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Booy EP, Gussakovsky D, Brown M, Shwaluk R, Nachtigal MW, McKenna SA. lncRNA BC200 is processed into a stable Alu monomer. RNA (NEW YORK, N.Y.) 2024; 30:1477-1494. [PMID: 39179355 PMCID: PMC11482611 DOI: 10.1261/rna.080152.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 08/08/2024] [Indexed: 08/26/2024]
Abstract
The noncoding RNA BC200 is elevated in human cancers and is implicated in translation regulation as well as cell survival and proliferation. Upon BC200 overexpression, we observed correlated expression of a second, smaller RNA species. This RNA is expressed endogenously and exhibits cell-type-dependent variability relative to BC200. Aptamer-tagged expression constructs confirmed that the RNA is a truncated form of BC200, and sequencing revealed a modal length of 120 nt; thus, we refer to the RNA fragment as BC120. We present a methodology for accurate and specific detection of BC120 and establish that BC120 is expressed in several normal human tissues and is also elevated in ovarian cancer. BC120 exhibits remarkable stability relative to BC200 and is resistant to knockdown strategies that target the 3' unique sequence of BC200. Combined knockdown of BC200 and BC120 exhibits greater phenotypic impacts than knockdown of BC200 alone, and overexpression of BC120 negatively impacts translation of a GFP reporter, providing insight into a potential translational regulatory role for this RNA. The presence of a novel, truncated, and stable form of BC200 adds complexity to the investigation of this noncoding RNA that must be considered in future studies of BC200 and other related Alu RNAs.
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Affiliation(s)
- Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Mira Brown
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Rowan Shwaluk
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Mark W Nachtigal
- Department of Biochemistry and Medical Genetics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada R3E 0J9
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, Manitoba, Canada R2H 2A6
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
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2
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Wang ZY, Ge LP, Ouyang Y, Jin X, Jiang YZ. Targeting transposable elements in cancer: developments and opportunities. Biochim Biophys Acta Rev Cancer 2024; 1879:189143. [PMID: 38936517 DOI: 10.1016/j.bbcan.2024.189143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 05/23/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Transposable elements (TEs), comprising nearly 50% of the human genome, have transitioned from being perceived as "genomic junk" to key players in cancer progression. Contemporary research links TE regulatory disruptions with cancer development, underscoring their therapeutic potential. Advances in long-read sequencing, computational analytics, single-cell sequencing, proteomics, and CRISPR-Cas9 technologies have enriched our understanding of TEs' clinical implications, notably their impact on genome architecture, gene regulation, and evolutionary processes. In cancer, TEs, including long interspersed element-1 (LINE-1), Alus, and long terminal repeat (LTR) elements, demonstrate altered patterns, influencing both tumorigenic and tumor-suppressive mechanisms. TE-derived nucleic acids and tumor antigens play critical roles in tumor immunity, bridging innate and adaptive responses. Given their central role in oncology, TE-targeted therapies, particularly through reverse transcriptase inhibitors and epigenetic modulators, represent a novel avenue in cancer treatment. Combining these TE-focused strategies with existing chemotherapy or immunotherapy regimens could enhance efficacy and offer a new dimension in cancer treatment. This review delves into recent TE detection advancements, explores their multifaceted roles in tumorigenesis and immune regulation, discusses emerging diagnostic and therapeutic approaches centered on TEs, and anticipates future directions in cancer research.
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Affiliation(s)
- Zi-Yu Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li-Ping Ge
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yang Ouyang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Jin
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yi-Zhou Jiang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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3
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Abstract
Alu RNA are implicated in the poor prognosis of several human disease states. These RNA are transcription products of primate specific transposable elements called Alu elements. These elements are extremely abundant, comprising over 10% of the human genome, and 100 to 1000 cytoplasmic copies of Alu RNA per cell. Alu RNA do not have a single universal functional role aside from selfish self-propagation. Despite this, Alu RNA have been found to operate in a diverse set of translational and transcriptional mechanisms. This review will focus on the current knowledge of Alu RNA involved in human disease states and known mechanisms of action. Examples of Alu RNA that are transcribed in a variety of contexts such as introns, mature mRNA, and non-coding transcripts will be discussed. Past and present challenges in studying Alu RNA, and the future directions of Alu RNA in basic and clinical research will also be examined.
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Affiliation(s)
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Canada
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4
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Sui Y, Peng S. A Mechanism Leading to Changes in Copy Number Variations Affected by Transcriptional Level Might Be Involved in Evolution, Embryonic Development, Senescence, and Oncogenesis Mediated by Retrotransposons. Front Cell Dev Biol 2021; 9:618113. [PMID: 33644055 PMCID: PMC7905054 DOI: 10.3389/fcell.2021.618113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/11/2021] [Indexed: 01/05/2023] Open
Abstract
In recent years, more and more evidence has emerged showing that changes in copy number variations (CNVs) correlated with the transcriptional level can be found during evolution, embryonic development, and oncogenesis. However, the underlying mechanisms remain largely unknown. The success of the induced pluripotent stem cell suggests that genome changes could bring about transformations in protein expression and cell status; conversely, genome alterations generated during embryonic development and senescence might also be the result of genome changes. With rapid developments in science and technology, evidence of changes in the genome affected by transcriptional level has gradually been revealed, and a rational and concrete explanation is needed. Given the preference of the HIV-1 genome to insert into transposons of genes with high transcriptional levels, we propose a mechanism based on retrotransposons facilitated by specific pre-mRNA splicing style and homologous recombination (HR) to explain changes in CNVs in the genome. This mechanism is similar to that of the group II intron that originated much earlier. Under this proposed mechanism, CNVs on genome are dynamically and spontaneously extended in a manner that is positively correlated with transcriptional level or contract as the cell divides during evolution, embryonic development, senescence, and oncogenesis, propelling alterations in them. Besides, this mechanism explains several critical puzzles in these processes. From evidence collected to date, it can be deduced that the message contained in genome is not just three-dimensional but will become four-dimensional, carrying more genetic information.
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Affiliation(s)
- Yunpeng Sui
- Department of Functional Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
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5
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Kerur N, Fukuda S, Banerjee D, Kim Y, Fu D, Apicella I, Varshney A, Yasuma R, Fowler BJ, Baghdasaryan E, Marion KM, Huang X, Yasuma T, Hirano Y, Serbulea V, Ambati M, Ambati VL, Kajiwara Y, Ambati K, Hirahara S, Bastos-Carvalho A, Ogura Y, Terasaki H, Oshika T, Kim KB, Hinton DR, Leitinger N, Cambier JC, Buxbaum JD, Kenney MC, Jazwinski SM, Nagai H, Hara I, West AP, Fitzgerald KA, Sadda SR, Gelfand BD, Ambati J. cGAS drives noncanonical-inflammasome activation in age-related macular degeneration. Nat Med 2017; 24:50-61. [PMID: 29176737 PMCID: PMC5760363 DOI: 10.1038/nm.4450] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/31/2017] [Indexed: 02/07/2023]
Abstract
Geographic atrophy is a blinding form of age-related macular degeneration characterized by death of the retinal pigmented epithelium (RPE). In this disease, the RPE displays evidence of DICER1 deficiency, resultant accumulation of endogenous Alu retroelement RNA, and NLRP3 inflammasome activation. How the inflammasome is activated in this untreatable disease is largely unknown. Here we demonstrate that RPE degeneration in human cell culture and in mouse models is driven by a non-canonical inflammasome pathway that results in activation of caspase-4 (caspase-11 in mice) and caspase-1, and requires cyclic GMP-AMP synthase (cGAS)-dependent interferon-β (IFN-β) production and gasdermin D-dependent interleukin-18 (IL-18) secretion. Reduction of DICER1 levelsor accumulation of Alu RNA triggers cytosolic escape of mitochondrial DNA, which engages cGAS. Moreover, caspase-4, gasdermin D, IFN-β, and cGAS levels are elevated in the RPE of human eyes with geographic atrophy. Collectively, these data highlight an unexpected role for cGAS in responding to mobile element transcripts, reveal cGAS-driven interferon signaling as a conduit for mitochondrial damage-induced inflammasome activation, expand the immune sensing repertoire of cGAS and caspase-4 to non-infectious human disease, and identify new potential targets for treatment of a major cause of blindness.
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Affiliation(s)
- Nagaraj Kerur
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Shinichi Fukuda
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Tsukuba, Ibaraki, Japan
| | - Daipayan Banerjee
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Younghee Kim
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Dongxu Fu
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ivana Apicella
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Akhil Varshney
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Reo Yasuma
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Benjamin J Fowler
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Elmira Baghdasaryan
- Doheny Eye Institute, Los Angeles, Los Angeles, California, USA.,Department of Ophthalmology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA
| | | | - Xiwen Huang
- Doheny Eye Institute, Los Angeles, Los Angeles, California, USA
| | - Tetsuhiro Yasuma
- Department of Ophthalmology, University of Tsukuba, Ibaraki, Japan.,Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshio Hirano
- Department of Ophthalmology, University of Tsukuba, Ibaraki, Japan.,Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Vlad Serbulea
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Meenakshi Ambati
- Center for Digital Image Evaluation, Charlottesville, Virginia, USA
| | - Vidya L Ambati
- Center for Digital Image Evaluation, Charlottesville, Virginia, USA
| | - Yuji Kajiwara
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Kameshwari Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Shuichiro Hirahara
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Ana Bastos-Carvalho
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - Yuichiro Ogura
- Department of Ophthalmology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuro Oshika
- Department of Ophthalmology, University of Tsukuba, Ibaraki, Japan
| | - Kyung Bo Kim
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky, USA
| | - David R Hinton
- Departments of Pathology and Ophthalmology, USC Roski Eye Institute, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
| | - Norbert Leitinger
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - John C Cambier
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Joseph D Buxbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - M Cristina Kenney
- Gavin Herbert Eye Institute, University of California Irvine, Irvine, California, USA
| | - S Michal Jazwinski
- Tulane Center for Aging and Department of Medicine, Tulane University Health Sciences Center, New Orleans, Louisiana, USA
| | - Hiroshi Nagai
- Division of Dermatology, Department of Internal Related, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Isao Hara
- Department of Urology, Wakayama Medical University, Wakayama, Japan
| | - A Phillip West
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, USA
| | - Katherine A Fitzgerald
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - SriniVas R Sadda
- Doheny Eye Institute, Los Angeles, Los Angeles, California, USA.,Department of Ophthalmology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, California, USA
| | - Bradley D Gelfand
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA.,Department of Biomedical Engineering, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Jayakrishna Ambati
- Center for Advanced Vision Science, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky, USA.,Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA.,Department of Microbiology, Immunology, and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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6
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Alu RNA accumulation induces epithelial-to-mesenchymal transition by modulating miR-566 and is associated with cancer progression. Oncogene 2017; 37:627-637. [PMID: 28991230 PMCID: PMC5799714 DOI: 10.1038/onc.2017.369] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/08/2017] [Accepted: 08/12/2017] [Indexed: 12/16/2022]
Abstract
Alu sequences are the most abundant short interspersed repeated elements in the human genome. Here we show that in a cell culture model of colorectal cancer (CRC) progression, we observe accumulation of Alu RNA that is associated with reduced DICER1 levels. Alu RNA induces epithelial-to-mesenchymal transition (EMT) by acting as a molecular sponge of miR-566. Moreover, Alu RNA accumulates as consequence of DICER1 deficit in colorectal, ovarian, renal and breast cancer cell lines. Interestingly, Alu RNA knockdown prevents DICER1 depletion-induced EMT despite global microRNA (miRNA) downregulation. Alu RNA expression is also induced by transforming growth factor-β1, a major driver of EMT. Corroborating this data, we found that non-coding Alu RNA significantly correlates with tumor progression in human CRC patients. Together, these findings reveal an unexpected DICER1-dependent, miRNA-independent role of Alu RNA in cancer progression that could bring mobile element transcripts in the fields of cancer therapeutic and prognosis.
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7
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Carnevali D, Dieci G. Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data. Noncoding RNA 2017; 3:ncrna3010015. [PMID: 29657287 PMCID: PMC5832001 DOI: 10.3390/ncrna3010015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/27/2017] [Accepted: 03/14/2017] [Indexed: 01/08/2023] Open
Abstract
Short Interspersed Element (SINE) retrotransposons are one of the most abundant DNA repeat elements in the human genome. They have been found to impact the expression of protein-coding genes, but the possible roles in cell physiology of their noncoding RNAs, generated by RNA polymerase (Pol) III, are just starting to be elucidated. For this reason, Short Interspersed Element (SINE) expression profiling is becoming mandatory to obtain a comprehensive picture of their regulatory roles. However, their repeated nature and frequent location within Pol II-transcribed genes represent a serious obstacle to the identification and quantification of genuine, Pol III-derived SINE transcripts at single-locus resolution on a genomic scale. Among the recent Next Generation Sequencing technologies, only RNA sequencing (RNA-Seq) holds the potential to solve these issues, even though both technical and biological matters need to be taken into account. A bioinformatic pipeline has been recently set up that, by exploiting RNA-seq features and knowledge of SINE transcription mechanisms, allows for easy identification and profiling of transcriptionally active genomic loci which are a source of genuine Pol III SINE transcripts.
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Affiliation(s)
- Davide Carnevali
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy.
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8
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Ivanova E, Berger A, Scherrer A, Alkalaeva E, Strub K. Alu RNA regulates the cellular pool of active ribosomes by targeted delivery of SRP9/14 to 40S subunits. Nucleic Acids Res 2015; 43:2874-87. [PMID: 25697503 PMCID: PMC4357698 DOI: 10.1093/nar/gkv048] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The human genome contains about 1.5 million Alu elements, which are transcribed into Alu RNAs by RNA polymerase III. Their expression is upregulated following stress and viral infection, and they associate with the SRP9/14 protein dimer in the cytoplasm forming Alu RNPs. Using cell-free translation, we have previously shown that Alu RNPs inhibit polysome formation. Here, we describe the mechanism of Alu RNP-mediated inhibition of translation initiation and demonstrate its effect on translation of cellular and viral RNAs. Both cap-dependent and IRES-mediated initiation is inhibited. Inhibition involves direct binding of SRP9/14 to 40S ribosomal subunits and requires Alu RNA as an assembly factor but its continuous association with 40S subunits is not required for inhibition. Binding of SRP9/14 to 40S prevents 48S complex formation by interfering with the recruitment of mRNA to 40S subunits. In cells, overexpression of Alu RNA decreases translation of reporter mRNAs and this effect is alleviated with a mutation that reduces its affinity for SRP9/14. Alu RNPs also inhibit the translation of cellular mRNAs resuming translation after stress and of viral mRNAs suggesting a role of Alu RNPs in adapting the translational output in response to stress and viral infection.
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Affiliation(s)
- Elena Ivanova
- Département de biologie cellulaire, Université de Genève, Sciences III, 1211 Genève, Switzerland
| | - Audrey Berger
- Département de biologie cellulaire, Université de Genève, Sciences III, 1211 Genève, Switzerland
| | - Anne Scherrer
- Département de biologie cellulaire, Université de Genève, Sciences III, 1211 Genève, Switzerland
| | - Elena Alkalaeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Katharina Strub
- Département de biologie cellulaire, Université de Genève, Sciences III, 1211 Genève, Switzerland
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9
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Conti A, Carnevali D, Bollati V, Fustinoni S, Pellegrini M, Dieci G. Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data. Nucleic Acids Res 2014; 43:817-35. [PMID: 25550429 PMCID: PMC4333407 DOI: 10.1093/nar/gku1361] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Of the ∼1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼1300 Alu loci corresponding to detectable transcripts, with ∼120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5′-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
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Affiliation(s)
- Anastasia Conti
- Department of Life Sciences, University of Parma, 43124 Parma, Italy Department of Clinical and Experimental Medicine, University of Parma, 43126 Parma, Italy
| | - Davide Carnevali
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy
| | - Silvia Fustinoni
- Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-7239, USA
| | - Giorgio Dieci
- Department of Life Sciences, University of Parma, 43124 Parma, Italy
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10
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Ade C, Roy-Engel AM, Deininger PL. Alu elements: an intrinsic source of human genome instability. Curr Opin Virol 2013; 3:639-45. [PMID: 24080407 PMCID: PMC3982648 DOI: 10.1016/j.coviro.2013.09.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
Abstract
Alu elements are ∼300bp sequences that have amplified via an RNA intermediate leading to the accumulation of over 1 million copies in the human genome. Although a few of the copies are active, Alu germline activity is the highest of all human retrotransposons and does significantly contribute to genetic disease and population diversity. There are two basic mechanisms by which Alu elements contribute to disease: through insertional mutagenesis and as a large source of repetitive sequences that contribute to nonallelic homologous recombination (NAHR) that cause genetic deletions and duplications.
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Affiliation(s)
- Catherine Ade
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
| | - Astrid M. Roy-Engel
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
| | - Prescott L. Deininger
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, Consortium Of Mobile Elements at Tulane)
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11
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Kerur N, Hirano Y, Tarallo V, Fowler BJ, Bastos-Carvalho A, Yasuma T, Yasuma R, Kim Y, Hinton DR, Kirschning CJ, Gelfand BD, Ambati J. TLR-independent and P2X7-dependent signaling mediate Alu RNA-induced NLRP3 inflammasome activation in geographic atrophy. Invest Ophthalmol Vis Sci 2013; 54:7395-401. [PMID: 24114535 DOI: 10.1167/iovs.13-12500] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
PURPOSE Accumulation of Alu RNA transcripts due to DICER1 deficiency in the retinal pigmented epithelium (RPE) promotes geographic atrophy. Recently we showed that Alu RNA activated the NLRP3 inflammasome, leading to RPE cell death via interleukin-18 (IL-18)-mediated MyD88 signaling. However, the molecular basis for NLRP3 inflammasome activation by Alu RNA is not well understood. We sought to decipher the key signaling events triggered by Alu RNA that lead to priming and activation of the NLRP3 inflammasome and, ultimately, to RPE degeneration by investigating the roles of the purinoreceptor P2X7, the transcription factor NF-κB, and the Toll-like receptors (TLRs) in these processes. METHODS Human and mouse RPE cells were transfected with a plasmid encoding an Alu element (pAlu) or an in vitro-transcribed Alu RNA. Inflammasome priming was assessed by measuring NLRP3 and IL18 mRNA levels by real-time quantitative PCR. Using immunoblotting, we assessed NF-κB activation by monitoring phosphorylation of its p65 subunit, and inflammasome activation by monitoring caspase-1 cleavage into its active form. RPE degeneration was induced in mice by subretinal transfection of pAlu or Alu RNA. The NF-κB inhibitor BAY 11-7082, the P2X7 receptor antagonist A-740003, and the NLRP3 inflammasome inhibitor glyburide were delivered by intravitreous injections. We studied wild-type (WT) C57Bl/6J, P2rx7(-/-), Nfkb1(-/-), and Tlr23479(-/-) mice. RPE degeneration was assessed by fundus photography and zonula occludens-1 (ZO-1) staining of mouse RPE. RESULTS Alu RNA-induced NF-κB activation, independent of TLR-1, -2, -3, -4, -6, -7, and -9 signaling, was required for priming the NLRP3 inflammasome. Nfkb1(-/-) and P2rx7(-/-) mice and WT mice treated with the pharmacological inhibitors of NF-κB, P2X7, or NLRP3, were protected against Alu RNA-induced RPE degeneration. CONCLUSIONS NF-κB and P2X7 are critical signaling intermediates in Alu RNA-induced inflammasome priming and RPE degeneration. These molecules are novel targets for rational drug development for geographic atrophy.
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Affiliation(s)
- Nagaraj Kerur
- Department of Ophthalmology and Visual Sciences, University of Kentucky, Lexington, Kentucky
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12
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Vossaert L, O'Leary T, Van Neste C, Heindryckx B, Vandesompele J, De Sutter P, Deforce D. Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Mol Biol 2013; 14:21. [PMID: 24028740 PMCID: PMC3848990 DOI: 10.1186/1471-2199-14-21] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 09/11/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Selecting stably expressed reference genes is essential for proper reverse transcription quantitative polymerase chain reaction gene expression analysis. However, this choice is not always straightforward. In the case of differentiating human embryonic stem (hES) cells, differentiation itself introduces changes whereby reference gene stability may be influenced. RESULTS In this study, we evaluated the stability of various references during retinoic acid-induced (2 microM) differentiation of hES cells. Out of 12 candidate references, beta-2-microglobulin, ribosomal protein L13A and Alu repeats are found to be the most stable for this experimental set-up. CONCLUSIONS Our results show that some of the commonly used reference genes are actually not amongst the most stable loci during hES cell differentiation promoted by retinoic acid. Moreover, a novel normalization strategy based on expressed Alu repeats is validated for use in hES cell experiments.
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Affiliation(s)
- Liesbeth Vossaert
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Harelbekestraat 72, Ghent 9000, Belgium.
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13
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Pascali C, Teichmann M. RNA polymerase III transcription - regulated by chromatin structure and regulator of nuclear chromatin organization. Subcell Biochem 2013; 61:261-287. [PMID: 23150255 DOI: 10.1007/978-94-007-4525-4_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
RNA polymerase III (Pol III) transcription is regulated by modifications of the chromatin. DNA methylation and post-translational modifications of histones, such as acetylation, phosphorylation and methylation have been linked to Pol III transcriptional activity. In addition to being regulated by modifications of DNA and histones, Pol III genes and its transcription factors have been implicated in the organization of nuclear chromatin in several organisms. In yeast, the ability of the Pol III transcription system to contribute to nuclear organization seems to be dependent on direct interactions of Pol III genes and/or its transcription factors TFIIIC and TFIIIB with the structural maintenance of chromatin (SMC) protein-containing complexes cohesin and condensin. In human cells, Pol III genes and transcription factors have also been shown to colocalize with cohesin and the transcription regulator and genome organizer CCCTC-binding factor (CTCF). Furthermore, chromosomal sites have been identified in yeast and humans that are bound by partial Pol III machineries (extra TFIIIC sites - ETC; chromosome organizing clamps - COC). These ETCs/COC as well as Pol III genes possess the ability to act as boundary elements that restrict spreading of heterochromatin.
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Affiliation(s)
- Chiara Pascali
- Institut Européen de Chimie et Biologie (IECB), Université Bordeaux Segalen / INSERM U869, 2, rue Robert Escarpit, 33607, Pessac, France
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14
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Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E. On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 2013; 5:578-90. [PMID: 23431001 PMCID: PMC3622293 DOI: 10.1093/gbe/evt028] [Citation(s) in RCA: 302] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/16/2013] [Indexed: 12/11/2022] Open
Abstract
A recent slew of ENCyclopedia Of DNA Elements (ENCODE) Consortium publications, specifically the article signed by all Consortium members, put forward the idea that more than 80% of the human genome is functional. This claim flies in the face of current estimates according to which the fraction of the genome that is evolutionarily conserved through purifying selection is less than 10%. Thus, according to the ENCODE Consortium, a biological function can be maintained indefinitely without selection, which implies that at least 80 - 10 = 70% of the genome is perfectly invulnerable to deleterious mutations, either because no mutation can ever occur in these "functional" regions or because no mutation in these regions can ever be deleterious. This absurd conclusion was reached through various means, chiefly by employing the seldom used "causal role" definition of biological function and then applying it inconsistently to different biochemical properties, by committing a logical fallacy known as "affirming the consequent," by failing to appreciate the crucial difference between "junk DNA" and "garbage DNA," by using analytical methods that yield biased errors and inflate estimates of functionality, by favoring statistical sensitivity over specificity, and by emphasizing statistical significance rather than the magnitude of the effect. Here, we detail the many logical and methodological transgressions involved in assigning functionality to almost every nucleotide in the human genome. The ENCODE results were predicted by one of its authors to necessitate the rewriting of textbooks. We agree, many textbooks dealing with marketing, mass-media hype, and public relations may well have to be rewritten.
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Affiliation(s)
- Dan Graur
- Department of Biology and Biochemistry, University of Houston, TX, USA.
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15
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Dieci G, Conti A, Pagano A, Carnevali D. Identification of RNA polymerase III-transcribed genes in eukaryotic genomes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:296-305. [PMID: 23041497 DOI: 10.1016/j.bbagrm.2012.09.010] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Revised: 09/20/2012] [Accepted: 09/21/2012] [Indexed: 12/16/2022]
Abstract
The RNA polymerase (Pol) III transcription system is devoted to the production of short, generally abundant noncoding (nc) RNAs in all eukaryotic cells. Previously thought to be restricted to a few housekeeping genes easily detectable in genome sequences, the set of known Pol III-transcribed genes (class III genes) has been expanding in the last ten years, and the issue of their detection, annotation and actual expression has been stimulated and revived by the results of recent high-resolution genome-wide location analyses of the mammalian Pol III machinery, together with those of Pol III-centered computational studies and of ncRNA-focused transcriptomic approaches. In this article, we provide an outline of distinctive features of Pol III-transcribed genes that have allowed and currently allow for their detection in genome sequences, we critically review the currently practiced strategies for the identification of novel class III genes and transcripts, and we discuss emerging themes in Pol III transcription regulation which might orient future transcriptomic studies. This article is part of a Special Issue entitled: Transcription by Odd Pols.
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Affiliation(s)
- Giorgio Dieci
- Dipartimento di Bioscienze, Università degli Studi di Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy.
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16
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Jády BE, Ketele A, Kiss T. Human intron-encoded Alu RNAs are processed and packaged into Wdr79-associated nucleoplasmic box H/ACA RNPs. Genes Dev 2012; 26:1897-910. [PMID: 22892240 PMCID: PMC3435494 DOI: 10.1101/gad.197467.112] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 07/16/2012] [Indexed: 11/25/2022]
Abstract
Alu repetitive sequences are the most abundant short interspersed DNA elements in the human genome. Full-length Alu elements are composed of two tandem sequence monomers, the left and right Alu arms, both derived from the 7SL signal recognition particle RNA. Since Alu elements are common in protein-coding genes, they are frequently transcribed into pre-mRNAs. Here, we demonstrate that the right arms of nascent Alu transcripts synthesized within pre-mRNA introns are processed into metabolically stable small RNAs. The intron-encoded Alu RNAs, termed AluACA RNAs, are structurally highly reminiscent of box H/ACA small Cajal body (CB) RNAs (scaRNAs). They are composed of two hairpin units followed by the essential H (AnAnnA) and ACA box motifs. The mature AluACA RNAs associate with the four H/ACA core proteins: dyskerin, Nop10, Nhp2, and Gar1. Moreover, the 3' hairpin of AluACA RNAs carries two closely spaced CB localization motifs, CAB boxes (UGAG), which bind Wdr79 in a cumulative fashion. In contrast to canonical H/ACA scaRNPs, which concentrate in CBs, the AluACA RNPs accumulate in the nucleoplasm. Identification of 348 human AluACA RNAs demonstrates that intron-encoded AluACA RNAs represent a novel, large subgroup of H/ACA RNAs, which are apparently confined to human or primate cells.
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Affiliation(s)
- Beáta E Jády
- Laboratoire de Biologie Moléculaire Eucaryote du CNRS, UMR5099, IFR109 CNRS, Université Paul Sabatier, 31062 Toulouse Cedex 9, France
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17
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Oler AJ, Traina-Dorge S, Derbes RS, Canella D, Cairns BR, Roy-Engel AM. Alu expression in human cell lines and their retrotranspositional potential. Mob DNA 2012; 3:11. [PMID: 22716230 PMCID: PMC3412727 DOI: 10.1186/1759-8753-3-11] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Accepted: 06/20/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The vast majority of the 1.1 million Alu elements are retrotranspositionally inactive, where only a few loci referred to as 'source elements' can generate new Alu insertions. The first step in identifying the active Alu sources is to determine the loci transcribed by RNA polymerase III (pol III). Previous genome-wide analyses from normal and transformed cell lines identified multiple Alu loci occupied by pol III factors, making them candidate source elements. FINDINGS Analysis of the data from these genome-wide studies determined that the majority of pol III-bound Alus belonged to the older subfamilies Alu S and Alu J, which varied between cell lines from 62.5% to 98.7% of the identified loci. The pol III-bound Alus were further scored for estimated retrotransposition potential (ERP) based on the absence or presence of selected sequence features associated with Alu retrotransposition capability. Our analyses indicate that most of the pol III-bound Alu loci candidates identified lack the sequence characteristics important for retrotransposition. CONCLUSIONS These data suggest that Alu expression likely varies by cell type, growth conditions and transformation state. This variation could extend to where the same cell lines in different laboratories present different Alu expression patterns. The vast majority of Alu loci potentially transcribed by RNA pol III lack important sequence features for retrotransposition and the majority of potentially active Alu loci in the genome (scored high ERP) belong to young Alu subfamilies. Our observations suggest that in an in vivo scenario, the contribution of Alu activity on somatic genetic damage may significantly vary between individuals and tissues.
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Affiliation(s)
- Andrew J Oler
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT USA.,Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stephen Traina-Dorge
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Rebecca S Derbes
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
| | - Donatella Canella
- Center for Integrative Genomics (CIG), Faculty of Biology and Medicine, University of Lausanne, Lausanne 1015, Switzerland
| | - Brad R Cairns
- Department of Oncological Sciences, Huntsman Cancer Institute, and Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Astrid M Roy-Engel
- Tulane Cancer Center SL-66, Dept. of Epidemiology, Tulane University, 1430 Tulane Ave, New Orleans, LA 70112, USA
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18
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Transcriptional regulation of human-specific SVAF₁ retrotransposons by cis-regulatory MAST2 sequences. Gene 2012; 505:128-36. [PMID: 22609064 DOI: 10.1016/j.gene.2012.05.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/03/2012] [Accepted: 05/04/2012] [Indexed: 12/11/2022]
Abstract
SVA elements represent the youngest family of hominid non-LTR retrotransposons. Recently, a human-specific subfamily (termed SVA(F1), CpG-SVA, or MAST2-SVA) was discovered representing fusion of the CpG island-containing exon 1 of the MAST2 gene and a 5'-truncated SVA. SVA(F1) includes at least 84 members, which suggests exceptionally high retrotransposition level. We investigated if the acquirement of the MAST2 CpG-island might play a role in the success of the SVA(F1) subfamily. We observed that in 16 samples representing seven human tissues, MAST2 was cotranscribed with the members of the SVA(F1) subfamily, but not with other retrotransposons. We found that the methylation status of the MAST2-derived sequences of SVA(F1) elements reversely correlates with the transcriptional activity of MAST2. The MAST2 sequence at the 5' end of SVA(F1) acts as a positive transcriptional regulator in human germ cells. Finally, in various testicular tissue samples we uncovered a transcriptional correlation of MAST2 with the human L1, Alu and SVA retrotransposons.
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19
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DICER1 loss and Alu RNA induce age-related macular degeneration via the NLRP3 inflammasome and MyD88. Cell 2012; 149:847-59. [PMID: 22541070 DOI: 10.1016/j.cell.2012.03.036] [Citation(s) in RCA: 469] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Revised: 02/19/2012] [Accepted: 03/26/2012] [Indexed: 02/06/2023]
Abstract
Alu RNA accumulation due to DICER1 deficiency in the retinal pigmented epithelium (RPE) is implicated in geographic atrophy (GA), an advanced form of age-related macular degeneration that causes blindness in millions of individuals. The mechanism of Alu RNA-induced cytotoxicity is unknown. Here we show that DICER1 deficit or Alu RNA exposure activates the NLRP3 inflammasome and triggers TLR-independent MyD88 signaling via IL18 in the RPE. Genetic or pharmacological inhibition of inflammasome components (NLRP3, Pycard, Caspase-1), MyD88, or IL18 prevents RPE degeneration induced by DICER1 loss or Alu RNA exposure. These findings, coupled with our observation that human GA RPE contains elevated amounts of NLRP3, PYCARD, and IL18 and evidence of increased Caspase-1 and MyD88 activation, provide a rationale for targeting this pathway in GA. Our findings also reveal a function of the inflammasome outside the immune system and an immunomodulatory action of mobile elements.
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20
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Roy-Engel AM. LINEs, SINEs and other retroelements: do birds of a feather flock together? Front Biosci (Landmark Ed) 2012; 17:1345-61. [PMID: 22201808 DOI: 10.2741/3991] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mobile elements account for almost half of the mass of the human genome. Only the retroelements from the non-LTR (long terminal repeat) retrotransposon family, which include the LINE-1 (L1) and its non-autonomous partners, are currently active and contributing to new insertions. Although these elements seem to share the same basic amplification mechanism, the activity and success of the different types of retroelements varies. For example, Alu-induced mutagenesis is responsible for the majority of the documented instances of human disease induced by insertion of retroelements. Using copy number in mammals as an indicator, some SINEs have been vastly more successful than other retroelements, such as the retropseudogenes and even L1, likely due to differences in post-insertion selection and ability to overcome cellular controls. SINE and LINE integration can be differentially influenced by cellular factors, indicating some differences between in their amplification mechanisms. We focus on the known aspects of this group of retroelements and highlight their similarities and differences that may significantly influence their biological impact.
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Affiliation(s)
- Astrid M Roy-Engel
- Tulane University, Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane Cancer Center, SL-66 1430 Tulane Ave., New Orleans, LA 70112.
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21
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Abstract
Alu elements are primate-specific repeats and comprise 11% of the human genome. They have wide-ranging influences on gene expression. Their contribution to genome evolution, gene regulation and disease is reviewed.
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22
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Hedges DJ, Belancio VP. Restless genomes humans as a model organism for understanding host-retrotransposable element dynamics. ADVANCES IN GENETICS 2011; 73:219-62. [PMID: 21310298 DOI: 10.1016/b978-0-12-380860-8.00006-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Since their initial discovery in maize, there have been various attempts to categorize the relationship between transposable elements (TEs) and their host organisms. These have ranged from TEs being selfish parasites to their role as essential, functional components of organismal biology. Research over the past several decades has, in many respects, only served to complicate the issue even further. On the one hand, investigators have amassed substantial evidence concerning the negative effects that TE-mutagenic activity can have on host genomes and organismal fitness. On the other hand, we find an increasing number of examples, across several taxa, of TEs being incorporated into functional biological roles for their host organism. Some 45% of our own genomes are comprised of TE copies. While many of these copies are dormant, having lost their ability to mobilize, several lineages continue to actively proliferate in modern human populations. With its complement of ancestral and active TEs, the human genome exhibits key aspects of the host-TE dynamic that has played out since early on in organismal evolution. In this review, we examine what insights the particularly well-characterized human system can provide regarding the nature of the host-TE interaction.
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Affiliation(s)
- Dale J Hedges
- Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, USA
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23
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Kaneko H, Dridi S, Tarallo V, Gelfand BD, Fowler BJ, Cho WG, Kleinman ME, Ponicsan SL, Hauswirth WW, Chiodo VA, Karikó K, Yoo JW, Lee DK, Hadziahmetovic M, Song Y, Misra S, Chaudhuri G, Buaas FW, Braun RE, Hinton DR, Zhang Q, Grossniklaus HE, Provis JM, Madigan MC, Milam AH, Justice NL, Albuquerque RJC, Blandford AD, Bogdanovich S, Hirano Y, Witta J, Fuchs E, Littman DR, Ambati BK, Rudin CM, Chong MMW, Provost P, Kugel JF, Goodrich JA, Dunaief JL, Baffi JZ, Ambati J. DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration. Nature 2011; 471:325-30. [PMID: 21297615 PMCID: PMC3077055 DOI: 10.1038/nature09830] [Citation(s) in RCA: 464] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2010] [Accepted: 01/18/2011] [Indexed: 12/15/2022]
Abstract
Geographic atrophy (GA), an untreatable advanced form of age-related macular degeneration, results from retinal pigmented epithelium (RPE) cell degeneration. Here we show that the microRNA (miRNA)-processing enzyme DICER1 is reduced in the RPE of humans with GA, and that conditional ablation of Dicer1, but not seven other miRNA-processing enzymes, induces RPE degeneration in mice. DICER1 knockdown induces accumulation of Alu RNA in human RPE cells and Alu-like B1 and B2 RNAs in mouse RPE. Alu RNA is increased in the RPE of humans with GA, and this pathogenic RNA induces human RPE cytotoxicity and RPE degeneration in mice. Antisense oligonucleotides targeting Alu/B1/B2 RNAs prevent DICER1 depletion-induced RPE degeneration despite global miRNA downregulation. DICER1 degrades Alu RNA, and this digested Alu RNA cannot induce RPE degeneration in mice. These findings reveal a miRNA-independent cell survival function for DICER1 involving retrotransposon transcript degradation, show that Alu RNA can directly cause human pathology, and identify new targets for a major cause of blindness.
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Affiliation(s)
- Hiroki Kaneko
- Department of Ophthalmology & Visual Sciences, University of Kentucky, Lexington, Kentucky 40506, USA
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24
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Berger A, Strub K. Multiple Roles of Alu-Related Noncoding RNAs. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:119-46. [PMID: 21287136 DOI: 10.1007/978-3-642-16502-3_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Repetitive Alu and Alu-related elements are present in primates, tree shrews (Scandentia), and rodents and have expanded to 1.3 million copies in the human genome by nonautonomous retrotransposition. Pol III transcription from these elements occurs at low levels under normal conditions but increases transiently after stress, indicating a function of Alu RNAs in cellular stress response. Alu RNAs assemble with cellular proteins into ribonucleoprotein complexes and can be processed into the smaller scAlu RNAs. Alu and Alu-related RNAs play a role in regulating transcription and translation. They provide a source for the biogenesis of miRNAs and, embedded into mRNAs, can be targeted by miRNAs. When present as inverted repeats in mRNAs, they become substrates of the editing enzymes, and their modification causes the nuclear retention of these mRNAs. Certain Alu elements evolved into unique transcription units with specific expression profiles producing RNAs with highly specific cellular functions.
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Affiliation(s)
- Audrey Berger
- Department of Cell Biology, University of Geneva, 30 quai Ernest Ansermet, 1211, Geneva 4, Switzerland
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25
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Kiesel P, Gibson TJ, Ciesielczyk B, Bodemer M, Kaup FJ, Bodemer W, Zischler H, Zerr I. Transcription of Alu DNA elements in blood cells of sporadic Creutzfeldt-Jakob disease (sCJD). Prion 2010; 4:87-93. [PMID: 20424511 DOI: 10.4161/pri.4.2.11965] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Alu DNA elements were long considered to be of no biological significance and thus have been only poorly defined. However, in the past Alu DNA elements with well-defined nucleotide sequences have been suspected to contribute to disease, but the role of Alu DNA element transcripts has rarely been investigated. For the first time, we determined in a real-time approach Alu DNA element transcription in buffy coat cells isolated from the blood of humans suffering from sporadic Creutzfeldt-Jakob disease (sCJD) and other neurodegenerative disorders. The reverse transcribed Alu transcripts were amplified and their cDNA sequences were aligned to genomic regions best fitted to database genomic Alu DNA element sequences deposited in the UCSC and NCBI data bases. Our cloned Alu RNA/cDNA sequences were widely distributed in the human genome and preferably belonged to the "young" Alu Y family. We also observed that some RNA/cDNA clones could be aligned to several chromosomes because of the same degree of identity and score to resident genomic Alu DNA elements. These elements, called paralogues, have purportedly been recently generated by retrotransposition. Along with cases of sCJD we also included cases of dementia and Alzheimer disease (AD). Each group revealed a divergent pattern of transcribed Alu elements. Chromosome 2 was the most preferred site in sCJD cases, besides chromosome 17; in AD cases chromosome 11 was overrepresented whereas chromosomes 2, 3 and 17 were preferred active Alu loci in controls. Chromosomes 2, 12 and 17 gave rise to Alu transcripts in dementia cases. The detection of putative Alu paralogues widely differed depending on the disease. A detailed data search revealed that some cloned Alu transcripts originated from RNA polymerase III transcription since the genomic sites of their Alu elements were found between genes. Other Alu DNA elements could be located close to or within coding regions of genes. In general, our observations suggest that identification and genomic localization of active Alu DNA elements could be further developed as a surrogate marker for differential gene expression in disease. A sufficient number of cases are necessary for statistical significance before Alu DNA elements can be considered useful to differentiate neurodegenerative diseases from controls.
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26
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Chelico L, Prochnow C, Erie DA, Chen XS, Goodman MF. Structural model for deoxycytidine deamination mechanisms of the HIV-1 inactivation enzyme APOBEC3G. J Biol Chem 2010; 285:16195-205. [PMID: 20212048 DOI: 10.1074/jbc.m110.107987] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
APOBEC3G (Apo3G) is a single-stranded DNA-dependent deoxycytidine deaminase, which, in the absence of the human immunodeficiency virus (HIV) viral infectivity factor, is encapsulated into HIV virions. Subsequently, Apo3G triggers viral inactivation by processively deaminating C-->U, with 3'-->5' polarity, on nascent minus-strand cDNA. Apo3G has a catalytically inactive N-terminal CD1 domain and an active C-terminal CD2 domain. Apo3G exists as monomers, dimers, tetramers, and higher order oligomers whose distributions depend on DNA substrate and salt. Here we use multiangle light scattering and atomic force microscopy to identify oligomerization states of Apo3G. A double mutant (F126A/W127A), designed to disrupt dimerization at the predicted CD1-CD1 dimer interface, predominantly converts Apo3G to a monomer that binds single-stranded DNA, Alu RNA, and catalyzes processive C-->U deaminations with 3'-->5' deamination polarity, similar to native Apo3G. The CD1 domain is essential for both processivity and polarity. We propose a structure-based model to explain the scanning and catalytic behavior of Apo3G.
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Affiliation(s)
- Linda Chelico
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089-2910, USA
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27
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Gu TJ, Yi X, Zhao XW, Zhao Y, Yin JQ. Alu-directed transcriptional regulation of some novel miRNAs. BMC Genomics 2009; 10:563. [PMID: 19943974 PMCID: PMC3087558 DOI: 10.1186/1471-2164-10-563] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Accepted: 11/30/2009] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Despite many studies on the biogenesis, molecular structure and biological functions of microRNAs, little is known about the transcriptional regulatory mechanisms controlling the spatiotemporal expression pattern of human miRNA gene loci. Several lines of experimental results have indicated that both polymerase II (Pol-II) and polymerase III (Pol-III) may be involved in transcribing miRNAs. Here, we assessed the genomic evidence for Alu-directed transcriptional regulation of some novel miRNA genes in humans. Our data demonstrate that the expression of these Alu-related miRNAs may be modulated by Pol-III. RESULTS We present a comprehensive exploration of the Alu-directed transcriptional regulation of some new miRNAs. Using a new computational approach, a variety of Alu-related sequences from multiple sources were pooled and filtered to obtain a subset containing Alu elements and characterized miRNA genes for which there is clear evidence of full-length transcription (embedded in EST). We systematically demonstrated that 73 miRNAs including five known ones may be transcribed by Pol-III through Alu or MIR. Among the new miRNAs, 33 were determined by high-throughput Solexa sequencing. Real-time TaqMan PCR and Northern blotting verified that three newly identified miRNAs could be induced to co-express with their upstream Alu transcripts by heat shock or cycloheximide. CONCLUSION Through genomic analysis, Solexa sequencing and experimental validation, we have identified candidate sequences for Alu-related miRNAs, and have found that the transcription of these miRNAs could be governed by Pol-III. Thus, this study may elucidate the mechanisms by which the expression of a class of small RNAs may be regulated by their upstream repeat elements.
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Affiliation(s)
- Tong J Gu
- National Laboratory of Biomacromolecules, Center for Computing and Systems Biology, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Beijing 100101, PR China.
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28
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Cordaux R, Batzer MA. The impact of retrotransposons on human genome evolution. Nat Rev Genet 2009; 10:691-703. [PMID: 19763152 DOI: 10.1038/nrg2640] [Citation(s) in RCA: 1138] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Their ability to move within genomes gives transposable elements an intrinsic propensity to affect genome evolution. Non-long terminal repeat (LTR) retrotransposons--including LINE-1, Alu and SVA elements--have proliferated over the past 80 million years of primate evolution and now account for approximately one-third of the human genome. In this Review, we focus on this major class of elements and discuss the many ways that they affect the human genome: from generating insertion mutations and genomic instability to altering gene expression and contributing to genetic innovation. Increasingly detailed analyses of human and other primate genomes are revealing the scale and complexity of the past and current contributions of non-LTR retrotransposons to genomic change in the human lineage.
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Affiliation(s)
- Richard Cordaux
- CNRS UMR 6556 Ecologie, Evolution, Symbiose, Université de Poitiers, 40 Avenue du Recteur Pineau, Poitiers, France
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29
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Koval AP, Kramerov DA. 5'-flanking sequences can dramatically influence 4.5SH RNA gene transcription by RNA-polymerase III. Gene 2009; 446:75-80. [PMID: 19619622 DOI: 10.1016/j.gene.2009.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 06/17/2009] [Accepted: 07/06/2009] [Indexed: 11/26/2022]
Abstract
4.5SH RNA is a 94 nt small nuclear RNA with an unknown function. Hundreds of its genes are present in the genomes of rodents of six families including Muridae. 4.5SH RNA genes contain an internal RNA-polymerase III promoter consisting of A and B boxes. Here we studied the influence of 5'-flanking sequences on the transcription of a mouse 4.5SH RNA gene. We found that replacement of the upstream sequence can dramatically change the 4.5SH RNA gene transcription efficiency. Various DNA fragments inserted immediately upstream from 4.5SH RNA gene completely inhibited its in vitro transcription, whereas others promoted it. The shortening of the native mouse 5'-flanking sequence of 4.5SH RNA gene to 42 bp resulted in the activation of an additional illegal transcription start site in upstream region. Transcription of the 4.5SH RNA gene with various upstream sequences in transfected HeLa cells revealed the differences between the tests performed in vivo and in vitro: in whole cells, only the construct with 5'-flanking native sequence could be transcribed. Apparently, at least some regions of the native 5'-flanking sequence of 4.5SH RNA genes have been selected during evolution for high transcription activity.
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Affiliation(s)
- Anastasia P Koval
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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30
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Comeaux MS, Roy-Engel AM, Hedges DJ, Deininger PL. Diverse cis factors controlling Alu retrotransposition: what causes Alu elements to die? Genome Res 2009; 19:545-55. [PMID: 19273617 DOI: 10.1101/gr.089789.108] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The human genome contains nearly 1.1 million Alu elements comprising roughly 11% of its total DNA content. Alu elements use a copy and paste retrotransposition mechanism that can result in de novo disease insertion alleles. There are nearly 900,000 old Alu elements from subfamilies S and J that appear to be almost completely inactive, and about 200,000 from subfamily Y or younger, which include a few thousand copies of the Ya5 subfamily which makes up the majority of current activity. Given the much higher copy number of the older Alu subfamilies, it is not known why all of the active Alu elements belong to the younger subfamilies. We present a systematic analysis evaluating the observed sequence variation in the different sections of an Alu element on retrotransposition. The length of the longest number of uninterrupted adenines in the A-tail, the degree of A-tail heterogeneity, the length of the 3' unique end after the A-tail and before the RNA polymerase III terminator, and random mutations found in the right monomer all modulate the retrotransposition efficiency. These changes occur over different evolutionary time frames. The combined impact of sequence changes in all of these regions explains why young Alus are currently causing disease through retrotransposition, and the old Alus have lost their ability to retrotranspose. We present a predictive model to evaluate the retrotransposition capability of individual Alu elements and successfully applied it to identify the first putative source element for a disease-causing Alu insertion in a patient with cystic fibrosis.
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Affiliation(s)
- Matthew S Comeaux
- Tulane Cancer Center and Dept. of Epidemiology, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA
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31
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Abstract
Non-protein-coding sequences increasingly dominate the genomes of multicellular organisms as their complexity increases, in contrast to protein-coding genes, which remain relatively static. Most of the mammalian genome and indeed that of all eukaryotes is expressed in a cell- and tissue-specific manner, and there is mounting evidence that much of this transcription is involved in the regulation of differentiation and development. Different classes of small and large noncoding RNAs (ncRNAs) have been shown to regulate almost every level of gene expression, including the activation and repression of homeotic genes and the targeting of chromatin-remodeling complexes. ncRNAs are involved in developmental processes in both simple and complex eukaryotes, and we illustrate this in the latter by focusing on the animal germline, brain, and eye. While most have yet to be systematically studied, the emerging evidence suggests that there is a vast hidden layer of regulatory ncRNAs that constitutes the majority of the genomic programming of multicellular organisms and plays a major role in controlling the epigenetic trajectories that underlie their ontogeny.
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32
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Mariner PD, Walters RD, Espinoza CA, Drullinger LF, Wagner SD, Kugel JF, Goodrich JA. Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock. Mol Cell 2008; 29:499-509. [PMID: 18313387 DOI: 10.1016/j.molcel.2007.12.013] [Citation(s) in RCA: 354] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2007] [Revised: 10/24/2007] [Accepted: 12/20/2007] [Indexed: 10/22/2022]
Abstract
Noncoding RNAs (ncRNAs) have recently been discovered to regulate mRNA transcription in trans, a role traditionally reserved for proteins. The breadth of ncRNAs as transacting transcriptional regulators and the diversity of signals to which they respond are only now becoming recognized. Here we show that human Alu RNA, transcribed from short interspersed elements (SINEs), is a transacting transcriptional repressor during the cellular heat shock response. Alu RNA blocks transcription by binding RNA polymerase II (Pol II) and entering complexes at promoters in vitro and in human cells. Transcriptional repression by Alu RNA involves two loosely structured domains that are modular, a property reminiscent of classical protein transcriptional regulators. Two other SINE RNAs, human scAlu RNA and mouse B1 RNA, also bind Pol II but do not repress transcription in vitro. These studies provide an explanation for why mouse cells harbor two major classes of SINEs, whereas human cells contain only one.
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Affiliation(s)
- Peter D Mariner
- Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, CO 80309-0215, USA
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Belancio VP, Hedges DJ, Deininger P. Mammalian non-LTR retrotransposons: for better or worse, in sickness and in health. Genome Res 2008; 18:343-58. [PMID: 18256243 DOI: 10.1101/gr.5558208] [Citation(s) in RCA: 224] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) have shared an exceptionally long coexistence with their host organisms and have come to occupy a significant fraction of eukaryotic genomes. The bulk of the expansion occurring within mammalian genomes has arisen from the activity of type I retrotransposons, which amplify in a "copy-and-paste" fashion through an RNA intermediate. For better or worse, the sequences of these retrotransposons are now wedded to the genomes of their mammalian hosts. Although there are several reported instances of the positive contribution of mobile elements to their host genomes, these discoveries have occurred alongside growing evidence of the role of TEs in human disease and genetic instability. Here we examine, with a particular emphasis on human retrotransposon activity, several newly discovered aspects of mammalian retrotransposon biology. We consider their potential impact on host biology as well as their ultimate implications for the nature of the TE-host relationship.
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Affiliation(s)
- Victoria P Belancio
- Tulane Cancer Center and Department of Epidemiology, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA
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34
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Abstract
Alus and B1s are short interspersed repeat elements (SINEs) derived from the 7SL RNA gene. Alus and B1s exist in the cytoplasm as non-coding RNA indicating that they are actively transcribed, but their function, if any, is unknown. Transcription of individual SINEs is a prerequisite for retroposition, but it is also possible that individual Alu and B1 elements have some cellular functions. Previous studies suggest that transcription of Alu elements depends on the presence of an RNA polymerase-III bipartite promoter and the poly-A tail. Sequencing of small RNAs has demonstrated that the members of the Y and S subfamily are expressed. We analyzed almost one million Alu sequences longer than 200 nucleotides for the presence of RNA polymerase-III bipartite promoter sequences. More than half contained a promoter indicating some potential for expression. We searched 7.7 million human EST sequences in dbEST for the presence of Alu non-coding RNAs and found evidence for the expression of 452. Analysis of mouse spermatogenic dbEST libraries revealed an apparent relationship between the level of differentiation and the level of B1-related sequences in the EST library.
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Affiliation(s)
- Boris Umylny
- Asia Pacific Bioinformatics Research Institute, Honolulu, HI, USA
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35
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Chiu YL, Witkowska HE, Hall SC, Santiago M, Soros VB, Esnault C, Heidmann T, Greene WC. High-molecular-mass APOBEC3G complexes restrict Alu retrotransposition. Proc Natl Acad Sci U S A 2006; 103:15588-93. [PMID: 17030807 PMCID: PMC1592537 DOI: 10.1073/pnas.0604524103] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
APOBEC3G (A3G) and related deoxycytidine deaminases are potent intrinsic antiretroviral factors. A3G is expressed either as an enzymatically active low-molecular-mass (LMM) form or as an enzymatically inactive high-molecular-mass (HMM) ribonucleoprotein complex. Resting CD4 T cells exclusively express LMM A3G, where it functions as a powerful postentry restriction factor for HIV-1. Activation of CD4 T cells promotes the recruitment of LMM A3G into 5- to 15-MDa HMM complexes whose function is unknown. Using tandem affinity purification techniques coupled with MS, we identified Staufen-containing RNA-transporting granules and Ro ribonucleoprotein complexes as specific components of HMM A3G complexes. Analysis of RNAs in these complexes revealed Alu and small Y RNAs, two of the most prominent nonautonomous mobile genetic elements in human cells. These retroelement RNAs are recruited into Staufen-containing RNA-transporting granules in the presence of A3G. Retrotransposition of Alu and hY RNAs depends on the reverse transcriptase machinery provided by long interspersed nucleotide elements 1 (L1). We now show that A3G greatly inhibits L1-dependent retrotransposition of marked Alu retroelements not by inhibiting L1 function but by sequestering Alu RNAs in cytoplasmic HMM A3G complexes away from the nuclear L1 enzymatic machinery. These findings identify nonautonomous Alu and hY retroelements as natural cellular targets of A3G and highlight how different forms of A3G uniquely protect cells from the threats posed by exogenous retroviruses (LMM A3G) and endogenous retroelements (HMM A3G).
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Affiliation(s)
- Ya-Lin Chiu
- *Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, CA 94158
| | - H. Ewa Witkowska
- Biomolecular Resource Center, Mass Spectrometry Facility, University of California, San Francisco, CA 94143; and
| | - Steven C. Hall
- Biomolecular Resource Center, Mass Spectrometry Facility, University of California, San Francisco, CA 94143; and
| | - Mario Santiago
- *Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, CA 94158
| | - Vanessa B. Soros
- *Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, CA 94158
| | - Cécile Esnault
- Unité des Rétrovirus Endogénes et Eléments Rétroïdes des Eucaryotes Supérieurs, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8122, Institut Gustave Roussy, 94805 Villejuif, France
| | - Thierry Heidmann
- Unité des Rétrovirus Endogénes et Eléments Rétroïdes des Eucaryotes Supérieurs, Centre National de la Recherche Scientifique Unité Mixte de Recherche 8122, Institut Gustave Roussy, 94805 Villejuif, France
| | - Warner C. Greene
- *Gladstone Institute of Virology and Immunology, 1650 Owens Street, San Francisco, CA 94158
- Departments of Medicine, Microbiology, and Immunology and
- To whom correspondence should be addressed. E-mail:
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Ludwig A, Rozhdestvensky TS, Kuryshev VY, Schmitz J, Brosius J. An Unusual Primate Locus that Attracted Two Independent Alu Insertions and Facilitates their Transcription. J Mol Biol 2005; 350:200-14. [PMID: 15922354 DOI: 10.1016/j.jmb.2005.03.058] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2005] [Revised: 03/18/2005] [Accepted: 03/21/2005] [Indexed: 10/25/2022]
Abstract
BC200 RNA, a neuronal, small non-messenger RNA that originated from a monomeric Alu element is specific to anthropoid primates. Tarsiers lack an insert at the orthologous genomic position, whereas strepsirrhines (Lemuriformes and Lorisiformes) acquired a dimeric Alu element, independently from anthropoids. In Galago moholi, the CpG dinucleotides are conspicuously conserved, while in Eulemur coronatus a large proportion is changed, indicating that the G.moholi Alu is under purifying selection and might be transcribed. Indeed, Northern blot analysis of total brain RNA from G.moholi with a specific probe revealed a prominent signal. In contrast, a corresponding signal was absent from brain RNA from E.coronatus. Isolation and sequence analysis of additional strepsirrhine loci confirmed the differential sequence conservation including CpG patterns of the orthologous dimeric Alu elements in Lorisiformes and Lemuriformes. Interestingly, all examined Alu elements from Lorisiformes were transcribed, while all from Lemuriformes were silent when transiently transfected into HeLa cells. Upstream sequences, especially those between the transcriptional start site and -22 upstream, were important for basal transcriptional activity. Thus, the BC200 RNA gene locus attracted two independent Alu insertions during its evolutionary history and provided upstream promoter elements required for their transcription.
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Affiliation(s)
- A Ludwig
- Institute of Experimental Pathology, ZMBE, University of Münster, Von-Esmarch-Str. 56, D-48149 Münster, Germany
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37
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Tang RB, Wang HY, Lu HY, Xiong J, Li HH, Qiu XH, Liu HQ. Increased level of polymerase III transcribed Alu RNA in hepatocellular carcinoma tissue. Mol Carcinog 2005; 42:93-6. [PMID: 15593371 DOI: 10.1002/mc.20057] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There have been extensive observations that RNA containing repetitive elements accumulates in transformed cells and tumor tissues. In the present study, we first obtained result consistent with previous observations by in situ hybridization. Then we used primer extension analysis to determine the level of polymerase III directed Alu RNA and found an increased expression of Alu RNA in hepatocellular carcinoma.
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Affiliation(s)
- Rui-Bao Tang
- Department of Histology and Embryology, the Second Military Medical University, Shanghai 200433, China
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38
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Evolution and distribution of RNA polymerase II regulatory sites from RNA polymerase III dependant mobile Alu elements. BMC Evol Biol 2004; 4:37. [PMID: 15461819 PMCID: PMC524483 DOI: 10.1186/1471-2148-4-37] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2004] [Accepted: 10/04/2004] [Indexed: 11/24/2022] Open
Abstract
Background The primate-specific Alu elements, which originated 65 million years ago, exist in over a million copies in the human genome. These elements have been involved in genome shuffling and various diseases not only through retrotransposition but also through large scale Alu-Alu mediated recombination. Only a few subfamilies of Alus are currently retropositionally active and show insertion/deletion polymorphisms with associated phenotypes. Retroposition occurs by means of RNA intermediates synthesised by a RNA polymerase III promoter residing in the A-Box and B-Box in these elements. Alus have also been shown to harbour a number of transcription factor binding sites, as well as hormone responsive elements. The distribution of Alus has been shown to be non-random in the human genome and these elements are increasingly being implicated in diverse functions such as transcription, translation, response to stress, nucleosome positioning and imprinting. Results We conducted a retrospective analysis of putative functional sites, such as the RNA pol III promoter elements, pol II regulatory elements like hormone responsive elements and ligand-activated receptor binding sites, in Alus of various evolutionary ages. We observe a progressive loss of the RNA pol III transcriptional potential with concomitant accumulation of RNA pol II regulatory sites. We also observe a significant over-representation of Alus harboring these sites in promoter regions of signaling and metabolism genes of chromosome 22, when compared to genes of information pathway components, structural and transport proteins. This difference is not so significant between functional categories in the intronic regions of the same genes. Conclusions Our study clearly suggests that Alu elements, through retrotransposition, could distribute functional and regulatable promoter elements, which in the course of subsequent selection might be stabilized in the genome. Exaptation of regulatory elements in the preexisting genes through Alus could thus have contributed to evolution of novel regulatory networks in the primate genomes. With such a wide spectrum of regulatory sites present in Alus, it also becomes imperative to screen for variations in these sites in candidate genes, which are otherwise repeat-masked in studies pertaining to identification of predisposition markers.
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39
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Pélissier T, Bousquet-Antonelli C, Lavie L, Deragon JM. Synthesis and processing of tRNA-related SINE transcripts in Arabidopsis thaliana. Nucleic Acids Res 2004; 32:3957-66. [PMID: 15282328 PMCID: PMC506818 DOI: 10.1093/nar/gkh738] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Despite the ubiquitous distribution of tRNA-related short interspersed elements (SINEs) in eukaryotic species, very little is known about the synthesis and processing of their RNAs. In this work, we have characterized in detail the different RNA populations resulting from the expression of a tRNA-related SINE S1 founder copy in Arabidopsis thaliana. The main population is composed of poly(A)-ending (pa) SINE RNAs, while two minor populations correspond to full-length (fl) or poly(A) minus [small cytoplasmic (sc)] SINE RNAs. Part of the poly(A) minus RNAs is modified by 3'-terminal addition of C or CA nucleotides. All three RNA populations accumulate in the cytoplasm. Using a mutagenesis approach, we show that the poly(A) region and the 3' end unique region, present at the founder locus, are both important for the maturation and the steady-state accumulation of the different S1 RNA populations. The observation that primary SINE transcripts can be post-transcriptionally processed in vivo into a poly(A)-ending species introduces the possibility that this paRNA is used as a retroposition intermediate.
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MESH Headings
- 3' Untranslated Regions
- Arabidopsis/genetics
- Base Sequence
- Cytoplasm/metabolism
- Gene Expression Regulation, Plant
- Molecular Sequence Data
- Polyadenylation
- RNA Processing, Post-Transcriptional
- RNA, Plant/biosynthesis
- RNA, Plant/chemistry
- RNA, Plant/metabolism
- RNA, Transfer/biosynthesis
- RNA, Transfer/chemistry
- RNA, Transfer/metabolism
- Regulatory Sequences, Ribonucleic Acid
- Short Interspersed Nucleotide Elements
- Transcription, Genetic
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Affiliation(s)
- Thierry Pélissier
- CNRS UMR 6547 BIOMOVE and GDR 2157, Université Blaise Pascal Clermont-Ferrand II, 63177 Aubière Cedex, France
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Abstract
The eukaryotic genome has undergone a series of epidemics of amplification of mobile elements that have resulted in most eukaryotic genomes containing much more of this 'junk' DNA than actual coding DNA. The majority of these elements utilize an RNA intermediate and are termed retroelements. Most of these retroelements appear to amplify in evolutionary waves that insert in the genome and then gradually diverge. In humans, almost half of the genome is recognizably derived from retroelements, with the two elements that are currently actively amplifying, L1 and Alu, making up about 25% of the genome and contributing extensively to disease. The mechanisms of this amplification process are beginning to be understood, although there are still more questions than answers. Insertion of new retroelements may directly damage the genome, and the presence of multiple copies of these elements throughout the genome has longer-term influences on recombination events in the genome and more subtle influences on gene expression.
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Affiliation(s)
- Prescott L Deininger
- Tulane Cancer Center, Department of Environmental Health Sciences, Tulane University Health Sciences Center, New Orleans, Louisiana 70112, USA.
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41
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Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, Batzer MA, Deininger PL. Active Alu element "A-tails": size does matter. Genome Res 2002; 12:1333-44. [PMID: 12213770 PMCID: PMC186649 DOI: 10.1101/gr.384802] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Long and short interspersed elements (LINEs and SINEs) are retroelements that make up almost half of the human genome. L1 and Alu represent the most prolific human LINE and SINE families, respectively. Only a few Alu elements are able to retropose, and the factors determining their retroposition capacity are poorly understood. The data presented in this paper indicate that the length of Alu "A-tails" is one of the principal factors in determining the retropositional capability of an Alu element. The A stretches of the Alu subfamilies analyzed, both old (Alu S and J) and young (Ya5), had a Poisson distribution of A-tail lengths with a mean size of 21 and 26, respectively. In contrast, the A-tails of very recent Alu insertions (disease causing) were all between 40 and 97 bp in length. The L1 elements analyzed displayed a similar tendency, in which the "disease"-associated elements have much longer A-tails (mean of 77) than do the elements even from the young Ta subfamily (mean of 41). Analysis of the draft sequence of the human genome showed that only about 1000 of the over one million Alu elements have tails of 40 or more adenosine residues in length. The presence of these long A stretches shows a strong bias toward the actively amplifying subfamilies, consistent with their playing a major role in the amplification process. Evaluation of the 19 Alu elements retrieved from the draft sequence of the human genome that are identical to the Alu Ya5a2 insert in the NF1 gene showed that only five have tails with 40 or more adenosine residues. Sequence analysis of the loci with the Alu elements containing the longest A-tails (7 of the 19) from the genomes of the NF1 patient and the father revealed that there are at least two loci with A-tails long enough to serve as source elements within our model. Analysis of the A-tail lengths of 12 Ya5a2 elements in diverse human population groups showed substantial variability in both the Alu A-tail length and sequence homogeneity. On the basis of these observations, a model is presented for the role of A-tail length in determining which Alu elements are active.
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Affiliation(s)
- Astrid M Roy-Engel
- Tulane Cancer Center, SL-66, Department of Environmental Health Sciences, Tulane University-Health Sciences Center, New Orleans, Louisiana 70112, USA
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42
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Abstract
During the past 65 million years, Alu elements have propagated to more than one million copies in primate genomes, which has resulted in the generation of a series of Alu subfamilies of different ages. Alu elements affect the genome in several ways, causing insertion mutations, recombination between elements, gene conversion and alterations in gene expression. Alu-insertion polymorphisms are a boon for the study of human population genetics and primate comparative genomics because they are neutral genetic markers of identical descent with known ancestral states.
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Affiliation(s)
- Mark A Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, Louisiana 70803, USA.
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43
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Abstract
L1 retrotransposons comprise 17% of the human genome. Although most L1s are inactive, some elements remain capable of retrotransposition. L1 elements have a long evolutionary history dating to the beginnings of eukaryotic existence. Although many aspects of their retrotransposition mechanism remain poorly understood, they likely integrate into genomic DNA by a process called target primed reverse transcription. L1s have shaped mammalian genomes through a number of mechanisms. First, they have greatly expanded the genome both by their own retrotransposition and by providing the machinery necessary for the retrotransposition of other mobile elements, such as Alus. Second, they have shuffled non-L1 sequence throughout the genome by a process termed transduction. Third, they have affected gene expression by a number of mechanisms. For instance, they occasionally insert into genes and cause disease both in humans and in mice. L1 elements have proven useful as phylogenetic markers and may find other practical applications in gene discovery following insertional mutagenesis in mice and in the delivery of therapeutic genes.
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Affiliation(s)
- E M Ostertag
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.
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44
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Li TH, Schmid CW. Differential stress induction of individual Alu loci: implications for transcription and retrotransposition. Gene 2001; 276:135-41. [PMID: 11591480 DOI: 10.1016/s0378-1119(01)00637-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
While human Alu repeats can be considered to be members of an extremely large, globally regulated, multigene family, each member of this family resides within a different sequence context that might uniquely modulate its transcription. Unique 3' flanking sequences for several transcriptionally active human Alu elements were identified by cDNA cloning and used for primer extension analysis to compare the basal and stress-induced expression of the corresponding Alu loci. Each of six Alu loci investigated exhibits a unique pattern of expression in three different human cell lines and in response to stress induction. The sequence context surrounding each Alu member uniquely determines its transcriptional regulation. In many cases, the individual Alu loci and total Alu RNA exhibit opposing patterns of expression implying that local rather than global regulation ultimately determines the expression of individual members. Some of the stresses, which induce Alu transcription, increase co-expression of LINE1 RNA, another requirement for Alu retrotransposition.
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Affiliation(s)
- T H Li
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535, USA
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45
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Alemán C, Roy-Engel AM, Shaikh TH, Deininger PL. Cis-acting influences on Alu RNA levels. Nucleic Acids Res 2000; 28:4755-61. [PMID: 11095687 PMCID: PMC115182 DOI: 10.1093/nar/28.23.4755] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The human short interspersed repeated element (SINE), Alu, amplifies through a poorly understood RNA-mediated mechanism, termed retroposition. There are over one million copies of Alu per haploid human genome. The copies show some internal variations in sequence and are very heterogeneous in chromosomal environment. However, very few Alu elements actively amplify. The amplification rate has decreased greatly in the last 40 million years. Factors influencing Alu transcription would directly affect an element's retroposition capability. Therefore, we evaluated several features that might influence expression from individual Alu elements. The influence of various internal sequence variations and 3' unique flanks on full-length Alu RNA steady-state levels was determined. Alu subfamily diagnostic mutations do not significantly alter the amount of Alu RNA observed. However, sequences containing random mutations throughout the right half of selected genomic Alu elements altered Alu RNA steady-state levels in cultured cells. In addition, sequence variations at the 3' unique end of the transcript also significantly altered the Alu RNA levels. In general, sequence mutations and 3' end sequences contribute to Alu RNA levels, suggesting that the master Alu element(s) have a multitude of individual differences that collectively gives them a selective advantage over other Alu elements.
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Affiliation(s)
- C Alemán
- Tulane Cancer Center, SL-66, and Department of Environmental Health Sciences, Tulane University-Health Sciences Center, 1430 Tulane Avenue, New Orleans, LA 70112, USA
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46
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Roy AM, Carroll ML, Nguyen SV, Salem AH, Oldridge M, Wilkie AO, Batzer MA, Deininger PL. Potential gene conversion and source genes for recently integrated Alu elements. Genome Res 2000; 10:1485-95. [PMID: 11042148 DOI: 10.1101/gr.152300] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Alu elements comprise >10% of the human genome. We have used a computational biology approach to analyze the human genomic DNA sequence databases to determine the impact of gene conversion on the sequence diversity of recently integrated Alu elements and to identify Alu elements that were potentially retroposition competent. We analyzed 269 Alu Ya5 elements and identified 23 members of a new Alu subfamily termed Ya5a2 with an estimated copy number of 35 members, including the de novo Alu insertion in the NF1 gene. Our analysis of Alu elements containing one to four (Ya1-Ya4) of the Ya5 subfamily-specific mutations suggests that gene conversion contributed as much as 10%-20% of the variation between recently integrated Alu elements. In addition, analysis of the middle A-rich region of the different Alu Ya5 members indicates a tendency toward expansion of this region and subsequent generation of simple sequence repeats. Mining the databases for putative retroposition-competent elements that share 100% nucleotide identity to the previously reported de novo Alu insertions linked to human diseases resulted in the retrieval of 13 exact matches to the NF1 Alu repeat, three to the Alu element in BRCA2, and one to the Alu element in FGFR2 (Apert syndrome). Transient transfections of the potential source gene for the Apert's Alu with its endogenous flanking genomic sequences demonstrated the transcriptional and presumptive transpositional competency of the element.
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Affiliation(s)
- A M Roy
- Tulane Cancer Center, Department of Environmental Health Sciences, Tulane University Medical Center, New Orleans, Louisiana 70112, USA
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Li TH, Kim C, Rubin CM, Schmid CW. K562 cells implicate increased chromatin accessibility in Alu transcriptional activation. Nucleic Acids Res 2000; 28:3031-9. [PMID: 10931917 PMCID: PMC108432 DOI: 10.1093/nar/28.16.3031] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Alu repeats in K562 cells are unusually hypomethylated and far more actively transcribed than those in other human cell lines and somatic tissues. Also, the level of Alu RNA in K562 cells is relatively insensitive to cell stresses, namely heat shock, adenovirus infection and treatment with cycloheximide, which increase the abundance of Alu RNA in HeLa and 293 cells. Recent advances in understanding the interactions between DNA methylation, transcriptional activation and chromatin conformation reveal reasons for the constitutively high level of Alu expression in K562 cells. Methylation represses transcription of transiently transfected Alu templates in all cell lines tested but cell stresses do not relieve this repression suggesting that they activate Alu transcription through another pathway. A relatively large fraction of the Alus within K562 chromatin is accessible to restriction enzyme cleavage and cell stresses increase the chromatin accessibility of Alus in HeLa and 293 cells. Cell stress evidently activates Alu transcription by rapidly remodeling chromatin to recruit additional templates.
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Affiliation(s)
- T H Li
- Section of Molecular and Cellular Biology and Department of Chemistry, University of California, Davis, CA 95616, USA
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Li T, Spearow J, Rubin CM, Schmid CW. Physiological stresses increase mouse short interspersed element (SINE) RNA expression in vivo. Gene 1999; 239:367-72. [PMID: 10548739 DOI: 10.1016/s0378-1119(99)00384-4] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possible functionality of short interspersed elements (SINEs) is investigated by assaying the effects of physiological stress on their RNA polymerase-III-directed transcriptional expression in vivo. B2 RNA is expressed at moderately high levels in all mouse tissues investigated, namely liver, spleen, kidney and testis. B1 RNA is expressed in testis but is nearly undetectable in the other tissues. Following hyperthermic shock, the amounts of B1 and B2 SINE RNAs transiently increase in all tissues by as much as 40-fold in certain cases. The kinetics of these increases resemble those of heat shock protein mRNAs. An acute dose of ethanol also transiently increases the abundance of B1 and B2 RNA in liver, showing that other physiological stresses increase SINE RNA expression. The constitutive expression of B2 RNA in all tissues and tissue-specific differences in expression of B1 RNA imply that these transcripts serve a normal physiological function(s). Moreover, increased SINE RNA expression is a vital response to stress and by the criterion of their inducibility, mammalian SINEs behave like regulated cell stress genes.
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Affiliation(s)
- T Li
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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Abstract
The 'master' human mobile element, the L1 retrotransposon, has come of age as a biological entity. Knowledge of how it retrotransposes in vivo, how its proteins act to retrotranspose other poly A elements and the extent of its role in shaping the human genome should emerge rapidly over the next few years. We review the impact of retrotransposons and how new insight is likely to lead to important practical applications for these intriguing mobile elements.
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Affiliation(s)
- H H Kazazian
- Department of Genetics, University of Pennsylvania, School of Medicine, Philadelphia 19104, USA.
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Abstract
Alu sequences are frequently encountered during study of human genomic nucleic acid and form a major component of repetitive DNA. This review describes the origin of Alu sequences and their subsequent amplification and evolution into distinct subfamilies. In recent years a number of different functional roles for Alu sequences have been described. The multiple influences of Alu sequences on RNA polymerase II-mediated gene expression and the presence of Alu sequences in RNA polymerase III-generated transcripts are discussed.
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Affiliation(s)
- A J Mighell
- Molecular Medicine Unit, The University of Leeds, St. James's University Hospital, UK.
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