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Garza AB, Lerat E, Girgis HZ. Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats. Mob DNA 2024; 15:8. [PMID: 38627766 PMCID: PMC11020628 DOI: 10.1186/s13100-024-00317-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 03/08/2024] [Indexed: 04/20/2024] Open
Abstract
Plant genomes include large numbers of transposable elements. One particular type of these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such elements are known as LTR-retrotransposons; they are the most abundant type of transposons in plant genomes. They have many important functions involving gene regulation and the rise of new genes and pseudo genes in response to severe stress. Additionally, LTR-retrotransposons have several applications in biotechnology. Due to the abundance and the importance of LTR-retrotransposons, multiple computational tools have been developed for their detection. However, none of these tools take advantages of the availability of related genomes; they process one chromosome at a time. Further, recently nested LTR-retrotransposons (multiple elements of the same family are inserted into each other) cannot be annotated accurately - or cannot be annotated at all - by the currently available tools. Motivated to overcome these two limitations, we built Look4LTRs, which can annotate LTR-retrotransposons in multiple related genomes simultaneously and discover recently nested elements. The methodology of Look4LTRs depends on techniques imported from the signal-processing field, graph algorithms, and machine learning with a minimal use of alignment algorithms. Four plant genomes were used in developing Look4LTRs and eight plant genomes for evaluating it in contrast to three related tools. Look4LTRs is the fastest while maintaining better or comparable F1 scores (the harmonic average of recall and precision) to those obtained by the other tools. Our results demonstrate the added benefit of annotating LTR-retrotransposons in multiple related genomes simultaneously and the ability to discover recently nested elements. Expert human manual examination of six elements - not included in the ground truth - revealed that three elements belong to known families and two elements are likely from new families. With respect to examining recently nested LTR-retrotransposons, three out of five were confirmed to be valid elements. Look4LTRs - with its speed, accuracy, and novel features - represents a true advancement in the annotation of LTR-retrotransposons, opening the door to many studies focused on understanding their functions in plants.
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Affiliation(s)
- Anthony B Garza
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA
| | - Emmanuelle Lerat
- The Biometrics and Evolutionary Biology Laboratory, University Lyon 1, Lyon, France
| | - Hani Z Girgis
- Bioinformatics Toolsmith Laboratory, Department of Electrical Engineering and Computer Science, Texas A &M University-Kingsville, Kingsville, Texas, USA.
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López JO, Quiñones JL, Martínez ED. Improved LINE-1 Detection through Pattern Matching by Increasing Probe Length. BIOLOGY 2024; 13:236. [PMID: 38666848 PMCID: PMC11047891 DOI: 10.3390/biology13040236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/22/2024] [Accepted: 03/04/2024] [Indexed: 04/28/2024]
Abstract
Long Interspersed Element-1 (LINE-1 or L1) is an autonomous transposable element that accounts for 17% of the human genome. Strong correlations between abnormal L1 expression and diseases, particularly cancer, have been documented by numerous studies. L1PD (LINE-1 Pattern Detection) had been previously created to detect L1s by using a fixed pre-determined set of 50-mer probes and a pattern-matching algorithm. L1PD uses a novel seed-and-pattern-match strategy as opposed to the well-known seed-and-extend strategy employed by other tools. This study discusses an improved version of L1PD that shows how increasing the size of the k-mer probes from 50 to 75 or to 100 yields better results, as evidenced by experiments showing higher precision and recall when compared to the 50-mers. The probe-generation process was updated and the corresponding software is now shared so that users may generate probes for other reference genomes (with certain limitations). Additionally, L1PD was applied to other non-human genomes, such as dogs, horses, and cows, to further validate the pattern-matching strategy. The improved version of L1PD proves to be an efficient and promising approach for L1 detection.
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Affiliation(s)
- Juan O. López
- Department of Computer Science, University of Puerto Rico at Arecibo, Arecibo 00612, Puerto Rico; (J.L.Q.); (E.D.M.)
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3
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Oomen ME, Torres-Padilla ME. Jump-starting life: balancing transposable element co-option and genome integrity in the developing mammalian embryo. EMBO Rep 2024; 25:1721-1733. [PMID: 38528171 PMCID: PMC11015026 DOI: 10.1038/s44319-024-00118-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/27/2024] Open
Abstract
Remnants of transposable elements (TEs) are widely expressed throughout mammalian embryo development. Originally infesting our genomes as selfish elements and acting as a source of genome instability, several of these elements have been co-opted as part of a complex system of genome regulation. Many TEs have lost transposition ability and their transcriptional potential has been tampered as a result of interactions with the host throughout evolutionary time. It has been proposed that TEs have been ultimately repurposed to function as gene regulatory hubs scattered throughout our genomes. In the early embryo in particular, TEs find a perfect environment of naïve chromatin to escape transcriptional repression by the host. As a consequence, it is thought that hosts found ways to co-opt TE sequences to regulate large-scale changes in chromatin and transcription state of their genomes. In this review, we discuss several examples of TEs expressed during embryo development, their potential for co-option in genome regulation and the evolutionary pressures on TEs and on our genomes.
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Affiliation(s)
- Marlies E Oomen
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany.
- Faculty of Biology, Ludwig-Maximilians Universität, München, Germany.
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4
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Singh S, Borkar MR, Bhatt LK. Transposable Elements: Emerging Therapeutic Targets in Neurodegenerative Diseases. Neurotox Res 2024; 42:9. [PMID: 38270797 DOI: 10.1007/s12640-024-00688-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/14/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Neurodegenerative diseases, such as Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are characterized by the progressive loss of neuronal function and structure. While several genetic and environmental factors have been implicated in the pathogenesis of these disorders, emerging evidence suggests that transposable elements (TEs), once considered "junk DNA," play a significant role in their development and progression. TEs are mobile genetic elements capable of moving within the genome, and their dysregulation has been associated with genomic instability, altered gene expression, and neuroinflammation. This review provides an overview of TEs, including long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and endogenous retroviruses (ERVs), mechanisms of repression and derepression, and their potential impact on neurodegeneration. The evidence linking TEs to AD, PD, and ALS by shedding light on the complex interactions between TEs and neurodegeneration has been discussed. Furthermore, the therapeutic potential of targeting TEs in neurodegenerative diseases has been explored. Understanding the role of TEs in neurodegeneration holds promise for developing novel therapeutic strategies aimed at mitigating disease progression and preserving neuronal health.
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Affiliation(s)
- Shrishti Singh
- Department of Pharmacology, Bhanuben Nanavati College of Pharmacy, SVKM's DrVile Parle (W), Mumbai, India
| | - Maheshkumar R Borkar
- Department of Pharmaceutical Chemistry, SVKM's Dr, Bhanuben Nanavati College of Pharmacy, Vile Parle (W), Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, Bhanuben Nanavati College of Pharmacy, SVKM's DrVile Parle (W), Mumbai, India.
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5
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Ge LP, Jin X, Ma D, Wang ZY, Liu CL, Zhou CZ, Zhao S, Yu TJ, Liu XY, Di GH, Shao ZM, Jiang YZ. ZNF689 deficiency promotes intratumor heterogeneity and immunotherapy resistance in triple-negative breast cancer. Cell Res 2024; 34:58-75. [PMID: 38168642 PMCID: PMC10770380 DOI: 10.1038/s41422-023-00909-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive disease characterized by remarkable intratumor heterogeneity (ITH), which poses therapeutic challenges. However, the clinical relevance and key determinant of ITH in TNBC are poorly understood. Here, we comprehensively characterized ITH levels using multi-omics data across our center's cohort (n = 260), The Cancer Genome Atlas cohort (n = 134), and four immunotherapy-treated cohorts (n = 109). Our results revealed that high ITH was associated with poor patient survival and immunotherapy resistance. Importantly, we identified zinc finger protein 689 (ZNF689) deficiency as a crucial determinant of ITH formation. Mechanistically, the ZNF689-TRIM28 complex was found to directly bind to the promoter of long interspersed element-1 (LINE-1), inducing H3K9me3-mediated transcriptional silencing. ZNF689 deficiency reactivated LINE-1 retrotransposition to exacerbate genomic instability, which fostered ITH. Single-cell RNA sequencing, spatially resolved transcriptomics and flow cytometry analysis confirmed that ZNF689 deficiency-induced ITH inhibited antigen presentation and T-cell activation, conferring immunotherapy resistance. Pharmacological inhibition of LINE-1 significantly reduced ITH, enhanced antitumor immunity, and eventually sensitized ZNF689-deficient tumors to immunotherapy in vivo. Consistently, ZNF689 expression positively correlated with favorable prognosis and immunotherapy response in clinical samples. Altogether, our study uncovers a previously unrecognized mechanism underlying ZNF689 deficiency-induced ITH and suggests LINE-1 inhibition combined with immunotherapy as a novel treatment strategy for TNBC.
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Affiliation(s)
- Li-Ping Ge
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zi-Yu Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao-Zheng Zhou
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian-Jian Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Human Phenome Institute, Fudan University, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Macke EL, Miller AR, Stonerock E, Olshefski R, Zajo K, Bedrosian TA, Mardis ER, Akkari YMN, Cottrell CE, Schieffer KM. A LINE-1 mediated deletion resulting in germline retinoblastoma predisposition. Neurooncol Adv 2024; 6:vdad163. [PMID: 38213835 PMCID: PMC10783486 DOI: 10.1093/noajnl/vdad163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024] Open
Abstract
Retinoblastoma is an ocular cancer associated with genomic variation in the RB1 gene. In individuals with bilateral retinoblastoma, a germline variant in RB1 is identified in virtually all cases. We describe herein an individual with bilateral retinoblastoma for whom multiple clinical lab assays performed by outside commercial laboratories failed to identify a germline RB1 variant. Paired tumor/normal exome sequencing, long-read whole genome sequencing, and long-read isoform sequencing was performed on a translational research basis ultimately identified a germline likely de novo Long Interspersed Nuclear Element (LINE)-1 mediated deletion resulting in a premature stop of translation of RB1 as the underlying genetic cause of retinoblastoma in this individual. Based on these research findings, the LINE-1 mediated deletion was confirmed via Sanger sequencing in our clinical laboratory, and results were reported in the patient's medical record to allow for appropriate genetic counseling.
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Affiliation(s)
- Erica L Macke
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Eileen Stonerock
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Randal Olshefski
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Kristin Zajo
- Division of Hematology/Oncology/BMT, Department of Pediatrics, Nationwide Children’s Hospital, Columbus, Ohio, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
| | - Yassmine M N Akkari
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio, USA
- Department of Pediatrics, The Ohio State University, Columbus, Ohio, USA
- Department of Pathology, The Ohio State University, Columbus, Ohio, USA
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7
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Milosevic I, Todorovic N, Filipovic A, Simic J, Markovic M, Stevanovic O, Malinic J, Katanic N, Mitrovic N, Nikolic N. HCV and HCC Tango-Deciphering the Intricate Dance of Disease: A Review Article. Int J Mol Sci 2023; 24:16048. [PMID: 38003240 PMCID: PMC10671156 DOI: 10.3390/ijms242216048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/12/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Hepatitis C virus (HCV) is a major cause of hepatocellular carcinoma (HCC) accounting for around one-third of all HCC cases. Prolonged inflammation in chronic hepatitis C (CHC), maintained through a variety of pro- and anti-inflammatory mediators, is one of the aspects of carcinogenesis, followed by mitochondrial dysfunction and oxidative stress. Immune response dysfunction including the innate and adaptive immunity also plays a role in the development, as well as in the recurrence of HCC after treatment. Some of the tumor suppressor genes inhibited by the HCV proteins are p53, p73, and retinoblastoma 1. Mutations in the telomerase reverse transcriptase promoter and the oncogene catenin beta 1 are two more important carcinogenic signaling pathways in HCC associated with HCV. Furthermore, in HCV-related HCC, numerous tumor suppressor and seven oncogenic genes are dysregulated by epigenetic changes. Epigenetic regulation of gene expression is considered as a lasting "epigenetic memory", suggesting that HCV-induced changes persist and are associated with liver carcinogenesis even after cure. Epigenetic changes and immune response dysfunction are recognized targets for potential therapy of HCC.
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Affiliation(s)
- Ivana Milosevic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Nevena Todorovic
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Ana Filipovic
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Jelena Simic
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Marko Markovic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Olja Stevanovic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Jovan Malinic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Natasa Katanic
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
- Faculty of Medicine, University of Pristina Situated in Kosovska Mitrovica, 28000 Kosovska Mitrovica, Serbia
| | - Nikola Mitrovic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
| | - Natasa Nikolic
- Faculty of Medicine, Department for Infectious Diseases, University of Belgrade, 11000 Belgrade, Serbia; (I.M.); (M.M.); (O.S.); (J.M.); (N.M.)
- University Clinic for Infectious and Tropical Diseases, University Clinical Center of Serbia, Bulevar Oslobodjenja 16, 11000 Belgrade, Serbia; (N.T.); (A.F.); (J.S.); (N.K.)
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Gebrie A. Transposable elements as essential elements in the control of gene expression. Mob DNA 2023; 14:9. [PMID: 37596675 PMCID: PMC10439571 DOI: 10.1186/s13100-023-00297-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Interspersed repetitions called transposable elements (TEs), commonly referred to as mobile elements, make up a significant portion of the genomes of higher animals. TEs contribute in controlling the expression of genes locally and even far away at the transcriptional and post-transcriptional levels, which is one of their significant functional effects on gene function and genome evolution. There are different mechanisms through which TEs control the expression of genes. First, TEs offer cis-regulatory regions in the genome with their inherent regulatory features for their own expression, making them potential factors for controlling the expression of the host genes. Promoter and enhancer elements contain cis-regulatory sites generated from TE, which function as binding sites for a variety of trans-acting factors. Second, a significant portion of miRNAs and long non-coding RNAs (lncRNAs) have been shown to have TEs that encode for regulatory RNAs, revealing the TE origin of these RNAs. Furthermore, it was shown that TE sequences are essential for these RNAs' regulatory actions, which include binding to the target mRNA. By being a member of cis-regulatory and regulatory RNA sequences, TEs therefore play essential regulatory roles. Additionally, it has been suggested that TE-derived regulatory RNAs and cis-regulatory regions both contribute to the evolutionary novelty of gene regulation. Additionally, these regulatory systems arising from TE frequently have tissue-specific functions. The objective of this review is to discuss TE-mediated gene regulation, with a particular emphasis on the processes, contributions of various TE types, differential roles of various tissue types, based mostly on recent studies on humans.
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Affiliation(s)
- Alemu Gebrie
- Department of Biomedical Sciences, School of Medicine, Debre Markos University, Debre Markos, Ethiopia.
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George S, Cassidy RN, Saintilnord WN, Fondufe-Mittendorf Y. Epigenomic reprogramming in iAs-mediated carcinogenesis. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2022; 96:319-365. [PMID: 36858778 DOI: 10.1016/bs.apha.2022.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Arsenic is a naturally occurring metal carcinogen found in the Earth's crust. Millions of people worldwide are chronically exposed to arsenic through drinking water and food. Exposure to inorganic arsenic has been implicated in many diseases ranging from acute toxicities to malignant transformations. Despite the well-known deleterious health effects of arsenic exposure, the molecular mechanisms in arsenic-mediated carcinogenesis are not fully understood. Since arsenic is non-mutagenic, the mechanism by which arsenic causes carcinogenesis is via alterations in epigenetic-regulated gene expression. There are two possible ways by which arsenic may modify the epigenome-indirectly through an arsenic-induced generation of reactive oxygen species which then impacts chromatin remodelers, or directly through interaction and modulation of chromatin remodelers. Whether directly or indirectly, arsenic modulates epigenetic gene regulation and our understanding of the direct effect of this modulation on chromatin structure is limited. In this chapter we will discuss the various ways by which inorganic arsenic affects the epigenome with consequences in health and disease.
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Affiliation(s)
- Smitha George
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Richard N Cassidy
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States
| | - Wesley N Saintilnord
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI, United States; Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
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10
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Lopez JO, Seguel J, Chamorro A, Ramos KS. Pattern matching for high precision detection of LINE-1s in human genomes. BMC Bioinformatics 2022; 23:375. [PMID: 36100885 PMCID: PMC9472350 DOI: 10.1186/s12859-022-04907-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 08/05/2022] [Indexed: 08/30/2023] Open
Abstract
Background Long interspersed element 1 (LINE-1 or L1) retrotransposons are mobile elements that constitute 17–20% of the human genome. Strong correlations between abnormal L1 expression and several human diseases have been reported. This has motivated increasing interest in accurate quantification of the number of L1 copies present in any given biologic specimen. A main obstacle toward this aim is that L1s are relatively long DNA segments with regions of high variability, or largely present in the human genome as truncated fragments. These particularities render traditional alignment strategies, such as seed-and-extend inefficient, as the number of segments that are similar to L1s explodes exponentially. This study uses the pattern matching methodology for more accurate identification of L1s. We validate experimentally the superiority of pattern matching for L1 detection over alternative methods and discuss some of its potential applications. Results Pattern matching detected full-length L1 copies with high precision, reasonable computational time, and no prior input information. It also detected truncated and significantly altered copies of L1 with relatively high precision. The method was effectively used to annotate L1s in a target genome and to calculate copy number variation with respect to a reference genome. Crucial to the success of implementation was the selection of a small set of k-mer probes from a set of sequences presenting a stable pattern of distribution in the genome. As in seed-and-extend methods, the pattern matching algorithm sowed these k-mer probes, but instead of using heuristic extensions around the seeds, the analysis was based on distribution patterns within the genome. The desired level of precision could be adjusted, with some loss of recall. Conclusion Pattern matching is more efficient than seed-and-extend methods for the detection of L1 segments whose characterization depends on a finite set of sequences with common areas of low variability. We propose that pattern matching may help establish correlations between L1 copy number and disease states associated with L1 mobilization and evolution.
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Affiliation(s)
- Juan O Lopez
- Department of Computer Science, University of Puerto Rico, Arecibo, Puerto Rico.
| | - Jaime Seguel
- Department of Computer Science and Engineering, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Andres Chamorro
- Department of Computer Science and Engineering, University of Puerto Rico, Mayagüez, Puerto Rico
| | - Kenneth S Ramos
- Institute of Biosciences and Technology, Texas A&M Health, Houston, TX, USA
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Kõks S, Pfaff AL, Singleton LM, Bubb VJ, Quinn JP. Non-reference genome transposable elements (TEs) have a significant impact on the progression of the Parkinson's disease. Exp Biol Med (Maywood) 2022; 247:1680-1690. [PMID: 36000172 PMCID: PMC9597212 DOI: 10.1177/15353702221117147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The pathophysiology of Parkinson's disease (PD) is a complex process of the interaction between genetic and environmental factors. Studies on the genetic component of PD have predominantly focused on single nucleotide polymorphisms (SNPs) using a cross-sectional case-control design in large genome-wide association studies. This approach while giving insight into a significant portion of the genetics of PD does not fully account for all the genetic components resulting in missing heritability. In this study, we approached this problem by focusing on the non-reference genome transposable elements (TEs) and their impact on the progression of PD using a longitudinal study design within the Parkinson's progression markers initiative (PPMI) cohort. We analyzed 2886 Alu repeats, 360 LINE1 and 128 SINE-VNTR-Alus (SVAs) that were called from the whole-genome sequence data which are not within the reference genome. The presence or absence of these non-reference TE variants is known as a retrotransposon insertion polymorphism, and measuring this polymorphism describes the impact of TEs on the traits. The variations for the presence or absence of the non-reference TE elements were modeled to align with the changes in the 114 outcome measures during the five-year follow-up period of the PPMI cohort. Linear mixed-effects models were used, and many TEs were found to have a highly significant effect on the longitudinal changes in the clinically important PD outcomes such as UPDRS subscale II, UPDRS total scores, and modified Schwab and England ADL scale. In addition, the progression of several imaging and functional measures, including the Caudate/Putamen ratio and levodopa equivalent daily dose (LEDD) were also significantly affected by the TEs. In conclusion, this study identified the overwhelming effect of the non-reference TEs on the progression of PD and is a good example of the impact the variations in the "junk DNA" have on complex diseases.
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Affiliation(s)
- Sulev Kõks
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia,Sulev Kõks.
| | - Abigail L Pfaff
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia,Centre for Molecular Medicine and
Innovative Therapeutics, Murdoch University, Perth, WA 6150, Australia
| | - Lewis M Singleton
- Perron Institute for Neurological and
Translational Science, Perth, WA 6009, Australia
| | - Vivien J Bubb
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
| | - John P Quinn
- Department of Pharmacology and
Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of
Liverpool, Liverpool L69 3BX, UK
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12
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Bhat A, Ghatage T, Bhan S, Lahane GP, Dhar A, Kumar R, Pandita RK, Bhat KM, Ramos KS, Pandita TK. Role of Transposable Elements in Genome Stability: Implications for Health and Disease. Int J Mol Sci 2022; 23:7802. [PMID: 35887150 PMCID: PMC9319628 DOI: 10.3390/ijms23147802] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/11/2022] Open
Abstract
Most living organisms have in their genome a sizable proportion of DNA sequences capable of mobilization; these sequences are commonly referred to as transposons, transposable elements (TEs), or jumping genes. Although long thought to have no biological significance, advances in DNA sequencing and analytical technologies have enabled precise characterization of TEs and confirmed their ubiquitous presence across all forms of life. These findings have ignited intense debates over their biological significance. The available evidence now supports the notion that TEs exert major influence over many biological aspects of organismal life. Transposable elements contribute significantly to the evolution of the genome by giving rise to genetic variations in both active and passive modes. Due to their intrinsic nature of mobility within the genome, TEs primarily cause gene disruption and large-scale genomic alterations including inversions, deletions, and duplications. Besides genomic instability, growing evidence also points to many physiologically important functions of TEs, such as gene regulation through cis-acting control elements and modulation of the transcriptome through epigenetic control. In this review, we discuss the latest evidence demonstrating the impact of TEs on genome stability and the underling mechanisms, including those developed to mitigate the deleterious impact of TEs on genomic stability and human health. We have also highlighted the potential therapeutic application of TEs.
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Affiliation(s)
- Audesh Bhat
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Trupti Ghatage
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Sonali Bhan
- Centre for Molecular Biology, Central University of Jammu, Jammu 181143, India;
| | - Ganesh P. Lahane
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Arti Dhar
- Department of Pharmacy, BITS-Pilani Hyderabad Campus, Hyderabad 500078, India; (T.G.); (G.P.L.); (A.D.)
| | - Rakesh Kumar
- Department of Biotechnology, Shri Mata Vaishnav Devi University, Katra 182320, India;
| | - Raj K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
| | - Krishna M. Bhat
- Department of Molecular Medicine, University of South Florida, Tampa, FL 33612, USA;
| | - Kenneth S. Ramos
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
| | - Tej K. Pandita
- Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA;
- Center for Genomics and Precision Medicine, Texas A&M College of Medicine, Houston, TX 77030, USA;
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13
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Meevassana J, Serirodom S, Prabsattru P, Boonsongserm P, Kamolratanakul S, Siritientong T, Mutirangura A, Angspatt A. Alu repetitive sequence CpG methylation changes in burn scars. Burns 2021; 48:1417-1424. [PMID: 34657766 DOI: 10.1016/j.burns.2021.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/25/2022]
Abstract
Alu elements are retrotransposons related to epigenetic modifications. To date, the role of epigenetics in hypertrophic scars from burn remains unknown. Here, our aim was to examine the pathophysiology of hypertrophic scars from an epigenetic perspective. For that, we performed a cross-sectional analytical study using tissue and blood samples from burned and healthy patients (n = 23 each) to detect Alu methylation levels and patterns. The results of the combined bisulfite restriction analysis technique were categorized into four groups based on the methylation status at the CpG dinucleotides from the 5' to the 3' ends of the Alu sequence: hypermethylated (mCmC), hypomethylated (uCuC), and partially methylated (uCmC and mCuC). Alu methylation levels were significantly lower in hypertrophic scar tissues than in normal skin (29.37 ± 2.49% vs. 35.56 ± 3.18%, p = 0.0002). In contrast, the levels were significantly higher in white blood cells from blood samples of burned patients than in those of control blood samples (26.92 ± 4.04% vs. 24.58 ± 3.34%, p = 0.0278). Alu total methylation (mC) and the uCmC pattern were significantly lower, whereas uCuC was significantly higher, in hypertrophic scar tissues than in normal skin (p < 0.0001). Receiver operating characteristic analysis indicated that the uCmC and uCuC patterns are useful as hypertrophic scar DNA methylation markers after burn, with 91.30% sensitivity and 96.23% specificity and 100% sensitivity and 94.23% specificity, respectively. Our findings suggest that epigenetic modifications play a major role in hypertrophic scar pathogenesis, and may be the starting point for developing a novel technique for burn scar treatment.
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Affiliation(s)
- Jiraroch Meevassana
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand.
| | - Siwat Serirodom
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Piyawan Prabsattru
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
| | - Papatson Boonsongserm
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Tippawan Siritientong
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand; Department of Food and Pharmaceutical Chemistry, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apichai Angspatt
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok, Thailand
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14
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Idiopathic Infertility as a Feature of Genome Instability. Life (Basel) 2021; 11:life11070628. [PMID: 34209597 PMCID: PMC8307193 DOI: 10.3390/life11070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
Genome instability may play a role in severe cases of male infertility, with disrupted spermatogenesis being just one manifestation of decreased general health and increased morbidity. Here, we review the data on the association of male infertility with genetic, epigenetic, and environmental alterations, the causes and consequences, and the methods for assessment of genome instability. Male infertility research has provided evidence that spermatogenic defects are often not limited to testicular dysfunction. An increased incidence of urogenital disorders and several types of cancer, as well as overall reduced health (manifested by decreased life expectancy and increased morbidity) have been reported in infertile men. The pathophysiological link between decreased life expectancy and male infertility supports the notion of male infertility being a systemic rather than an isolated condition. It is driven by the accumulation of DNA strand breaks and premature cellular senescence. We have presented extensive data supporting the notion that genome instability can lead to severe male infertility termed “idiopathic oligo-astheno-teratozoospermia.” We have detailed that genome instability in men with oligo-astheno-teratozoospermia (OAT) might depend on several genetic and epigenetic factors such as chromosomal heterogeneity, aneuploidy, micronucleation, dynamic mutations, RT, PIWI/piRNA regulatory pathway, pathogenic allelic variants in repair system genes, DNA methylation, environmental aspects, and lifestyle factors.
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15
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Chen D, Cremona MA, Qi Z, Mitra RD, Chiaromonte F, Makova KD. Human L1 Transposition Dynamics Unraveled with Functional Data Analysis. Mol Biol Evol 2021; 37:3576-3600. [PMID: 32722770 DOI: 10.1093/molbev/msaa194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. To fill this gap, we investigated three genome-wide data sets of L1s that integrated at different evolutionary times: 17,037 de novo L1s (from an L1 insertion cell-line experiment conducted in-house), and 1,212 polymorphic and 1,205 human-specific L1s (from public databases). We characterized 49 genomic features-proxying chromatin accessibility, transcriptional activity, replication, recombination, etc.-in the ±50 kb flanks of these elements. These features were contrasted between the three L1 data sets and L1-free regions using state-of-the-art Functional Data Analysis statistical methods, which treat high-resolution data as mathematical functions. Our results indicate that de novo, polymorphic, and human-specific L1s are surrounded by different genomic features acting at specific locations and scales. This led to an integrative model of L1 transposition, according to which L1s preferentially integrate into open-chromatin regions enriched in non-B DNA motifs, whereas they are fixed in regions largely free of purifying selection-depleted of genes and noncoding most conserved elements. Intriguingly, our results suggest that L1 insertions modify local genomic landscape by extending CpG methylation and increasing mononucleotide microsatellite density. Altogether, our findings substantially facilitate understanding of L1 integration and fixation preferences, pave the way for uncovering their role in aging and cancer, and inform their use as mutagenesis tools in genetic studies.
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Affiliation(s)
- Di Chen
- Intercollege Graduate Degree Program in Genetics, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA
| | - Marzia A Cremona
- Department of Statistics, The Pennsylvania State University, University Park, PA.,Department of Operations and Decision Systems, Université Laval, Québec, Canada
| | - Zongtai Qi
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Robi D Mitra
- Department of Genetics and Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Francesca Chiaromonte
- Department of Statistics, The Pennsylvania State University, University Park, PA.,EMbeDS, Sant'Anna School of Advanced Studies, Pisa, Italy.,The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA
| | - Kateryna D Makova
- The Huck Institutes of the Life Sciences, Center for Medical Genomics, The Pennsylvania State University, University Park, PA.,Department of Biology, The Pennsylvania State University, University Park, PA
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16
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Spector LP, Tiffany M, Ferraro NM, Abell NS, Montgomery SB, Kay MA. Evaluating the Genomic Parameters Governing rAAV-Mediated Homologous Recombination. Mol Ther 2021; 29:1028-1046. [PMID: 33248247 PMCID: PMC7934627 DOI: 10.1016/j.ymthe.2020.11.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 10/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique ability to promote targeted integration of transgenes via homologous recombination at specified genomic sites, reaching frequencies of 0.1%-1%. We studied genomic parameters that influence targeting efficiencies on a large scale. To do this, we generated more than 1,000 engineered, doxycycline-inducible target sites in the human HAP1 cell line and infected this polyclonal population with a library of AAV-DJ targeting vectors, with each carrying a unique barcode. The heterogeneity of barcode integration at each target site provided an assessment of targeting efficiency at that locus. We compared targeting efficiency with and without target site transcription for identical chromosomal positions. Targeting efficiency was enhanced by target site transcription, while chromatin accessibility was associated with an increased likelihood of targeting. ChromHMM chromatin states characterizing transcription and enhancers in wild-type K562 cells were also associated with increased AAV-HR efficiency with and without target site transcription, respectively. Furthermore, the amenability of a site to targeting was influenced by the endogenous transcriptional level of intersecting genes. These results define important parameters that may not only assist in designing optimal targeting vectors for genome editing, but also provide new insights into the mechanism of AAV-mediated homologous recombination.
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Affiliation(s)
- Laura P Spector
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew Tiffany
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Nicole M Ferraro
- Biomedical Informatics Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Nathan S Abell
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Stephen B Montgomery
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
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17
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Zimak J, Wagoner ZW, Nelson N, Waechtler B, Schlosser H, Kopecky M, Wu J, Zhao W. Epigenetic silencing directs expression heterogeneity of stably integrated multi-transcript unit genetic circuits. Sci Rep 2021; 11:2424. [PMID: 33510302 PMCID: PMC7844226 DOI: 10.1038/s41598-021-81975-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/08/2021] [Indexed: 12/19/2022] Open
Abstract
We report that epigenetic silencing causes the loss of function of multi-transcript unit constructs that are integrated using CRISPR-Cas9. Using a modular two color reporter system flanked by selection markers, we demonstrate that expression heterogeneity does not correlate with sequence alteration but instead correlates with chromosomal accessibility. We partially reverse this epigenetic silencing via small-molecule inhibitors of methylation and histone deacetylation. We then correlate each heterogeneously-expressing phenotype with its expected epigenetic state by employing ATAC-seq. The stability of each expression phenotype is reinforced by selective pressure, which indicates that ongoing epigenetic remodeling can occur for over one month after integration. Collectively, our data suggests that epigenetic silencing limits the utility of multi-transcript unit constructs that are integrated via double-strand repair pathways. Our research implies that mammalian synthetic biologists should consider localized epigenetic outcomes when designing complex genetic circuits.
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Affiliation(s)
- Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Zachary W Wagoner
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Nellie Nelson
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Brooke Waechtler
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Hana Schlosser
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Morgan Kopecky
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA
| | - Jie Wu
- Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA.,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA, 92697, USA. .,Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, 92697, USA. .,Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.
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18
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Kohlrausch FB, Berteli TS, Wang F, Navarro PA, Keefe DL. Control of LINE-1 Expression Maintains Genome Integrity in Germline and Early Embryo Development. Reprod Sci 2021; 29:328-340. [PMID: 33481218 DOI: 10.1007/s43032-021-00461-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/06/2021] [Indexed: 11/28/2022]
Abstract
Maintenance of genome integrity in the germline and in preimplantation embryos is crucial for mammalian development. Epigenetic remodeling during primordial germ cell (PGC) and preimplantation embryo development may contribute to genomic instability in these cells, since DNA methylation is an important mechanism to silence retrotransposons. Long interspersed elements 1 (LINE-1 or L1) are the most common autonomous retrotransposons in mammals, corresponding to approximately 17% of the human genome. Retrotransposition events are more frequent in germ cells and in early stages of embryo development compared with somatic cells. It has been shown that L1 activation and expression occurs in germline and is essential for preimplantation development. In this review, we focus on the role of L1 retrotransposon in mouse and human germline and early embryo development and discuss the possible relationship between L1 expression and genomic instability during these stages. Although several studies have addressed L1 expression at different stages of development, the developmental consequences of this expression remain poorly understood. Future research is still needed to highlight the relationship between L1 retrotransposition events and genomic instability during germline and early embryo development.
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Affiliation(s)
- Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Biologia Geral, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Thalita S Berteli
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.,Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Fang Wang
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA
| | - Paula A Navarro
- Departamento de Ginecologia e Obstetrícia, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, New York University Langone Medical Center, 462 1st Avenue, New York, NY, 10016, USA.
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19
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Rymen B, Ferrafiat L, Blevins T. Non-coding RNA polymerases that silence transposable elements and reprogram gene expression in plants. Transcription 2020; 11:172-191. [PMID: 33180661 PMCID: PMC7714444 DOI: 10.1080/21541264.2020.1825906] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Multisubunit RNA polymerase (Pol) complexes are the core machinery for gene expression in eukaryotes. The enzymes Pol I, Pol II and Pol III transcribe distinct subsets of nuclear genes. This family of nuclear RNA polymerases expanded in terrestrial plants by the duplication of Pol II subunit genes. Two Pol II-related enzymes, Pol IV and Pol V, are highly specialized in the production of regulatory, non-coding RNAs. Pol IV and Pol V are the central players of RNA-directed DNA methylation (RdDM), an RNA interference pathway that represses transposable elements (TEs) and selected genes. Genetic and biochemical analyses of Pol IV/V subunits are now revealing how these enzymes evolved from ancestral Pol II to sustain non-coding RNA biogenesis in silent chromatin. Intriguingly, Pol IV-RdDM regulates genes that influence flowering time, reproductive development, stress responses and plant–pathogen interactions. Pol IV target genes vary among closely related taxa, indicating that these regulatory circuits are often species-specific. Data from crops like maize, rice, tomato and Brassicarapa suggest that dynamic repositioning of TEs, accompanied by Pol IV targeting to TE-proximal genes, leads to the reprogramming of plant gene expression over short evolutionary timescales.
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Affiliation(s)
- Bart Rymen
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Laura Ferrafiat
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
| | - Todd Blevins
- Institut de biologie moléculaire des plantes, Université de Strasbourg , Strasbourg, France
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20
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Hitti-Malin RJ, Burmeister LM, Ricketts SL, Lewis TW, Pettitt L, Boursnell M, Schofield EC, Sargan D, Mellersh CS. A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs. BMC Genet 2020; 21:100. [PMID: 32894063 PMCID: PMC7487703 DOI: 10.1186/s12863-020-00911-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/30/2020] [Indexed: 12/30/2022] Open
Abstract
Background Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lhasa Apso (LA) dog has not previously been clinically characterised or described in the literature, but owners in the UK are advised to have their dog examined through the British Veterinary Association/ Kennel Club/ International Sheep Dog Society (BVA/KC/ISDS) eye scheme annually, and similar schemes that are in operation in other countries. After the exclusion of 25 previously reported canine retinal mutations in LA PRA-affected dogs, we sought to identify the genetic cause of PRA in this breed. Results Analysis of whole-exome sequencing data of three PRA-affected LA and three LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal variant was non-exonic. We subsequently undertook a genome-wide association study (GWAS), which identified a 1.3 Mb disease-associated region on canine chromosome 33, followed by whole-genome sequencing analysis that revealed a long interspersed element-1 (LINE-1) insertion upstream of the IMPG2 gene. IMPG2 has previously been implicated in human retinal disease; however, until now no canine PRAs have been associated with this gene. The identification of this PRA-associated variant has enabled the development of a DNA test for this form of PRA in the breed, here termed PRA4 to distinguish it from other forms of PRA described in other breeds. This test has been used to determine the genotypes of over 900 LA dogs. A large cohort of genotyped dogs was used to estimate the allele frequency as between 0.07–0.1 in the UK LA population. Conclusions Through the use of GWAS and subsequent sequencing of a PRA case, we have identified a LINE-1 insertion in the retinal candidate gene IMPG2 that is associated with a form of PRA in the LA dog. Validation of this variant in 447 dogs of 123 breeds determined it was private to LA dogs. We envisage that, over time, the developed DNA test will offer breeders the opportunity to avoid producing dogs affected with this form of PRA.
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Affiliation(s)
- Rebekkah J Hitti-Malin
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK. .,Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK.
| | - Louise M Burmeister
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Sally L Ricketts
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Thomas W Lewis
- The Kennel Club, London, W1J 8AB, UK.,School of Veterinary Medicine and Science, The University of Nottingham, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Louise Pettitt
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Mike Boursnell
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - Ellen C Schofield
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
| | - David Sargan
- Department of Veterinary Medicine, University of Cambridge, Cambridge, CB3 0ES, UK
| | - Cathryn S Mellersh
- Kennel Club Genetics Centre, Animal Health Trust, Lanwades Park, Newmarket, Suffolk, CB8 7UU, UK
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Zeng Y, Cao Y, Halevy RS, Nguyen P, Liu D, Zhang X, Ahituv N, Han JDJ. Characterization of functional transposable element enhancers in acute myeloid leukemia. SCIENCE CHINA-LIFE SCIENCES 2020; 63:675-687. [PMID: 32170627 DOI: 10.1007/s11427-019-1574-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 10/24/2019] [Indexed: 12/15/2022]
Abstract
Transposable elements (TEs) have been shown to have important gene regulatory functions and their alteration could lead to disease phenotypes. Acute myeloid leukemia (AML) develops as a consequence of a series of genetic changes in hematopoietic precursor cells, including mutations in epigenetic factors. Here, we set out to study the gene regulatory role of TEs in AML. We first explored the epigenetic landscape of TEs in AML patients using ATAC-seq data. We show that a large number of TEs in general, and more specifically mammalian-wide interspersed repeats (MIRs), are more enriched in AML cells than in normal blood cells. We obtained a similar finding when analyzing histone modification data in AML patients. Gene Ontology enrichment analysis showed that genes near MIRs in open chromatin regions are involved in leukemogenesis. To functionally validate their regulatory role, we selected 19 MIR regions in AML cells, and tested them for enhancer activity in an AML cell line (Kasumi-1) and a chronic myeloid leukemia (CML) cell line (K562); the results revealed several MIRs to be functional enhancers. Taken together, our results suggest that TEs are potentially involved in myeloid leukemogenesis and highlight these sequences as potential candidates harboring AML-associated variation.
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Affiliation(s)
- Yingying Zeng
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rivka Sukenik Halevy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.,Sackler School of Medicine, Tel-Aviv University, Tel Aviv, 6997801, Israel
| | - Picard Nguyen
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA.,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA
| | - Denghui Liu
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoli Zhang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, 94158, USA. .,Institute for Human Genetics, University of California San Francisco, San Francisco, 94143, USA.
| | - Jing-Dong J Han
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology, Peking University, Beijing, 100871, China.
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22
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Khosraviani N, Ostrowski LA, Mekhail K. Roles for Non-coding RNAs in Spatial Genome Organization. Front Cell Dev Biol 2019; 7:336. [PMID: 31921848 PMCID: PMC6930868 DOI: 10.3389/fcell.2019.00336] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 11/29/2019] [Indexed: 12/15/2022] Open
Abstract
Genetic loci are non-randomly arranged in the nucleus of the cell. This order, which is important to overall genome expression and stability, is maintained by a growing number of factors including the nuclear envelope, various genetic elements and dedicated protein complexes. Here, we review evidence supporting roles for non-coding RNAs (ncRNAs) in the regulation of spatial genome organization and its impact on gene expression and cell survival. Specifically, we discuss how ncRNAs from single-copy and repetitive DNA loci contribute to spatial genome organization by impacting perinuclear chromosome tethering, major nuclear compartments, chromatin looping, and various chromosomal structures. Overall, our analysis of the literature highlights central functions for ncRNAs and their transcription in the modulation of spatial genome organization with connections to human health and disease.
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Affiliation(s)
- Negin Khosraviani
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Lauren A. Ostrowski
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Karim Mekhail
- Department of Laboratory Medicine and Pathobiology, MaRS Centre, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Canada Research Chairs Program, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
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23
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Drongitis D, Aniello F, Fucci L, Donizetti A. Roles of Transposable Elements in the Different Layers of Gene Expression Regulation. Int J Mol Sci 2019; 20:ijms20225755. [PMID: 31731828 PMCID: PMC6888579 DOI: 10.3390/ijms20225755] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/12/2019] [Accepted: 11/14/2019] [Indexed: 02/03/2023] Open
Abstract
The biology of transposable elements (TEs) is a fascinating and complex field of investigation. TEs represent a substantial fraction of many eukaryotic genomes and can influence many aspects of DNA function that range from the evolution of genetic information to duplication, stability, and gene expression. Their ability to move inside the genome has been largely recognized as a double-edged sword, as both useful and deleterious effects can result. A fundamental role has been played by the evolution of the molecular processes needed to properly control the expression of TEs. Today, we are far removed from the original reductive vision of TEs as “junk DNA”, and are more convinced that TEs represent an essential element in the regulation of gene expression. In this review, we summarize some of the more recent findings, mainly in the animal kingdom, concerning the active roles that TEs play at every level of gene expression regulation, including chromatin modification, splicing, and protein translation.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale delle Ricerche, 80131 Naples, Italy;
| | - Francesco Aniello
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Laura Fucci
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
| | - Aldo Donizetti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy; (F.A.); (L.F.)
- Correspondence:
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24
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Zheng Y, Hlady RA, Joyce BT, Robertson KD, He C, Nannini DR, Kibbe WA, Achenbach CJ, Murphy RL, Roberts LR, Hou L. DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma. Clin Epigenetics 2019; 11:145. [PMID: 31639042 PMCID: PMC6802191 DOI: 10.1186/s13148-019-0733-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background The two most common repetitive elements (REs) in humans, long interspersed nuclear element-1 (LINE-1) and Alu element (Alu), have been linked to various cancers. Hepatitis C virus (HCV) may cause hepatocellular carcinoma (HCC) by suppressing host defenses, through DNA methylation that controls the mobilization of REs. We aimed to investigate the role of RE methylation in HCV-induced HCC (HCV-HCC). Results We studied methylation of over 30,000 locus-specific REs across the genome in HCC, cirrhotic, and healthy liver tissues obtained by surgical resection. Relative to normal liver tissue, we observed the largest number of differentially methylated REs in HCV-HCC followed by alcohol-induced HCC (EtOH-HCC). After excluding EtOH-HCC-associated RE methylation (FDR < 0.001) and those unable to be validated in The Cancer Genome Atlas (TCGA), we identified 13 hypomethylated REs (11 LINE-1 and 2 Alu) and 2 hypermethylated REs (1 LINE-1 and 1 Alu) in HCV-HCC (FDR < 0.001). A majority of these REs were located in non-coding regions, preferentially enriched with chromatin repressive marks H3K27me3, and positively associated with gene expression (median correlation r = 0.32 across REs). We further constructed an HCV-HCC RE methylation score that distinguished HCV-HCC (lowest score), HCV-cirrhosis, and normal liver (highest score) in a dose-responsive manner (p for trend < 0.001). HCV-cirrhosis had a lower score than EtOH-cirrhosis (p = 0.038) and HCV-HCC had a lower score than EtOH-HCC in TCGA (p = 0.024). Conclusions Our findings indicate that HCV infection is associated with loss of DNA methylation in specific REs, which could implicate molecular mechanisms in liver cancer development. If our findings are validated in larger sample sizes, methylation of these REs may be useful as an early detection biomarker for HCV-HCC and/or a target for prevention of HCC in HCV-positive individuals. Electronic supplementary material The online version of this article (10.1186/s13148-019-0733-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yinan Zheng
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA.
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Brian T Joyce
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Chunyan He
- University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, University of Kentucky, Lexington, KY, USA
| | - Drew R Nannini
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Warren A Kibbe
- Duke Cancer Institute and Duke School of Medicine, Duke University, Durham, NC, USA
| | - Chad J Achenbach
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Robert L Murphy
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lifang Hou
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
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25
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Michalak EM, Burr ML, Bannister AJ, Dawson MA. The roles of DNA, RNA and histone methylation in ageing and cancer. Nat Rev Mol Cell Biol 2019; 20:573-589. [PMID: 31270442 DOI: 10.1038/s41580-019-0143-1] [Citation(s) in RCA: 308] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2019] [Indexed: 12/17/2022]
Abstract
Chromatin is a macromolecular complex predominantly comprising DNA, histone proteins and RNA. The methylation of chromatin components is highly conserved as it helps coordinate the regulation of gene expression, DNA repair and DNA replication. Dynamic changes in chromatin methylation are essential for cell-fate determination and development. Consequently, inherited or acquired mutations in the major factors that regulate the methylation of DNA, RNA and/or histones are commonly observed in developmental disorders, ageing and cancer. This has provided the impetus for the clinical development of epigenetic therapies aimed at resetting the methylation imbalance observed in these disorders. In this Review, we discuss the cellular functions of chromatin methylation and focus on how this fundamental biological process is corrupted in cancer. We discuss methylation-based cancer therapies and provide a perspective on the emerging data from early-phase clinical trial therapies that target regulators of DNA and histone methylation. We also highlight promising therapeutic strategies, including monitoring chromatin methylation for diagnostic purposes and combination epigenetic therapy strategies that may improve immune surveillance in cancer and increase the efficacy of conventional and targeted anticancer drugs.
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Affiliation(s)
- Ewa M Michalak
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Marian L Burr
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Mark A Dawson
- Cancer Research Division, Peter MacCallum Cancer Centre, Melbourne, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia.
- Centre for Cancer Research, The University of Melbourne, Melbourne, Australia.
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26
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Kaul T, Morales ME, Smither E, Baddoo M, Belancio VP, Deininger P. RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level. J Vis Exp 2019. [PMID: 31157783 DOI: 10.3791/59771] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Long INterspersed Elements-1 (LINEs/L1s) are repetitive elements that can copy and randomly insert in the genome resulting in genomic instability and mutagenesis. Understanding the expression patterns of L1 loci at the individual level will lend to the understanding of the biology of this mutagenic element. This autonomous element makes up a significant portion of the human genome with over 500,000 copies, though 99% are truncated and defective. However, their abundance and dominant number of defective copies make it challenging to identify authentically expressed L1s from L1-related sequences expressed as part of other genes. It is also challenging to identify which specific L1 locus is expressed due to the repetitive nature of the elements. Overcoming these challenges, we present an RNA-Seq bioinformatic approach to identify L1 expression at the locus specific level. In summary, we collect cytoplasmic RNA, select for polyadenylated transcripts, and utilize strand-specific RNA-Seq analyses to uniquely map reads to L1 loci in the human reference genome. We visually curate each L1 locus with uniquely mapped reads to confirm transcription from its own promoter and adjust mapped transcript reads to account for mappability of each individual L1 locus. This approach was applied to a prostate tumor cell line, DU145, to demonstrate the ability of this protocol to detect expression from a small number of the full-length L1 elements.
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Affiliation(s)
| | | | | | - Melody Baddoo
- Tulane Cancer Center, Tulane University; Department of Pathology, Tulane University
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane University; Department of Structural and Cellular Biology, Tulane University
| | - Prescott Deininger
- Tulane Cancer Center, Tulane University; Department of Epidemiology, Tulane University;
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27
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Lin YL, Gokcumen O. Fine-Scale Characterization of Genomic Structural Variation in the Human Genome Reveals Adaptive and Biomedically Relevant Hotspots. Genome Biol Evol 2019; 11:1136-1151. [PMID: 30887040 PMCID: PMC6475128 DOI: 10.1093/gbe/evz058] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/16/2019] [Indexed: 12/25/2022] Open
Abstract
Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2,504 genomes to construct a refined map of 1,148 SV hotspots in human genomes. We confirmed that segmental duplication-related nonallelic homologous recombination is an important mechanistic driver of SV hotspot formation. However, to our surprise, we also found that a majority of SVs in hotspots do not form through such recombination-based mechanisms, suggesting diverse mechanistic and selective forces shaping hotspots. Indeed, our evolutionary analyses showed that the majority of SV hotspots are within gene-poor regions and evolve under relaxed negative selection or neutrality. However, we still found a small subset of SV hotspots harboring genes that are enriched for anthropologically crucial functions and evolve under geography-specific and balancing adaptive forces. These include two independent hotspots on different chromosomes affecting alpha and beta hemoglobin gene clusters. Biomedically, we found that the SV hotspots coincide with breakpoints of clinically relevant, large de novo SVs, significantly more often than genome-wide expectations. For example, we showed that the breakpoints of multiple large SVs, which lead to idiopathic short stature, coincide with SV hotspots. Therefore, the mutational instability in SV hotpots likely enables chromosomal breaks that lead to pathogenic structural variation formations. Overall, our study contributes to a better understanding of the mutational and adaptive landscape of the genome.
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Affiliation(s)
- Yen-Lung Lin
- Department of Biological Sciences, University at Buffalo
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo
- Corresponding author: E-mail: or
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28
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Latent infection with Kaposi's sarcoma-associated herpesvirus enhances retrotransposition of long interspersed element-1. Oncogene 2019; 38:4340-4351. [PMID: 30770900 DOI: 10.1038/s41388-019-0726-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/18/2019] [Indexed: 12/14/2022]
Abstract
Kaposi's sarcoma (KS)-associated herpesvirus (KSHV), a gamma-2 herpesvirus, is the causative agent of KS, primary effusion lymphoma (PEL), and a plasma cell variant of multicentric Castleman's disease. Although KSHV latency is detected in KS-related tumors, oncogenic pathways activated by KSHV latent infection are not fully understood. Here, we found that retrotransposition of long interspersed element-1 (L1), a retrotransposon in the human genome, was enhanced in PEL cells. Among the KSHV latent genes, viral FLICE-inhibitory protein (vFLIP) enhanced L1 retrotransposition in an NF-κB-dependent manner. Intracellular cell adhesion molecule-1 (ICAM-1), an NF-κB target, regulated the vFLIP-mediated enhancement of L1 retrotransposition. Furthermore, ICAM-1 downregulated the expression of Moloney leukemia virus 10 (MOV10), an L1 restriction factor. Knockdown of ICAM-1 or overexpression of MOV10 relieved the vFLIP-mediated enhancement of L1 retrotransposition. Collectively, during KSHV latency, vFLIP upregulates ICAM-1 in an NF-κB-dependent manner, which, in turn, downregulates MOV10 expression and thereby enhances L1 retrotransposition. Because active L1 retrotransposition can lead to genomic instability, which is commonly found in KS and PEL, activation of L1 retrotransposition during KSHV latency may accelerate oncogenic processes through enhancing genomic instability. Our results suggest that L1 retrotransposition may be a novel target for impeding tumor development in KSHV-infected patients.
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29
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Childebayeva A, Jones TR, Goodrich JM, Leon-Velarde F, Rivera-Chira M, Kiyamu M, Brutsaert TD, Dolinoy DC, Bigham AW. LINE-1 and EPAS1 DNA methylation associations with high-altitude exposure. Epigenetics 2019; 14:1-15. [PMID: 30574831 DOI: 10.1080/15592294.2018.1561117] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Recent discoveries indicate a genetic basis for high-altitude adaptation among human groups who have resided at high altitude for millennia, including Andeans, Tibetans, and Ethiopians. Yet, genetics alone does not explain the extent of variation in altitude-adaptive phenotypes. Current and past environments may also play a role, and one way to determine the effect of the environment is through the epigenome. To characterize if Andean adaptive responses to high altitude have an epigenetic component, we analyzed DNA methylation of the promoter region of EPAS1 and LINE-1 repetitive element among 572 Quechua individuals from high- (4,388 m) and low-altitude (0 m) in Peru. Participants recruited at high altitude had lower EPAS1 DNA methylation and higher LINE-1 methylation. Altitude of birth was associated with higher LINE-1 methylation, not with EPAS1 methylation. The number of years lived at high altitude was negatively associated with EPAS1 methylation and positively associated with LINE-1 methylation. We found four one-carbon metabolism SNPs (MTHFD1 rs2236225, TYMS rs502396, FOLH1 rs202676, GLDC rs10975681) that cumulatively explained 11.29% of the variation in average LINE-1 methylation. And identified an association between LINE-1 methylation and genome-wide SNP principal component 1 that distinguishes European from Indigenous American ancestry suggesting that European admixture decreases LINE-1 methylation. Our results indicate that both current and lifetime exposure to high-altitude hypoxia have an effect on EPAS1 and LINE-1 methylation among Andean Quechua, suggesting that epigenetic modifications may play a role in high-altitude adaptation.
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Affiliation(s)
- Ainash Childebayeva
- a Department of Anthropology , University of Michigan , Ann Arbor , MI , USA.,b Department of Environmental Health Sciences , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Tamara R Jones
- b Department of Environmental Health Sciences , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Jaclyn M Goodrich
- b Department of Environmental Health Sciences , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Fabiola Leon-Velarde
- c Departamento de Ciencias Biológicas y Fisiológicas , Universidad Peruana Cayetano Heredia , Lima , Peru
| | - Maria Rivera-Chira
- c Departamento de Ciencias Biológicas y Fisiológicas , Universidad Peruana Cayetano Heredia , Lima , Peru
| | - Melisa Kiyamu
- c Departamento de Ciencias Biológicas y Fisiológicas , Universidad Peruana Cayetano Heredia , Lima , Peru
| | - Tom D Brutsaert
- d Department of Exercise Science , Syracuse University , Syracuse , NY , USA
| | - Dana C Dolinoy
- b Department of Environmental Health Sciences , School of Public Health, University of Michigan , Ann Arbor , MI , USA.,e Department of Nutritional Sciences , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Abigail W Bigham
- a Department of Anthropology , University of Michigan , Ann Arbor , MI , USA
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30
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DNA methylation changes and somatic mutations as tumorigenic events in Lynch syndrome-associated adenomas retaining mismatch repair protein expression. EBioMedicine 2018; 39:280-291. [PMID: 30578081 PMCID: PMC6355728 DOI: 10.1016/j.ebiom.2018.12.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 12/04/2018] [Accepted: 12/11/2018] [Indexed: 12/13/2022] Open
Abstract
Background DNA mismatch repair (MMR) defects are a major factor in colorectal tumorigenesis in Lynch syndrome (LS) and 15% of sporadic cases. Some adenomas from carriers of inherited MMR gene mutations have intact MMR protein expression implying other mechanisms accelerating tumorigenesis. We determined roles of DNA methylation changes and somatic mutations in cancer-associated genes as tumorigenic events in LS-associated colorectal adenomas with intact MMR. Methods We investigated 122 archival colorectal specimens of normal mucosae, adenomas and carcinomas from 57 LS patients. MMR-deficient (MMR-D, n = 49) and MMR-proficient (MMR-P, n = 18) adenomas were of particular interest and were interrogated by methylation-specific multiplex ligation-dependent probe amplification and Ion Torrent sequencing. Findings Promoter methylation of CpG island methylator phenotype (CIMP)-associated marker genes and selected colorectal cancer (CRC)-associated tumor suppressor genes (TSGs) increased and LINE-1 methylation decreased from normal mucosa to MMR-P adenomas to MMR-D adenomas. Methylation differences were statistically significant when either adenoma group was compared with normal mucosa, but not between MMR-P and MMR-D adenomas. Significantly increased methylation was found in multiple CIMP marker genes (IGF2, NEUROG1, CRABP1, and CDKN2A) and TSGs (SFRP1 and SFRP2) in MMR-P adenomas already. Furthermore, certain CRC-associated somatic mutations, such as KRAS, were prevalent in MMR-P adenomas. Interpretation We conclude that DNA methylation changes and somatic mutations of cancer-associated genes might serve as an alternative pathway accelerating LS-associated tumorigenesis in the presence of proficient MMR. Fund Jane and Aatos Erkko Foundation, Academy of Finland, Cancer Foundation Finland, Sigrid Juselius Foundation, and HiLIFE.
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31
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Wagstaff BJ, Wang L, Lai S, Derbes RS, Roy-Engel AM. Reviving a 60 million year old LINE-1 element. GENE REPORTS 2018; 11:74-78. [PMID: 30221208 DOI: 10.1016/j.genrep.2018.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Mobile elements have significantly impacted genome structure of most organisms. The continued activity of the mobile element, LINE-1 (L1), through time has contributed to the accumulation of over half a million L1 copies in the human genome. Most copies in the human genome belong to evolutionary older extinct L1s. Here we apply our previous published approach to "revive" the extinct L1 PA13A; an L1 family that was active about 60 million year ago (mya). The reconstructed L1PA13A is retrocompentent in culture, but shows a significantly lower level of activity in HeLa cells when compared to the modern L1 element (L1PA1) and a 40 million year old L1PA8. L1 elements code for two proteins (ORF1p and ORF2p) that are necessary for retrotransposition. Using PA13A-PA1 and PA13A-PA8 L1 chimeric elements, we determined that both the ORF1p and ORF2p contribute to the observed decrease in retrotransposition efficiency of L1PA13A. The lower retrotransposition rate of L1PA13A is consistent in both human and rodent cell lines. However, in rodent cells, the chimeric element L1PA:1-13 containing the modern L1PA1 ORF1p shows a recovery in the retrotransposition rate, suggestive that the L1PA13A ORF2p efficiently drives retrotransposition in these cells. The functionality of the L1PA13A ORF2p was further confirmed by demonstrating its ability to drive Alu retrotransposition in rodent cells. The variation in L1PA13A retrotransposition rates observed between rodent and human cells are suggestive that cellular environment significantly affects retrotransposition efficiency, which may be mediated through an interaction with ORF1p. Based on these observations, we speculate that the observed differences between cell lines may reflect an evolutionary adaptation of the L1 element to its host cell.
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Affiliation(s)
- Bradley J Wagstaff
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Linda Wang
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Susan Lai
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112
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32
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Szafranski P, Kośmider E, Liu Q, Karolak JA, Currie L, Parkash S, Kahler SG, Roeder E, Littlejohn RO, DeNapoli TS, Shardonofsky FR, Henderson C, Powers G, Poisson V, Bérubé D, Oligny L, Michaud JL, Janssens S, De Coen K, Van Dorpe J, Dheedene A, Harting MT, Weaver MD, Khan AM, Tatevian N, Wambach J, Gibbs KA, Popek E, Gambin A, Stankiewicz P. LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV. Hum Mutat 2018; 39:1916-1925. [PMID: 30084155 DOI: 10.1002/humu.23608] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/01/2018] [Accepted: 08/02/2018] [Indexed: 01/20/2023]
Abstract
Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue-specific enhancer. Eighty-five percent of 45 ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements. We describe a novel ∼35 kb-large genomic instability hotspot at 16q24.1, involving two evolutionarily young LINE-1 (L1) elements, L1PA2 and L1PA3, flanking AluY, two AluSx, AluSx1, and AluJr elements. The occurrence of L1s at this location coincided with the branching out of the Homo-Pan-Gorilla clade, and was preceded by the insertion of AluSx, AluSx1, and AluJr. Our data show that, in addition to mediating recurrent CNVs, L1 and Alu retrotransposons can predispose the human genome to formation of variably sized CNVs, both of clinical and evolutionary relevance. Nonetheless, epigenetic or other genomic features of this locus might also contribute to its increased instability.
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Affiliation(s)
- Przemyslaw Szafranski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Ewelina Kośmider
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, Poznan, Poland
| | - Lauren Currie
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Sandhya Parkash
- Maritime Medical Genetics Service, IWK Health Centre, Halifax, Canada
| | - Stephen G Kahler
- Section of Genetics and Metabolism, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Elizabeth Roeder
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas
| | | | - Thomas S DeNapoli
- Department of Pathology, Children's Hospital of San Antonio, San Antonio, Texas
| | - Felix R Shardonofsky
- Pediatric Pulmonary Center, Children's Hospital of San Antonio, San Antonio, Texas
| | - Cody Henderson
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | - George Powers
- Department of Pediatrics, Baylor College of Medicine, San Antonio, Texas.,Neonatal-Perinatal Medicine, Children's Hospital of San Antonio, San Antonio, Texas
| | | | | | | | | | - Sandra Janssens
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Kris De Coen
- Department of Neonatal Intensive Care, Ghent University, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University, Ghent, Belgium
| | | | | | | | - Amir M Khan
- McGovern Medical School at UTHealth, Houston, Texas
| | | | - Jennifer Wambach
- Edward Mallinckrodt Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Kathleen A Gibbs
- Children's Hospital of Philadelphia, and University of Pennsylvania, Philadelphia, Pennsylvania
| | - Edwina Popek
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas
| | - Anna Gambin
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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33
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Li S, Wehrenberg B, Waldman BC, Waldman AS. Mismatch tolerance during homologous recombination in mammalian cells. DNA Repair (Amst) 2018; 70:25-36. [PMID: 30103093 DOI: 10.1016/j.dnarep.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/19/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022]
Abstract
We investigated the homology dependency of recombination in thymidine kinase (tk)-deficient mouse fibroblasts. Cells were transfected with DNA constructs harboring a herpes tk gene (the "recipient") rendered non-functional by an oligonucleotide containing the recognition site for endonuclease I-SceI. Constructs also contained a "donor" tk sequence that could restore function to the recipient gene through spontaneous gene conversion or via repair of a double-strand break (DSB) at the I-SceI site. Recombination events were recoverable by selection for tk-positive clones. Three different donors were used containing 16, 25, or 33 mismatches relative to the recipient. The mismatches were clustered, forming an interval of "homeology" relative to the recipient sequences. We show that when homeologous sequences were surrounded by high homology, mismatches were frequently included in gene conversion events. Notably, conversion tracts from spontaneous recombination included either all or none of the mismatches, suggesting that recombination must begin and end in high homology. This requirement was relaxed for events that occurred near an induced DSB, as a significant number of these latter conversion tracts had one end positioned within homeology. Knock-down of mismatch repair showed that incorporation of mismatches into gene conversion tracts can involve repair of mismatched heteroduplex intermediates, indicating that mismatch repair does not necessarily impede homeologous genetic exchange. Our results illustrate (1) genetic exchange between homeologous sequences in a mammalian genome is enabled by nearby homology, (2) proximity to a DSB impacts the homology requirements for where genetic exchange may begin and end, and (3) mismatch correction and previously documented anti-recombination activity are separable functions of the mismatch repair machinery in mammalian cells.
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Affiliation(s)
- Shen Li
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Bryan Wehrenberg
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Barbara C Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA
| | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Coker Life Sciences Building, 700 Sumter Street, Columbia, South Carolina, 29208, USA.
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34
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Sookdeo A, Ruiz-García M, Schneider H, Boissinot S. Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family. Cytogenet Genome Res 2018; 154:217-228. [PMID: 29991050 DOI: 10.1159/000490481] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2018] [Indexed: 11/19/2022] Open
Abstract
LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.
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35
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Abstract
Stress conditions such as UV irradiation, exposure to genotoxic agents, stalled DNA replication, and even tumors trigger the release of cytosolic genomic DNA (cgDNA). Classically, cgDNA induces interferon response via its binding to proteins such as STING. In this study, we found previously reported cgDNA (cg721) exists in the cytosol of the mouse cell lines, cultured under no stress conditions. The overexpression of cg721 suppressed the complementary RNA expression using strand selection and knockdown of DNA/RNA hybrid R-loop removing enzyme RNase H and three prime repair exonuclease 1 TREX1 increased the expression levels of cg721 and thus, inhibited the target Naa40 transcript, as well as protein expression, with a phenotypic effect. In addition, cgDNA was incorporated into extracellular vesicles (EVs), and the EV-derived cg721 inhibited gene expression of the acceptor cells. Thus, our findings suggest that cg721 functions as a natural antisense DNA and play a role in cell-to-cell gene regulation once it secreted outside the cell as EVs.
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36
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Suarez NA, Macia A, Muotri AR. LINE-1 retrotransposons in healthy and diseased human brain. Dev Neurobiol 2017; 78:434-455. [PMID: 29239145 DOI: 10.1002/dneu.22567] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/12/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is a transposable element with the ability to self-mobilize throughout the human genome. The L1 elements found in the human brain is hypothesized to date back 56 million years ago and has survived evolution, currently accounting for 17% of the human genome. L1 retrotransposition has been theorized to contribute to somatic mosaicism. This review focuses on the presence of L1 in the healthy and diseased human brain, such as in autism spectrum disorders. Throughout this exploration, we will discuss the impact L1 has on neurological disorders that can occur throughout the human lifetime. With this, we hope to better understand the complex role of L1 in the human brain development and its implications to human cognition. © 2017 Wiley Periodicals, Inc. Develop Neurobiol 78: 434-455, 2018.
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Affiliation(s)
- Nicole A Suarez
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Angela Macia
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
| | - Alysson R Muotri
- Department of Pediatrics/Rady Children's Hospital San Diego, University of California San Diego, La Jolla, California, 92093
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37
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Lizardi PM, Yan Q, Wajapeyee N. High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation. Cold Spring Harb Protoc 2017; 2017:pdb.prot094862. [PMID: 27852842 DOI: 10.1101/pdb.prot094862] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This protocol describes methylation mapping analysis by paired-end sequencing (Methyl-MAPS). In addition to the sequence information, paired-end sequencing provides information about the physical distance between the two reads in the genome. Methyl-MAPS typically samples ~80% of the CpG dinucleotides in the genome and is also able to report the methylation status of individual genomic loci harboring repetitive elements. This is achieved by enzymatic fractionation of the genome into methylated and unmethylated compartments. Because the method avoids the use of bisulfite modification, DNA fragments of relatively large size are preserved, permitting the generation of paired-end libraries with DNA inserts of known size in the ranges of 0.8-1.5, 1.5-3, and 3-6 kb. The paired-end configurations can be uniquely mapped to the genome in most instances, because the paired reads will span most repetitive element sequences.
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38
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Gardner A, Úbeda F. The meaning of intragenomic conflict. Nat Ecol Evol 2017; 1:1807-1815. [PMID: 29109471 DOI: 10.1038/s41559-017-0354-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 09/22/2017] [Indexed: 01/30/2023]
Abstract
Recent years have seen an explosion of interest in genes that function for their own good and to the detriment of other genes that reside in the same genome. Such intragenomic conflicts are increasingly recognized to underpin maladaptation and disease. However, progress has been impeded by a lack of clear understanding regarding what intragenomic conflict actually means, and an associated obscurity concerning its fundamental drivers. Here we develop a general theory of intragenomic conflict in which genes are viewed as inclusive-fitness-maximizing agents that come into conflict when their inclusive-fitness interests disagree. This yields a classification of all intragenomic conflicts into three categories according to whether genes disagree about where they have come from, where they are going, or where they currently are. We illustrate each of these three basic categories, survey and classify all known forms of intragenomic conflict, and discuss the implications for organismal maladaptation and human disease.
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Affiliation(s)
- Andy Gardner
- School of Biology, University of St Andrews, St Andrews, KY16 9TH, UK.
| | - Francisco Úbeda
- School of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK.
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39
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Everson R, Pettitt L, Forman OP, Dower-Tylee O, McLaughlin B, Ahonen S, Kaukonen M, Komáromy AM, Lohi H, Mellersh CS, Sansom J, Ricketts SL. An intronic LINE-1 insertion in MERTK is strongly associated with retinopathy in Swedish Vallhund dogs. PLoS One 2017; 12:e0183021. [PMID: 28813472 PMCID: PMC5558984 DOI: 10.1371/journal.pone.0183021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 07/30/2017] [Indexed: 12/31/2022] Open
Abstract
The domestic dog segregates a significant number of inherited progressive retinal diseases, several of which mirror human retinal diseases and which are collectively termed progressive retinal atrophy (PRA). In 2014, a novel form of PRA was reported in the Swedish Vallhund breed, and the disease was mapped to canine chromosome 17. The causal mutation was not identified, but expression analyses of the retinas of affected Vallhunds demonstrated a 6-fold increased expression of the MERTK gene compared to unaffected dogs. Using 24 retinopathy cases and 97 controls with no clinical signs of retinopathy, we replicated the chromosome 17 association in Swedish Vallhunds from the UK and aimed to elucidate the causal variant underlying this association using whole genome sequencing (WGS) of an affected dog. This revealed a 6-8 kb insertion in intron 1 of MERTK that was not present in WGS of 49 dogs of other breeds. Sequencing and BLASTN analysis of the inserted segment was consistent with the insertion comprising a full-length intact LINE-1 retroelement. Testing of the LINE-1 insertion for association with retinopathy in the UK set of 24 cases and 97 controls revealed a strong statistical association (P-value 6.0 x 10-11) that was subsequently replicated in the original Finnish study set (49 cases and 89 controls (P-value 4.3 x 10-19). In a pooled analysis of both studies (73 cases and 186 controls), the LINE-1 insertion was associated with a ~20-fold increased risk of retinopathy (odds ratio 23.41, 95% confidence intervals 10.99-49.86, P-value 1.3 x 10-27). Our study adds further support for regulatory disruption of MERTK in Swedish Vallhund retinopathy; however, further work is required to establish a functional overexpression model. Future work to characterise the mechanism by which this intronic mutation disrupts gene regulation will further improve the understanding of MERTK biology and its role in retinal function.
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Affiliation(s)
- Richard Everson
- Centre for Small Animal Studies–Ophthalmology Unit, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Louise Pettitt
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Oliver P. Forman
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Olivia Dower-Tylee
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Bryan McLaughlin
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Saija Ahonen
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maria Kaukonen
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - András M. Komáromy
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, United States of America
- Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Cathryn S. Mellersh
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Jane Sansom
- Centre for Small Animal Studies–Ophthalmology Unit, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
| | - Sally L. Ricketts
- Canine Genetics Research Group, Kennel Club Genetics Centre, Animal Health Trust, Kentford, Newmarket, Suffolk, United Kingdom
- * E-mail:
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40
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Deininger P, Morales ME, White TB, Baddoo M, Hedges DJ, Servant G, Srivastav S, Smither ME, Concha M, DeHaro DL, Flemington EK, Belancio VP. A comprehensive approach to expression of L1 loci. Nucleic Acids Res 2017; 45:e31. [PMID: 27899577 PMCID: PMC5389711 DOI: 10.1093/nar/gkw1067] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/09/2016] [Indexed: 11/14/2022] Open
Abstract
L1 elements represent the only currently active, autonomous retrotransposon in the human genome, and they make major contributions to human genetic instability. The vast majority of the 500 000 L1 elements in the genome are defective, and only a relatively few can contribute to the retrotransposition process. However, there is currently no comprehensive approach to identify the specific loci that are actively transcribed separate from the excess of L1-related sequences that are co-transcribed within genes. We have developed RNA-Seq procedures, as well as a 1200 bp 5΄ RACE product coupled with PACBio sequencing that can identify the specific L1 loci that contribute most of the L1-related RNA reads. At least 99% of L1-related sequences found in RNA do not arise from the L1 promoter, instead representing pieces of L1 incorporated in other cellular RNAs. In any given cell type a relatively few active L1 loci contribute to the 'authentic' L1 transcripts that arise from the L1 promoter, with significantly different loci seen expressed in different tissues.
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Affiliation(s)
- Prescott Deininger
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.,Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA
| | - Maria E Morales
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | - Travis B White
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | - Melody Baddoo
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | - Dale J Hedges
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA
| | | | - Sudesh Srivastav
- Department of Structural and Cellular Biology, Tulane University, New Orleans, LA 70112, USA
| | | | - Monica Concha
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.,Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA 70112, USA
| | - Dawn L DeHaro
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.,Department of Pathology, Tulane University, New Orleans, LA 70112, USA
| | - Erik K Flemington
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.,Department of Biostatistics and Bioinformatics, Tulane University, New Orleans, LA 70112, USA
| | - Victoria P Belancio
- Tulane Cancer Center, Tulane University, New Orleans, LA 70112, USA.,Department of Pathology, Tulane University, New Orleans, LA 70112, USA
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41
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Meyer TJ, Held U, Nevonen KA, Klawitter S, Pirzer T, Carbone L, Schumann GG. The Flow of the Gibbon LAVA Element Is Facilitated by the LINE-1 Retrotransposition Machinery. Genome Biol Evol 2016; 8:3209-3225. [PMID: 27635049 PMCID: PMC5174737 DOI: 10.1093/gbe/evw224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
LINE-Alu-VNTR-Alu-like (LAVA) elements comprise a family of non-autonomous, composite, non-LTR retrotransposons specific to gibbons and may have played a role in the evolution of this lineage. A full-length LAVA element consists of portions of repeats found in most primate genomes: CT-rich, Alu-like, and VNTR regions from the SVA retrotransposon, and portions of the AluSz and L1ME5 elements. To evaluate whether the gibbon genome currently harbors functional LAVA elements capable of mobilization by the endogenous LINE-1 (L1) protein machinery and which LAVA components are important for retrotransposition, we established a trans-mobilization assay in HeLa cells. Specifically, we tested if a full-length member of the older LAVA subfamily C that was isolated from the gibbon genome and named LAVAC, or its components, can be mobilized in the presence of the human L1 protein machinery. We show that L1 proteins mobilize the LAVAC element at frequencies exceeding processed pseudogene formation and human SVAE retrotransposition by > 100-fold and ≥3-fold, respectively. We find that only the SVA-derived portions confer activity, and truncation of the 3′ L1ME5 portion increases retrotransposition rates by at least 100%. Tagged de novo insertions integrated into intronic regions in cell culture, recapitulating findings in the gibbon genome. Finally, we present alternative models for the rise of the LAVA retrotransposon in the gibbon lineage.
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Affiliation(s)
- Thomas J Meyer
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
| | - Ulrike Held
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Kimberly A Nevonen
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon
| | - Sabine Klawitter
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
- Present address: Division of Inborn Metabolic Diseases, University Children's Hospital, Heidelberg, Germany
| | - Thomas Pirzer
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
| | - Lucia Carbone
- Division of Neuroscience, Oregon National Primate Research Center, Beaverton, Oregon
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health & Science University, Portland, Oregon
- Department of Medicine, Oregon Health & Science University, Portland, Oregon
| | - Gerald G Schumann
- Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, Germany
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42
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Nascimento FF, Rodrigo AG. Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution. PLoS One 2016; 11:e0162454. [PMID: 27649303 PMCID: PMC5029938 DOI: 10.1371/journal.pone.0162454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 08/02/2016] [Indexed: 02/05/2023] Open
Abstract
Transposable elements (TEs) are DNA sequences that are able to replicate and move within and between host genomes. Their mechanism of replication is also shared with endogenous retroviruses (ERVs), which are also a type of TE that represent an ancient retroviral infection within animal genomes. Two models have been proposed to explain TE proliferation in host genomes: the strict master model (SMM), and the random template (or transposon) model (TM). In SMM only a single copy of a given TE lineage is able to replicate, and all other genomic copies of TEs are derived from that master copy. In TM, any element of a given family is able to replicate in the host genome. In this paper, we simulated ERV phylogenetic trees under variations of SMM and TM. To test whether current phylogenetic programs can recover the simulated ERV phylogenies, DNA sequence alignments were simulated and maximum likelihood trees were reconstructed and compared to the simulated phylogenies. Results indicate that visual inspection of phylogenetic trees alone can be misleading. However, if a set of statistical summaries is calculated, we are able to distinguish between models with high accuracy by using a data mining algorithm that we introduce here. We also demonstrate the use of our data mining algorithm with empirical data for the porcine endogenous retrovirus (PERV), an ERV that is able to replicate in human and pig cells in vitro.
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Affiliation(s)
| | - Allen G. Rodrigo
- National Evolutionary Synthesis Center, Durham, NC, United States of America
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43
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Christian CM, Kines KJ, Belancio VP. The importance of L1 ORF2p cryptic sequence to ORF2p fragment-mediated cytotoxicity. Mob Genet Elements 2016; 6:e1198300. [PMID: 27583184 PMCID: PMC4993571 DOI: 10.1080/2159256x.2016.1198300] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 11/18/2022] Open
Abstract
The Long Interspersed Element 1 (LINE1 or L1) ORF2 protein (ORF2p) can cause DNA damage through the activity of its endonuclease domain (EN). The DNA double-strand breaks (DSB) introduced by the ORF2p EN have the potential to be mutagenic. Previously, our lab has shown that ORF2p fragments containing the EN domain could be expressed in mammalian cells and have variable cytotoxicity. Inclusion of the ORF2p sequence C-terminal to the EN domain in these fragments both reduced the cytotoxicity of these fragments and increased their presence in the nucleus as detected by Western blot analysis. Here, we identify the amino acids (aa 270-274) in the newly-identified ORF2p Cryptic region (Cry) that may be important to the subcellular localization and cytotoxic potential of these EN-containing ORF2p fragments.
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Affiliation(s)
- Claiborne M. Christian
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA, USA
| | - Kristine J. Kines
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA, USA
| | - Victoria P. Belancio
- Structural and Cellular Biology, Tulane University School of Medicine, Tulane Cancer Center, Tulane Center for Aging, New Orleans, LA, USA
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44
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Kim NH, Lee G, Sherer NA, Martini KM, Goldenfeld N, Kuhlman TE. Real-time transposable element activity in individual live cells. Proc Natl Acad Sci U S A 2016; 113:7278-83. [PMID: 27298350 PMCID: PMC4932956 DOI: 10.1073/pnas.1601833113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The excision and reintegration of transposable elements (TEs) restructure their host genomes, generating cellular diversity involved in evolution, development, and the etiology of human diseases. Our current knowledge of TE behavior primarily results from bulk techniques that generate time and cell ensemble averages, but cannot capture cell-to-cell variation or local environmental and temporal variability. We have developed an experimental system based on the bacterial TE IS608 that uses fluorescent reporters to directly observe single TE excision events in individual cells in real time. We find that TE activity depends upon the TE's orientation in the genome and the amount of transposase protein in the cell. We also find that TE activity is highly variable throughout the lifetime of the cell. Upon entering stationary phase, TE activity increases in cells hereditarily predisposed to TE activity. These direct observations demonstrate that real-time live-cell imaging of evolution at the molecular and individual event level is a powerful tool for the exploration of genome plasticity in stressed cells.
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Affiliation(s)
- Neil H Kim
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Gloria Lee
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nicholas A Sherer
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - K Michael Martini
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Nigel Goldenfeld
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Institute for Universal Biology NASA Astrobiology Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
| | - Thomas E Kuhlman
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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Amarillo IE, Nievera I, Hagan A, Huchthagowder V, Heeley J, Hollander A, Koenig J, Austin P, Wang T. Integrated small copy number variations and epigenome maps of disorders of sex development. Hum Genome Var 2016; 3:16012. [PMID: 27340555 PMCID: PMC4899613 DOI: 10.1038/hgv.2016.12] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 03/24/2016] [Accepted: 03/26/2016] [Indexed: 02/03/2023] Open
Abstract
Small copy number variations (CNVs) have typically not been analyzed or reported in clinical settings and hence have remained underrepresented in databases and the literature. Here, we focused our investigations on these small CNVs using chromosome microarray analysis (CMA) data previously obtained from patients with atypical characteristics or disorders of sex development (DSD). Using our customized CMA track targeting 334 genes involved in the development of urogenital and reproductive structures and a less stringent analysis filter, we uncovered small genes with recurrent and overlapping CNVs as small as 1 kb, and small regions of homozygosity (ROHs), imprinting and position effects. Detailed analysis of these high-resolution data revealed CNVs and ROHs involving structural and functional domains, repeat elements, active transcription sites and regulatory regions. Integration of these genomic data with DNA methylation, histone modification and predicted RNA expression profiles in normal testes and ovaries suggested spatiotemporal and tissue-specific gene regulation. This study emphasized a DSD-specific and gene-targeted CMA approach that uncovered previously unanalyzed or unreported small genes and CNVs, contributing to the growing resources on small CNVs and facilitating the narrowing of the genomic gap for identifying candidate genes or regions. This high-resolution analysis tool could improve the diagnostic utility of CMA, not only in patients with DSD but also in other clinical populations. These integrated data provided a better genomic-epigenomic landscape of DSD and greater opportunities for downstream research.
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Affiliation(s)
- Ina E Amarillo
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine, St Louis, MO, USA; Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA
| | - Isabelle Nievera
- Washington University in St Louis School of Medicine DSD Team , St Louis, MO, USA
| | - Andrew Hagan
- Division of Biology and Biomedical Sciences, Washington University in St Louis , St Louis, MO, USA
| | - Vishwa Huchthagowder
- Cytogenomics and Molecular Pathology Laboratory, Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University in St Louis School of Medicine , St Louis, MO, USA
| | - Jennifer Heeley
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Abby Hollander
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Pediatrics, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Joel Koenig
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Paul Austin
- Washington University in St Louis School of Medicine DSD Team, St Louis, MO, USA; Department of Surgery, Washington University in St Louis School of Medicine, St Louis, MO, USA
| | - Ting Wang
- Department of Genetics, Washington University in St Louis School of Medicine , St Louis, MO, USA
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Udomsinprasert W, Kitkumthorn N, Mutirangura A, Chongsrisawat V, Poovorawan Y, Honsawek S. Global methylation, oxidative stress, and relative telomere length in biliary atresia patients. Sci Rep 2016; 6:26969. [PMID: 27243754 PMCID: PMC4886632 DOI: 10.1038/srep26969] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/11/2016] [Indexed: 12/25/2022] Open
Abstract
Alu and LINE-1 elements are retrotransposons with a ubiquitous presence in the human genome that can cause genomic instability, specifically relating to telomere length. Genotoxic agents may induce methylation of retrotransposons, in addition to oxidative DNA damage in the form of 8-hydroxy-2′-deoxyguanosine (8-OHdG). Methylation of retrotransposons induced by these agents may contribute to biliary atresia (BA) etiology. Here, we investigated correlations between global methylation, 8-OHdG, and relative telomere length, as well as reporting on Alu and LINE-1 hypomethylation in BA patients. Alu and LINE-1 hypomethylation were found to be associated with elevated risk of BA (OR = 4.07; 95% CI: 2.27–7.32; P < 0.0001 and OR = 3.51; 95% CI: 1.87–6.59; P < 0.0001, respectively). Furthermore, LINE-1 methylation was associated with liver stiffness in BA patients (β coefficient = −0.17; 95% CI: −0.24 to −0.10; P < 0.0001). Stratified analysis revealed negative correlations between Alu and LINE-1 methylation and 8-OHdG in BA patients (P < 0.0001). In contrast, positive relationships were identified between Alu and LINE-1 methylation and relative telomere length in BA patients (P < 0.0001). These findings suggest that retrotransposon hypomethylation is associated with plasma 8-OHdG and telomere length in BA patients.
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Affiliation(s)
- Wanvisa Udomsinprasert
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral and Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voranush Chongsrisawat
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Yong Poovorawan
- Center of Excellence in Clinical Virology, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Bangkok, Thailand
| | - Sittisak Honsawek
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
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Wang Y, Li S, Smith K, Waldman BC, Waldman AS. Intrachromosomal recombination between highly diverged DNA sequences is enabled in human cells deficient in Bloom helicase. DNA Repair (Amst) 2016; 41:73-84. [PMID: 27100209 DOI: 10.1016/j.dnarep.2016.03.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 03/21/2016] [Indexed: 11/30/2022]
Abstract
Mutation of Bloom helicase (BLM) causes Bloom syndrome (BS), a rare human genetic disorder associated with genome instability, elevation of sister chromatid exchanges, and predisposition to cancer. Deficiency in BLM homologs in Drosophila and yeast brings about significantly increased rates of recombination between imperfectly matched sequences ("homeologous recombination," or HeR). To assess whether BLM deficiency provokes an increase in HeR in human cells, we transfected an HeR substrate into a BLM-null cell line derived from a BS patient. The substrate contained a thymidine kinase (tk)-neo fusion gene disrupted by the recognition site for endonuclease I-SceI, as well as a functional tk gene to serve as a potential recombination partner for the tk-neo gene. The two tk sequences on the substrate displayed 19% divergence. A double-strand break was introduced by expression of I-SceI and repair events were recovered by selection for G418-resistant clones. Among 181 events recovered, 30 were accomplished via HeR with the balance accomplished by nonhomologous end-joining. The frequency of HeR events in the BS cells was elevated significantly compared to that seen in normal human fibroblasts or in BS cells complemented for BLM expression. We conclude that BLM deficiency enables HeR in human cells.
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Affiliation(s)
- Yibin Wang
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Shen Li
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Krissy Smith
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | | | - Alan S Waldman
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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Identification of transposable element-mediated deletions in 27 Korean individuals based on whole genome sequencing data. Genes Genomics 2016. [DOI: 10.1007/s13258-015-0370-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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White TB, Morales ME, Deininger PL. Alu elements and DNA double-strand break repair. Mob Genet Elements 2015; 5:81-85. [PMID: 26942043 DOI: 10.1080/2159256x.2015.1093067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/31/2015] [Accepted: 09/04/2015] [Indexed: 12/30/2022] Open
Abstract
Alu elements represent one of the most common sources of homology and homeology in the human genome. Homeologous recombination between Alu elements represents a major form of genetic instability leading to deletions and duplications. Although these types of events have been studied extensively through genomic sequencing to assess the impact of Alu elements on disease mutations and genome evolution, the overall abundance of Alu elements in the genome often makes it difficult to assess the relevance of the Alu elements to specific recombination events. We recently reported a powerful new reporter gene system that allows the assessment of various cis and trans factors on the contribution of Alu elements to various forms of genetic instability. This allowed a quantitative measurement of the influence of mismatches on Alu elements and instability. It also confirmed that homeologous Alu elements are able to stimulate non-homologous end joining events in their vicinity. This appears to be dependent on portions of the mismatch repair pathway. We are now in a position to begin to unravel the complex influences of Alu density, mismatch and location with alterations of DNA repair processes in various tissues and tumors.
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Affiliation(s)
- Travis B White
- Tulane Cancer Center; Tulane University Health Sciences Center ; New Orleans, LA USA
| | - Maria E Morales
- Tulane Cancer Center; Tulane University Health Sciences Center ; New Orleans, LA USA
| | - Prescott L Deininger
- Tulane Cancer Center; Tulane University Health Sciences Center ; New Orleans, LA USA
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