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Łabno A, Warkocki Z, Kuliński T, Krawczyk PS, Bijata K, Tomecki R, Dziembowski A. Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs. Nucleic Acids Res 2016; 44:10437-10453. [PMID: 27431325 PMCID: PMC5137419 DOI: 10.1093/nar/gkw649] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 07/09/2016] [Accepted: 07/11/2016] [Indexed: 01/02/2023] Open
Abstract
The exosome-independent exoribonuclease DIS3L2 is mutated in Perlman syndrome. Here, we used extensive global transcriptomic and targeted biochemical analyses to identify novel DIS3L2 substrates in human cells. We show that DIS3L2 regulates pol II transcripts, comprising selected canonical and histone-coding mRNAs, and a novel FTL_short RNA from the ferritin mRNA 5' UTR. Importantly, DIS3L2 contributes to surveillance of maturing snRNAs during their cytoplasmic processing. Among pol III transcripts, DIS3L2 particularly targets vault and Y RNAs and an Alu-like element BC200 RNA, but not Alu repeats, which are removed by exosome-associated DIS3. Using 3' RACE-Seq, we demonstrate that all novel DIS3L2 substrates are uridylated in vivo by TUT4/TUT7 poly(U) polymerases. Uridylation-dependent DIS3L2-mediated decay can be recapitulated in vitro, thus reinforcing the tight cooperation between DIS3L2 and TUTases. Together these results indicate that catalytically inactive DIS3L2, characteristic of Perlman syndrome, can lead to deregulation of its target RNAs to disturb transcriptome homeostasis.
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Affiliation(s)
- Anna Łabno
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Zbigniew Warkocki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz Kuliński
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Paweł Szczepan Krawczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Krystian Bijata
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland.,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Rafał Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland .,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland .,Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
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52
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Conti A, Rota F, Ragni E, Favero C, Motta V, Lazzari L, Bollati V, Fustinoni S, Dieci G. Hydroquinone induces DNA hypomethylation-independent overexpression of retroelements in human leukemia and hematopoietic stem cells. Biochem Biophys Res Commun 2016; 474:691-695. [DOI: 10.1016/j.bbrc.2016.05.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
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53
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Hancks DC, Kazazian HH. Roles for retrotransposon insertions in human disease. Mob DNA 2016; 7:9. [PMID: 27158268 PMCID: PMC4859970 DOI: 10.1186/s13100-016-0065-9] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 04/14/2016] [Indexed: 12/12/2022] Open
Abstract
Over evolutionary time, the dynamic nature of a genome is driven, in part, by the activity of transposable elements (TE) such as retrotransposons. On a shorter time scale it has been established that new TE insertions can result in single-gene disease in an individual. In humans, the non-LTR retrotransposon Long INterspersed Element-1 (LINE-1 or L1) is the only active autonomous TE. In addition to mobilizing its own RNA to new genomic locations via a "copy-and-paste" mechanism, LINE-1 is able to retrotranspose other RNAs including Alu, SVA, and occasionally cellular RNAs. To date in humans, 124 LINE-1-mediated insertions which result in genetic diseases have been reported. Disease causing LINE-1 insertions have provided a wealth of insight and the foundation for valuable tools to study these genomic parasites. In this review, we provide an overview of LINE-1 biology followed by highlights from new reports of LINE-1-mediated genetic disease in humans.
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Affiliation(s)
- Dustin C. Hancks
- />Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Haig H. Kazazian
- />McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins School of Medicine, Baltimore, MD USA
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54
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Morales-Hernández A, González-Rico FJ, Román AC, Rico-Leo E, Alvarez-Barrientos A, Sánchez L, Macia Á, Heras SR, García-Pérez JL, Merino JM, Fernández-Salguero PM. Alu retrotransposons promote differentiation of human carcinoma cells through the aryl hydrocarbon receptor. Nucleic Acids Res 2016; 44:4665-83. [PMID: 26883630 PMCID: PMC4889919 DOI: 10.1093/nar/gkw095] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 02/09/2016] [Indexed: 12/18/2022] Open
Abstract
Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, their role in gene regulation is poorly understood. Here, we show that the dioxin receptor (AHR) leads to differentiation of human carcinoma cells through the transcriptional upregulation of Alu retrotransposons, whose RNA transcripts can repress pluripotency genes. Despite the genome-wide presence of Alu elements, we provide evidences that those located at the NANOG and OCT4 promoters bind AHR, are transcribed by RNA polymerase-III and repress NANOG and OCT4 in differentiated cells. OCT4 and NANOG repression likely involves processing of Alu-derived transcripts through the miRNA machinery involving the Microprocessor and RISC. Consistently, stable AHR knockdown led to basal undifferentiation, impaired Alus transcription and blockade of OCT4 and NANOG repression. We suggest that transcripts produced from AHR-regulated Alu retrotransposons may control the expression of stemness genes OCT4 and NANOG during differentiation of carcinoma cells. The control of discrete Alu elements by specific transcription factors may have a dynamic role in genome regulation under physiological and diseased conditions.
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Affiliation(s)
- Antonio Morales-Hernández
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071-Badajoz, Spain
| | - Francisco J González-Rico
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071-Badajoz, Spain
| | - Angel C Román
- Instituto Cajal, Consejo Superior de Investigaciones Científicas, Avenida Doctor Arce 37, 28002-Madrid, Spain
| | - Eva Rico-Leo
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071-Badajoz, Spain
| | - Alberto Alvarez-Barrientos
- Servicio de Técnicas Aplicadas a las Biociencias, Universidad de Extremadura, Avenida de Elvas s/n 06071-Badajoz, Spain
| | - Laura Sánchez
- GENYO. Centro de Genómica e Investigación Oncológica: Pfizer/Universidad de Granada/Junta de Andalucía, Avda. de la Ilustración 114, PTS Granada, 18016-Granada, Spain
| | - Ángela Macia
- GENYO. Centro de Genómica e Investigación Oncológica: Pfizer/Universidad de Granada/Junta de Andalucía, Avda. de la Ilustración 114, PTS Granada, 18016-Granada, Spain
| | - Sara R Heras
- GENYO. Centro de Genómica e Investigación Oncológica: Pfizer/Universidad de Granada/Junta de Andalucía, Avda. de la Ilustración 114, PTS Granada, 18016-Granada, Spain
| | - José L García-Pérez
- GENYO. Centro de Genómica e Investigación Oncológica: Pfizer/Universidad de Granada/Junta de Andalucía, Avda. de la Ilustración 114, PTS Granada, 18016-Granada, Spain
| | - Jaime M Merino
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071-Badajoz, Spain
| | - Pedro M Fernández-Salguero
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias, Universidad de Extremadura, Avenida de Elvas s/n, 06071-Badajoz, Spain
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Varshney D, Vavrova-Anderson J, Oler AJ, Cairns BR, White RJ. Selective repression of SINE transcription by RNA polymerase III. Mob Genet Elements 2015; 5:86-91. [PMID: 26942044 DOI: 10.1080/2159256x.2015.1096997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 10/23/2022] Open
Abstract
A million copies of the Alu short interspersed nuclear element (SINE) are scattered throughout the human genome, providing ∼11% of our total DNA. SINEs spread by retrotransposition, using a transcript generated by RNA polymerase (pol) III from an internal promoter. Levels of these pol III-dependent Alu transcripts are far lower than might be expected from the abundance of the template. This was believed to reflect transcriptional suppression through DNA methylation, denying pol III access to most SINEs through chromatin-mediated effects. Contrary to expectations, our recent study found no evidence that methylation of SINE DNA reduces its occupancy or expression by pol III. However, histone H3 associated with SINEs is prominently methylated on lysine 9, a mark that correlates with transcriptional silencing. The SUV39 methyltransferases that deposit this mark can be found at many SINEs. Furthermore, a selective inhibitor of SUV39 stimulates pol III recruitment to these loci, as well as SINE expression. These data suggest that methylation of histone H3 rather than DNA may mediate repression of SINE transcription by pol III, at least under the conditions we studied.
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Affiliation(s)
- Dhaval Varshney
- Centre for Gene Regulation and Expression; University of Dundee ; Dundee, UK
| | - Jana Vavrova-Anderson
- College of Medical; Veterinary and Life Sciences; University of Glasgow ; Glasgow, UK
| | - Andrew J Oler
- 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 USA
| | - Bradley R Cairns
- Department of Oncological Sciences; Huntsman Cancer Institute; University of Utah School of Medicine; Salt Lake City, UT USA; Howard Hughes Medical Institute; University of Utah School of Medicine; Salt Lake City, UT USA
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56
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Pickl JMA, Kamel W, Ciftci S, Punga T, Akusjärvi G. Opposite expression of CYP51A1 and its natural antisense transcript AluCYP51A1 in adenovirus type 37 infected retinal pigmented epithelial cells. FEBS Lett 2015; 589:1383-8. [PMID: 25907535 DOI: 10.1016/j.febslet.2015.04.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 03/26/2015] [Accepted: 04/10/2015] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 family member CYP51A1 is a key enzyme in cholesterol biosynthesis whose deregulation is implicated in numerous diseases, including retinal degeneration. Here we describe that HAdV-37 infection leads to downregulation of CYP51A1 expression and overexpression of its antisense non-coding Alu element (AluCYP51A1) in retinal pigment epithelium (RPE) cells. This change in gene expression is associated with a reversed accumulation of a positive histone mark at the CYP51A1 and AluCYP51A1 promoters. Further, transient AluCYP51A1 RNA overexpression correlates with reduced CYP51A1 mRNA accumulation. Collectively, our data suggest that AluCYP51A1 might control CYP51A1 gene expression in HAdV-37-infected RPE cells.
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Affiliation(s)
- Julia Maria Anna Pickl
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, 75123 Uppsala, Sweden
| | - Wael Kamel
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, 75123 Uppsala, Sweden
| | - Sibel Ciftci
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, 75123 Uppsala, Sweden
| | - Tanel Punga
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, 75123 Uppsala, Sweden
| | - Göran Akusjärvi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Husargatan 3, BMC, Box 582, 75123 Uppsala, Sweden.
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