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Favasuli VK, Ronchetti D, Silvestris I, Puccio N, Fabbiano G, Traini V, Todoerti K, Erratico S, Ciarrocchi A, Fragliasso V, Giannandrea D, Tumiatti F, Chiaramonte R, Torrente Y, Finelli P, Morelli E, Munshi NC, Bolli N, Neri A, Taìana E. DIS3 depletion in multiple myeloma causes extensive perturbation in cell cycle progression and centrosome amplification. Haematologica 2024; 109:231-244. [PMID: 37439377 PMCID: PMC10772536 DOI: 10.3324/haematol.2023.283274] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
DIS3 gene mutations occur in approximately 10% of patients with multiple myeloma (MM); furthermore, DIS3 expression can be affected by monosomy 13 and del(13q), found in roughly 40% of MM cases. Despite the high incidence of DIS3 mutations and deletions, the biological significance of DIS3 and its contribution to MM pathogenesis remain poorly understood. In this study we investigated the functional role of DIS3 in MM, by exploiting a loss-of-function approach in human MM cell lines. We found that DIS3 knockdown inhibits proliferation in MM cell lines and largely affects cell cycle progression of MM plasma cells, ultimately inducing a significant increase in the percentage of cells in the G0/G1 phase and a decrease in the S and G2/M phases. DIS3 plays an important role not only in the control of the MM plasma cell cycle, but also in the centrosome duplication cycle, which are strictly co-regulated in physiological conditions in the G1 phase. Indeed, DIS3 silencing leads to the formation of supernumerary centrosomes accompanied by the assembly of multipolar spindles during mitosis. In MM, centrosome amplification is present in about a third of patients and may represent a mechanism leading to genomic instability. These findings strongly prompt further studies investigating the relevance of DIS3 in the centrosome duplication process. Indeed, a combination of DIS3 defects and deficient spindle-assembly checkpoint can allow cells to progress through the cell cycle without proper chromosome segregation, generating aneuploid cells which ultimately lead to the development of MM.
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Affiliation(s)
- Vanessa K Favasuli
- Department of Oncology and Hemato-oncology, University of Milan, Italy; Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Noemi Puccio
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, 41121
| | - Giuseppina Fabbiano
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Valentina Traini
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Katia Todoerti
- Department of Pathology and Laboratory Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan
| | - Silvia Erratico
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Novystem Spa, Milan
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia
| | - Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia
| | | | - Francesca Tumiatti
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | | | - Yvan Torrente
- Stem Cell Laboratory, Department of Pathophysiology and Transplantation, University of Milan, Centro Dino Ferrari, Unit of Neurology, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Palma Finelli
- Medical Genetics Laboratory, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; Department of Medical Biotechnology and Translational Medicine, University of Milan, Segrate, 20090 Milan
| | - Eugenio Morelli
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Nikhil C Munshi
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Niccolò Bolli
- Department of Oncology and Hemato-oncology, University of Milan, Italy; Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
| | - Antonino Neri
- Scientific Directorate, Azienda USL-IRCCS Reggio Emilia, 42123 Reggio Emilia.
| | - Elisa Taìana
- Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan
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2
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Hojka-Osinska A, Chlebowski A, Grochowska J, Owczarek EP, Affek K, Kłosowska-Kosicka K, Szczesny RJ, Dziembowski A. Landscape of functional interactions of human processive ribonucleases revealed by high-throughput siRNA screenings. iScience 2021; 24:103036. [PMID: 34541468 PMCID: PMC8437785 DOI: 10.1016/j.isci.2021.103036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/09/2021] [Accepted: 08/23/2021] [Indexed: 11/24/2022] Open
Abstract
Processive exoribonucleases are executors of RNA decay. In humans, their physical but not functional interactions were thoughtfully investigated. Here we have screened cells deficient in DIS3, XRN2, EXOSC10, DIS3L, and DIS3L2 with a custom siRNA library and determined their genetic interactions (GIs) with diverse pathways of RNA metabolism. We uncovered a complex network of positive interactions that buffer alterations in RNA degradation and reveal reciprocal cooperation with genes involved in transcription, RNA export, and splicing. Further, we evaluated the functional distinctness of nuclear DIS3 and cytoplasmic DIS3L using a library of all known genes associated with RNA metabolism. Our analysis revealed that DIS3 mutation suppresses RNA splicing deficiency, while DIS3L GIs disclose the interplay of cytoplasmic RNA degradation with nuclear RNA processing. Finally, genome-wide DIS3 GI map uncovered relations with genes not directly involved in RNA metabolism, like microtubule organization or regulation of telomerase activity.
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Affiliation(s)
- Anna Hojka-Osinska
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Aleksander Chlebowski
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Joanna Grochowska
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Ewelina P. Owczarek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Kamila Affek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | | | - Roman J. Szczesny
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Andrzej Dziembowski
- International Institute of Molecular and Cell Biology, 02-109 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 02-106 Warsaw, Poland
- Department of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland
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3
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Milbury KL, Paul B, Lari A, Fowler C, Montpetit B, Stirling PC. Exonuclease domain mutants of yeast DIS3 display genome instability. Nucleus 2020; 10:21-32. [PMID: 30724665 PMCID: PMC6380420 DOI: 10.1080/19491034.2019.1578600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The exosome functions to regulate the cellular transcriptome through RNA biogenesis, surveillance, and decay. Mutations in Dis3, a catalytic subunit of the RNA exosome with separable endonuclease and exonuclease activities, are linked to multiple myeloma. Here we report that a cancer-associated DIS3 allele, dis3E729K, provides evidence for DIS3 functioning in mitotic fidelity in yeast. This dis3E729K allele does not induce defects in 7S→5.8S rRNA processing, although it elicits a requirement for P-body function. While it does not significantly influence cell cycle progression alone, the allele reduces the efficiency of cell cycle arrest in strains with defects in kinetochore assembly. Finally, point mutations in the exonuclease domains of yeast Dis3 elicit genome instability phenotypes; however, these DIS3 mutations do not increase DNA damage or RNA processing defects that lead to the accumulation of polyadenylated RNA in the nucleus. These data suggest that specific DIS3 activities support mitotic fidelity in yeast.
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Affiliation(s)
- Karissa L Milbury
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Biplab Paul
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Azra Lari
- b Department of Cell Biology , University of Alberta , Edmonton , Canada
| | - Claire Fowler
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada
| | - Ben Montpetit
- b Department of Cell Biology , University of Alberta , Edmonton , Canada.,c Department of Viticulture and Enology , University of California , Davis , CA , USA
| | - Peter C Stirling
- a Terry Fox Laboratory , British Columbia Cancer Agency , Vancouver , Canada.,d Department of Medical Genetics , University of British Columbia , Vancouver , BC , Canada
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Abstract
The evolutionarily conserved RNA exosome is a multisubunit ribonuclease complex that processes and/or degrades numerous RNAs. Recently, mutations in genes encoding both structural and catalytic subunits of the RNA exosome have been linked to human disease. Mutations in the structural exosome gene EXOSC2 cause a distinct syndrome that includes retinitis pigmentosa, hearing loss, and mild intellectual disability. In contrast, mutations in the structural exosome genes EXOSC3 and EXOSC8 cause pontocerebellar hypoplasia type 1b (PCH1b) and type 1c (PCH1c), respectively, which are related autosomal recessive, neurodegenerative diseases. In addition, mutations in the structural exosome gene EXOSC9 cause a PCH-like disease with cerebellar atrophy and spinal motor neuronopathy. Finally, mutations in the catalytic exosome gene DIS3 have been linked to multiple myeloma, a neoplasm of plasma B cells. How mutations in these RNA exosome genes lead to distinct, tissue-specific diseases is not currently well understood. In this chapter, we examine the role of the RNA exosome complex in human disease and discuss the mechanisms by which mutations in different exosome subunit genes could impair RNA exosome function and give rise to diverse diseases.
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Affiliation(s)
- Milo B Fasken
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
| | - Derrick J Morton
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Emily G Kuiper
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Stephanie K Jones
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA
| | - Sara W Leung
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA
| | - Anita H Corbett
- Department of Biology, RRC 1021, Emory University, Atlanta, GA, USA.
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Identification of Recessive Lethal Alleles in the Diploid Genome of a Candida albicans Laboratory Strain Unveils a Potential Role of Repetitive Sequences in Buffering Their Deleterious Impact. mSphere 2019; 4:4/1/e00709-18. [PMID: 30760617 PMCID: PMC6374597 DOI: 10.1128/msphere.00709-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heterozygous diploid genome of Candida albicans is highly plastic, with frequent loss of heterozygosity (LOH) events. In the SC5314 laboratory strain, while LOH events are ubiquitous, a chromosome homozygosis bias is observed for certain chromosomes, whereby only one of the two homologs can occur in the homozygous state. This suggests the occurrence of recessive lethal allele(s) (RLA) preventing large-scale LOH events on these chromosomes from being stably maintained. To verify the presence of an RLA on chromosome 7 (Chr7), we utilized a system that allows (i) DNA double-strand break (DSB) induction on Chr7 by the I-SceI endonuclease and (ii) detection of the resulting long-range homozygosis. I-SceI successfully induced a DNA DSB on both Chr7 homologs, generally repaired by gene conversion. Notably, cells homozygous for the right arm of Chr7B were not recovered, confirming the presence of RLA(s) in this region. Genome data mining for RLA candidates identified a premature nonsense-generating single nucleotide polymorphism (SNP) within the HapB allele of C7_03400c whose Saccharomyces cerevisiae ortholog encodes the essential Mtr4 RNA helicase. Complementation with a wild-type copy of MTR4 rescued cells homozygous for the right arm of Chr7B, demonstrating that the mtr4K880* RLA is responsible for the Chr7 homozygosis bias in strain SC5314. Furthermore, we observed that the major repeat sequences (MRS) on Chr7 acted as hot spots for interhomolog recombination. Such recombination events provide C. albicans with increased opportunities to survive DNA DSBs whose repair can lead to homozygosis of recessive lethal or deleterious alleles. This might explain the maintenance of MRS in this species.IMPORTANCE Candida albicans is a major fungal pathogen, whose mode of reproduction is mainly clonal. Its genome is highly tolerant to rearrangements, in particular loss of heterozygosity events, known to unmask recessive lethal and deleterious alleles in heterozygous diploid organisms such as C. albicans By combining a site-specific DSB-inducing system and mining genome sequencing data of 182 C. albicans isolates, we were able to ascribe the chromosome 7 homozygosis bias of the C. albicans laboratory strain SC5314 to an heterozygous SNP introducing a premature STOP codon in the MTR4 gene. We have also proposed genome-wide candidates for new recessive lethal alleles. We additionally observed that the major repeat sequences (MRS) on chromosome 7 acted as hot spots for interhomolog recombination. Maintaining MRS in C. albicans could favor haplotype exchange, of vital importance to LOH events, leading to homozygosis of recessive lethal or deleterious alleles that inevitably accumulate upon clonality.
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Towler BP, Newbury SF. Regulation of cytoplasmic RNA stability: Lessons from Drosophila. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1499. [PMID: 30109918 DOI: 10.1002/wrna.1499] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/06/2018] [Accepted: 07/01/2018] [Indexed: 12/19/2022]
Abstract
The process of RNA degradation is a critical level of regulation contributing to the control of gene expression. In the last two decades a number of studies have shown the specific and targeted nature of RNA decay and its importance in maintaining homeostasis. The key players within the pathways of RNA decay are well conserved with their mutation or disruption resulting in distinct phenotypes as well as human disease. Model organisms including Drosophila melanogaster have played a substantial role in elucidating the mechanisms conferring control over RNA stability. A particular advantage of this model organism is that the functions of ribonucleases can be assessed in the context of natural cells within tissues in addition to individual immortalized cells in culture. Drosophila RNA stability research has demonstrated how the cytoplasmic decay machines, such as the exosome, Dis3L2 and Xrn1, are responsible for regulating specific processes including apoptosis, proliferation, wound healing and fertility. The work discussed here has begun to identify specific mRNA transcripts that appear sensitive to specific decay pathways representing mechanisms through which the ribonucleases control mRNA stability. Drosophila research has also contributed to our knowledge of how specific RNAs are targeted to the ribonucleases including AU rich elements, miRNA targeting and 3' tailing. Increased understanding of these mechanisms is critical to elucidating the control elicited by the cytoplasmic ribonucleases which is relevant to human disease. This article is categorized under: RNA in Disease and Development > RNA in Development RNA Turnover and Surveillance > Regulation of RNA Stability RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms.
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Affiliation(s)
- Benjamin P Towler
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
| | - Sarah F Newbury
- Brighton and Sussex Medical School, University of Sussex, Brighton, UK
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Onderak AM, Anderson JT. Loss of the RNA helicase SKIV2L2 impairs mitotic progression and replication-dependent histone mRNA turnover in murine cell lines. RNA (NEW YORK, N.Y.) 2017; 23:910-926. [PMID: 28351885 PMCID: PMC5435864 DOI: 10.1261/rna.060640.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 03/02/2017] [Indexed: 06/06/2023]
Abstract
RNA surveillance via the nuclear exosome requires cofactors such as the helicase SKIV2L2 to process and degrade certain noncoding RNAs. This research aimed to characterize the phenotype associated with RNAi knockdown of Skiv2l2 in two murine cancer cell lines: Neuro2A and P19. SKIV2L2 depletion in Neuro2A and P19 cells induced changes in gene expression indicative of cell differentiation and reduced cellular proliferation by 30%. Propidium iodide-based cell-cycle analysis of Skiv2l2 knockdown cells revealed defective progression through the G2/M phase and an accumulation of mitotic cells, suggesting SKIV2L2 contributes to mitotic progression. Since SKIV2L2 targets RNAs to the nuclear exosome for processing and degradation, we identified RNA targets elevated in cells depleted of SKIV2L2 that could account for the observed twofold increase in mitotic cells. Skiv2l2 knockdown cells accumulated replication-dependent histone mRNAs, among other RNAs, that could impede mitotic progression and indirectly trigger differentiation.
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Affiliation(s)
- Alexis M Onderak
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
| | - James T Anderson
- Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin 53201, USA
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8
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Hoskins JW, Ibrahim A, Emmanuel MA, Manmiller SM, Wu Y, O’Neill M, Jia J, Collins I, Zhang M, Thomas JV, Rost LM, Das S, Parikh H, Haake JM, Matters GL, Kurtz RC, Bamlet WR, Klein A, Stolzenberg-Solomon R, Wolpin BM, Yarden R, Wang Z, Smith J, Olson SH, Andresson T, Petersen GM, Amundadottir LT. Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects on DIS3 expression. Hum Mol Genet 2016; 25:4726-4738. [PMID: 28172817 PMCID: PMC5815622 DOI: 10.1093/hmg/ddw300] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 07/08/2016] [Accepted: 08/26/2016] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWAS) have identified multiple common susceptibility loci for pancreatic cancer. Here we report fine-mapping and functional analysis of one such locus residing in a 610 kb gene desert on chr13q22.1 (marked by rs9543325). The closest candidate genes, KLF5, KLF12, PIBF1, DIS3 and BORA, range in distance from 265-586 kb. Sequencing three sub-regions containing the top ranked SNPs by imputation P-value revealed a 30 bp insertion/deletion (indel) variant that was significantly associated with pancreatic cancer risk (rs386772267, P = 2.30 × 10-11, OR = 1.22, 95% CI 1.15-1.28) and highly correlated to rs9543325 (r2 = 0.97 in the 1000 Genomes EUR population). This indel was the most significant cis-eQTL variant in a set of 222 histologically normal pancreatic tissue samples (β = 0.26, P = 0.004), with the insertion (risk-increasing) allele associated with reduced DIS3 expression. DIS3 encodes a catalytic subunit of the nuclear RNA exosome complex that mediates RNA processing and decay, and is mutated in several cancers. Chromosome conformation capture revealed a long range (570 kb) physical interaction between a sub-region of the risk locus, containing rs386772267, and a region ∼6 kb upstream of DIS3 Finally, repressor regulatory activity and allele-specific protein binding by transcription factors of the TCF/LEF family were observed for the risk-increasing allele of rs386772267, indicating that expression regulation at this risk locus may be influenced by the Wnt signaling pathway. In conclusion, we have identified a putative functional indel variant at chr13q22.1 that associates with decreased DIS3 expression in carriers of pancreatic cancer risk-increasing alleles, and could therefore affect nuclear RNA processing and/or decay.
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Affiliation(s)
- Jason W. Hoskins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Abdisamad Ibrahim
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mickey A. Emmanuel
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sarah M. Manmiller
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yinglun Wu
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Maura O’Neill
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Jinping Jia
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Irene Collins
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mingfeng Zhang
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Janelle V. Thomas
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lauren M. Rost
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sudipto Das
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Hemang Parikh
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jefferson M. Haake
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Gail L. Matters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, USA
| | - Robert C. Kurtz
- Department of Medicine, Memorial Sloan-Kettering Cancer Center, New York, New York, USA
| | - William R. Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Alison Klein
- Department of Oncology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Epidemiology, the Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Rachael Stolzenberg-Solomon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Brian M. Wolpin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Ronit Yarden
- Department of Human Science, NHS, Georgetown University Medical Center, NW, Washington DC, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Jill Smith
- Department of Medicine, Georgetown University Hospital, Washington, DC, and Department of Medicine, Penn State University College of Medicine, Hershey PA, USA
| | - Sara H. Olson
- Department of Epidemiology and Biostatistics, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gloria M. Petersen
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | - Laufey T. Amundadottir
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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Robinson SR, Oliver AW, Chevassut TJ, Newbury SF. The 3' to 5' Exoribonuclease DIS3: From Structure and Mechanisms to Biological Functions and Role in Human Disease. Biomolecules 2015; 5:1515-39. [PMID: 26193331 PMCID: PMC4598762 DOI: 10.3390/biom5031515] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/01/2015] [Accepted: 07/06/2015] [Indexed: 12/03/2022] Open
Abstract
DIS3 is a conserved exoribonuclease and catalytic subunit of the exosome, a protein complex involved in the 3' to 5' degradation and processing of both nuclear and cytoplasmic RNA species. Recently, aberrant expression of DIS3 has been found to be implicated in a range of different cancers. Perhaps most striking is the finding that DIS3 is recurrently mutated in 11% of multiple myeloma patients. Much work has been done to elucidate the structural and biochemical characteristics of DIS3, including the mechanistic details of its role as an effector of RNA decay pathways. Nevertheless, we do not understand how DIS3 mutations can lead to cancer. There are a number of studies that pertain to the function of DIS3 at the organismal level. Mutant phenotypes in S. pombe, S. cerevisiae and Drosophila suggest DIS3 homologues have a common role in cell-cycle progression and microtubule assembly. DIS3 has also recently been implicated in antibody diversification of mouse B-cells. This article aims to review current knowledge of the structure, mechanisms and functions of DIS3 as well as highlighting the genetic patterns observed within myeloma patients, in order to yield insight into the putative role of DIS3 mutations in oncogenesis.
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Affiliation(s)
- Sophie R Robinson
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK.
| | - Timothy J Chevassut
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
| | - Sarah F Newbury
- Medical Research Building, Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PS, UK.
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Tsanova B, Spatrick P, Jacobson A, van Hoof A. The RNA exosome affects iron response and sensitivity to oxidative stress. RNA (NEW YORK, N.Y.) 2014; 20:1057-1067. [PMID: 24860016 PMCID: PMC4114685 DOI: 10.1261/rna.043257.113] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 04/01/2014] [Indexed: 06/03/2023]
Abstract
RNA degradation plays important roles for maintaining temporal control and fidelity of gene expression, as well as processing of transcripts. In Saccharomyces cerevisiae the RNA exosome is a major 3'-to-5' exoribonuclease and also has an endonuclease domain of unknown function. Here we report a physiological role for the exosome in response to a stimulus. We show that inactivating the exoribonuclease active site of Rrp44 up-regulates the iron uptake regulon. This up-regulation is caused by increased levels of reactive oxygen species (ROS) in the mutant. Elevated ROS also causes hypersensitivity to H2O2, which can be reduced by the addition of iron to H2O2 stressed cells. Finally, we show that the previously characterized slow growth phenotype of rrp44-exo(-) is largely ameliorated during fermentative growth. While the molecular functions of Rrp44 and the RNA exosome have been extensively characterized, our studies characterize how this molecular function affects the physiology of the organism.
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Affiliation(s)
- Borislava Tsanova
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center–Houston and The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
| | - Phyllis Spatrick
- Department of Microbiology and Physiological Systems, Albert Sherman Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Allan Jacobson
- Department of Microbiology and Physiological Systems, Albert Sherman Center, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
| | - Ambro van Hoof
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center–Houston and The University of Texas Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
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Mechanisms of genome instability induced by RNA-processing defects. Trends Genet 2014; 30:245-53. [PMID: 24794811 DOI: 10.1016/j.tig.2014.03.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 03/25/2014] [Accepted: 03/26/2014] [Indexed: 12/20/2022]
Abstract
The role of normal transcription and RNA processing in maintaining genome integrity is becoming increasingly appreciated in organisms ranging from bacteria to humans. Several mutations in RNA biogenesis factors have been implicated in human cancers, but the mechanisms and potential connections to tumor genome instability are not clear. Here, we discuss how RNA-processing defects could destabilize genomes through mutagenic R-loop structures and by altering expression of genes required for genome stability. A compelling body of evidence now suggests that researchers should be directly testing these mechanisms in models of human cancer.
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Wurtmann EJ, Ratushny AV, Pan M, Beer KD, Aitchison JD, Baliga NS. An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation. Mol Microbiol 2014; 92:369-82. [PMID: 24612392 PMCID: PMC4060883 DOI: 10.1111/mmi.12564] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2014] [Indexed: 01/27/2023]
Abstract
It is known that environmental context influences the degree of regulation at the transcriptional and post-transcriptional levels. However, the principles governing the differential usage and interplay of regulation at these two levels are not clear. Here, we show that the integration of transcriptional and post-transcriptional regulatory mechanisms in a characteristic network motif drives efficient environment-dependent state transitions. Through phenotypic screening, systems analysis, and rigorous experimental validation, we discovered an RNase (VNG2099C) in Halobacterium salinarum that is transcriptionally co-regulated with genes of the aerobic physiologic state but acts on transcripts of the anaerobic state. Through modelling and experimentation we show that this arrangement generates an efficient state-transition switch, within which RNase-repression of a transcriptional positive autoregulation (RPAR) loop is critical for shutting down ATP-consuming active potassium uptake to conserve energy required for salinity adaptation under aerobic, high potassium, or dark conditions. Subsequently, we discovered that many Escherichia coli operons with energy-associated functions are also putatively controlled by RPAR indicating that this network motif may have evolved independently in phylogenetically distant organisms. Thus, our data suggest that interplay of transcriptional and post-transcriptional regulation in the RPAR motif is a generalized principle for efficient environment-dependent state transitions across prokaryotes.
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Affiliation(s)
| | - Alexander V. Ratushny
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Seattle Biomedical Research Institute, Seattle, WA, 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - John D. Aitchison
- Institute for Systems Biology, Seattle, WA, 98109, USA
- Seattle Biomedical Research Institute, Seattle, WA, 98109, USA
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Reis FP, Pobre V, Silva IJ, Malecki M, Arraiano CM. The RNase II/RNB family of exoribonucleases: putting the 'Dis' in disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 4:607-15. [PMID: 23776156 DOI: 10.1002/wrna.1180] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/03/2013] [Accepted: 05/14/2013] [Indexed: 12/21/2022]
Abstract
Important findings over the last years have shed new light onto the mechanistic details of RNA degradation by members of the RNase II/RNB family of exoribonucleases. Members of this family have been shown to be involved in growth, normal chloroplast biogenesis, mitotic control and cancer. Recently, different publications have linked human orthologs (Dis3 and Dis3L2) to important human diseases. This article describes the structural and biochemical characteristics of members of this family of enzymes, and the physiological implications that relate them with disease.
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Affiliation(s)
- Filipa P Reis
- Instituto de Tecnologia Química e Biológica-ITQB, Universidade Nova de Lisboa, Oeiras, Portugal
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Abstract
Most RNAs in eukaryotic cells are produced as precursors that undergo processing at the 3' and/or 5' end to generate the mature transcript. In addition, many transcripts are degraded not only as part of normal recycling, but also when recognized as aberrant by the RNA surveillance machinery. The exosome, a conserved multiprotein complex containing two nucleases, is involved in both the 3' processing and the turnover of many RNAs in the cell. A series of factors, including the TRAMP (Trf4-Air2-Mtr4 polyadenylation) complex, Mpp6 and Rrp47, help to define the targets to be processed and/or degraded and assist in exosome function. The majority of the data on the exosome and RNA maturation/decay have been derived from work performed in the yeast Saccharomyces cerevisiae. In the present paper, we provide an overview of the exosome and its role in RNA processing/degradation and discuss important new insights into exosome composition and function in human cells.
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Hou D, Ruiz M, Andrulis ED. The ribonuclease Dis3 is an essential regulator of the developmental transcriptome. BMC Genomics 2012; 13:359. [PMID: 22853036 PMCID: PMC3434026 DOI: 10.1186/1471-2164-13-359] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 07/11/2012] [Indexed: 11/24/2022] Open
Abstract
Background Dis3 is ribonuclease that acts directly in the processing, turnover, and surveillance of a large number of distinct RNA species. Evolutionarily conserved from eubacteria to eukaryotes and a crucial component of the RNA processing exosome, Dis3 has been shown to be essential in yeast and fly S2 cells. However, it is not known whether Dis3 has essential functions in a metazoan. This study inquires whether Dis3 is required for Drosophila development and viability and how Dis3 regulates the transcriptome in the developing fly. Results Using transgenic flies, we show that Dis3 knock down (Dis3KD) retards growth, induces melanotic tumor formation, and ultimately results in 2nd instar larval lethality. In order to determine whether Dis3KD fly phenotypes were a consequence of disrupting developmentally regulated RNA turnover, we performed RNA deep sequencing analysis on total RNA isolated from developmentally staged animals. Bioinformatic analysis of transcripts from Dis3KD flies reveals substantial transcriptomic changes, most notably down-regulation in early expressed RNAs. Finally, gene ontology analysis of this early stage shows that Dis3 regulates transcripts related to extracellular structure and remodelling, neurogenesis, and nucleotide metabolism. Conclusions We conclude that Dis3 is essential for early Drosophila melanogaster development and has specific and important stage-specific roles in regulating RNA metabolism. In showing for the first time that Dis3 is required for the development of a multicellular organism, our work provides mechanistic insight into how Dis3—either independent of or associated with the RNA processing exosome—participates in cell type-specific RNA turnover in metazoan development.
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Affiliation(s)
- Dezhi Hou
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
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Dis3- and exosome subunit-responsive 3' mRNA instability elements. Biochem Biophys Res Commun 2012; 423:461-6. [PMID: 22668878 DOI: 10.1016/j.bbrc.2012.05.141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 05/26/2012] [Indexed: 11/20/2022]
Abstract
Eukaryotic RNA turnover is regulated in part by the exosome, a nuclear and cytoplasmic complex of ribonucleases (RNases) and RNA-binding proteins. The major RNase of the complex is thought to be Dis3, a multi-functional 3'-5' exoribonuclease and endoribonuclease. Although it is known that Dis3 and core exosome subunits are recruited to transcriptionally active genes and to messenger RNA (mRNA) substrates, this recruitment is thought to occur indirectly. We sought to discover cis-acting elements that recruit Dis3 or other exosome subunits. Using a bioinformatic tool called RNA SCOPE to screen the 3' untranslated regions of up-regulated transcripts from our published Dis3 depletion-derived transcriptomic data set, we identified several motifs as candidate instability elements. Secondary screening using a luciferase reporter system revealed that one cassette-harboring four elements-destabilized the reporter transcript. RNAi-based depletion of Dis3, Rrp6, Rrp4, Rrp40, or Rrp46 diminished the efficacy of cassette-mediated destabilization. Truncation analysis of the cassette showed that two exosome subunit-sensitive elements (ESSEs) destabilized the reporter. Point-directed mutagenesis of ESSE abrogated the destabilization effect. An examination of the transcriptomic data from exosome subunit depletion-based microarrays revealed that mRNAs with ESSEs are found in every up-regulated mRNA data set but are underrepresented or missing from the down-regulated data sets. Taken together, our findings imply a potentially novel mechanism of mRNA turnover that involves direct Dis3 and other exosome subunit recruitment to and/or regulation on mRNA substrates.
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Kim IK, Roldão A, Siewers V, Nielsen J. A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 2012; 12:228-48. [DOI: 10.1111/j.1567-1364.2011.00779.x] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Revised: 12/05/2011] [Accepted: 12/09/2011] [Indexed: 12/01/2022] Open
Affiliation(s)
- Il-Kwon Kim
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - António Roldão
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Verena Siewers
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
| | - Jens Nielsen
- Department of Chemical and Biological Engineering; Chalmers University of Technology; Gothenburg; Sweden
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