101
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Jacob-Hirsch J, Eyal E, Knisbacher BA, Roth J, Cesarkas K, Dor C, Farage-Barhom S, Kunik V, Simon AJ, Gal M, Yalon M, Moshitch-Moshkovitz S, Tearle R, Constantini S, Levanon EY, Amariglio N, Rechavi G. Whole-genome sequencing reveals principles of brain retrotransposition in neurodevelopmental disorders. Cell Res 2018; 28:187-203. [PMID: 29327725 DOI: 10.1038/cr.2018.8] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 11/10/2017] [Accepted: 11/20/2017] [Indexed: 02/07/2023] Open
Abstract
Neural progenitor cells undergo somatic retrotransposition events, mainly involving L1 elements, which can be potentially deleterious. Here, we analyze the whole genomes of 20 brain samples and 80 non-brain samples, and characterized the retrotransposition landscape of patients affected by a variety of neurodevelopmental disorders including Rett syndrome, tuberous sclerosis, ataxia-telangiectasia and autism. We report that the number of retrotranspositions in brain tissues is higher than that observed in non-brain samples and even higher in pathologic vs normal brains. The majority of somatic brain retrotransposons integrate into pre-existing repetitive elements, preferentially A/T rich L1 sequences, resulting in nested insertions. Our findings document the fingerprints of encoded endonuclease independent mechanisms in the majority of L1 brain insertion events. The insertions are "non-classical" in that they are truncated at both ends, integrate in the same orientation as the host element, and their target sequences are enriched with a CCATT motif in contrast to the classical endonuclease motif of most other retrotranspositions. We show that L1Hs elements integrate preferentially into genes associated with neural functions and diseases. We propose that pre-existing retrotransposons act as "lightning rods" for novel insertions, which may give fine modulation of gene expression while safeguarding from deleterious events. Overwhelmingly uncontrolled retrotransposition may breach this safeguard mechanism and increase the risk of harmful mutagenesis in neurodevelopmental disorders.
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Affiliation(s)
- Jasmine Jacob-Hirsch
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Eran Eyal
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | | | - Jonathan Roth
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Karen Cesarkas
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Chen Dor
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sarit Farage-Barhom
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Vered Kunik
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Amos J Simon
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Moran Gal
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Michal Yalon
- Department of Pediatric Hematology-Oncology, Edmond and Lily Safra Children's Hospital, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Sharon Moshitch-Moshkovitz
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Rick Tearle
- Complete Genomics, 2071 Stierlin Court, Mountain View, CA 94043, USA
| | - Shlomi Constantini
- Department of Pediatric Neurosurgery, Dana Children's Hospital, Tel Aviv Medical Center, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Ninette Amariglio
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, Israel
| | - Gideon Rechavi
- Cancer Research Center and the Wohl Institute of Translational Medicine, the Chaim Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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102
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Mita P, Wudzinska A, Sun X, Andrade J, Nayak S, Kahler DJ, Badri S, LaCava J, Ueberheide B, Yun CY, Fenyö D, Boeke JD. LINE-1 protein localization and functional dynamics during the cell cycle. eLife 2018; 7:30058. [PMID: 29309036 PMCID: PMC5821460 DOI: 10.7554/elife.30058] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 01/04/2018] [Indexed: 01/12/2023] Open
Abstract
LINE-1/L1 retrotransposon sequences comprise 17% of the human genome. Among the many classes of mobile genetic elements, L1 is the only autonomous retrotransposon that still drives human genomic plasticity today. Through its co-evolution with the human genome, L1 has intertwined itself with host cell biology. However, a clear understanding of L1’s lifecycle and the processes involved in restricting its insertion and intragenomic spread remains elusive. Here we identify modes of L1 proteins’ entrance into the nucleus, a necessary step for L1 proliferation. Using functional, biochemical, and imaging approaches, we also show a clear cell cycle bias for L1 retrotransposition that peaks during the S phase. Our observations provide a basis for novel interpretations about the nature of nuclear and cytoplasmic L1 ribonucleoproteins (RNPs) and the potential role of DNA replication in L1 retrotransposition. Only two percent of our genetic material or genome are occupied by genes, while between 60-70 percent are made up of hundreds of thousands of copies of very similar DNA sequences. These repetitive sequences evolved from genetic elements called transposons. Transposons are often referred to as ‘jumping genes’, as they can randomly move within the genome and thereby create dangerous mutations that may lead to cancer or other genetic diseases. LINE-1 is the only remaining active transposon in humans, and it expands by copying and pasting itself to new locations via a process called 'retrotransposition'. To do so, it is first transcribed into RNA – the molecules that help to make proteins – and then converted back into identical DNA sequences. Previous research has shown that LINE-1 can form complexes with a series of proteins, including the two encoded by LINE-1 RNA itself: ORF1p and ORF2p. The LINE-1 complexes can enter the nucleus of the cell and insert a new copy of LINE-1 into the genome. However, until now it was not known how they do this. To investigate this further, Mita et al. used human cancer cells grown in the lab and tracked LINE-1 during the different stages of the cell cycle. The results showed that LINE-1 enters the nucleus as the cell starts to divide and the membrane of the nucleus breaks down. The LINE-1 complexes are then retained in the nucleus while the membrane of the nucleus reforms. Later, as the cell duplicates its genetic material, LINE-1 starts to copy and paste itself. Mita et al., together with another group of researchers, also found that during this process, only LINE-1 RNA and ORF2p were found in the nucleus. This shows that the cell cycle dictates both where the LINE-1 complexes gather and when LINE-1 is active. A next step will be to further investigate how the ‘copy and paste’ mechanisms of LINE-1 and the two LINE-1 proteins are regulated during the cell cycle. In future, this may help to identify LINE-1’s role in processes like aging or in diseases such as cancer.
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Affiliation(s)
- Paolo Mita
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Aleksandra Wudzinska
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Xiaoji Sun
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Joshua Andrade
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - Shruti Nayak
- Proteomics laboratory, NYU Langone Health, New York, United States
| | - David J Kahler
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - Sana Badri
- Department of Pathology, NYU Langone Health, New York, United States
| | - John LaCava
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, United States
| | - Beatrix Ueberheide
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States.,Proteomics laboratory, NYU Langone Health, New York, United States
| | - Chi Y Yun
- High Throughput Biology (HTB) Laboratory, NYU Langone Health, New York, United States
| | - David Fenyö
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
| | - Jef D Boeke
- Institute of Systems Genetics (ISG), Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, United States
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103
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Dai Q, Shen Y, Wang Y, Wang X, Francisco JC, Luo Z, Lin C. Striking a balance: regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells. Nucleic Acids Res 2017; 45:12301-12310. [PMID: 29036642 PMCID: PMC5716208 DOI: 10.1093/nar/gkx841] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/12/2017] [Indexed: 01/22/2023] Open
Abstract
Transposable elements (TEs) compose about 40% of the murine genome. Retrotransposition of active TEs such as LINE-1 (L1) tremendously impacts genetic diversification and genome stability. Therefore, transcription and transposition activities of retrotransposons are tightly controlled. Here, we show that the Krüppel-like zinc finger protein Zfp281 directly binds and suppresses a subset of retrotransposons, including the active young L1 repeat elements, in mouse embryonic stem (ES) cells. In addition, we find that Zfp281-regulated L1s are highly enriched for 5-hydroxymethylcytosine (5hmC) and H3K4me3. The COMPASS-like H3K4 methyltransferase Mll2 is the major H3K4me3 methylase at the Zfp281-regulated L1s and required for their proper expression. Our studies also reveal that Zfp281 functions partially through recruiting the L1 regulators DNA hydroxymethylase Tet1 and Sin3A, and restricting Mll2 at these active L1s, leading to their balanced expression. In summary, our data indicate an instrumental role of Zfp281 in suppressing the young active L1s in mouse ES cells.
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Affiliation(s)
- Qian Dai
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Yang Shen
- Bioinformatics Group, A*STAR Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Yan Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xin Wang
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Joel Celio Francisco
- Transcriptional Control in Development and Disease Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
| | - Zhuojuan Luo
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Chengqi Lin
- Institute of Life Sciences, the Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.,Transcriptional Control in Development and Disease Laboratory, A*STAR Institute of Molecular and Cell Biology, 61 Biopolis Drive Proteos, Singapore 138673, Singapore
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104
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Honda T. Potential Links between Hepadnavirus and Bornavirus Sequences in the Host Genome and Cancer. Front Microbiol 2017; 8:2537. [PMID: 29312227 PMCID: PMC5742130 DOI: 10.3389/fmicb.2017.02537] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/06/2017] [Indexed: 12/26/2022] Open
Abstract
Various viruses leave their sequences in the host genomes during infection. Such events occur mainly in retrovirus infection but also sometimes in DNA and non-retroviral RNA virus infections. If viral sequences are integrated into the genomes of germ line cells, the sequences can become inherited as endogenous viral elements (EVEs). The integration events of viral sequences may have oncogenic potential. Because proviral integrations of some retroviruses and/or reactivation of endogenous retroviruses are closely linked to cancers, viral insertions related to non-retroviral viruses also possibly contribute to cancer development. This article focuses on genomic viral sequences derived from two non-retroviral viruses, whose endogenization is already reported, and discusses their possible contributions to cancer. Viral insertions of hepatitis B virus play roles in the development of hepatocellular carcinoma. Endogenous bornavirus-like elements, the only non-retroviral RNA virus-related EVEs found in the human genome, may also be involved in cancer formation. In addition, the possible contribution of the interactions between viruses and retrotransposons, which seem to be a major driving force for generating EVEs related to non-retroviral RNA viruses, to cancers will be discussed. Future studies regarding the possible links described here may open a new avenue for the development of novel therapeutics for tumor virus-related cancers and/or provide novel insights into EVE functions.
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Affiliation(s)
- Tomoyuki Honda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Osaka, Japan
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105
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Attig J, Young GR, Stoye JP, Kassiotis G. Physiological and Pathological Transcriptional Activation of Endogenous Retroelements Assessed by RNA-Sequencing of B Lymphocytes. Front Microbiol 2017; 8:2489. [PMID: 29312197 PMCID: PMC5733090 DOI: 10.3389/fmicb.2017.02489] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/29/2017] [Indexed: 12/20/2022] Open
Abstract
In addition to evolutionarily-accrued sequence mutation or deletion, endogenous retroelements (EREs) in eukaryotic genomes are subject to epigenetic silencing, preventing or reducing their transcription, particularly in the germplasm. Nevertheless, transcriptional activation of EREs, including endogenous retroviruses (ERVs) and long interspersed nuclear elements (LINEs), is observed in somatic cells, variably upon cellular differentiation and frequently upon cellular transformation. ERE transcription is modulated during physiological and pathological immune cell activation, as well as in immune cell cancers. However, our understanding of the potential consequences of such modulation remains incomplete, partly due to the relative scarcity of information regarding genome-wide ERE transcriptional patterns in immune cells. Here, we describe a methodology that allows probing RNA-sequencing (RNA-seq) data for genome-wide expression of EREs in murine and human cells. Our analysis of B cells reveals that their transcriptional response during immune activation is dominated by induction of gene transcription, and that EREs respond to a much lesser extent. The transcriptional activity of the majority of EREs is either unaffected or reduced by B cell activation both in mice and humans, albeit LINEs appear considerably more responsive in the latter host. Nevertheless, a small number of highly distinct ERVs are strongly and consistently induced during B cell activation. Importantly, this pattern contrasts starkly with B cell transformation, which exhibits widespread induction of EREs, including ERVs that minimally overlap with those responsive to immune stimulation. The distinctive patterns of ERE induction suggest different underlying mechanisms and will help separate physiological from pathological expression.
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Affiliation(s)
- Jan Attig
- Retroviral Immunology, The Francis Crick Institute, London, United Kingdom
| | - George R Young
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom
| | - Jonathan P Stoye
- Retrovirus-Host Interactions, The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - George Kassiotis
- Retroviral Immunology, The Francis Crick Institute, London, United Kingdom.,Department of Medicine, Faculty of Medicine, Imperial College London, London, United Kingdom
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106
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Habibi L, Salmani H. Pivotal Impacts of Retrotransposon Based Invasive RNAs on Evolution. Front Microbiol 2017; 8:1957. [PMID: 29067016 PMCID: PMC5641331 DOI: 10.3389/fmicb.2017.01957] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 09/22/2017] [Indexed: 11/16/2022] Open
Abstract
RNAs have long been described as the mediators of gene expression; they play a vital role in the structure and function of cellular complexes. Although the role of RNAs in the prokaryotes is mainly confined to these basic functions, the effects of these molecules in regulating the gene expression and enzymatic activities have been discovered in eukaryotes. Recently, a high-resolution analysis of the DNA obtained from different organisms has revealed a fundamental impact of the RNAs in shaping the genomes, heterochromatin formation, and gene creation. Deep sequencing of the human genome revealed that about half of our DNA is comprised of repetitive sequences (remnants of transposable element movements) expanded mostly through RNA-mediated processes. ORF2 encoded by L1 retrotransposons is a cellular reverse transcriptase which is mainly responsible for RNA invasion of various transposable elements (L1s, Alus, and SVAs) and cellular mRNAs in to the genomic DNA. In addition to increasing retroelements copy number; genomic expansion in association with centromere, telomere, and heterochromatin formation as well as pseudogene creation are the evolutionary consequences of this RNA-based activity. Threatening DNA integrity by disrupting the genes and forming excessive double strand breaks is another effect of this invasion. Therefore, repressive mechanisms have been evolved to control the activities of these invasive intracellular RNAs. All these mechanisms now have essential roles in the complex cellular functions. Therefore, it can be concluded that without direct action of RNA networks in shaping the genome and in the development of different cellular mechanisms, the evolution of higher eukaryotes would not be possible.
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107
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Levy O, Knisbacher BA, Levanon EY, Havlin S. Integrating networks and comparative genomics reveals retroelement proliferation dynamics in hominid genomes. SCIENCE ADVANCES 2017; 3:e1701256. [PMID: 29043294 PMCID: PMC5640379 DOI: 10.1126/sciadv.1701256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/20/2017] [Indexed: 05/28/2023]
Abstract
Retroelements (REs) are mobile DNA sequences that multiply and spread throughout genomes by a copy-and-paste mechanism. These parasitic elements are active in diverse genomes, from yeast to humans, where they promote diversity, cause disease, and accelerate evolution. Because of their high copy number and sequence similarity, studying their activity and tracking their proliferation dynamics is a challenge. It is particularly difficult to pinpoint the few REs in a genome that are still active in the haystack of degenerate and suppressed elements. We develop a computational framework based on network theory that tracks the path of RE proliferation throughout evolution. We analyze SVA (SINE-VNTR-Alu), the youngest RE family in human genomes, to understand RE dynamics across hominids. Integrating comparative genomics and network tools enables us to track the course of SVA proliferation, identify yet unknown active communities, and detect tentative "master REs" that played key roles in SVA propagation, providing strong support for the fundamental "master gene" model of RE proliferation. The method is generic and thus can be applied to REs of any of the thousands of available genomes to identify active RE communities and master REs that were pivotal in the evolution of their host genomes.
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Affiliation(s)
- Orr Levy
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Binyamin A. Knisbacher
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Erez Y. Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
| | - Shlomo Havlin
- Department of Physics, Bar-Ilan University, Ramat Gan 52900, Israel
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108
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Dong Y, Huang Z, Kuang Q, Wen Z, Liu Z, Li Y, Yang Y, Li M. Expression dynamics and relations with nearby genes of rat transposable elements across 11 organs, 4 developmental stages and both sexes. BMC Genomics 2017; 18:666. [PMID: 28851270 PMCID: PMC5576108 DOI: 10.1186/s12864-017-4078-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/21/2017] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND TEs pervade mammalian genomes. However, compared with mice, fewer studies have focused on the TE expression patterns in rat, particularly the comparisons across different organs, developmental stages and sexes. In addition, TEs can influence the expression of nearby genes. The temporal and spatial influences of TEs remain unclear yet. RESULTS To evaluate the TEs transcription patterns, we profiled their transcript levels in 11 organs for both sexes across four developmental stages of rat. The results show that most short interspersed elements (SINEs) are commonly expressed in all conditions, which are also the major TE types with commonly expression patterns. In contrast, long terminal repeats (LTRs) are more likely to exhibit specific expression patterns. The expression tendency of TEs and genes are similar in most cases. For example, few specific genes and TEs are in the liver, muscle and heart. However, TEs perform superior over genes on classing organ, which imply their higher organ specificity than genes. By associating the TEs with the closest genes in genome, we find their expression levels are correlated, independent of their distance in some cases. CONCLUSIONS TEs sex-dependently associate with nearest genes. A gene would be associated with more than one TE. Our works can help to functionally annotate the genome and further understand the role of TEs in gene regulation.
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Affiliation(s)
- Yongcheng Dong
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Ziyan Huang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Qifan Kuang
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zhining Wen
- College of Chemistry, Sichuan University, Chengdu, 610064, China
| | - Zhibin Liu
- College of Life Science, Sichuan University, Chengdu, 610064, China
| | - Yizhou Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yi Yang
- College of Life Science, Sichuan University, Chengdu, 610064, China.
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, 610064, China
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109
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Abstract
In modern molecular biology, RNA has emerged as a versatile macromolecule capable of mediating an astonishing number of biological functions beyond its role as a transient messenger of genetic information. The recent discovery and functional analyses of new classes of noncoding RNAs (ncRNAs) have revealed their widespread use in many pathways, including several in the nucleus. This Review focuses on the mechanisms by which nuclear ncRNAs directly contribute to the maintenance of genome stability. We discuss how ncRNAs inhibit spurious recombination among repetitive DNA elements, repress mobilization of transposable elements (TEs), template or bridge DNA double-strand breaks (DSBs) during repair, and direct developmentally regulated genome rearrangements in some ciliates. These studies reveal an unexpected repertoire of mechanisms by which ncRNAs contribute to genome stability and even potentially fuel evolution by acting as templates for genome modification.
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110
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Lv J, Zhao Z. Binding of LINE-1 RNA to PSF transcriptionally promotes GAGE6 and regulates cell proliferation and tumor formation in vitro. Exp Ther Med 2017; 14:1685-1691. [PMID: 28810637 DOI: 10.3892/etm.2017.4667] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has one of the highest mortality rates among numerous types of cancer. It has been demonstrated that in hepatitis B (HBV)-associated HCC, the expression of chimeric fusion transcript HBx-long interspersed nuclear element-1 (LINE-1) initiated by HBV integration is correlated with hepatocarcinogenesis and poor patient survival rates. Furthermore, increased rates of LINE-1 hypomethylation have been detected in HCC tissues compared with adjacent tissues. This suggests that individual LINE-1 RNA (L1 RNA) serves an important role in the processes of hepatocarcinogenesis. The present study assessed the epigenic interaction between L1 RNA and polypyrimidine tract-binding protein-associated splicing factor (PSF) in the A549 human alveolar epithelial and 16HBE human bronchial epithelial cell lines. In addition, changes in the transcriptional regulatory activity of PSF on its target gene, proto-oncogene G antigen 6 (GAGE6), were investigated following overexpression of L1 RNA, as well as its impact on cell-proliferative capacity, carried out by plotting cell growth curves and 5-ethynyl-2'-deoxyuridine assay. It was observed that L1 RNA specifically bound to the RNA binding domain of PSF and released the GAGE6 promoter region from the DNA-binding domain of PSF. This increased the transcription of GAGE6 and led to the promotion of cell proliferation as well as colony formation. Furthermore, at least two binding sites specific for PSF were identified on L1 RNA. In conclusion, the transcriptional regulatory activity of L1 RNA may partially result in cell transformation, and endogenous L1 RNA may function as an important regulatory factor in the process of tumorigenesis.
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Affiliation(s)
- Jiao Lv
- Center for Functional Genomics and Bioinformatics, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China.,Center for Translational Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Ziyi Zhao
- Central Laboratory, The Teaching Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan 610072, P.R. China
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111
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Comparative Principles of DNA Methylation Reprogramming during Human and Mouse In Vitro Primordial Germ Cell Specification. Dev Cell 2017; 39:104-115. [PMID: 27728778 PMCID: PMC5064768 DOI: 10.1016/j.devcel.2016.09.015] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 08/24/2016] [Accepted: 09/14/2016] [Indexed: 12/22/2022]
Abstract
Primordial germ cell (PGC) development is characterized by global epigenetic remodeling, which resets genomic potential and establishes an epigenetic ground state. Here we recapitulate PGC specification in vitro from naive embryonic stem cells and characterize the early events of epigenetic reprogramming during the formation of the human and mouse germline. Following rapid de novo DNA methylation during priming to epiblast-like cells, methylation is globally erased in PGC-like cells. Repressive chromatin marks (H3K9me2/3) and transposable elements are enriched at demethylation-resistant regions, while active chromatin marks (H3K4me3 or H3K27ac) are more prominent at regions that demethylate faster. The dynamics of specification and epigenetic reprogramming show species-specific differences, in particular markedly slower reprogramming kinetics in the human germline. Differences in developmental kinetics may be explained by differential regulation of epigenetic modifiers. Our work establishes a robust and faithful experimental system of the early events of epigenetic reprogramming and regulation in the germline.
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112
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Hunter DR, Bao L, Poss M. Assignment of endogenous retrovirus integration sites using a mixture model. Ann Appl Stat 2017. [DOI: 10.1214/16-aoas1016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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113
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Agarwal P, Enroth S, Teichmann M, Jernberg Wiklund H, Smit A, Westermark B, Singh U. Growth signals employ CGGBP1 to suppress transcription of Alu-SINEs. Cell Cycle 2017; 15:1558-71. [PMID: 25483050 PMCID: PMC4934077 DOI: 10.4161/15384101.2014.967094] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
CGGBP1 (CGG triplet repeat-binding protein 1) regulates cell proliferation, stress response, cytokinesis, telomeric integrity and transcription. It could affect these processes by modulating target gene expression under different conditions. Identification of CGGBP1-target genes and their regulation could reveal how a transcription regulator affects such diverse cellular processes. Here we describe the mechanisms of differential gene expression regulation by CGGBP1 in quiescent or growing cells. By studying global gene expression patterns and genome-wide DNA-binding patterns of CGGBP1, we show that a possible mechanism through which it affects the expression of RNA Pol II-transcribed genes in trans depends on Alu RNA. We also show that it regulates Alu transcription in cis by binding to Alu promoter. Our results also indicate that potential phosphorylation of CGGBP1 upon growth stimulation facilitates its nuclear retention, Alu-binding and dislodging of RNA Pol III therefrom. These findings provide insights into how Alu transcription is regulated in response to growth signals.
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Affiliation(s)
- Prasoon Agarwal
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Stefan Enroth
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Martin Teichmann
- b University of Bordeaux, IECB , ARNA laboratory, Equipe Labellisée Contre le Cancer , Pessac , France
| | - Helena Jernberg Wiklund
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Arian Smit
- c Institute for Systems Biology , Seattle , WA , USA
| | - Bengt Westermark
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
| | - Umashankar Singh
- a Department of Immunology, Genetics and Pathology, Rudbeck Laboratory , Uppsala University , Uppsala , Sweden
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114
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Adrion JR, Song MJ, Schrider DR, Hahn MW, Schaack S. Genome-Wide Estimates of Transposable Element Insertion and Deletion Rates in Drosophila Melanogaster. Genome Biol Evol 2017; 9:1329-1340. [PMID: 28338986 PMCID: PMC5447328 DOI: 10.1093/gbe/evx050] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/08/2017] [Indexed: 02/06/2023] Open
Abstract
Knowing the rate at which transposable elements (TEs) insert and delete is critical for understanding their role in genome evolution. We estimated spontaneous rates of insertion and deletion for all known, active TE superfamilies present in a set of Drosophila melanogaster mutation-accumulation (MA) lines using whole genome sequence data. Our results demonstrate that TE insertions far outpace TE deletions in D. melanogaster. We found a significant effect of background genotype on TE activity, with higher rates of insertions in one MA line. We also found significant rate heterogeneity between the chromosomes, with both insertion and deletion rates elevated on the X relative to the autosomes. Further, we identified significant associations between TE activity and chromatin state, and tested for associations between TE activity and other features of the local genomic environment such as TE content, exon content, GC content, and recombination rate. Our results provide the most detailed assessment of TE mobility in any organism to date, and provide a useful benchmark for both addressing theoretical predictions of TE dynamics and for exploring large-scale patterns of TE movement in D. melanogaster and other species.
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Affiliation(s)
| | - Michael J. Song
- Department of Integrative Biology, University of California, Berkeley, CA
| | - Daniel R. Schrider
- Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN
- School of Informatics and Computing, Indiana University, Bloomington, IN
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115
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Ruggles KV, Krug K, Wang X, Clauser KR, Wang J, Payne SH, Fenyö D, Zhang B, Mani DR. Methods, Tools and Current Perspectives in Proteogenomics. Mol Cell Proteomics 2017; 16:959-981. [PMID: 28456751 DOI: 10.1074/mcp.mr117.000024] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Indexed: 12/20/2022] Open
Abstract
With combined technological advancements in high-throughput next-generation sequencing and deep mass spectrometry-based proteomics, proteogenomics, i.e. the integrative analysis of proteomic and genomic data, has emerged as a new research field. Early efforts in the field were focused on improving protein identification using sample-specific genomic and transcriptomic sequencing data. More recently, integrative analysis of quantitative measurements from genomic and proteomic studies have identified novel insights into gene expression regulation, cell signaling, and disease. Many methods and tools have been developed or adapted to enable an array of integrative proteogenomic approaches and in this article, we systematically classify published methods and tools into four major categories, (1) Sequence-centric proteogenomics; (2) Analysis of proteogenomic relationships; (3) Integrative modeling of proteogenomic data; and (4) Data sharing and visualization. We provide a comprehensive review of methods and available tools in each category and highlight their typical applications.
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Affiliation(s)
- Kelly V Ruggles
- From the ‡Department of Medicine, New York University School of Medicine, New York, New York 10016
| | - Karsten Krug
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Xiaojing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Karl R Clauser
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Jing Wang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030.,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Samuel H Payne
- **Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354
| | - David Fenyö
- ‡‡Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016; .,§§Institute for Systems Genetics, New York University School of Medicine, New York, New York 10016
| | - Bing Zhang
- ¶Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, Texas 77030; .,‖Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - D R Mani
- §The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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116
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Sekridova AV, Varizhuk AM, Tatarinova ON, Severov VV, Barinov NA, Smirnov IP, Lazarev VN, Klinov DV, Pozmogova GE. Conformational polymorphysm of G-rich fragments of DNA Alu-repeats. I. Noncanonical structures. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2017. [DOI: 10.1134/s1990750817010097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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117
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Saavedra JT, Schwartzman JA, Gilmore MS. Mapping Transposon Insertions in Bacterial Genomes by Arbitrarily Primed PCR. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2017; 118:15.15.1-15.15.15. [PMID: 28369678 PMCID: PMC5679462 DOI: 10.1002/cpmb.38] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Transposons can be used to easily generate and label the location of mutations throughout bacterial and other genomes. Transposon insertion mutants may be screened for a phenotype as individual isolates, or by selection applied to a pool of thousands of mutants. Identifying the location of a transposon insertion is critical for connecting phenotype to the genetic lesion. In this unit, we present an easy and detailed approach for mapping transposon insertion sites using arbitrarily-primed PCR (AP-PCR). Two rounds of PCR are used to (1) amplify DNA spanning the transposon insertion junction, and (2) increase the specific yield of transposon insertion junction fragments for sequence analysis. The resulting sequence is mapped to a bacterial genome to identify the site of transposon insertion. In this protocol, AP-PCR as it is routinely used to map sites of transposon insertion within Staphylococcus aureus, is used to illustrate the principle. Guidelines are provided for adapting this protocol for mapping insertions in other bacterial genomes. Mapping transposon insertions using this method is typically achieved in 2 to 3 days if starting from a culture of the transposon insertion mutant. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- José T Saavedra
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
| | - Julia A Schwartzman
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
- Department of Ophthalmology, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
| | - Michael S Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts
- Department of Ophthalmology, and Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute, Cambridge, Massachusetts
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118
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Papin C, Ibrahim A, Gras SL, Velt A, Stoll I, Jost B, Menoni H, Bronner C, Dimitrov S, Hamiche A. Combinatorial DNA methylation codes at repetitive elements. Genome Res 2017; 27:934-946. [PMID: 28348165 PMCID: PMC5453327 DOI: 10.1101/gr.213983.116] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 03/21/2017] [Indexed: 12/30/2022]
Abstract
DNA methylation is an essential epigenetic modification, present in both unique DNA sequences and repetitive elements, but its exact function in repetitive elements remains obscure. Here, we describe the genome-wide comparative analysis of the 5mC, 5hmC, 5fC, and 5caC profiles of repetitive elements in mouse embryonic fibroblasts and mouse embryonic stem cells. We provide evidence for distinct and highly specific DNA methylation/oxidation patterns of the repetitive elements in both cell types, which mainly affect CA repeats and evolutionarily conserved mouse-specific transposable elements including IAP-LTRs, SINEs B1m/B2m, and L1Md-LINEs. DNA methylation controls the expression of these retroelements, which are clustered at specific locations in the mouse genome. We show that TDG is implicated in the regulation of their unique DNA methylation/oxidation signatures and their dynamics. Our data suggest the existence of a novel epigenetic code for the most recently acquired evolutionarily conserved repeats that could play a major role in cell differentiation.
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Affiliation(s)
- Christophe Papin
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Abdulkhaleg Ibrahim
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Stéphanie Le Gras
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Amandine Velt
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Isabelle Stoll
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Bernard Jost
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Hervé Menoni
- Institut Albert Bonniot, Université de Grenoble Alpes /INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Christian Bronner
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
| | - Stefan Dimitrov
- Institut Albert Bonniot, Université de Grenoble Alpes /INSERM U1209/CNRS UMR 5309, 38042 Grenoble Cedex 9, France
| | - Ali Hamiche
- Département de Génomique Fonctionnelle et Cancer, Institut de Génétique et Biologie Moléculaire et Cellulaire (IGBMC), UdS, CNRS, INSERM, Equipe labellisée Ligue contre le Cancer, 67404 Illkirch Cedex, France
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119
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Sekridova AV, Varizhuk AM, Tatarinova ON, Severov VV, Barinov NA, Smirnov IP, Lazarev VN, Klinov DV, Pozmogova GE. [Conformational polymorphysm of G-rich fragments of DNA ALU-repeats. I. Potential noncanonical structures]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 62:535-543. [PMID: 27797328 DOI: 10.18097/pbmc20166205535] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this paper, we report results of systematic studies of conformational polymorphism of G-rich DNA fragments from Alu repeats. Alu retrotransposones are primate-specific short interspersed elements. Using the Alu sequence from the prooncogen bcl2 intron and the consensus AluSx sequence as representative examples, we determined characteristic Alu sites that are capable of adopting G-quadruplex (GQ) conformations (i.e., potential quadruplex sites - PQSAlu), and demonstrated by bioinformatics methods that those sites are Alu-specific in the human genome. Genomic frequencies of PQSAlu were assessed (~1/10000 b.p.). The sites were found to be characteristic of young (active) Alu families (Alu-Y). A recombinant DNA sequence bearing the Alu element from the human bcl2 gene (304 b.p.) and its PQS-mutant (Alu-PQS) were constructed. The formation of noncanonical structures in Alubcl2 dsDNA and the absence of such structures in the case of Alu-PQS were shown using DMS-footprinting and AFM microscopy. Expression vectors bearing wild-type and mutant Alu insertions in the promoter regions were obtained, and the effects of these insertions on the expression of the reporter gene in НЕК293 and HeLa cell lines were compared. Our findings on the spatial organization of Alu repeats may provide insight into the mechanisms of genomic rearrangements which underlie many oncological and neurodegenerative diseases.
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Affiliation(s)
- A V Sekridova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - A M Varizhuk
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - O N Tatarinova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - V V Severov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - N A Barinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - I P Smirnov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - V N Lazarev
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - D V Klinov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - G E Pozmogova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
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120
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Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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121
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Ardeljan D, Taylor MS, Ting DT, Burns KH. The Human Long Interspersed Element-1 Retrotransposon: An Emerging Biomarker of Neoplasia. Clin Chem 2017; 63:816-822. [PMID: 28188229 DOI: 10.1373/clinchem.2016.257444] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/22/2016] [Indexed: 02/06/2023]
Abstract
BACKGROUND A large portion of intronic and intergenic space in our genome consists of repeated sequences. One of the most prevalent is the long interspersed element-1 (LINE-1, L1) mobile DNA. LINE-1 is rightly receiving increasing interest as a cancer biomarker. CONTENT Intact LINE-1 elements are self-propagating. They code for RNA and proteins that function to make more copies of the genomic element. Our current understanding is that this process is repressed in most normal cells, but that LINE-1 expression is a hallmark of many types of malignancy. Here, we will consider features of cancer cells when cellular defense mechanisms repressing LINE-1 go awry. We will review evidence that genomic LINE-1 methylation, LINE-1-encoded RNAs, and LINE-1 ORF1p (open reading frame 1 protein) may be useful in cancer diagnosis. SUMMARY The repetitive and variable nature of LINE-1 DNA sequences poses unique challenges to studying them, but recent advances in reagents and next generation sequencing present opportunities to characterize LINE-1 expression and activity in cancers and to identify clinical applications.
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Affiliation(s)
- Daniel Ardeljan
- McKusick-Nathans Institute of Genetic Medicine (IGM) and.,Medical Scientist Training Program (MSTP), Johns Hopkins University School of Medicine, Baltimore, MD
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - David T Ting
- Department of Medicine and the Massachusetts General Hospital Cancer Center, Boston, MA
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine (IGM) and .,Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
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122
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Human transposon insertion profiling: Analysis, visualization and identification of somatic LINE-1 insertions in ovarian cancer. Proc Natl Acad Sci U S A 2017; 114:E733-E740. [PMID: 28096347 DOI: 10.1073/pnas.1619797114] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mammalian genomes are replete with interspersed repeats reflecting the activity of transposable elements. These mobile DNAs are self-propagating, and their continued transposition is a source of both heritable structural variation as well as somatic mutation in human genomes. Tailored approaches to map these sequences are useful to identify insertion alleles. Here, we describe in detail a strategy to amplify and sequence long interspersed element-1 (LINE-1, L1) retrotransposon insertions selectively in the human genome, transposon insertion profiling by next-generation sequencing (TIPseq). We also report the development of a machine-learning-based computational pipeline, TIPseqHunter, to identify insertion sites with high precision and reliability. We demonstrate the utility of this approach to detect somatic retrotransposition events in high-grade ovarian serous carcinoma.
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123
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Rishishwar L, Wang L, Clayton EA, Mariño-Ramírez L, McDonald JF, Jordan IK. Population and clinical genetics of human transposable elements in the (post) genomic era. Mob Genet Elements 2017; 7:1-20. [PMID: 28228978 PMCID: PMC5305044 DOI: 10.1080/2159256x.2017.1280116] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 10/26/2022] Open
Abstract
Recent technological developments-in genomics, bioinformatics and high-throughput experimental techniques-are providing opportunities to study ongoing human transposable element (TE) activity at an unprecedented level of detail. It is now possible to characterize genome-wide collections of TE insertion sites for multiple human individuals, within and between populations, and for a variety of tissue types. Comparison of TE insertion site profiles between individuals captures the germline activity of TEs and reveals insertion site variants that segregate as polymorphisms among human populations, whereas comparison among tissue types ascertains somatic TE activity that generates cellular heterogeneity. In this review, we provide an overview of these new technologies and explore their implications for population and clinical genetic studies of human TEs. We cover both recent published results on human TE insertion activity as well as the prospects for future TE studies related to human evolution and health.
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Affiliation(s)
- Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; PanAmerican Bioinformatics Institute, Cali, Colombia; Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lu Wang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; PanAmerican Bioinformatics Institute, Cali, Colombia
| | - Evan A Clayton
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; Ovarian Cancer Institute, Atlanta, GA, USA
| | - Leonardo Mariño-Ramírez
- PanAmerican Bioinformatics Institute, Cali, Colombia; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - John F McDonald
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; Ovarian Cancer Institute, Atlanta, GA, USA
| | - I King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA; PanAmerican Bioinformatics Institute, Cali, Colombia; Applied Bioinformatics Laboratory, Atlanta, GA, USA
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124
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Mita P, Savas JN, Briggs EM, Ha S, Gnanakkan V, Yates JR, Robins DM, David G, Boeke JD, Garabedian MJ, Logan SK. URI Regulates KAP1 Phosphorylation and Transcriptional Repression via PP2A Phosphatase in Prostate Cancer Cells. J Biol Chem 2016; 291:25516-25528. [PMID: 27780869 PMCID: PMC5207251 DOI: 10.1074/jbc.m116.741660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/21/2016] [Indexed: 11/06/2022] Open
Abstract
URI (unconventional prefoldin RPB5 interactor protein) is an unconventional prefoldin, RNA polymerase II interactor that functions as a transcriptional repressor and is part of a larger nuclear protein complex. The components of this complex and the mechanism of transcriptional repression have not been characterized. Here we show that KAP1 (KRAB-associated protein 1) and the protein phosphatase PP2A interact with URI. Mechanistically, we show that KAP1 phosphorylation is decreased following recruitment of PP2A by URI. We functionally characterize the novel URI-KAP1-PP2A complex, demonstrating a role of URI in retrotransposon repression, a key function previously demonstrated for the KAP1-SETDB1 complex. Microarray analysis of annotated transposons revealed a selective increase in the transcription of LINE-1 and L1PA2 retroelements upon knockdown of URI. These data unveil a new nuclear function of URI and identify a novel post-transcriptional regulation of KAP1 protein that may have important implications in reactivation of transposable elements in prostate cancer cells.
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Affiliation(s)
- Paolo Mita
- From the Institute of Systems Genetics and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jeffrey N Savas
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Erica M Briggs
- the Departments of Biochemistry and Molecular Pharmacology
| | - Susan Ha
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Veena Gnanakkan
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
| | - John R Yates
- the Department of Chemical Physiology, Scripps Research Institute, La Jolla, California 92037
| | - Diane M Robins
- the Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Gregory David
- the Departments of Biochemistry and Molecular Pharmacology
| | - Jef D Boeke
- From the Institute of Systems Genetics and
- the Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and
- the Departments of Biochemistry and Molecular Pharmacology
| | - Michael J Garabedian
- Urology, and
- Microbiology at New York University School of Medicine, New York, New York 10016
| | - Susan K Logan
- Urology, and
- the Departments of Biochemistry and Molecular Pharmacology
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125
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Shen XD, Hou F, Chen J, Jiang XY, Zou SM. Identification of nuclear localization signal within goldfish Tgf2 transposase. Gene 2016; 593:21-27. [PMID: 27468946 DOI: 10.1016/j.gene.2016.07.060] [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: 05/30/2016] [Revised: 07/12/2016] [Accepted: 07/24/2016] [Indexed: 10/21/2022]
Abstract
The structure of goldfish (Carassius auratus) Tgf2 transposase is still poorly understood, although it can mediate efficient gene transfer in teleost fish. We hypothesized the existence of a nuclear localization signal (NLS) within Tgf2 transposase to assist transport into the nucleus. To explore this, 15 consecutive amino acid residues (656-670 aa) within the C-terminus of Tgf2 transposase were predicted in silico to be a NLS domain. The pEGFP-C1-Tgf2TP(△31C) plasmid encoding the NLS-domain-deleted Tgf2 transposase fused to EGFP was constructed, and transfected into 293T cells. After transfection with pEGFP-C1-Tgf2TP(△31C), EGFP was not detected in the nucleus alone, while 67.0% of cells expressed EGFP only in the cytoplasm. In contrast, after transfection with control plasmids containing C- or N-terminal truncated Tgf2 transposases with an intact NLS domain, EGFP was not detected in the cytoplasm alone, while approximately 40% of cells expressed EGFP only in the nucleus, and the remaining 60% expressed EGFP in both the nucleus and cytoplasm. Our results demonstrated that loss of the NLS domain results in expression in the cytoplasm but not in the nucleus. These findings suggest that 15 aa residues located from 656 to 670 aa within the C-terminus of Tgf2 transposase can function as a NLS to assist the transfer of the transposase into the nucleus where it mediates DNA transposition.
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Affiliation(s)
- Xiao-Dan Shen
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Fei Hou
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Jie Chen
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China
| | - Xia-Yun Jiang
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.
| | - Shu-Ming Zou
- Key Laboratory of Genetic Resources for Freshwater Aquaculture and Fisheries, Shanghai Ocean University, 999 Huchenghuan Road, Shanghai 201306, China.
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126
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Achanta P, Steranka JP, Tang Z, Rodić N, Sharma R, Yang WR, Ma S, Grivainis M, Huang CRL, Schneider AM, Gallia GL, Riggins GJ, Quinones-Hinojosa A, Fenyö D, Boeke JD, Burns KH. Somatic retrotransposition is infrequent in glioblastomas. Mob DNA 2016; 7:22. [PMID: 27843500 PMCID: PMC5105304 DOI: 10.1186/s13100-016-0077-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/13/2016] [Indexed: 11/10/2022] Open
Abstract
Background Gliomas are the most common primary brain tumors in adults. We sought to understand the roles of endogenous transposable elements in these malignancies by identifying evidence of somatic retrotransposition in glioblastomas (GBM). We performed transposon insertion profiling of the active subfamily of Long INterspersed Element-1 (LINE-1) elements by deep sequencing (TIPseq) on genomic DNA of low passage oncosphere cell lines derived from 7 primary GBM biopsies, 3 secondary GBM tissue samples, and matched normal intravenous blood samples from the same individuals. Results We found and PCR validated one somatically acquired tumor-specific insertion in a case of secondary GBM. No LINE-1 insertions present in primary GBM oncosphere cultures were missing from corresponding blood samples. However, several copies of the element (11) were found in genomic DNA from blood and not in the oncosphere cultures. SNP 6.0 microarray analysis revealed deletions or loss of heterozygosity in the tumor genomes over the intervals corresponding to these LINE-1 insertions. Conclusions These findings indicate that LINE-1 retrotransposon can act as an infrequent insertional mutagen in secondary GBM, but that retrotransposition is uncommon in these central nervous system tumors as compared to other neoplasias. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0077-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pragathi Achanta
- Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Zuojian Tang
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: Yale University, New Haven, CT USA
| | - Reema Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
| | - Sisi Ma
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA
| | - Mark Grivainis
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Cheng Ran Lisa Huang
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: L.E.K. Consulting, Boston, MA USA
| | - Anna M Schneider
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,Present address: BioNTech AG, Mainz, Germany
| | - Gary L Gallia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Gregory J Riggins
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Alfredo Quinones-Hinojosa
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD USA.,Present address: Mayo Clinic, Jacksonville, FL USA
| | - David Fenyö
- Center for Health Informatics and Bioinformatics, New York University Langone Medical Center, New York, NY USA.,Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone Medical Center, ACLSW Room 503, 430 East 29th Street, New York, NY 10016 USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Miller Research Building (MRB) Room 447, 733 North Broadway, Baltimore, MD 21205 USA
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127
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Zampella JG, Rodić N, Yang WR, Huang CRL, Welch J, Gnanakkan VP, Cornish TC, Boeke JD, Burns KH. A map of mobile DNA insertions in the NCI-60 human cancer cell panel. Mob DNA 2016; 7:20. [PMID: 27807467 PMCID: PMC5087121 DOI: 10.1186/s13100-016-0078-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/21/2016] [Indexed: 11/13/2022] Open
Abstract
Background The National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy. Method We used Transposon Insertion Profiling by microarray (TIP-chip) to map Long INterspersed Element-1 (LINE-1, L1) and Alu Short INterspersed Element (SINE) insertions in cancer genes in NCI-60 cells. We focused this discovery effort on annotated Cancer Gene Index loci. Results We catalogued a total of 749 and 2,100 loci corresponding to candidate LINE-1 and Alu insertion sites, respectively. As expected, these numbers encompass previously known insertions, polymorphisms shared in unrelated tumor cell lines, as well as unique, potentially tumor-specific insertions. We also conducted association analyses relating individual insertions to a variety of cellular phenotypes. Conclusions These data provide a resource for investigators with interests in specific cancer gene loci or mobile element insertion effects more broadly. Our data underscore that significant genetic variation in cancer genomes is owed to LINE-1 and Alu retrotransposons. Our findings also indicate that as large numbers of cancer genomes become available, it will be possible to associate individual transposable element insertion variants with molecular and phenotypic features of these malignancies. Electronic supplementary material The online version of this article (doi:10.1186/s13100-016-0078-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John G Zampella
- Department of Dermatology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Wan Rou Yang
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Cheng Ran Lisa Huang
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Jane Welch
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Veena P Gnanakkan
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Toby C Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
| | - Jef D Boeke
- McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; Present address: Institute for Systems Genetics, NYU Langone University School of Medicine, New York, NY 10016 USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA
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128
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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129
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Huntriss J, Lu J, Hemmings K, Bayne R, Anderson R, Rutherford A, Balen A, Elder K, Picton HM. Isolation and expression of the human gametocyte-specific factor 1 gene (GTSF1) in fetal ovary, oocytes, and preimplantation embryos. J Assist Reprod Genet 2016; 34:23-31. [PMID: 27646122 PMCID: PMC5330970 DOI: 10.1007/s10815-016-0795-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/16/2016] [Indexed: 01/23/2023] Open
Abstract
Purpose Gametocyte-specific factor 1 has been shown in other species to be required for the silencing of retrotransposons via the Piwi-interacting RNA (piRNA) pathway. In this study, we aimed to isolate and assess expression of transcripts of the gametocyte-specific factor 1 (GTSF1) gene in the human female germline and in preimplantation embryos. Methods Complementary DNA (cDNA) libraries from human fetal ovaries and testes, human oocytes and preimplantation embryos and ovarian follicles isolated from an adult ovarian cortex biopsy were used to as templates for PCR, cloning and sequencing, and real time PCR experiments of GTSF1 expression. Results GTSF1 cDNA clones that covered the entire coding region were isolated from human oocytes and preimplantation embryos. GTSF1 mRNA expression was detected in archived cDNAs from staged human ovarian follicles, germinal vesicle (GV) stage oocytes, metaphase II oocytes, and morula and blastocyst stage preimplantation embryos. Within the adult female germline, expression was highest in GV oocytes. GTSF1 mRNA expression was also assessed in human fetal ovary and was observed to increase during gestation, from 8 to 21 weeks, during which time oogonia enter meiosis and primordial follicle formation first occurs. In human fetal testis, GTSF1 expression also increased from 8 to 19 weeks. Conclusions To our knowledge, this report is the first to describe the expression of the human GTSF1 gene in human gametes and preimplantation embryos. Electronic supplementary material The online version of this article (doi:10.1007/s10815-016-0795-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John Huntriss
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK.
| | - Jianping Lu
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Karen Hemmings
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
| | - Rosemary Bayne
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Richard Anderson
- MRC Centre for Reproductive Health, University of Edinburgh, Queen's Medical Research Institute, Edinburgh, EH16 4TJ, UK
| | - Anthony Rutherford
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Adam Balen
- Leeds Centre for Reproductive Medicine, Leeds Teaching Hospital NHS Trust, Seacroft Hospital, York Road, Leeds, LS14 6UH, UK
| | - Kay Elder
- Bourn Hall Clinic, Cambridge, CB23 2TN, UK
| | - Helen M Picton
- Division of Reproduction and Early Development, Leeds Institute of Cardiovascular and Metabolic Medicine, Clarendon Way, University of Leeds, Leeds, LS2 9JT, UK
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130
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Dufresne F. Don't throw the baby out with the bathwater: identifying and mapping paralogs in salmonids. Mol Ecol Resour 2016; 16:7-9. [PMID: 26768194 DOI: 10.1111/1755-0998.12477] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/02/2015] [Indexed: 11/28/2022]
Abstract
Many eukaryotic genomes contain a large fraction of gene duplicates (or paralogs) as a result of ancient or recent whole-genome duplications (Ohno 1970; Jaillon et al. 2004; Kellis et al. 2004). Identifying paralogs with NGS data is a pervasive problem in both ancient polyploids and neopolyploids. Likewise, paralogs are often treated as a nuisance that has to be detected and removed (Everett et al. 2012). In this issue of Molecular Ecology Resources, Waples et al. (2015) show that exclusion might not be necessary and how we may miss out on important genomic information in doing so. They present a novel statistical approach to detect paralogs based on the segregation of RAD loci in haploid offspring and test their method by constructing linkage maps with and without these duplicated loci in chum salmon, Oncorhynchus keta (Fig.1). Their linkage map including the resolved paralogs shows that these are mostly located in the distal regions of several linkage groups. Particularly intriguing is their finding that these homoeologous regions appear impoverished in transposable elements (TE). Given the role that TE play in genome remodelling, it is noteworthy that these elements are of low abundance in regions showing residual tetrasomic inheritance. This raises the question whether re-diploidization is constrained in these regions and whether they might have a role to play in salmonid speciation. This study provides an original approach to identifying duplicated loci in species with a pedigree, as well as providing a dense linkage map for chum salmon, and interesting insights into the retention of gene duplicates in an ancient polyploid.
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Affiliation(s)
- France Dufresne
- Département de biologie, Université du Québec à Rimouski, 300 allée des ursulines, Rimouski, Quebec, Canada, G5L3A1
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131
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Abstract
Retrotransposons have generated about 40 % of the human genome. This review examines the strategies the cell has evolved to coexist with these genomic "parasites", focussing on the non-long terminal repeat retrotransposons of humans and mice. Some of the restriction factors for retrotransposition, including the APOBECs, MOV10, RNASEL, SAMHD1, TREX1, and ZAP, also limit replication of retroviruses, including HIV, and are part of the intrinsic immune system of the cell. Many of these proteins act in the cytoplasm to degrade retroelement RNA or inhibit its translation. Some factors act in the nucleus and involve DNA repair enzymes or epigenetic processes of DNA methylation and histone modification. RISC and piRNA pathway proteins protect the germline. Retrotransposon control is relaxed in some cell types, such as neurons in the brain, stem cells, and in certain types of disease and cancer, with implications for human health and disease. This review also considers potential pitfalls in interpreting retrotransposon-related data, as well as issues to consider for future research.
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Affiliation(s)
- John L. Goodier
- McKusick-Nathans Institute for Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD USA 212051
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132
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Kassiotis G, Stoye JP. Immune responses to endogenous retroelements: taking the bad with the good. Nat Rev Immunol 2016; 16:207-19. [PMID: 27026073 DOI: 10.1038/nri.2016.27] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The ultimate form of parasitism and evasion of host immunity is for the parasite genome to enter the germ line of the host species. Retroviruses have invaded the host germ line on the grandest scale, and this is evident in the extraordinary abundance of endogenous retroelements in the genome of all vertebrate species that have been studied. Many of these endogenous retroelements have retained viral characteristics; some also the capacity to replicate and, consequently, the potential to trigger host innate and adaptive immune responses. However, although retroelements are mainly recognized for their pathogenic potential, recent evidence suggests that this 'enemy within' may also have beneficial roles in tuning host immune reactivity. In this Review, we discuss how the immune system recognizes and is shaped by endogenous retroelements.
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Affiliation(s)
- George Kassiotis
- Retroviral Immunology, the Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK.,Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK
| | - Jonathan P Stoye
- Department of Medicine, Faculty of Medicine, Imperial College London, London W2 1PG, UK.,Retrovirus-Host Interactions, the Francis Crick Institute, Mill Hill Laboratory, London NW7 1AA, UK
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133
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Ardeljan D, Taylor MS, Burns KH, Boeke JD, Espey MG, Woodhouse EC, Howcroft TK. Meeting Report: The Role of the Mobilome in Cancer. Cancer Res 2016; 76:4316-9. [PMID: 27527733 DOI: 10.1158/0008-5472.can-15-3421] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/13/2016] [Indexed: 11/16/2022]
Abstract
Approximately half of the human genome consists of repetitive sequence attributed to the activities of mobile DNAs, including DNA transposons, RNA transposons, and endogenous retroviruses. Of these, only long interspersed elements (LINE-1 or L1) and sequences copied by LINE-1 remain mobile in our species today. Although cells restrict L1 activity by both transcriptional and posttranscriptional mechanisms, L1 derepression occurs in developmental and pathologic contexts, including many types of cancers. However, we have limited knowledge of the extent and consequences of L1 expression in premalignancies and cancer. Participants in this NIH strategic workshop considered key questions to enhance our understanding of mechanisms and roles the mobilome may play in cancer biology. Cancer Res; 76(15); 4316-9. ©2016 AACR.
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Affiliation(s)
- Daniel Ardeljan
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland. Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Kathleen H Burns
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland. Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jef D Boeke
- Institute for Systems Genetics, New York University Langone Medical Center, New York, New York
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134
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Restriction of Retrotransposon Mobilization in Schizosaccharomyces pombe by Transcriptional Silencing and Higher-Order Chromatin Organization. Genetics 2016; 203:1669-78. [PMID: 27343236 PMCID: PMC4981269 DOI: 10.1534/genetics.116.189118] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/20/2016] [Indexed: 12/23/2022] Open
Abstract
Uncontrolled propagation of retrotransposons is potentially detrimental to host genome integrity. Therefore, cells have evolved surveillance mechanisms to restrict the mobility of these elements. In Schizosaccharomyces pombe the Tf2 LTR retrotransposons are transcriptionally silenced and are also clustered in the nucleus into structures termed Tf bodies. Here we describe the impact of silencing and clustering on the mobility of an endogenous Tf2 element. Deletion of genes such as set1+ (histone H3 lysine 4 methyltransferase) or abp1+ (CENP-B homolog) that both alleviate silencing and clustering, result in a corresponding increase in mobilization. Furthermore, expression of constitutively active Sre1, a transcriptional activator of Tf2 elements, also alleviates clustering and induces mobilization. In contrast, clustering is not disrupted by loss of the HIRA histone chaperone, despite high levels of expression, and in this background, mobilization frequency is only marginally increased. Thus, mutations that compromise transcriptional silencing but not Tf bodies are insufficient to drive mobilization. Furthermore, analyses of mutant alleles that separate the transcriptional repression and clustering functions of Set1 are consistent with control of Tf2 propagation via a combination of silencing and spatial organization. Our results indicate that host surveillance mechanisms operate at multiple levels to restrict Tf2 retrotransposon mobilization.
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135
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Criscione SW, Theodosakis N, Micevic G, Cornish TC, Burns KH, Neretti N, Rodić N. Genome-wide characterization of human L1 antisense promoter-driven transcripts. BMC Genomics 2016; 17:463. [PMID: 27301971 PMCID: PMC4908685 DOI: 10.1186/s12864-016-2800-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/26/2016] [Indexed: 11/23/2022] Open
Abstract
Background Long INterspersed Element-1 (LINE-1 or L1) is the only autonomously active, transposable element in the human genome. L1 sequences comprise approximately 17 % of the human genome, but only the evolutionarily recent, human-specific subfamily is retrotransposition competent. The L1 promoter has a bidirectional orientation containing a sense promoter that drives the transcription of two proteins required for retrotransposition and an antisense promoter. The L1 antisense promoter can drive transcription of chimeric transcripts: 5’ L1 antisense sequences spliced to the exons of neighboring genes. Results The impact of L1 antisense promoter activity on cellular transcriptomes is poorly understood. To investigate this, we analyzed GenBank ESTs for messenger RNAs that initiate in the L1 antisense promoter. We identified 988 putative L1 antisense chimeric transcripts, 911 of which have not been previously reported. These appear to be alternative genic transcripts, sense-oriented with respect to gene and initiating near, but typically downstream of, the gene transcriptional start site. In multiple cell lines, L1 antisense promoters display enrichment for YY1 transcription factor and histone modifications associated with active promoters. Global run-on sequencing data support the activity of the L1 antisense promoter. We independently detected 124 L1 antisense chimeric transcripts using long read Pacific Biosciences RNA-seq data. Furthermore, we validated four chimeric transcripts by quantitative RT-PCR and Sanger sequencing and demonstrated that they are readily detectable in many normal human tissues. Conclusions We present a comprehensive characterization of human L1 antisense promoter-driven transcripts and provide substantial evidence that they are transcribed in a variety of human cell-types. Our findings reveal a new wide-reaching aspect of L1 biology by identifying antisense transcripts affecting as many as 4 % of all human genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2800-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Steven W Criscione
- Department of Molecular Biology, Cell Biology, and Biochemistry, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA
| | - Nicholas Theodosakis
- Department of Pathology, Yale University, New Haven, CT, 06510, USA.,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA
| | - Goran Micevic
- Department of Pathology, Yale University, New Haven, CT, 06510, USA.,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA
| | - Toby C Cornish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,High Throughput (HiT) Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology, and Biochemistry, Center for Computational Molecular Biology, Brown University, Providence, RI, 02912, USA.
| | - Nemanja Rodić
- Department of Pathology, Yale University, New Haven, CT, 06510, USA. .,Department of Dermatology, Division of Dermatopathology, Yale University, New Haven, CT, 06510, USA.
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136
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Guffanti G, Gaudi S, Klengel T, Fallon JH, Mangalam H, Madduri R, Rodriguez A, DeCrescenzo P, Glovienka E, Sobell J, Klengel C, Pato M, Ressler KJ, Pato C, Macciardi F. LINE1 insertions as a genomic risk factor for schizophrenia: Preliminary evidence from an affected family. Am J Med Genet B Neuropsychiatr Genet 2016; 171:534-45. [PMID: 26990047 DOI: 10.1002/ajmg.b.32437] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 02/11/2016] [Indexed: 02/02/2023]
Abstract
Recent studies show that human-specific LINE1s (L1HS) play a key role in the development of the central nervous system (CNS) and its disorders, and that their transpositions within the human genome are more common than previously thought. Many polymorphic L1HS, that is, present or absent across individuals, are not annotated in the current release of the genome and are customarily termed "non-reference L1s." We developed an analytical workflow to identify L1 polymorphic insertions with next-generation sequencing (NGS) using data from a family in which SZ segregates. Our workflow exploits two independent algorithms to detect non-reference L1 insertions, performs local de novo alignment of the regions harboring predicted L1 insertions and resolves the L1 subfamily designation from the de novo assembled sequence. We found 110 non-reference L1 polymorphic loci exhibiting Mendelian inheritance, the vast majority of which are already reported in dbRIP and/or euL1db, thus, confirming their status as non-reference L1 polymorphic insertions. Four previously undetected L1 polymorphic loci were confirmed by PCR amplification and direct sequencing of the insert. A large fraction of our non-reference L1s is located within the open reading frame of protein-coding genes that belong to pathways already implicated in the pathogenesis of schizophrenia. The finding of these polymorphic variants among SZ offsprings is intriguing and suggestive of putative pathogenic role. Our data show the utility of NGS to uncover L1 polymorphic insertions, a neglected type of genetic variants with the potential to influence the risk to develop schizophrenia like SNVs and CNVs. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Guia Guffanti
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Simona Gaudi
- Department of Infectious, Parasitic and Immune-Mediated Diseases, Italian National Institute of Health, Rome, Italy
| | - Torsten Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - James H Fallon
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Harry Mangalam
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California
| | - Ravi Madduri
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Alex Rodriguez
- Division of Mathematics and Computer Science, Argonne National Laboratory, Lemont, Illinois.,Computation Institute, University of Chicago, Chicago, Illinois
| | - Paula DeCrescenzo
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Emily Glovienka
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, New York
| | - Janet Sobell
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Claudia Klengel
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Michele Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Kerry J Ressler
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, Massachusetts
| | - Carlos Pato
- SUNY Downstate, College of Medicine, Brooklyn, New York
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, California.,Center for Autism Research and Treatment (CART), University of California, Irvine, California.,Center for Epigenetics and Metabolism, University of California, Irvine, California
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137
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Honda T. Links between Human LINE-1 Retrotransposons and Hepatitis Virus-Related Hepatocellular Carcinoma. Front Chem 2016; 4:21. [PMID: 27242996 PMCID: PMC4863659 DOI: 10.3389/fchem.2016.00021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for approximately 80% of liver cancers, the third most frequent cause of cancer mortality. The most prevalent risk factors for HCC are infections by hepatitis B or hepatitis C virus. Findings suggest that hepatitis virus-related HCC might be a cancer in which LINE-1 retrotransposon, often termed L1, activity plays a potential role. Firstly, hepatitis viruses can suppress host defense factors that also control L1 mobilization. Secondly, many recent studies also have indicated that hypomethylation of L1 affects the prognosis of HCC patients. Thirdly, endogenous L1 retrotransposition was demonstrated to activate oncogenic pathways in HCC. Fourthly, several L1 chimeric transcripts with host or viral genes are found in hepatitis virus-related HCC. Such lines of evidence suggest a linkage between L1 retrotransposons and hepatitis virus-related HCC. Here, I briefly summarize current understandings of the association between hepatitis virus-related HCC and L1. Then, I discuss potential mechanisms of how hepatitis viruses drive the development of HCC via L1 retrotransposons. An increased understanding of the contribution of L1 to hepatitis virus-related HCC may provide unique insights related to the development of novel therapeutics for this disease.
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Affiliation(s)
- Tomoyuki Honda
- Department of Viral Oncology, Institute for Virus Research, Kyoto UniversityKyoto, Japan; Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of MedicineSuita, Japan
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138
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Philippe C, Vargas-Landin DB, Doucet AJ, van Essen D, Vera-Otarola J, Kuciak M, Corbin A, Nigumann P, Cristofari G. Activation of individual L1 retrotransposon instances is restricted to cell-type dependent permissive loci. eLife 2016; 5. [PMID: 27016617 PMCID: PMC4866827 DOI: 10.7554/elife.13926] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 03/25/2016] [Indexed: 12/26/2022] Open
Abstract
LINE-1 (L1) retrotransposons represent approximately one sixth of the human genome, but only the human-specific L1HS-Ta subfamily acts as an endogenous mutagen in modern humans, reshaping both somatic and germline genomes. Due to their high levels of sequence identity and the existence of many polymorphic insertions absent from the reference genome, the transcriptional activation of individual genomic L1HS-Ta copies remains poorly understood. Here we comprehensively mapped fixed and polymorphic L1HS-Ta copies in 12 commonly-used somatic cell lines, and identified transcriptional and epigenetic signatures allowing the unambiguous identification of active L1HS-Ta copies in their genomic context. Strikingly, only a very restricted subset of L1HS-Ta loci - some being polymorphic among individuals - significantly contributes to the bulk of L1 expression, and these loci are differentially regulated among distinct cell lines. Thus, our data support a local model of L1 transcriptional activation in somatic cells, governed by individual-, locus-, and cell-type-specific determinants. DOI:http://dx.doi.org/10.7554/eLife.13926.001 Retrotransposons, also known as jumping genes, have invaded the genomes of most living organisms. These fragments of DNA have the ability to move or copy themselves from one location of a chromosome to another. Depending on where they insert themselves, retrotransposons can modify the sequence of nearby genes, which can alter or even abolish their activity. Although these genetic modifications have contributed significantly to the evolution of different species, retrotransposons can also have detrimental effects; for example, by causing new cases of genetic diseases. Adult human cells have a number of mechanisms that work to keep the activity of retrotransposons at a very low level. However, in many types of cancers retrotransposons escape these defense mechanisms and ‘jump’ actively. This is thought to contribute to the development and spread of cancerous tumors. To understand how jumping genes are mobilized, a fundamental question must be answered: is the high jumping gene activity observed in some cell types a result of activating many copies of the retrotransposons, or only a few of them? This question has been difficult to address because there are more than one hundred copies of retrotransposons that could potentially move in humans, many of which have not even been referenced in the human genome map. Furthermore, each copy is almost identical to another one, making it difficult to discriminate between them. Philippe et al. have now developed an approach that can map where individual retrotransposons are located in the genome of normal and cancerous cells and measure how active these jumping genes are. This revealed that only a very restricted number of them are active in any given cell type. Moreover, different subsets of jumping genes are active in different cell types, and their locations in the genome often do not overlap. Thus, whether jumping genes are activated depends on the cell type and their position in the genome. These results are in contrast to the prevalent view that retrotransposons are activated in a more widespread manner across the genome, at least in cancerous cells. Overall, Philippe et al.’s findings pave the way towards characterizing the chromosome regions in which retrotransposons are frequently activated and understanding how they contribute to cancer and other diseases. DOI:http://dx.doi.org/10.7554/eLife.13926.002
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Affiliation(s)
- Claude Philippe
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dulce B Vargas-Landin
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure, Paris, France
| | - Aurélien J Doucet
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
| | - Dominic van Essen
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Jorge Vera-Otarola
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Monika Kuciak
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,Ecole Normale Supérieure de Lyon, Lyon, France
| | | | - Pilvi Nigumann
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France
| | - Gaël Cristofari
- INSERM U1081, CNRS UMR 7284, Institute for Research on Cancer and Aging of Nice, Nice, France.,Faculty of Medicine, University of Nice-Sophia Antipolis, Nice, France.,FHU OncoAge, University of Nice-Sophia Antipolis, Nice, France
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139
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Abstract
Transposable elements have had a profound impact on the structure and function of mammalian genomes. The retrotransposon Long INterspersed Element-1 (LINE-1 or L1), by virtue of its replicative mobilization mechanism, comprises ∼17% of the human genome. Although the vast majority of human LINE-1 sequences are inactive molecular fossils, an estimated 80-100 copies per individual retain the ability to mobilize by a process termed retrotransposition. Indeed, LINE-1 is the only active, autonomous retrotransposon in humans and its retrotransposition continues to generate both intra-individual and inter-individual genetic diversity. Here, we briefly review the types of transposable elements that reside in mammalian genomes. We will focus our discussion on LINE-1 retrotransposons and the non-autonomous Short INterspersed Elements (SINEs) that rely on the proteins encoded by LINE-1 for their mobilization. We review cases where LINE-1-mediated retrotransposition events have resulted in genetic disease and discuss how the characterization of these mutagenic insertions led to the identification of retrotransposition-competent LINE-1s in the human and mouse genomes. We then discuss how the integration of molecular genetic, biochemical, and modern genomic technologies have yielded insight into the mechanism of LINE-1 retrotransposition, the impact of LINE-1-mediated retrotransposition events on mammalian genomes, and the host cellular mechanisms that protect the genome from unabated LINE-1-mediated retrotransposition events. Throughout this review, we highlight unanswered questions in LINE-1 biology that provide exciting opportunities for future research. Clearly, much has been learned about LINE-1 and SINE biology since the publication of Mobile DNA II thirteen years ago. Future studies should continue to yield exciting discoveries about how these retrotransposons contribute to genetic diversity in mammalian genomes.
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140
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Solovei I, Thanisch K, Feodorova Y. How to rule the nucleus: divide et impera. Curr Opin Cell Biol 2016; 40:47-59. [PMID: 26938331 DOI: 10.1016/j.ceb.2016.02.014] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/04/2016] [Accepted: 02/14/2016] [Indexed: 01/14/2023]
Abstract
Genome-wide molecular studies have provided new insights into the organization of nuclear chromatin by revealing the presence of chromatin domains of differing transcriptional activity, frequency of cis-interactions, proximity to scaffolding structures and replication timing. These studies have not only brought our understanding of genome function to a new level, but also offered functional insight for many phenomena observed in microscopic studies. In this review, we discuss the major principles of nuclear organization based on the spatial segregation of euchromatin and heterochromatin, as well as the dynamic genome rearrangements occurring during cell differentiation and development. We hope to unite the existing molecular and microscopic data on genome organization to get a holistic view of the nucleus, and propose a model, in which repeat repertoire together with scaffolding structures blueprint the functional nuclear architecture.
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Affiliation(s)
- Irina Solovei
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany.
| | - Katharina Thanisch
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany
| | - Yana Feodorova
- Department of Biology II, Ludwig Maximilians University Munich, Grosshadernerstrasse 2, Planegg-Martinsried 82152, Germany; Department of Medical Biology, Medical University-Plovdiv, Boulevard Vasil Aprilov 15A, Plovdiv 4000, Bulgaria
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141
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Konkel MK, Ullmer B, Arceneaux EL, Sanampudi S, Brantley SA, Hubley R, Smit AFA, Batzer MA. Discovery of a new repeat family in the Callithrix jacchus genome. Genome Res 2016; 26:649-59. [PMID: 26916108 PMCID: PMC4864456 DOI: 10.1101/gr.199075.115] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 02/23/2016] [Indexed: 11/24/2022]
Abstract
We identified a novel repeat family, termed Platy-1, in the Callithrix jacchus (common marmoset) genome that arose around the time of the divergence of platyrrhines and catarrhines and established itself as a repeat family in New World monkeys (NWMs). A full-length Platy-1 element is ∼100 bp in length, making it the shortest known short interspersed element (SINE) in primates, and harbors features characteristic of non-LTR retrotransposons. We identified 2268 full-length Platy-1 elements across 62 subfamilies in the common marmoset genome. Our subfamily reconstruction and phylogenetic analyses support Platy-1 propagation throughout the evolution of NWMs in the lineage leading to C. jacchus Platy-1 appears to have reached its amplification peak in the common ancestor of current day marmosets and has since moderately declined. However, identification of more than 200 Platy-1 elements identical to their respective consensus sequence, and the presence of polymorphic elements within common marmoset populations, suggests ongoing retrotransposition activity. Platy-1, a SINE, appears to have originated from an Alu element, and hence is likely derived from 7SL RNA. Our analyses illustrate the birth of a new repeat family and its propagation dynamics in the lineage leading to the common marmoset over the last 40 million years.
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Affiliation(s)
- Miriam K Konkel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Brygg Ullmer
- School of Electrical Engineering and Computer Science, Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Erika L Arceneaux
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Sreeja Sanampudi
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Sarah A Brantley
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Robert Hubley
- Institute for Systems Biology, Seattle, Washington 98109-5263, USA
| | - Arian F A Smit
- Institute for Systems Biology, Seattle, Washington 98109-5263, USA
| | - Mark A Batzer
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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142
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Naville M, Warren IA, Haftek-Terreau Z, Chalopin D, Brunet F, Levin P, Galiana D, Volff JN. Not so bad after all: retroviruses and long terminal repeat retrotransposons as a source of new genes in vertebrates. Clin Microbiol Infect 2016; 22:312-323. [PMID: 26899828 DOI: 10.1016/j.cmi.2016.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/24/2022]
Abstract
Viruses and transposable elements, once considered as purely junk and selfish sequences, have repeatedly been used as a source of novel protein-coding genes during the evolution of most eukaryotic lineages, a phenomenon called 'molecular domestication'. This is exemplified perfectly in mammals and other vertebrates, where many genes derived from long terminal repeat (LTR) retroelements (retroviruses and LTR retrotransposons) have been identified through comparative genomics and functional analyses. In particular, genes derived from gag structural protein and envelope (env) genes, as well as from the integrase-coding and protease-coding sequences, have been identified in humans and other vertebrates. Retroelement-derived genes are involved in many important biological processes including placenta formation, cognitive functions in the brain and immunity against retroelements, as well as in cell proliferation, apoptosis and cancer. These observations support an important role of retroelement-derived genes in the evolution and diversification of the vertebrate lineage.
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Affiliation(s)
- M Naville
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - I A Warren
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - Z Haftek-Terreau
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Chalopin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France; Department of Genetics, University of Georgia, Athens, GA, USA
| | - F Brunet
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - P Levin
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - D Galiana
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France
| | - J-N Volff
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR5242, Université Lyon 1, Lyon, France.
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143
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Mita P, Boeke JD. How retrotransposons shape genome regulation. Curr Opin Genet Dev 2016; 37:90-100. [PMID: 26855260 DOI: 10.1016/j.gde.2016.01.001] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 12/30/2015] [Accepted: 01/17/2016] [Indexed: 12/30/2022]
Abstract
Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA.
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry & Molecular Pharmacology, NYU Langone Medical Center, 430 East 29 Street, NY, NY 10016, USA
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144
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Conover HN, Argueso JL. Contrasting mechanisms of de novo copy number mutagenesis suggest the existence of different classes of environmental copy number mutagens. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2016; 57:3-9. [PMID: 26247157 DOI: 10.1002/em.21967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 07/05/2015] [Accepted: 07/07/2015] [Indexed: 05/23/2023]
Abstract
While gene copy number variations (CNVs) are abundant in the human genome, and often are associated with disease consequences, the mutagenic pathways and environmental exposures that cause these large structural mutations are understudied relative to conventional nucleotide substitutions in DNA. The members of the environmental mutagenesis community are currently seeking to remedy this deficiency, and there is a renewed interest in the development of mutagenicity assays to identify and characterize compounds that may induce de novo CNVs in humans. To achieve this goal, it is critically important to acknowledge that CNVs exist in two very distinct classes: nonrecurrent and recurrent CNVs. The goal of this commentary is to emphasize the deep contrasts that exist between the proposed pathways that lead to these two mutation classes. Nonrecurrent de novo CNVs originate primarily in mitotic cells through replication-dependent DNA repair pathways that involve microhomologies (<10 bp), and are detected at higher frequency in children of older fathers. In contrast, recurrent de novo CNVs are most often formed in meiotic cells through homologous recombination between nonallelic large low-copy repeats (>10,000 bp), without an associated paternal age effect. Given the biological differences between the two CNV classes, it is our belief that nonrecurrent and recurrent CN mutagens will probably differ substantially in their modes of action. Therefore, each CNV class may require their own uniquely designed assays, so that we as a field may succeed in uncovering the broadest possible spectrum of environmental CN mutagens.
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Affiliation(s)
- Hailey N Conover
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Cell and Molecular Biology Graduate Program, Institute for Genome Architecture and Function, Colorado State University, Fort Collins, Colorado
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145
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Abstract
The LINE-1 retrotransposon (L1) encodes two proteins, ORF1p and ORF2p, which bind to the L1 RNA in cis, forming a ribonucleoprotein (RNP) complex that is critical for retrotransposition. Interactions with both permissive and repressive host factors pervade every step of the L1 life cycle. Until recently, limitations in detection and production precluded in-depth characterization of L1 RNPs. Inducible expression and recombinant engineering of epitope tags have made detection of both L1 ORFs routine. Here, we describe large-scale production of L1-expressing HEK-293T cells in suspension cell culture, cryomilling and affinity capture of L1 RNP complexes, sample preparation for analysis by mass spectrometry, and assay using the L1 element amplification protocol (LEAP) and qRT-PCR.
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146
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Sharma R, Rodić N, Burns KH, Taylor MS. Immunodetection of Human LINE-1 Expression in Cultured Cells and Human Tissues. Methods Mol Biol 2016; 1400:261-80. [PMID: 26895059 DOI: 10.1007/978-1-4939-3372-3_17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Long interspersed element-1 (LINE-1) is the only active protein-coding retrotransposon in humans. It is not expressed in somatic tissue but is aberrantly expressed in a wide variety of human cancers. ORF1p protein is the most robust indicator of LINE-1 expression; the protein accumulates in large quantities in cellular cytoplasm. Recently, monoclonal antibodies have allowed more complete characterizations of ORF1p expression and indicated potential for developing ORF1p as a clinical biomarker. Here, we describe a mouse monoclonal antibody specific for human LINE-1 ORF1p and its application in immunofluorescence and immunohistochemistry of both cells and human tissues. We also describe detection of tagged LINE-1 ORF2p via immunofluorescence. These general methods may be readily adapted to use with many other proteins and antibodies.
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Affiliation(s)
- Reema Sharma
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, MRB 469, Baltimore, MD, 21205, USA
| | - Nemanja Rodić
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, MRB 469, Baltimore, MD, 21205, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, MRB 469, Baltimore, MD, 21205, USA.
| | - Martin S Taylor
- Department of Pathology, Johns Hopkins University School of Medicine, 733 N. Broadway, MRB 469, Baltimore, MD, 21205, USA. .,Department of Pathology, Massachusetts General Hospital, Boston, MA, USA.
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147
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Lin S, Zhang L, Luo W, Zhang X. Characteristics of Antisense Transcript Promoters and the Regulation of Their Activity. Int J Mol Sci 2015; 17:E9. [PMID: 26703594 PMCID: PMC4730256 DOI: 10.3390/ijms17010009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 11/23/2015] [Accepted: 12/16/2015] [Indexed: 02/07/2023] Open
Abstract
Recently, an increasing number of studies on natural antisense transcripts have been reported, especially regarding their classification, temporal and spatial expression patterns, regulatory functions and mechanisms. It is well established that natural antisense transcripts are produced from the strand opposite to the strand encoding a protein. Despite the pivotal roles of natural antisense transcripts in regulating the expression of target genes, the transcriptional mechanisms initiated by antisense promoters (ASPs) remain unknown. To date, nearly all of the studies conducted on this topic have focused on the ASP of a single gene of interest, whereas no study has systematically analyzed the locations of ASPs in the genome, ASP activity, or factors influencing this activity. This review focuses on elaborating on and summarizing the characteristics of ASPs to extend our knowledge about the mechanisms of antisense transcript initiation.
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Affiliation(s)
- Shudai Lin
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Li Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
- Agricultural College, Guangdong Ocean University, Zhanjiang 524088, China.
| | - Wen Luo
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
| | - Xiquan Zhang
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
- Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, Guangzhou 510642, China.
- Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, China.
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148
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Vijaya Chandra SH, Makhija H, Peter S, Myint Wai CM, Li J, Zhu J, Ren Z, D'Alcontres MS, Siau JW, Chee S, Ghadessy FJ, Dröge P. Conservative site-specific and single-copy transgenesis in human LINE-1 elements. Nucleic Acids Res 2015; 44:e55. [PMID: 26673710 PMCID: PMC4824084 DOI: 10.1093/nar/gkv1345] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/17/2015] [Indexed: 12/22/2022] Open
Abstract
Genome engineering of human cells plays an important role in biotechnology and molecular medicine. In particular, insertions of functional multi-transgene cassettes into suitable endogenous sequences will lead to novel applications. Although several tools have been exploited in this context, safety issues such as cytotoxicity, insertional mutagenesis and off-target cleavage together with limitations in cargo size/expression often compromise utility. Phage λ integrase (Int) is a transgenesis tool that mediates conservative site-specific integration of 48 kb DNA into a safe harbor site of the bacterial genome. Here, we show that an Int variant precisely recombines large episomes into a sequence, term edattH4X, found in 1000 human Long INterspersed Elements-1 (LINE-1). We demonstrate single-copy transgenesis through attH4X-targeting in various cell lines including hESCs, with the flexibility of selecting clones according to transgene performance and downstream applications. This is exemplified with pluripotency reporter cassettes and constitutively expressed payloads that remain functional in LINE1-targeted hESCs and differentiated progenies. Furthermore, LINE-1 targeting does not induce DNA damage-response or chromosomal aberrations, and neither global nor localized endogenous gene expression is substantially affected. Hence, this simple transgene addition tool should become particularly useful for applications that require engineering of the human genome with multi-transgenes.
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Affiliation(s)
| | - Harshyaa Makhija
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Cho Mar Myint Wai
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Jinming Li
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | - Jindong Zhu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | - Zhonglu Ren
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Tonghe GuangZhou 510515, People's Republic of China State Key Laboratory of Organ Failure Research, Division of Nephrology, Nanfang Hospital, Tonghe, Guangzhou 510515, People's Republic of China
| | | | - Jia Wei Siau
- p53Lab, Agency for Science Technology and Research, Singapore 138673
| | - Sharon Chee
- p53Lab, Agency for Science Technology and Research, Singapore 138673
| | | | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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149
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A Small RNA-Based Immune System Defends Germ Cells against Mobile Genetic Elements. Stem Cells Int 2015; 2016:7595791. [PMID: 26681955 PMCID: PMC4670677 DOI: 10.1155/2016/7595791] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 06/11/2015] [Indexed: 11/17/2022] Open
Abstract
Transposons are mobile genetic elements that threaten the survival of species by destabilizing the germline genomes. Limiting the spread of these selfish elements is imperative. Germ cells employ specialized small regulatory RNA pathways to restrain transposon activity. PIWI proteins and Piwi-interacting RNAs (piRNAs) silence transposons at the transcriptional and posttranscriptional level with loss-of-function mutant animals universally exhibiting sterility often associated with germ cell defects. This short review aims to illustrate basic strategies of piRNA-guided defense against transposons. Mechanisms of piRNA silencing are most readily studied in Drosophila melanogaster, which serves as a model to delineate molecular concepts and as a reference for mammalian piRNA systems. PiRNA pathways utilize two major strategies to handle the challenges of transposon control: (1) the hard-wired molecular memory of prior transpositions enables recognition of mobile genetic elements and discriminates transposons from host genes; (2) a feed-forward adaptation mechanism shapes piRNA populations to selectively combat the immediate threat of transposon transcripts. In flies, maternally contributed PIWI-piRNA complexes bolster both of these lines of defense and ensure transgenerational immunity. While recent studies have provided a conceptual framework of what could be viewed as an ancient immune system, we are just beginning to appreciate its many molecular innovations.
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Ahl V, Keller H, Schmidt S, Weichenrieder O. Retrotransposition and Crystal Structure of an Alu RNP in the Ribosome-Stalling Conformation. Mol Cell 2015; 60:715-727. [PMID: 26585389 DOI: 10.1016/j.molcel.2015.10.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/14/2015] [Accepted: 10/01/2015] [Indexed: 10/22/2022]
Abstract
The Alu element is the most successful human genomic parasite affecting development and causing disease. It originated as a retrotransposon during early primate evolution of the gene encoding the signal recognition particle (SRP) RNA. We defined a minimal Alu RNA sufficient for effective retrotransposition and determined a high-resolution structure of its complex with the SRP9/14 proteins. The RNA adopts a compact, closed conformation that matches the envelope of the SRP Alu domain in the ribosomal translation elongation factor-binding site. Conserved structural elements in SRP RNAs support an ancient function of the closed conformation that predates SRP9/14. Structure-based mutagenesis shows that retrotransposition requires the closed conformation of the Alu ribonucleoprotein particle and is consistent with the recognition of stalled ribosomes. We propose that ribosome stalling is a common cause for the cis-preference of the mammalian L1 retrotransposon and for the efficiency of the Alu RNA in hijacking nascent L1 reverse transcriptase.
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Affiliation(s)
- Valentina Ahl
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Heiko Keller
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Steffen Schmidt
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany
| | - Oliver Weichenrieder
- Department of Biochemistry, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.
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