Postmitotic neurons require persistently active controls to maintain terminal differentiation. Unlike dividing cells, aberrant cell cycle activation in mature neurons causes apoptosis rather than transformation. In Alzheimer's disease (AD) and related tauopathies, evidence suggests that pathogenic forms of tau drive neurodegeneration via neuronal cell cycle re-entry. Multiple interconnected mechanisms linking tau to cell cycle activation have been identified, including, but not limited to, tau-induced overstabilization of the actin cytoskeleton, consequent changes to nuclear architecture, and disruption of heterochromatin-mediated gene silencing. Cancer- and development-associated pathways are upregulated in human and cellular models of tauopathy, and many tau-induced cellular phenotypes are also present in various cancers and progenitor/stem cells. In this review, I delve into mechanistic parallels between tauopathies, cancer, and development, and highlight the role of tau in cancer and in the developing brain. Based on these studies, I put forth a model by which pathogenic forms of tau disrupt the program that maintains terminal neuronal differentiation, driving cell cycle re-entry and consequent neuronal death. This framework presents tauopathies as conditions involving the profound toxic disruption of neuronal identity.
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Affiliation(s)
- Bess Frost
- Sam & Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, TX, USA; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, TX, USA; Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA.
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18
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Rybacki K, Xia M, Ahsan MU, Xing J, Wang K. Assessing the Expression of Long INterspersed Elements (LINEs) via Long-Read Sequencing in Diverse Human Tissues and Cell Lines. Genes (Basel) 2023; 14:1893. [PMID: 37895242 PMCID: PMC10606529 DOI: 10.3390/genes14101893] [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: 09/04/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Transposable elements, such as Long INterspersed Elements (LINEs), are DNA sequences that can replicate within genomes. LINEs replicate using an RNA intermediate followed by reverse transcription and are typically a few kilobases in length. LINE activity creates genomic structural variants in human populations and leads to somatic alterations in cancer genomes. Long-read RNA sequencing technologies, including Oxford Nanopore and PacBio, can directly sequence relatively long transcripts, thus providing the opportunity to examine full-length LINE transcripts. This study focuses on the development of a new bioinformatics pipeline for the identification and quantification of active, full-length LINE transcripts in diverse human tissues and cell lines. In our pipeline, we utilized RepeatMasker to identify LINE-1 (L1) transcripts from long-read transcriptome data and incorporated several criteria, such as transcript start position, divergence, and length, to remove likely false positives. Comparisons between cancerous and normal cell lines, as well as human tissue samples, revealed elevated expression levels of young LINEs in cancer, particularly at intact L1 loci. By employing bioinformatics methodologies on long-read transcriptome data, this study demonstrates the landscape of L1 expression in tissues and cell lines.
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Affiliation(s)
- Karleena Rybacki
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Mingyi Xia
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
| | - Jinchuan Xing
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
- Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Kai Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; (K.R.); (M.X.)
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA;
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19
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Fu J, Qin T, Li C, Zhu J, Ding Y, Zhou M, Yang Q, Liu X, Zhou J, Chen F. Research progress of LINE-1 in the diagnosis, prognosis, and treatment of gynecologic tumors. Front Oncol 2023; 13:1201568. [PMID: 37546391 PMCID: PMC10399582 DOI: 10.3389/fonc.2023.1201568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/19/2023] [Indexed: 08/08/2023] Open
Abstract
The retrotransposon known as long interspersed nuclear element-1 (LINE-1), which is currently the sole autonomously mobile transposon in the human genome, can result in insertional mutations, chromosomal rearrangements, and genomic instability. In recent years, numerous studies have shown that LINE-1 is involved in the development of various diseases and also plays an important role in the immune regulation of the organism. The expression of LINE-1 in gynecologic tumors suggests that it is expected to be an independent indicator for early diagnosis and prognosis, and also, as a therapeutic target, LINE-1 is closely associated with gynecologic tumor prognosis. This article discusses the function of LINE-1 in the diagnosis, treatment, and prognosis of ovarian, cervical, and endometrial malignancies, as well as other gynecologic malignancies. It offers fresh perspectives on the early detection of tumors and the creation of novel anti-tumor medications.
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Affiliation(s)
- Jiaojiao Fu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Tiansheng Qin
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
- The First Clinical Medical School, Lanzhou University, Lanzhou, Gansu, China
- National Health Commission (NHC) Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Chaoming Li
- The First People’s Hospital of Longnan, Longnan City Hospital, Longnan, Gansu, China
| | - Jiaojiao Zhu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Yaoyao Ding
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Meiying Zhou
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Qing Yang
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Xiaofeng Liu
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Juanhong Zhou
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Fan Chen
- The First Clinical Medical College of Gansu University of Chinese Medicine, Gansu Provincial Hospital, Lanzhou, China
- Department of Obstetrics and Gynecology, Gansu Provincial Hospital, Lanzhou, Gansu, China
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20
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Veschetti L, Treccani M, De Tomi E, Malerba G. Genomic Instability Evolutionary Footprints on Human Health: Driving Forces or Side Effects? Int J Mol Sci 2023; 24:11437. [PMID: 37511197 PMCID: PMC10380557 DOI: 10.3390/ijms241411437] [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: 05/11/2023] [Revised: 06/30/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
In this work, we propose a comprehensive perspective on genomic instability comprising not only the accumulation of mutations but also telomeric shortening, epigenetic alterations and other mechanisms that could contribute to genomic information conservation or corruption. First, we present mechanisms playing a role in genomic instability across the kingdoms of life. Then, we explore the impact of genomic instability on the human being across its evolutionary history and on present-day human health, with a particular focus on aging and complex disorders. Finally, we discuss the role of non-coding RNAs, highlighting future approaches for a better living and an expanded healthy lifespan.
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Affiliation(s)
| | | | | | - Giovanni Malerba
- GM Lab, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, 37134 Verona, Italy; (L.V.); (M.T.); (E.D.T.)
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21
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Laufer VA, Glover TW, Wilson TE. Applications of advanced technologies for detecting genomic structural variation. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108475. [PMID: 37931775 PMCID: PMC10792551 DOI: 10.1016/j.mrrev.2023.108475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/07/2023] [Accepted: 11/02/2023] [Indexed: 11/08/2023]
Abstract
Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that "telomere-to-telomere" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.
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Affiliation(s)
- Vincent A Laufer
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas W Glover
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
| | - Thomas E Wilson
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
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22
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Singh M, Kondrashkina AM, Widmann TJ, Cortes JL, Bansal V, Wang J, Römer C, Garcia-Canadas M, Garcia-Perez JL, Hurst LD, Izsvák Z. A new human embryonic cell type associated with activity of young transposable elements allows definition of the inner cell mass. PLoS Biol 2023; 21:e3002162. [PMID: 37339119 DOI: 10.1371/journal.pbio.3002162] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 05/12/2023] [Indexed: 06/22/2023] Open
Abstract
There remains much that we do not understand about the earliest stages of human development. On a gross level, there is evidence for apoptosis, but the nature of the affected cell types is unknown. Perhaps most importantly, the inner cell mass (ICM), from which the foetus is derived and hence of interest in reproductive health and regenerative medicine, has proven hard to define. Here, we provide a multi-method analysis of the early human embryo to resolve these issues. Single-cell analysis (on multiple independent datasets), supported by embryo visualisation, uncovers a common previously uncharacterised class of cells lacking commitment markers that segregates after embryonic gene activation (EGA) and shortly after undergo apoptosis. The discovery of this cell type allows us to clearly define their viable ontogenetic sisters, these being the cells of the ICM. While ICM is characterised by the activity of an Old non-transposing endogenous retrovirus (HERVH) that acts to suppress Young transposable elements, the new cell type, by contrast, expresses transpositionally competent Young elements and DNA-damage response genes. As the Young elements are RetroElements and the cells are excluded from the developmental process, we dub these REject cells. With these and ICM being characterised by differential mobile element activities, the human embryo may be a "selection arena" in which one group of cells selectively die, while other less damaged cells persist.
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Affiliation(s)
- Manvendra Singh
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
- Max Planck Institute of Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | | | - Thomas J Widmann
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Cortes
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Vikas Bansal
- German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Jichang Wang
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Christine Römer
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
| | - Marta Garcia-Canadas
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
| | - Jose L Garcia-Perez
- GENYO, Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, PTS Granada, Granada, Spain
- Institute of Genetics and Molecular Medicine (IGMM), University of Edinburgh, Crewe Road, Edinburgh, United Kingdom
| | - Laurence D Hurst
- The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, United Kingdom
| | - Zsuzsanna Izsvák
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Society, Berlin, Germany
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23
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Mosaddeghi P, Farahmandnejad M, Zarshenas MM. The role of transposable elements in aging and cancer. Biogerontology 2023:10.1007/s10522-023-10028-z. [PMID: 37017895 DOI: 10.1007/s10522-023-10028-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023]
Abstract
Transposable elements (TEs) constitute a large portion of the human genome. Various mechanisms at the transcription and post-transcription levels developed to suppress TE activity in healthy conditions. However, a growing body of evidence suggests that TE dysregulation is involved in various human diseases, including age-related diseases and cancer. In this review, we explained how sensing TEs by the immune system could induce innate immune responses, chronic inflammation, and following age-related diseases. We also noted that inflammageing and exogenous carcinogens could trigger the upregulation of TEs in precancerous cells. Increased inflammation could enhance epigenetic plasticity and upregulation of early developmental TEs, which rewires the transcriptional networks and gift the survival advantage to the precancerous cells. In addition, upregulated TEs could induce genome instability, activation of oncogenes, or inhibition of tumor suppressors and consequent cancer initiation and progression. So, we suggest that TEs could be considered therapeutic targets in aging and cancer.
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Affiliation(s)
- Pouria Mosaddeghi
- Medicinal Plants Processing Research Center, School of Pharmacy, Shiraz University of Medical Science, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mitra Farahmandnejad
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
- Quality Control of Drug Products Department, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad M Zarshenas
- Department of Phytopharmaceuticals (Traditional Pharmacy), School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. J Autism Dev Disord 2023; 53:1091-1106. [PMID: 35759154 DOI: 10.1007/s10803-022-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.
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25
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Wang H, Wang LS, Schellenberg G, Lee WP. The role of structural variations in Alzheimer's disease and other neurodegenerative diseases. Front Aging Neurosci 2023; 14:1073905. [PMID: 36846102 PMCID: PMC9944073 DOI: 10.3389/fnagi.2022.1073905] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/31/2022] [Indexed: 02/10/2023] Open
Abstract
Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can be a major contributor to the missing heritability of AD; while SV in AD remains largely unexplored as the accurate detection of SVs from the widely used array-based and short-read technology are still far from perfect. Here, we briefly summarized the strengths and weaknesses of available SV detection methods. We reviewed the current landscape of SV analysis in AD and SVs that have been found associated with AD. Particularly, the importance of currently less explored SVs, including insertions, inversions, short tandem repeats, and transposable elements in neurodegenerative diseases were highlighted.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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26
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Gruhn WH, Tang WW, Dietmann S, Alves-Lopes JP, Penfold CA, Wong FC, Ramakrishna NB, Surani MA. Epigenetic resetting in the human germ line entails histone modification remodeling. SCIENCE ADVANCES 2023; 9:eade1257. [PMID: 36652508 PMCID: PMC9848478 DOI: 10.1126/sciadv.ade1257] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human primordial germ cells (hPGCs) to reveal mechanisms preventing the widespread derepression of genes and transposable elements (TEs). Along with the loss of DNA methylation, we show that hPGCs exhibit a profound reduction of repressive histone modifications resulting in diminished heterochromatic signatures at most genes and TEs and the acquisition of a neutral or paused epigenetic state without transcriptional activation. Efficient maintenance of a heterochromatic state is limited to a subset of genomic loci, such as evolutionarily young TEs and some developmental genes, which require H3K9me3 and H3K27me3, respectively, for efficient transcriptional repression. Accordingly, transcriptional repression in hPGCs presents an exemplary balanced system relying on local maintenance of heterochromatic features and a lack of inductive cues.
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Affiliation(s)
- Wolfram H. Gruhn
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Walfred W.C. Tang
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Sabine Dietmann
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO, USA
| | - João P. Alves-Lopes
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- NORDFERTIL Research Lab Stockholm, Childhood Cancer Research Unit, J9:30, Department of Women’s and Children’s Health, Karolinska Institutet and Karolinska University Hospital, Visionsgatan 4, 17164, Solna, Stockholm, Sweden
| | - Christopher A. Penfold
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Frederick C. K. Wong
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
| | - Navin B. Ramakrishna
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Genome Institute of Singapore, A*STAR, Biopolis, Singapore 138672, Singapore
| | - M. Azim Surani
- Wellcome Trust/Cancer Research UK Gurdon Institute, Henry Wellcome Building of Cancer and Developmental Biology, Cambridge CB2 1QN, UK
- Physiology, Development and Neuroscience Department, University of Cambridge, Cambridge CB2 3EL, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge Biomedical Campus, Cambridge CB2 0AW, UK
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27
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Lesack K, Mariene GM, Andersen EC, Wasmuth JD. Different structural variant prediction tools yield considerably different results in Caenorhabditis elegans. PLoS One 2022; 17:e0278424. [PMID: 36584177 PMCID: PMC9803319 DOI: 10.1371/journal.pone.0278424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 11/15/2022] [Indexed: 01/01/2023] Open
Abstract
The accurate characterization of structural variation is crucial for our understanding of how large chromosomal alterations affect phenotypic differences and contribute to genome evolution. Whole-genome sequencing is a popular approach for identifying structural variants, but the accuracy of popular tools remains unclear due to the limitations of existing benchmarks. Moreover, the performance of these tools for predicting variants in non-human genomes is less certain, as most tools were developed and benchmarked using data from the human genome. To evaluate the use of long-read data for the validation of short-read structural variant calls, the agreement between predictions from a short-read ensemble learning method and long-read tools were compared using real and simulated data from Caenorhabditis elegans. The results obtained from simulated data indicate that the best performing tool is contingent on the type and size of the variant, as well as the sequencing depth of coverage. These results also highlight the need for reference datasets generated from real data that can be used as 'ground truth' in benchmarks.
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Affiliation(s)
- Kyle Lesack
- Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Alberta, Canada
| | - Grace M. Mariene
- Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Alberta, Canada
| | - Erik C. Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, United States of America
| | - James D. Wasmuth
- Faculty of Veterinary Medicine, University of Calgary, Alberta, Canada
- Host-Parasite Interactions Research Training Network, University of Calgary, Alberta, Canada
- * E-mail:
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28
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Remnants of SIRE1 retrotransposons in human genome? J Genet 2022. [DOI: 10.1007/s12041-022-01398-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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29
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Almeida da Paz M, Taher L. T3E: a tool for characterising the epigenetic profile of transposable elements using ChIP-seq data. Mob DNA 2022; 13:29. [PMID: 36451223 PMCID: PMC9710123 DOI: 10.1186/s13100-022-00285-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/14/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Despite the advent of Chromatin Immunoprecipitation Sequencing (ChIP-seq) having revolutionised our understanding of the mammalian genome's regulatory landscape, many challenges remain. In particular, because of their repetitive nature, the sequencing reads derived from transposable elements (TEs) pose a real bioinformatics challenge, to the point that standard analysis pipelines typically ignore reads whose genomic origin cannot be unambiguously ascertained. RESULTS We show that discarding ambiguously mapping reads may lead to a systematic underestimation of the number of reads associated with young TE families/subfamilies. We also provide evidence suggesting that the strategy of randomly permuting the location of the read mappings (or the TEs) that is often used to compute the background for enrichment calculations at TE families/subfamilies can result in both false positive and negative enrichments. To address these problems, we present the Transposable Element Enrichment Estimator (T3E), a tool that makes use of ChIP-seq data to characterise the epigenetic profile of associated TE families/subfamilies. T3E weights the number of read mappings assigned to the individual TE copies of a family/subfamily by the overall number of genomic loci to which the corresponding reads map, and this is done at the single nucleotide level. In addition, T3E computes ChIP-seq enrichment relative to a background estimated based on the distribution of the read mappings in the input control DNA. We demonstrated the capabilities of T3E on 23 different ChIP-seq libraries. T3E identified enrichments that were consistent with previous studies. Furthermore, T3E detected context-specific enrichments that are likely to pinpoint unexplored TE families/subfamilies with individual TE copies that have been frequently exapted as cis-regulatory elements during the evolution of mammalian regulatory networks. CONCLUSIONS T3E is a novel open-source computational tool (available for use at: https://github.com/michelleapaz/T3E ) that overcomes some of the pitfalls associated with the analysis of ChIP-seq data arising from the repetitive mammalian genome and provides a framework to shed light on the epigenetics of entire TE families/subfamilies.
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Affiliation(s)
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria.
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30
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Savage AL, Iacoangeli A, Schumann GG, Rubio-Roldan A, Garcia-Perez JL, Al Khleifat A, Koks S, Bubb VJ, Al-Chalabi A, Quinn JP. Characterisation of retrotransposon insertion polymorphisms in whole genome sequencing data from individuals with amyotrophic lateral sclerosis. Gene 2022; 843:146799. [PMID: 35963498 DOI: 10.1016/j.gene.2022.146799] [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: 03/24/2022] [Revised: 07/15/2022] [Accepted: 08/05/2022] [Indexed: 11/15/2022]
Abstract
The genetics of an individual is a crucial factor in understanding the risk of developing the neurodegenerative disease amyotrophic lateral sclerosis (ALS). There is still a large proportion of the heritability of ALS, particularly in sporadic cases, to be understood. Among others, active transposable elements drive inter-individual variability, and in humans long interspersed element 1 (LINE1, L1), Alu and SINE-VNTR-Alu (SVA) retrotransposons are a source of polymorphic insertions in the population. We undertook a pilot study to characterise the landscape of non-reference retrotransposon insertion polymorphisms (non-ref RIPs) in 15 control and 15 ALS individuals' whole genomes from Project MinE, an international project to identify potential genetic causes of ALS. The combination of two bioinformatics tools (mobile element locator tool (MELT) and TEBreak) identified on average 1250 Alu, 232 L1 and 77 SVA non-ref RIPs per genome across the 30 analysed. Further PCR validation of individual polymorphic retrotransposon insertions showed a similar level of accuracy for MELT and TEBreak. Our preliminary study did not identify a specific RIP or a significant difference in the total number of non-ref RIPs in ALS compared to control genomes. The use of multiple bioinformatic tools improved the accuracy of non-ref RIP detection and our study highlights the potential importance of studying these elements further in ALS.
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Affiliation(s)
- Abigail L Savage
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Alfredo Iacoangeli
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Biostatistics and Health Informatics, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 8AF, UK
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen 63225, Germany
| | - Alejandro Rubio-Roldan
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain
| | - Jose L Garcia-Perez
- Department of Genomic Medicine and Department of Oncology, GENYO, Centre for Genomics & Oncology, PTS Granada, 18007, Spain; MRC-HGU Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ahmad Al Khleifat
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, Western Australia 6009, Australia; Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, Western Australia 6150, Australia
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK
| | - Ammar Al-Chalabi
- Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London SE5 9RT, UK; Department of Neurology, King's College Hospital, London SE5 9RS, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, UK.
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31
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Lee H, Min JW, Mun S, Han K. Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101583. [PMID: 36295018 PMCID: PMC9605557 DOI: 10.3390/life12101583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/03/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are classified into two classes according to their mobilization mechanism. Compared to DNA transposons that move by the "cut and paste" mechanism, retrotransposons mobilize via the "copy and paste" method. They have been an essential research topic because some of the active elements, such as Long interspersed element 1 (LINE-1), Alu, and SVA elements, have contributed to the genetic diversity of primates beyond humans. In addition, they can cause genetic disorders by altering gene expression and generating structural variations (SVs). The development and rapid technological advances in next-generation sequencing (NGS) have led to new perspectives on detecting retrotransposon-mediated SVs, especially insertions. Moreover, various computational methods have been developed based on NGS data to precisely detect the insertions and deletions in the human genome. Therefore, this review discusses details about the recently studied and utilized NGS technologies and the effective computational approaches for discovering retrotransposons through it. The final part covers a diverse range of computational methods for detecting retrotransposon insertions with human NGS data. This review will give researchers insights into understanding the TEs and how to investigate them and find connections with research interests.
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Affiliation(s)
- Haeun Lee
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
| | - Jun Won Min
- Department of Surgery, Dankook University College of Medicine, Cheonan 31116, Korea
| | - Seyoung Mun
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- Correspondence: (S.M.); (K.H.)
| | - Kyudong Han
- Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea
- Department of Microbiology, College of Science & Technology, Dankook University, Cheonan 31116, Korea
- Center for Bio Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
- HuNbiome Co., Ltd., R&D Center, Seoul 08507, Korea
- Correspondence: (S.M.); (K.H.)
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Tong X, Han MJ, Lu K, Tai S, Liang S, Liu Y, Hu H, Shen J, Long A, Zhan C, Ding X, Liu S, Gao Q, Zhang B, Zhou L, Tan D, Yuan Y, Guo N, Li YH, Wu Z, Liu L, Li C, Lu Y, Gai T, Zhang Y, Yang R, Qian H, Liu Y, Luo J, Zheng L, Lou J, Peng Y, Zuo W, Song J, He S, Wu S, Zou Y, Zhou L, Cheng L, Tang Y, Cheng G, Yuan L, He W, Xu J, Fu T, Xiao Y, Lei T, Xu A, Yin Y, Wang J, Monteiro A, Westhof E, Lu C, Tian Z, Wang W, Xiang Z, Dai F. High-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation. Nat Commun 2022; 13:5619. [PMID: 36153338 PMCID: PMC9509368 DOI: 10.1038/s41467-022-33366-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.
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33
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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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34
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Saeliw T, Permpoon T, Iadsee N, Tencomnao T, Hu VW, Sarachana T, Green D, Sae-Lee C. LINE-1 and Alu methylation signatures in autism spectrum disorder and their associations with the expression of autism-related genes. Sci Rep 2022; 12:13970. [PMID: 35978033 PMCID: PMC9385849 DOI: 10.1038/s41598-022-18232-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Long interspersed nucleotide element-1 (LINE-1) and Alu elements are retrotransposons whose abilities cause abnormal gene expression and genomic instability. Several studies have focused on DNA methylation profiling of gene regions, but the locus-specific methylation of LINE-1 and Alu elements has not been identified in autism spectrum disorder (ASD). Here we interrogated locus- and family-specific methylation profiles of LINE-1 and Alu elements in ASD whole blood using publicly-available Illumina Infinium 450 K methylation datasets from heterogeneous ASD and ASD variants (Chromodomain Helicase DNA-binding 8 (CHD8) and 16p11.2del). Total DNA methylation of repetitive elements were notably hypomethylated exclusively in ASD with CHD8 variants. Methylation alteration in a family-specific manner including L1P, L1H, HAL, AluJ, and AluS families were observed in the heterogeneous ASD and ASD with CHD8 variants. Moreover, LINE-1 and Alu methylation within target genes is inversely related to the expression level in each ASD variant. The DNA methylation signatures of the LINE-1 and Alu elements in ASD whole blood, as well as their associations with the expression of ASD-related genes, have been identified. If confirmed in future larger studies, these findings may contribute to the identification of epigenomic biomarkers of ASD.
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Affiliation(s)
- Thanit Saeliw
- The Ph.D. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Tiravut Permpoon
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nutta Iadsee
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Tewin Tencomnao
- Natural Products for Neuroprotection and Anti-Ageing Research Unit, Chulalongkorn University, Bangkok, Thailand.,Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Valerie W Hu
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Tewarit Sarachana
- Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand.,SYstems Neuroscience of Autism and PSychiatric Disorders (SYNAPS) Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Daniel Green
- Institute of Life Course and Medical Sciences, Faculty of Health and Life Sciences, University of Liverpool, Liverpool, UK
| | - Chanachai Sae-Lee
- Research Division, SiMR, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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35
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
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Smith RD, Puzey JR, Conradi Smith GD. Population genetics of transposable element load: A mechanistic account of observed overdispersion. PLoS One 2022; 17:e0270839. [PMID: 35834543 PMCID: PMC9282655 DOI: 10.1371/journal.pone.0270839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/20/2022] [Indexed: 11/18/2022] Open
Abstract
In an empirical analysis of transposable element (TE) abundance within natural populations of Mimulus guttatus and Drosophila melanogaster, we found a surprisingly high variance of TE count (e.g., variance-to-mean ratio on the order of 10 to 300). To obtain insight regarding the evolutionary genetic mechanisms that underlie the overdispersed population distributions of TE abundance, we developed a mathematical model of TE population genetics that includes the dynamics of element proliferation and purifying selection on TE load. The modeling approach begins with a master equation for a birth-death process and extends the predictions of the classical theory of TE dynamics in several ways. In particular, moment-based analyses of population distributions of TE load reveal that overdispersion is likely to arise via copy-and-paste proliferation dynamics, especially when the elementary processes of proliferation and excision are approximately balanced. Parameter studies and analytic work confirm this result and further suggest that overdispersed population distributions of TE abundance are probably not a consequence of purifying selection on total element load.
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Affiliation(s)
- Ronald D. Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
| | - Joshua R. Puzey
- Department of Biology, William & Mary, Williamsburg, VA, United States of America
| | - Gregory D. Conradi Smith
- Department of Applied Science, William & Mary, Williamsburg, VA, United States of America
- * E-mail:
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Ametrano A, Picchietti S, Guerra L, Giacomelli S, Oreste U, Coscia MR. Comparative Analysis of the pIgR Gene from the Antarctic Teleost Trematomus bernacchii Reveals Distinctive Features of Cold-Adapted Notothenioidei. Int J Mol Sci 2022; 23:ijms23147783. [PMID: 35887127 PMCID: PMC9321927 DOI: 10.3390/ijms23147783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
The IgM and IgT classes were previously identified and characterized in the Antarctic teleost Trematomus bernacchii, a species belonging to the Perciform suborder Notothenoidei. Herein, we characterized the gene encoding the polymeric immunoglobulin receptor (pIgR) in the same species and compared it to the pIgR of multiple teleost species belonging to five perciform suborders, including 11 Antarctic and 1 non-Antarctic (Cottoperca gobio) notothenioid species, the latter living in the less-cold peri-Antarctic sea. Antarctic pIgR genes displayed particularly long introns marked by sites of transposable elements and transcription factors. Furthermore, analysis of T. bernacchii pIgR cDNA unveiled multiple amino acid substitutions unique to the Antarctic species, all introducing adaptive features, including N-glycosylation sequons. Interestingly, C. gobio shared most features with the other perciforms rather than with the cold-adapted relatives. T. bernacchii pIgR transcripts were predominantly expressed in mucosal tissues, as indicated by q-PCR and in situ hybridization analysis. These results suggest that in cold-adapted species, pIgR preserved its fundamental role in mucosal immune defense, although remarkable gene structure modifications occurred.
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Affiliation(s)
- Alessia Ametrano
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Simona Picchietti
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Laura Guerra
- Department for Innovation in Biological, Agro-Food and Forest Systems, University of Tuscia, Largo dell’Università snc, 01100 Viterbo, Italy; (S.P.); (L.G.)
| | - Stefano Giacomelli
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Umberto Oreste
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
| | - Maria Rosaria Coscia
- Institute of Biochemistry and Cell Biology, National Research Council of Italy, Via P. Castellino 111, 80131 Naples, Italy; (A.A.); (S.G.); (U.O.)
- Correspondence: ; Tel.: +39-081-6132556
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Halabian R, Makałowski W. A Map of 3' DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes. BIOLOGY 2022; 11:biology11071032. [PMID: 36101413 PMCID: PMC9311842 DOI: 10.3390/biology11071032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 05/03/2023]
Abstract
As one of the major structural constituents, mobile elements comprise more than half of the human genome, among which Alu, L1, and SVA elements are still active and continue to generate new offspring. One of the major characteristics of L1 and SVA elements is their ability to co-mobilize adjacent downstream sequences to new loci in a process called 3' DNA transduction. Transductions influence the structure and content of the genome in different ways, such as increasing genome variation, exon shuffling, and gene duplication. Moreover, given their mutagenicity capability, 3' transductions are often involved in tumorigenesis or in the development of some diseases. In this study, we analyzed 3202 genomes sequenced at high coverage by the New York Genome Center to catalog and characterize putative 3' transduced segments mediated by L1s and SVAs. Here, we present a genome-wide map of inter/intrachromosomal 3' transduction variants, including their genomic and functional location, length, progenitor location, and allelic frequency across 26 populations. In total, we identified 7103 polymorphic L1s and 3040 polymorphic SVAs. Of these, 268 and 162 variants were annotated as high-confidence L1 and SVA 3' transductions, respectively, with lengths that ranged from 7 to 997 nucleotides. We found specific loci within chromosomes X, 6, 7, and 6_GL000253v2_alt as master L1s and SVAs that had yielded more transductions, among others. Together, our results demonstrate the dynamic nature of transduction events within the genome and among individuals and their contribution to the structural variations of the human genome.
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Chiang VSC, DeRosa H, Park JH, Hunter RG. The Role of Transposable Elements in Sexual Development. Front Behav Neurosci 2022; 16:923732. [PMID: 35874645 PMCID: PMC9301316 DOI: 10.3389/fnbeh.2022.923732] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/20/2022] [Indexed: 11/19/2022] Open
Abstract
Up to 50% of most mammalian genomes are made up of transposable elements (TEs) that have the potential to mobilize around the genome. Despite this prevalence, research on TEs is only beginning to gain traction within the field of neuroscience. While TEs have long been regarded as “junk” or parasitic DNA, it has become evident that they are adaptive DNA and RNA regulatory elements. In addition to their vital role in normal development, TEs can also interact with steroid receptors, which are key elements to sexual development. In this review, we provide an overview of the involvement of TEs in processes related to sexual development- from TE activity in the germline to TE accumulation in sex chromosomes. Moreover, we highlight sex differences in TE activity and their regulation of genes related to sexual development. Finally, we speculate on the epigenetic mechanisms that may govern TEs’ role in sexual development. In this context, we emphasize the need to further the understanding of sexual development through the lens of TEs including in a variety of organs at different developmental stages, their molecular networks, and evolution.
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Yu H, Chen M, Hu Y, Ou S, Yu X, Liang S, Li N, Yang M, Kong X, Sun C, Jia S, Zhang Q, Liu L, Hurst LD, Li R, Wang W, Wang J. Dynamic reprogramming of H3K9me3 at hominoid-specific retrotransposons during human preimplantation development. Cell Stem Cell 2022; 29:1031-1050.e12. [PMID: 35803225 DOI: 10.1016/j.stem.2022.06.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 04/06/2022] [Accepted: 06/08/2022] [Indexed: 12/13/2022]
Abstract
Reprogramming of H3K9me3-dependent heterochromatin is required for early development. How H3K9me3 is involved in early human development remains, however, largely unclear. Here, we resolve the temporal landscape of H3K9me3 during human preimplantation development and its regulation for diverse hominoid-specific retrotransposons. At the 8-cell stage, H3K9me3 reprogramming at hominoid-specific retrotransposons termed SINE-VNTR-Alu (SVA) facilitates interaction between certain promoters and SVA-derived enhancers, promoting the zygotic genome activation. In trophectoderm, de novo H3K9me3 domains prevent pluripotent transcription factors from binding to hominoid-specific retrotransposons-derived regulatory elements for inner cell mass (ICM)-specific genes. H3K9me3 re-establishment at SVA elements in the ICM is associated with higher transcription of DNA repair genes, when compared with naive human pluripotent stem cells. Our data demonstrate that species-specific reorganization of H3K9me3-dependent heterochromatin at hominoid-specific retrotransposons plays important roles during early human development, shedding light on how the epigenetic regulation for early development has evolved in mammals.
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Affiliation(s)
- Hanwen Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Manqi Chen
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Yuanlang Hu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China; The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Songbang Ou
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiu Yu
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Shiqi Liang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Niannian Li
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Mingzhu Yang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Xuhui Kong
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
| | - Chuanbo Sun
- Laboratory of Medical Systems Biology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shiqi Jia
- The First Affiliated Hospital, Jinan University, Guangzhou 510630, China
| | - Qingxue Zhang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Liu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China; Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China
| | - Laurence D Hurst
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
| | - Ruiqi Li
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Wenjun Wang
- Department of Obstetrics and Gynaecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Jichang Wang
- Department of Histology and Embryology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Key Laboratory for Stem Cells and Tissue Engineering (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China.
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Li W, Pandya D, Pasternack N, Garcia-Montojo M, Henderson L, Kozak CA, Nath A. Retroviral Elements in Pathophysiology and as Therapeutic Targets for Amyotrophic Lateral Sclerosis. Neurotherapeutics 2022; 19:1085-1101. [PMID: 35415778 PMCID: PMC9587200 DOI: 10.1007/s13311-022-01233-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2022] [Indexed: 10/18/2022] Open
Abstract
The study of the role of retroviruses in amyotrophic lateral sclerosis (ALS) dates back to the 1960s shortly after transposable elements themselves were first discovered. It was quickly realized that in wild mice both horizontal and vertical transmissions of retroviral elements were key to the development of an ALS-like syndrome leading to the postulate that endogenous retroviruses (ERVs) contribute significantly to the pathogenicity of this disease. Subsequent studies identified retroviral reverse transcriptase activity in brains of individuals with ALS from Guam. However, except for a single study from the former Soviet Union, ALS could not be transmitted to rhesus macaques. The discovery of an ALS-like syndrome in human immunodeficiency virus (HIV) and human T cell leukemia virus infected individuals led to renewed interest in the field and reverse transcriptase activity was found in the blood and cerebrospinal fluid of individuals with sporadic ALS. However, exogenous retroviruses could not be found in individuals with ALS which further reinforced the possibility of involvement of a human ERV (HERV). The first demonstration of the involvement of a HERV was the discovery of the activation of human endogenous retrovirus-K subtype HML-2 in the brains of individuals with ALS. The envelope protein of HML-2 is neurotoxic and transgenic animals expressing the envelope protein develop an ALS-like syndrome. Activation of HML-2 occurs in the context of generalized transposable element activation and is not specific for ALS. Individuals with HIV-associated ALS show a remarkable response to antiretroviral therapy; however, antiretroviral trials in ALS down-regulate HML-2 without ameliorating the disease. This highlights the need for specific drugs to be developed against HML-2 as a novel therapeutic target for ALS. Other approaches might include antisense oligonucleotides, shRNA targeted against the envelope gene or antibodies that can target the extracellular envelope protein. Future clinical trials in ALS should consider combination therapies to control these ERVs.
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Affiliation(s)
- Wenxue Li
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Darshan Pandya
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Nicholas Pasternack
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Marta Garcia-Montojo
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Lisa Henderson
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Christine A Kozak
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA.
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Abstract
Human endogenous retroviruses (HERVs) occupy approximately 8% of the human genome. HERVs, transcribed in early embryos, are epigenetically silenced in somatic cells, except under pathological conditions. HERV-K is thought to protect embryos from exogenous viral infection. However, uncontrolled HERV-K expression in somatic cells has been implicated in several diseases. Here, we show that SOX2, which plays a key role in maintaining the pluripotency of stem cells, is critical for HERV-K LTR5Hs. HERV-K undergoes retrotransposition within producer cells in the absence of Env expression. Furthermore, we identified new HERV-K integration sites in long-term culture of induced pluripotent stem cells that express SOX2. These results suggest that the strict dependence of HERV-K on SOX2 has allowed HERV-K to protect early embryos during evolution while limiting the potentially harmful effects of HERV-K retrotransposition on host genome integrity in these early embryos. IMPORTANCE Human endogenous retroviruses (HERVs) account for approximately 8% of the human genome; however, the physiological role of HERV-K remains unknown. This study found that HERV-K LTR5Hs and LTR5B were transactivated by SOX2, which is essential for maintaining and reestablishing pluripotency. HERV-K can undergo retrotransposition within producer cells without env expression, and new integration sites may affect cell proliferation. In induced pluripotent stem cells (iPSCs), genomic impairment due to HERV-K retrotransposition has been identified, but it is a rare event. Considering the retention of SOX2-responsive elements in the HERV-K long terminal repeat (LTR) for over 20 million years, we conclude that HERV-K may play important physiological roles in SOX2-expressing cells.
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Structural and genome-wide analyses suggest that transposon-derived protein SETMAR alters transcription and splicing. J Biol Chem 2022; 298:101894. [PMID: 35378129 PMCID: PMC9062482 DOI: 10.1016/j.jbc.2022.101894] [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: 12/18/2021] [Revised: 03/25/2022] [Accepted: 03/26/2022] [Indexed: 11/22/2022] Open
Abstract
Extensive portions of the human genome have unknown function, including those derived from transposable elements. One such element, the DNA transposon Hsmar1, entered the primate lineage approximately 50 million years ago leaving behind terminal inverted repeat (TIR) sequences and a single intact copy of the Hsmar1 transposase, which retains its ancestral TIR-DNA-binding activity, and is fused with a lysine methyltransferase SET domain to constitute the chimeric SETMAR gene. Here, we provide a structural basis for recognition of TIRs by SETMAR and investigate the function of SETMAR through genome-wide approaches. As elucidated in our 2.37 Å crystal structure, SETMAR forms a dimeric complex with each DNA-binding domain bound specifically to TIR-DNA through the formation of 32 hydrogen bonds. We found that SETMAR recognizes primarily TIR sequences (∼5000 sites) within the human genome as assessed by chromatin immunoprecipitation sequencing analysis. In two SETMAR KO cell lines, we identified 163 shared differentially expressed genes and 233 shared alternative splicing events. Among these genes are several pre–mRNA-splicing factors, transcription factors, and genes associated with neuronal function, and one alternatively spliced primate-specific gene, TMEM14B, which has been identified as a marker for neocortex expansion associated with brain evolution. Taken together, our results suggest a model in which SETMAR impacts differential expression and alternative splicing of genes associated with transcription and neuronal function, potentially through both its TIR-specific DNA-binding and lysine methyltransferase activities, consistent with a role for SETMAR in simian primate development.
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Garland W, Müller I, Wu M, Schmid M, Imamura K, Rib L, Sandelin A, Helin K, Jensen TH. Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression. Mol Cell 2022; 82:1691-1707.e8. [PMID: 35349793 PMCID: PMC9433625 DOI: 10.1016/j.molcel.2022.03.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/14/2021] [Accepted: 03/01/2022] [Indexed: 12/12/2022]
Abstract
Transposable elements (TEs) are widespread genetic parasites known to be kept under tight transcriptional control. Here, we describe a functional connection between the mouse-orthologous “nuclear exosome targeting” (NEXT) and “human silencing hub” (HUSH) complexes, involved in nuclear RNA decay and the epigenetic silencing of TEs, respectively. Knocking out the NEXT component ZCCHC8 in embryonic stem cells results in elevated TE RNA levels. We identify a physical interaction between ZCCHC8 and the MPP8 protein of HUSH and establish that HUSH recruits NEXT to chromatin at MPP8-bound TE loci. However, while NEXT and HUSH both dampen TE RNA expression, their activities predominantly affect shorter non-polyadenylated and full-length polyadenylated transcripts, respectively. Indeed, our data suggest that the repressive action of HUSH promotes a condition favoring NEXT RNA decay activity. In this way, transcriptional and post-transcriptional machineries synergize to suppress the genotoxic potential of TE RNAs. Garland et al. report a physical and functional connection between the NEXT complex, involved in RNA decay, and the HUSH complex, involved in chromatin regulation. Together, NEXT and HUSH cooperate to control transposable element (TE) RNA expression in embryonic stem cells, suppressing pA− and pA+ transcripts, respectively.
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Affiliation(s)
- William Garland
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Iris Müller
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mengjun Wu
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark; SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Katsutoshi Imamura
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Leonor Rib
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Albin Sandelin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Novo Nordisk Foundation for Stem Cell Biology, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark; Cell Biology Program and Center for Epigenetics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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Niu Y, Teng X, Zhou H, Shi Y, Li Y, Tang Y, Zhang P, Luo H, Kang Q, Xu T, He S. Characterizing mobile element insertions in 5675 genomes. Nucleic Acids Res 2022; 50:2493-2508. [PMID: 35212372 PMCID: PMC8934628 DOI: 10.1093/nar/gkac128] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/07/2022] [Accepted: 02/11/2022] [Indexed: 12/30/2022] Open
Abstract
Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.
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Affiliation(s)
- Yiwei Niu
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyi Teng
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yirong Shi
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanyan Li
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiheng Tang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Huaxia Luo
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Quan Kang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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46
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Ying H, Hayward DC, Klimovich A, Bosch TCG, Baldassarre L, Neeman T, Forêt S, Huttley G, Reitzel AM, Fraune S, Ball EE, Miller DJ. The role of DNA methylation in genome defense in Cnidaria and other invertebrates. Mol Biol Evol 2022; 39:6516040. [PMID: 35084499 PMCID: PMC8857917 DOI: 10.1093/molbev/msac018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Considerable attention has recently been focused on the potential involvement of DNA methylation in regulating gene expression in cnidarians. Much of this work has been centered on corals, in the context of changes in methylation perhaps facilitating adaptation to higher seawater temperatures and other stressful conditions. Although first proposed more than 30 years ago, the possibility that DNA methylation systems function in protecting animal genomes against the harmful effects of transposon activity has largely been ignored since that time. Here, we show that transposons are specifically targeted by the DNA methylation system in cnidarians, and that the youngest transposons (i.e., those most likely to be active) are most highly methylated. Transposons in longer and highly active genes were preferentially methylated and, as transposons aged, methylation levels declined, reducing the potentially harmful side effects of CpG methylation. In Cnidaria and a range of other invertebrates, correlation between the overall extent of methylation and transposon content was strongly supported. Present transposon burden is the dominant factor in determining overall level of genomic methylation in a range of animals that diverged in or before the early Cambrian, suggesting that genome defense represents the ancestral role of CpG methylation.
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Affiliation(s)
- Hua Ying
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David C Hayward
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Thomas C G Bosch
- Zoological Institute, Christian Albrechts University, Kiel, Germany.,Collaborative Research Center for the Origin and Function of Metaorganisms, Christian Albrechts University, Kiel, Germany
| | - Laura Baldassarre
- Department of Zoology and Organismal Interactions, Heinrich-Heine-University Düsseldorf, Germany
| | - Teresa Neeman
- Biological Data Institute, Australian National University, Canberra, ACT, Australia
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - Gavin Huttley
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, USA
| | - Sebastian Fraune
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia
| | - Eldon E Ball
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,ARC Centre of Excellence for Coral Reef Studies, Australian National University, Canberra, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Queensland, Australia.,College of Public Health, Medical and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Townsville, Queensland, Australia.,Marine Climate Change Unit, Okinawa Institute of Science and Technology, Japan
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47
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Peze-Heidsieck E, Bonnifet T, Znaidi R, Ravel-Godreuil C, Massiani-Beaudoin O, Joshi RL, Fuchs J. Retrotransposons as a Source of DNA Damage in Neurodegeneration. Front Aging Neurosci 2022; 13:786897. [PMID: 35058771 PMCID: PMC8764243 DOI: 10.3389/fnagi.2021.786897] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/30/2021] [Indexed: 01/09/2023] Open
Abstract
The etiology of aging-associated neurodegenerative diseases (NDs), such as Parkinson’s disease (PD) and Alzheimer’s disease (AD), still remains elusive and no curative treatment is available. Age is the major risk factor for PD and AD, but the molecular link between aging and neurodegeneration is not fully understood. Aging is defined by several hallmarks, some of which partially overlap with pathways implicated in NDs. Recent evidence suggests that aging-associated epigenetic alterations can lead to the derepression of the LINE-1 (Long Interspersed Element-1) family of transposable elements (TEs) and that this derepression might have important implications in the pathogenesis of NDs. Almost half of the human DNA is composed of repetitive sequences derived from TEs and TE mobility participated in shaping the mammalian genomes during evolution. Although most TEs are mutated and no longer mobile, more than 100 LINE-1 elements have retained their full coding potential in humans and are thus retrotransposition competent. Uncontrolled activation of TEs has now been reported in various models of neurodegeneration and in diseased human brain tissues. We will discuss in this review the potential contribution of LINE-1 elements in inducing DNA damage and genomic instability, which are emerging pathological features in NDs. TEs might represent an important molecular link between aging and neurodegeneration, and a potential target for urgently needed novel therapeutic disease-modifying interventions.
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Affiliation(s)
- Eugenie Peze-Heidsieck
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Tom Bonnifet
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rania Znaidi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Camille Ravel-Godreuil
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Olivia Massiani-Beaudoin
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Rajiv L Joshi
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
| | - Julia Fuchs
- Center for Interdisciplinary Research in Biology (CIRB), CNRS, INSERM, Collège de France, Université PSL, Paris, France
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48
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Pradhan RK, Ramakrishna W. Transposons: Unexpected players in cancer. Gene 2022; 808:145975. [PMID: 34592349 DOI: 10.1016/j.gene.2021.145975] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 12/21/2022]
Abstract
Transposons are repetitive DNA sequences encompassing about half of the human genome. They play a vital role in genome stability maintenance and contribute to genomic diversity and evolution. Their activity is regulated by various mechanisms considering the deleterious effects of these mobile elements. Various genetic risk factors and environmental stress conditions affect the regulatory pathways causing alteration of transposon expression. Our knowledge of the biological role of transposons is limited especially in various types of cancers. Retrotransposons of different types (LTR-retrotransposons, LINEs and SINEs) regulate a plethora of genes that have a role in cell reprogramming, tumor suppression, cell cycle, apoptosis, cell adhesion and migration, and DNA repair. The regulatory mechanisms of transposons, their deregulation and different mechanisms underlying transposon-mediated carcinogenesis in humans focusing on the three most prevalent types, lung, breast and colorectal cancers, were reviewed. The modes of regulation employed include alternative splicing, deletion, insertion, duplication in genes and promoters resulting in upregulation, downregulation or silencing of genes.
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49
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Ramirez P, Zuniga G, Sun W, Beckmann A, Ochoa E, DeVos SL, Hyman B, Chiu G, Roy ER, Cao W, Orr M, Buggia-Prevot V, Ray WJ, Frost B. Pathogenic tau accelerates aging-associated activation of transposable elements in the mouse central nervous system. Prog Neurobiol 2022; 208:102181. [PMID: 34670118 PMCID: PMC8712387 DOI: 10.1016/j.pneurobio.2021.102181] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 01/03/2023]
Abstract
Transposable elements comprise almost half of the mammalian genome. A growing body of evidence suggests that transposable element dysregulation accompanies brain aging and neurodegenerative disorders, and that transposable element activation is neurotoxic. Recent studies have identified links between pathogenic forms of tau, a protein that accumulates in Alzheimer's disease and related "tauopathies," and transposable element-induced neurotoxicity. Starting with transcriptomic analyses, we find that age- and tau-induced transposable element activation occurs in the mouse brain. Among transposable elements that are activated at the RNA level in the context of brain aging and tauopathy, we find that the endogenous retrovirus (ERV) class of retrotransposons is particularly enriched. We show that protein encoded by Intracisternal A-particle, a highly active mouse ERV, is elevated in brains of tau transgenic mice. Using two complementary approaches, we find that brains of tau transgenic mice contain increased DNA copy number of transposable elements, raising the possibility that these elements actively retrotranspose in the context of tauopathy. Taken together, our study lays the groundwork for future mechanistic studies focused on transposable element regulation in the aging mouse brain and in mouse models of tauopathy and provides support for ongoing therapeutic efforts targeting transposable element activation in patients with Alzheimer's disease.
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Affiliation(s)
- Paulino Ramirez
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Gabrielle Zuniga
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Wenyan Sun
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Adrian Beckmann
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Elizabeth Ochoa
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas
| | - Sarah L. DeVos
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Bradley Hyman
- Department of Neurology, MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts
| | - Gabriel Chiu
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Ethan R. Roy
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Wei Cao
- Huffington Center on Aging, Baylor College of Medicine, Houston, TX
| | - Miranda Orr
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC,WG Hefner VA Medical Center, Salisbury, NC
| | - Virginie Buggia-Prevot
- The Neurodegeneration Consortium, Therapeutics Discovery Division, University of Texas MD Anderson Cancer Center, Houston, TX
| | - William J. Ray
- The Neurodegeneration Consortium, Therapeutics Discovery Division, University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bess Frost
- Barshop Institute for Longevity and Aging Studies, University of Texas Health San Antonio, San Antonio, Texas,Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health San Antonio, San Antonio, Texas,Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, Texas,Corresponding Author and Lead Contact: Bess Frost, Ph.D., Associate Professor, 4939 Charles Katz, Barshop Institute, rm 1041, University of Texas Health San Antonio, San Antonio, TX 78229, Phone: 210-562-5037,
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50
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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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