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Lacuna M, Hortal AM, Cifuentes C, Gonzalo T, Alcoceba M, Bastos M, Bustelo XR, González M, Alarcón B. Characterization of Three Somatic Mutations in the 3'UTR of RRAS2 and Their Inverse Correlation with Lymphocytosis in Chronic Lymphocytic Leukemia. Cells 2023; 12:2687. [PMID: 38067115 PMCID: PMC10705375 DOI: 10.3390/cells12232687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Chronic lymphocytic leukemia (CLL) is a hematologic malignancy characterized by progressive accumulation of a rare population of CD5+ B-lymphocytes in peripheral blood, bone marrow, and lymphoid tissues. CLL exhibits remarkable clinical heterogeneity, with some patients presenting with indolent disease and others progressing rapidly to aggressive CLL. The significant heterogeneity of CLL underscores the importance of identifying novel prognostic markers. Recently, the RAS-related gene RRAS2 has emerged as both a driver oncogene and a potential marker for CLL progression, with higher RRAS2 expression associated with poorer disease prognosis. Although missense somatic mutations in the coding sequence of RRAS2 have not been described in CLL, this study reports the frequent detection of three somatic mutations in the 3' untranslated region (3'UTR) affecting positions +26, +53, and +180 downstream of the stop codon in the mRNA. An inverse relationship was observed between these three somatic mutations and RRAS2 mRNA expression, which correlated with lower blood lymphocytosis. These findings highlight the importance of RRAS2 overexpression in CLL development and prognosis and point to somatic mutations in its 3'UTR as novel mechanistic clues. Our results may contribute to the development of targeted therapeutic strategies and improved risk stratification for CLL patients.
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Affiliation(s)
- Marta Lacuna
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Alejandro M. Hortal
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Claudia Cifuentes
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Tania Gonzalo
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
| | - Miguel Alcoceba
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Miguel Bastos
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Xosé R. Bustelo
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Marcos González
- Departamento de Hematología, Hospital Universitario de Salamanca (HUS-IBSAL), 37007 Salamanca, Spain; (M.A.); (M.B.); (M.G.)
- Centro de Investigación del Cáncer, Instituto de Biología Molecular y Celular del Cáncer and Centro de Investigación Biomédica en Red de Cáncer, CSIC, Universidad de Salamanca, 37007 Salamanca, Spain;
| | - Balbino Alarcón
- Immune System Development and Function Program, Centro Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)-Universidad Autónoma de Madrid, 28049 Madrid, Spain; (M.L.); (A.M.H.); (C.C.); (T.G.)
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Xiao S, Kai Z, Murphy D, Li D, Patel D, Bielowka AM, Bernabeu-Herrero ME, Abdulmogith A, Mumford AD, Westbury SK, Aldred MA, Vargesson N, Caulfield MJ, Shovlin CL. Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA. Am J Hum Genet 2023; 110:1903-1918. [PMID: 37816352 PMCID: PMC10645545 DOI: 10.1016/j.ajhg.2023.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 10/12/2023] Open
Abstract
Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY, an analytic tool that integrates coordinates for regions with experimental evidence of functionality. Applied to WGS data from solved and unsolved hereditary hemorrhagic telangiectasia (HHT) recruits to the 100,000 Genomes Project, GROFFFY-based filtration reduced the mean number of variants/DNA from 4,867,167 to 21,486, without deleting disease-causal variants. In three unsolved cases (two related), GROFFFY identified ultra-rare deletions within the 3' untranslated region (UTR) of the tumor suppressor SMAD4, where germline loss-of-function alleles cause combined HHT and colonic polyposis (MIM: 175050). Sited >5.4 kb distal to coding DNA, the deletions did not modify or generate microRNA binding sites, but instead disrupted the sequence context of the final cleavage and polyadenylation site necessary for protein production: By iFoldRNA, an AAUAAA-adjacent 16-nucleotide deletion brought the cleavage site into inaccessible neighboring secondary structures, while a 4-nucleotide deletion unfolded the downstream RNA polymerase II roadblock. SMAD4 RNA expression differed to control-derived RNA from resting and cycloheximide-stressed peripheral blood mononuclear cells. Patterns predicted the mutational site for an unrelated HHT/polyposis-affected individual, where a complex insertion was subsequently identified. In conclusion, we describe a functional rare variant type that impacts regulatory systems based on RNA polyadenylation. Extension of coding sequence-focused gene panels is required to capture these variants.
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Affiliation(s)
- Sihao Xiao
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK.
| | - Zhentian Kai
- Topgen Biopharm Technology Co. Ltd., Shanghai 201203, China
| | - Daniel Murphy
- National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK; Women's, Children's & Clinical Support (Pharmacy), Imperial College Healthcare NHS Trust, W2 1NY London, UK
| | - Dongyang Li
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Dilip Patel
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Adrianna M Bielowka
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Maria E Bernabeu-Herrero
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Awatif Abdulmogith
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK
| | - Andrew D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1QU Bristol, UK
| | - Sarah K Westbury
- School of Cellular and Molecular Medicine, University of Bristol, BS8 1QU Bristol, UK
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep & Occupational Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Neil Vargesson
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, AB25 2ZD Aberdeen, UK
| | - Mark J Caulfield
- William Harvey Research Institute, Queen Mary University of London, E1 4NS London, UK
| | - Claire L Shovlin
- National Heart and Lung Institute, Imperial College London, W12 ONN London, UK; National Institute for Health Research (NIHR) Imperial Biomedical Research Centre, W2 1NY London, UK; Specialist Medicine, Imperial College Healthcare NHS Trust, W12 OHS London, UK.
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3
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Muir WM, Lo CL, Bell RL, Zhou FC. Multi-animal-model study reveals mutations in neural plasticity and nociception genes linked to excessive alcohol drinking. Alcohol Clin Exp Res (Hoboken) 2023; 47:1478-1493. [PMID: 37336636 PMCID: PMC10728351 DOI: 10.1111/acer.15131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/10/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
BACKGROUND The basis for familial alcohol use disorder (AUD) remains an enigma due to various biological and societal confounds. The present study used three of the most adopted and documented rat models, combining the alcohol-preferring/non-alcohol-preferring (P/NP) lines and high alcohol-drinking/low alcohol-drinking (HAD/LAD) replicated lines, of AUD as examined through the lens of whole genomic analyses. METHODS We used complete genome sequencing of the P/NP lines and previously published sequences of the HAD/LAD replicates to enhance the discovery of variants associated with AUD and to remove confounding with genetic background and random genetic drift. Specifically, we used high-order statistical methods to search for genetic variants whose frequency changes in whole sets of gene ontologies corresponded with phenotypic changes in the direction of selection, that is, ethanol-drinking preference. RESULTS Our first finding was that in addition to variants causing translational changes, the principal genetic changes associated with drinking predisposition were silent mutations and mutations in the 3' untranslated regions (3'UTR) of genes. Neither of these types of mutations alters the amino acid sequence of the translated protein but they influence both the rate and conformation of gene transcription, including its stability and posttranslational events that alter gene efficacy. This finding argues for refocusing human genomic studies on changes in gene efficacy. Among the key ontologies identified were the central genes associated with the Na+ voltage-gated channels of neurons and glia (including the Scn1a, Scn2a, Scn2b, Scn3a, Scn7a, and Scn9a subtypes) and excitatory glutamatergic secretion (including Grm2 and Myo6), both of which are essential in neuroplasticity. In addition, we identified "Nociception or Sensory Perception of Pain," which contained variants in nociception (Arrb1, Ccl3, Ephb1) and enlist sodium (Scn1a, Scn2a, Scn2b, Scn3a, Scn7a), pain activation (Scn9a), and potassium channel (Kcna1) genes. CONCLUSION The multi-model analyses used herein reduced the confounding effects of random drift and the "founders" genetic background. The most differentiated bidirectionally selected genes across all three animal models were Scn9a, Scn1a, and Kcna, all of which are annotated in the nociception ontology. The complexity of neuroplasticity and nociception adds strength to the hypothesis that neuroplasticity and pain (physical or psychological) are prominent phenotypes genetically linked to the development of AUD.
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Affiliation(s)
- William M. Muir
- Indiana Alcohol Research Center, Indiana University School of Medicine
- Department of Medicine, School of Medicine, Indiana University, Indianapolis, IN, 46202, USA
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Chiao-Ling Lo
- Indiana Alcohol Research Center, Indiana University School of Medicine
| | - Richard L. Bell
- Indiana Alcohol Research Center, Indiana University School of Medicine
- Stark Neuroscience Research Institute, Indianapolis, Indiana, USA
| | - Feng C. Zhou
- Indiana Alcohol Research Center, Indiana University School of Medicine
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Stark Neuroscience Research Institute, Indianapolis, Indiana, USA
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Liang M, Hody C, Yammine V, Soin R, Sun Y, Lin X, Tian X, Meurs R, Perdrau C, Delacourt N, Oumalis M, Andris F, Conrard L, Kruys V, Gueydan C. eIF4EHP promotes Ldh mRNA translation in and fruit fly adaptation to hypoxia. EMBO Rep 2023; 24:e56460. [PMID: 37144276 PMCID: PMC10328074 DOI: 10.15252/embr.202256460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/16/2023] [Accepted: 04/21/2023] [Indexed: 05/06/2023] Open
Abstract
Hypoxia induces profound modifications in the gene expression program of eukaryotic cells due to lowered ATP supply resulting from the blockade of oxidative phosphorylation. One significant consequence of oxygen deprivation is the massive repression of protein synthesis, leaving a limited set of mRNAs to be translated. Drosophila melanogaster is strongly resistant to oxygen fluctuations; however, the mechanisms allowing specific mRNA to be translated into hypoxia are still unknown. Here, we show that Ldh mRNA encoding lactate dehydrogenase is highly translated into hypoxia by a mechanism involving a CA-rich motif present in its 3' untranslated region. Furthermore, we identified the cap-binding protein eIF4EHP as a main factor involved in 3'UTR-dependent translation under hypoxia. In accordance with this observation, we show that eIF4EHP is necessary for Drosophila development under low oxygen concentrations and contributes to Drosophila mobility after hypoxic challenge. Altogether, our data bring new insight into mechanisms contributing to LDH production and Drosophila adaptation to oxygen variations.
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Affiliation(s)
- Manfei Liang
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
- Present address:
Medical Science and Technology Innovation CenterShandong First Medical UniversityJinanChina
| | - Clara Hody
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Vanessa Yammine
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romuald Soin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Yuqiu Sun
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xing Lin
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Xiaoying Tian
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Romane Meurs
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Camille Perdrau
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Nadège Delacourt
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Marina Oumalis
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Fabienne Andris
- Laboratoire d'Immunobiologie, Faculté des SciencesUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Louise Conrard
- Center of Microscopy and Molecular Imaging (CMMI)Université libre de Bruxelles (ULB)GosseliesBelgium
| | - Véronique Kruys
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
| | - Cyril Gueydan
- Laboratoire de Biologie Moléculaire du GèneUniversité libre de Bruxelles (ULB)GosseliesBelgium
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Zhao D, Wang Q, Wang M, Lyu L, Liu S, Jiang Y, Zhou S, Liu F. A putative wild-type or wild-type-like hairpin structure is required within 3' untranslated region of Senecavirus A for virus replication. Virology 2023; 585:72-77. [PMID: 37307649 DOI: 10.1016/j.virol.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/18/2023] [Accepted: 05/22/2023] [Indexed: 06/14/2023]
Abstract
The 3' untranslated region (UTR) of Senecavirus A (SVA) was predicted to harbor two hairpin structures, hairpin-I and -II. The former is composed of two internal loops, one terminal loop and three stem regions; the latter comprises one internal loop, one terminal loop and two stem regions. In this study, we constructed a total of nine SVA cDNA clones, which contained different point mutations within a stem-formed motif in the hairpin-I or -II, for rescuing replication-competent viruses. Only three mutants were successfully rescued and moreover genetically stable during at least five serial passages. Computer-aided prediction showed these three mutants bearing either a wild-type or a wild-type-like hairpin-I in their individual 3' UTRs. Neither wild-type nor wild-type-like hairpin-I could be computationally predicted to exist in 3' UTRs of the other six unviable "viruses". The results suggested that the wild-type or wild-type-like hairpin-I was necessary in the 3' UTR for SVA replication.
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Affiliation(s)
- Di Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot, 010018, China
| | - Qianqian Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China; College of Veterinary Medicine, Inner Mongolia Agricultural University, Huhhot, 010018, China
| | - Mengyao Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Liangpeng Lyu
- Qingdao Workstation of Animal Husbandry, Qingdao, 266199, China
| | - Shuqing Liu
- Qingdao Center for Animal Disease Control & Prevention, Qingdao, 266199, China
| | - Yujia Jiang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuning Zhou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, 266109, China.
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Savinov A, Brandsen BM, Angell BE, Cuperus JT, Fields S. Effects of sequence motifs in the yeast 3' untranslated region determined from massively parallel assays of random sequences. Genome Biol 2021; 22:293. [PMID: 34663436 PMCID: PMC8522215 DOI: 10.1186/s13059-021-02509-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/30/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The 3' untranslated region (UTR) plays critical roles in determining the level of gene expression through effects on activities such as mRNA stability and translation. Functional elements within this region have largely been identified through analyses of native genes, which contain multiple co-evolved sequence features. RESULTS To explore the effects of 3' UTR sequence elements outside of native sequence contexts, we analyze hundreds of thousands of random 50-mers inserted into the 3' UTR of a reporter gene in the yeast Saccharomyces cerevisiae. We determine relative protein expression levels from the fitness of transformants in a growth selection. We find that the consensus 3' UTR efficiency element significantly boosts expression, independent of sequence context; on the other hand, the consensus positioning element has only a small effect on expression. Some sequence motifs that are binding sites for Puf proteins substantially increase expression in the library, despite these proteins generally being associated with post-transcriptional downregulation of native mRNAs. Our measurements also allow a systematic examination of the effects of point mutations within efficiency element motifs across diverse sequence backgrounds. These mutational scans reveal the relative in vivo importance of individual bases in the efficiency element, which likely reflects their roles in binding the Hrp1 protein involved in cleavage and polyadenylation. CONCLUSIONS The regulatory effects of some 3' UTR sequence features, like the efficiency element, are consistent regardless of sequence context. In contrast, the consequences of other 3' UTR features appear to be strongly dependent on their evolved context within native genes.
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Affiliation(s)
- Andrew Savinov
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA
- Present address: Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Benjamin M Brandsen
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA
- Department of Chemistry and Biochemistry, Creighton University, Omaha, NE, 68178, USA
| | - Brooke E Angell
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA
- Present address: Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, 60208, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA.
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Box 355065, Seattle, WA, 98195, USA.
- Department of Medicine, University of Washington, Box 357720, Seattle, WA, 98195, USA.
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Xing J, Zhang Y, Lin Z, Liu L, Xu Q, Liang J, Yuan Z, Huang C, Liao M, Qi W. 3'UTR SL-IV and DB1 Regions Contribute to Japanese Encephalitis Virus Replication and Pathogenicity. Front Vet Sci 2021; 8:703147. [PMID: 34409089 PMCID: PMC8366024 DOI: 10.3389/fvets.2021.703147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/07/2021] [Indexed: 11/29/2022] Open
Abstract
Japanese encephalitis virus (JEV), a mosquito-borne flavivirus that causes fatal neurological disease in humans, is one of the most important emerging pathogens of public health significance. JEV is maintained in an enzootic cycle and causes reproductive failure in pigs. Notably, the shift in JEV genotypes is not fully protected by existing vaccines, so the development of a candidate vaccine is urgently needed. In this study, we compared pathogenicity between Japanese encephalitis virus SA14 and BJB (isolated from humans in the 1970s) strains. We found that the BJB strain was attenuated in mice and that there was no case fatality rate. The growth rate of BJB was higher than SA14 virus in BHK-21 cells. Based on the sequence alignment of the viral genome between the SA14 and BJB virus strains, some mutations at sites 248, 254, 258, and 307 were observed in the 3′ untranslated region (3′UTR). The 3′UTR of JEV plays a very important role in the viral life cycle. Furthermore, using a reverse genetic system, we conducted and rescued the parental JEV strain SA14 (T248, A254, and A258) and the mutant virus rSA14-3′UTRmut (T248C, A254G, A258G, and 307G). Through an analysis of the RNA secondary structure model of the 3′UTR, we discovered that the mutations of T248C, A254G, and A258G reduced the apiculus ring and increased the lateral ring significantly in the stem-loop structures IV (SL-IV) structure region of 3′UTR. Moreover, the insertion of 307G added a ring to the dumbbell structure 1 (DB1) structure region. Strikingly, these RNA secondary structure changes in 3′UTR of rSA14-3′UTRmut increased viral negative chain RNA production and enhanced the replication ability of the virus in BHK-21 cells. However, in vivo mouse experiments illustrated that the rSA14-3′UTRmut virus significantly decreased the neurovirulence of JEV. These results affirmed that the JEV SL-IV and DB1 regions play an important role in viral proliferation and pathogenicity. Taken together, we complement the study of RNA element function in the 3′UTR region of JEV by providing a new target for the rational design of live attenuated candidate vaccines and the increase of virus production.
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Affiliation(s)
- Jinchao Xing
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Youyue Zhang
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Ziying Lin
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China
| | - Lele Liu
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China
| | - Qiang Xu
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China
| | - Jiaqi Liang
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China
| | - Zhaoxia Yuan
- College of Animal Sciences and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Cuiqin Huang
- The Key Laboratory of Fujian Animal Diseases Control, Longyan University, Longyan, China
| | - Ming Liao
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
| | - Wenbao Qi
- Key Laboratory of Zoonoses, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, China.,National and Regional Joint Engineering Laboratory for Medicament of Zoonoses Prevention and Control, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Key Laboratory of Zoonoses Prevention and Control of Guangdong Province, Guangzhou, China
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Hwang S, Lee N, Choe D, Lee Y, Kim W, Jeong Y, Cho S, Palsson BO, Cho BK. Elucidating the Regulatory Elements for Transcription Termination and Posttranscriptional Processing in the Streptomyces clavuligerus Genome. mSystems 2021; 6:e01013-20. [PMID: 33947798 DOI: 10.1128/mSystems.01013-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Identification of transcriptional regulatory elements in the GC-rich Streptomyces genome is essential for the production of novel biochemicals from secondary metabolite biosynthetic gene clusters (smBGCs). Despite many efforts to understand the regulation of transcription initiation in smBGCs, information on the regulation of transcription termination and posttranscriptional processing remains scarce. In this study, we identified the transcriptional regulatory elements in β-lactam antibiotic-producing Streptomyces clavuligerus ATCC 27064 by determining a total of 1,427 transcript 3'-end positions (TEPs) using the term-seq method. Termination of transcription was governed by three classes of TEPs, of which each displayed unique sequence features. The data integration with transcription start sites and transcriptome data generated 1,648 transcription units (TUs) and 610 transcription unit clusters (TUCs). TU architecture showed that the transcript abundance in TU isoforms of a TUC was potentially affected by the sequence context of their TEPs, suggesting that the regulatory elements of TEPs could control the transcription level in additional layers. We also identified TU features of a xenobiotic response element (XRE) family regulator and DUF397 domain-containing protein, particularly showing the abundance of bidirectional TEPs. Finally, we found that 189 noncoding TUs contained potential cis- and trans-regulatory elements that played a major role in regulating the 5' and 3' UTR. These findings highlight the role of transcriptional regulatory elements in transcription termination and posttranscriptional processing in Streptomyces sp.IMPORTANCE Streptomyces sp. is a great source of bioactive secondary metabolites, including antibiotics, antifungal agents, antiparasitic agents, immunosuppressant compounds, and other drugs. Secondary metabolites are synthesized via multistep conversions of the precursor molecules from primary metabolism, governed by multicomplex enzymes from secondary metabolite biosynthetic gene clusters. As their production is closely related with the growth phase and dynamic cellular status in response to various intra- and extracellular signals, complex regulatory systems tightly control the gene expressions related to secondary metabolism. In this study, we determined genome-wide transcript 3'-end positions and transcription units in the β-lactam antibiotic producer Streptomyces clavuligerus ATCC 27064 to elucidate the transcriptional regulatory elements in transcription termination and posttranscriptional processing by integration of multiomics data. These unique features, such as transcript 3'-end sequence, potential riboregulators, and potential 3'-untranslated region (UTR) cis-regulatory elements, can be potentially used to design engineering tools that can regulate the transcript abundance of genes for enhancing secondary metabolite production.
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9
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Dayananda PD, de Silva H, Fernando L, de Silva BGDNK. Genetic Variation in the Domain II, 3' Untranslated Region of Human and Mosquito Derived Dengue Virus Strains in Sri Lanka. Viruses 2021; 13:421. [PMID: 33807922 DOI: 10.3390/v13030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Genetic variations in dengue virus (DENV) play a distinct role in epidemic emergence. The DENV 3′ UTR has become a recent interest in research. The objective of the study was to examine the genetic variation in the domain II, 3′ UTR region of human and mosquito-derived DENV. DENV-infected human sera were orally infected to laboratory reared Aedes aegypti mosquitoes. The domain II, 3′ UTR of each human- and mosquito-derived sample was amplified. The nucleotide sequence variation, phylogenetic and secondary structure analysis was carried out incorporating respective regions of so far recorded Sri Lankan and the reference genotype strains of the DENV3 and DENV1 serotypes. The human- and mosquito-derived domain II, 3′ UTR were identical in nucleotide sequences within the serotypes isolated, indicating the conserved nature of the region during host switch. The sequence analysis revealed distinct variations in study isolates compared to so far recorded Sri Lankan isolates. However, despite single nucleotide variations, the maintenance of structural integrity was evident in related strains within the serotypes in the secondary structure analysis. The phylogenetic analysis revealed distinct clade segregation of the study sequences from so far reported Sri Lankan isolates and illustrated the phylogenetic relations of the study sequences to the available global isolates of respective serotypes.
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10
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Karliuk Y, Vom Hemdt A, Wieseler J, Pfeffer M, Kümmerer BM. Characterization and Vector Competence Studies of Chikungunya Virus Lacking Repetitive Motifs in the 3' Untranslated Region of the Genome. Viruses 2021; 13:v13030403. [PMID: 33806267 PMCID: PMC7999577 DOI: 10.3390/v13030403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/26/2021] [Accepted: 02/27/2021] [Indexed: 12/27/2022] Open
Abstract
Using reverse genetics, we analyzed a chikungunya virus (CHIKV) isolate of the Indian Ocean lineage lacking direct repeat (DR) elements in the 3′ untranslated region, namely DR1a and DR2a. While this deletion mutant CHIKV-∆DR exhibited growth characteristics comparable to the wild-type virus in Baby Hamster Kidney cells, replication of the mutant was reduced in Aedes albopictus C6/36 and Ae. aegypti Aag2 cells. Using oral and intrathoracic infection of mosquitoes, viral infectivity, dissemination, and transmission of CHIKV-∆DR could be shown for the well-known CHIKV vectors Ae. aegypti and Ae. albopictus. Oral infection of Ae. vexans and Culex pipiens mosquitoes with mutant or wild-type CHIKV showed very limited infectivity. Dissemination, transmission, and transmission efficiencies as determined via viral RNA in the saliva were slightly higher in Ae. vexans for the wild-type virus than for CHIKV-∆DR. However, both Ae. vexans and Cx. pipiens allowed efficient viral replication after intrathoracic injection confirming that the midgut barrier is an important determinant for the compromised infectivity after oral infection. Transmission efficiencies were neither significantly different between Ae. vexans and Cx. pipiens nor between wild-type and CHIKV-∆DR. With a combined transmission efficiency of 6%, both Ae. vexans and Cx. pipiens might serve as potential vectors in temperate regions.
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Affiliation(s)
- Yauhen Karliuk
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Anja Vom Hemdt
- Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Janett Wieseler
- Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
| | - Martin Pfeffer
- Institute of Animal Hygiene and Veterinary Public Health, Faculty of Veterinary Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Beate M Kümmerer
- Institute of Virology, Medical Faculty, University of Bonn, 53127 Bonn, Germany
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11
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Jiang W, Zhu D, Wang C, Zhu Y. Tumor suppressing effects of tristetraprolin and its small double-stranded RNAs in bladder cancer. Cancer Med 2021; 10:269-285. [PMID: 33259133 PMCID: PMC7826468 DOI: 10.1002/cam4.3622] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/20/2020] [Accepted: 10/25/2020] [Indexed: 12/23/2022] Open
Abstract
Bladder cancer (BCa) is a common malignant tumor of urinary system with few treatments, so more useful therapeutic targets are still needed. Antitumor effects of tristetraprolin (TTP) have been explored in many type tumors, but its roles in bladder cancer are still unknown until now. In this study, public expression profiles and tissue microarray analysis showed that TTP mRNA and protein levels decreased in BCa relative to the normal bladder tissue. To explore biological functions of TTP in BCa, 488 TTP target genes, which could be both suppressed and bound by TTP, were identified by comprehensively analyzing publicly available high-throughput data obtained from Gene Expression Omnibus (GEO). Gene enrichment analysis showed that these genes were enriched in pathways such as cell cycle, epithelial to mesenchymal transition (EMT), and Wnt signaling. Clustering analysis and gene set variation analysis indicated that patients with high expression of TTP target genes had poorer prognosis and stronger tumor proliferation ability relative to the BCa patients with low expression of TTP target genes. In vitro experiments validated that TTP could suppress proliferation, migration, and invasiveness of BCa cells. And TTP could suppress mRNA expression of cyclin-dependent kinase 1 (CDK1) in BCa cells by target its 3' UTR. Then, we identified a new small double-stranded RNA (dsRNA) named dsTTP-973 which could increase TTP expression in BCa cells, in vivo and in vitro experiments revealed that dsTTP-973 could suppress aggressiveness of BCa. In conclusion, TTP played a role of tumor suppressor gene in BCa like other tumors, and its dsRNA named dsTTP-973 could induce TTP expression in BCa and suppress aggressiveness of BCa. With the help of materials science, dsTTP-973 may become a potential treatment for BCa in the future.
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Affiliation(s)
- Wen Jiang
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Dandan Zhu
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Chenghe Wang
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Yu Zhu
- Department of UrologyRuijin HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
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12
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Wu X, Liu T, Ye C, Ye W, Ji G. scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data. Brief Bioinform 2020; 22:5952304. [PMID: 33142319 DOI: 10.1093/bib/bbaa273] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/17/2020] [Accepted: 09/20/2020] [Indexed: 02/06/2023] Open
Abstract
Alternative polyadenylation (APA) generates diverse mRNA isoforms, which contributes to transcriptome diversity and gene expression regulation by affecting mRNA stability, translation and localization in cells. The rapid development of 3' tag-based single-cell RNA-sequencing (scRNA-seq) technologies, such as CEL-seq and 10x Genomics, has led to the emergence of computational methods for identifying APA sites and profiling APA dynamics at single-cell resolution. However, existing methods fail to detect the precise location of poly(A) sites or sites with low read coverage. Moreover, they rely on priori genome annotation and can only detect poly(A) sites located within or near annotated genes. Here we proposed a tool called scAPAtrap for detecting poly(A) sites at the whole genome level in individual cells from 3' tag-based scRNA-seq data. scAPAtrap incorporates peak identification and poly(A) read anchoring, enabling the identification of the precise location of poly(A) sites, even for sites with low read coverage. Moreover, scAPAtrap can identify poly(A) sites without using priori genome annotation, which helps locate novel poly(A) sites in previously overlooked regions and improve genome annotation. We compared scAPAtrap with two latest methods, scAPA and Sierra, using scRNA-seq data from different experimental technologies and species. Results show that scAPAtrap identified poly(A) sites with higher accuracy and sensitivity than competing methods and could be used to explore APA dynamics among cell types or the heterogeneous APA isoform expression in individual cells. scAPAtrap is available at https://github.com/BMILAB/scAPAtrap.
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Affiliation(s)
- Xiaohui Wu
- Department of Automation in Xiamen University
| | - Tao Liu
- Department of Automation in Xiamen University
| | - Congting Ye
- College of the Environment and Ecology in Xiamen University
| | - Wenbin Ye
- Department of Automation in Xiamen University
| | - Guoli Ji
- Department of Automation in Xiamen University
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13
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Takeuchi A, Takahashi Y, Iida K, Hosokawa M, Irie K, Ito M, Brown JB, Ohno K, Nakashima K, Hagiwara M. Identification of Qk as a Glial Precursor Cell Marker that Governs the Fate Specification of Neural Stem Cells to a Glial Cell Lineage. Stem Cell Reports 2020; 15:883-897. [PMID: 32976762 PMCID: PMC7562946 DOI: 10.1016/j.stemcr.2020.08.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023] Open
Abstract
During brain development, neural stem cells (NSCs) initially produce neurons and change their fate to generate glias. While the regulation of neurogenesis is well characterized, specific markers for glial precursor cells (GPCs) and the master regulators for gliogenesis remain unidentified. Accumulating evidence suggests that RNA-binding proteins (RBPs) have significant roles in neuronal development and function, as they comprehensively regulate the expression of target genes in a cell-type-specific manner. We systematically investigated the expression profiles of 1,436 murine RBPs in the developing mouse brain and identified quaking (Qk) as a marker of the putative GPC population. Functional analysis of the NSC-specific Qk-null mutant mouse revealed the key role of Qk in astrocyte and oligodendrocyte generation and differentiation from NSCs. Mechanistically, Qk upregulates gliogenic genes via quaking response elements in their 3′ untranslated regions. These results provide crucial directions for identifying GPCs and deciphering the regulatory mechanisms of gliogenesis from NSCs. Differential expression analysis identified Qk as a glial precursor cell marker Loss of Qk ablated both astrocyte and OL production from neural stem cells Qk−/− NSCs failed to become glia and aberrantly expressed neural genes Qk comprehensively upregulates essential genes for gliogenesis as regulons via QREs
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Affiliation(s)
- Akihide Takeuchi
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Yuji Takahashi
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kei Iida
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan; Medical Research Support Center, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Motoyasu Hosokawa
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Koichiro Irie
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Mikako Ito
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - J B Brown
- Laboratory for Molecular Biosciences, Life Science Informatics Research Unit, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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14
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Hosny N, Matson AW, Kumbha R, Steinhoff M, Sushil Rao J, El-Abaseri TB, Sabek NA, Mahmoud MA, Hering BJ, Burlak C. 3'UTR enhances hCD47 cell surface expression, self-signal function, and reduces ER stress in porcine fibroblasts. Xenotransplantation 2020; 28:e12641. [PMID: 32892439 DOI: 10.1111/xen.12641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/08/2020] [Accepted: 08/17/2020] [Indexed: 12/13/2022]
Abstract
INTRODUCTION Macrophages contribute to xenograft rejection by direct cytotoxicity and by amplifying T cell-mediated immune responses. It has been shown that transgenic expression of hCD47 protects porcine cells from human macrophages by restoring the CD47-SIRPα self-recognition signal. It has also been reported that the long 3' untranslated region (3'UTR) of the hCD47 gene, which is missing from constructs previously used to make hCD47 transgenic pigs, is critical for efficient cell surface expression in human cells. The aim of this study was to investigate the impact of a modified form of the 3'UTR on the expression, localization, and function of hCD47 in transfected porcine cells. METHODS hCD47 constructs with and without the modified 3'UTR were knocked into the GGTA1 locus in porcine fetal fibroblasts using CRISPR. Flow cytometry of the transfected cells was used to analyze hCD47 localization. Endoplasmic reticulum (ER), mitochondrial, and oxidative stress were examined by gene expression analysis and confocal microscopy. Phagocytosis of transfected cells by human macrophages was measured by flow cytometry, and stimulation of human/non-human (NHP) primate lymphocytes by the cells was examined using a PBMCs proliferation assay. RESULTS Cells transfected with the construct lacking the 3'UTR (hCD47(3'UTR-)) exhibited predominantly intracellular expression of hCD47, and showed evidence of ER stress, dysregulated mitochondrial biogenesis, oxidative stress, and autophagy. Inclusion of the 3'UTR (hCD47(3'UTR+)) decreased intracellular expression of hCD47 by 36% and increased cell surface expression by 53%. This was associated with a significant reduction in cellular stress markers and a higher level of protection from phagocytosis by human macrophages. Furthermore, hCD47(3'UTR+) porcine cells stimulated significantly less proliferation of human/NHP T cells than hCD47(3'UTR-) cells. CONCLUSION Our results suggest the potential benefits of using hCD47 constructs containing the 3'UTR to generate genetically engineered hCD47-expressing donor pigs.
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Affiliation(s)
- Nora Hosny
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Anders W Matson
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Ramesh Kumbha
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Magie Steinhoff
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Joseph Sushil Rao
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA.,Division of Solid Organ Transplantation, Department of Surgery, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Taghrid B El-Abaseri
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Nagwan A Sabek
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Moushira A Mahmoud
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Bernhard J Hering
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA
| | - Christopher Burlak
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota School of Medicine, Minneapolis, MN, USA
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15
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Ge S, Dan C, Xiong Y, Gong G, Mei J, Guo W, Li X. Identifying difference in primordial germ cells between XX female and XY male yellow catfish embryos. Gene 2020; 761:145037. [PMID: 32777526 DOI: 10.1016/j.gene.2020.145037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 08/02/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022]
Abstract
Primordial germ cells (PGCs) are singled out from somatic cells very early during embryogenesis, then they migrate towards the genital ridge and differentiate into gametes through oogenesis or spermatogenesis. Labeling PGCs with Localized RNAexpression (LRE) technique by fluorescent proteins has been widely applied among teleost species to study the germ cell development and gonad differentiation. In this study, we first cloned and characterized the 3' untranslated regions (3'UTRs) of nanos homolog 1-like (nos1l), dead end (dnd), and vasa in yellow catfish (Pelteobagrus fulvidraco), and then synthesized the GFP-nos1l/dnd/vasa 3'UTR mRNAs. Each of these three 3'UTRs could label PGCs in yellow catfish embryos, of which, vasa 3'UTR exhibited the highest labeling efficiency. To identify the differences in PGCs at embryonic stage, XX all-female and XY all-male yellow catfish embryos were produced and injected with GFP-vasa 3'UTR mRNA. We observed the PGC migration route in these two monosex embryos from 24 hpf to 7 dpf, and found there was no difference between them. Besides, the PGC number was counted at 48 hpf, and the result showed that the average PGC number in XX females (11.3) was significantly larger than that in XY males (8.1).These findings provide an insight into the development of PGCs in yellow catfish embryos and the relationship between embryonicPGCnumberand thelatergonaddifferentiation.
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Affiliation(s)
- Si Ge
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Cheng Dan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430070, China
| | - Yang Xiong
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gaorui Gong
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jie Mei
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjie Guo
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaohui Li
- College of Fisheries, Huazhong Agricultural University, Wuhan, 430070, China.
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16
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Oliveira LC, Dias Barros AL, Boldt ABW, Adelman Cipolla G. Lack of Association between LCT_rs140433552*CA>del Indel Polymorphism and Lactose Intolerance in a Southern Brazilian Population. Lifestyle Genom 2020; 13:129-133. [PMID: 32659776 DOI: 10.1159/000508509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/07/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND/AIMS Polymorphisms in the enhancer of the lactase gene (LCT) are strongly associated with lactase persistence, but not always predictive of the phenotype. We investigated a possible association between the regulatory rs140433552*CA>del variant of LCT and lactose intolerance (LI). METHODS We genotyped 122 individuals for rs140433552 and rs4988235 (-13910*C>T). RESULTS Associations of rs140433552*CA>del with LI depend on -13910*C>T. Homozygous individuals for the C-CA haplotype, as well as C-CA+/C individuals, seem more likely to manifest LI (OR 3.33 [95% CI 1.32-8.35], p = 0.011, and OR 3.93 [95% CI 1.61-9.61], p = 0.003, respectively), while homozygous individuals for the T-CA haplotype seem more likely to be lactose tolerant (OR 0.04 [95% CI 0.002-0.70], p = 8 × 10-4). CONCLUSIONS rs140433552*CA>del is not independently associated with LI.
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Affiliation(s)
- Luana Caroline Oliveira
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil.,Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Andrey Lucas Dias Barros
- Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Angelica Beate Winter Boldt
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil.,Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | - Gabriel Adelman Cipolla
- Postgraduate Program in Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil, .,Laboratory of Human Molecular Genetics, Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil,
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17
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Browning JWL, Rambo TME, McKay BC. Comparative genomic analysis of the 3' UTR of human MDM2 identifies multiple transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences that arose during primate evolution. Gene 2020; 741:144557. [PMID: 32171824 DOI: 10.1016/j.gene.2020.144557] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 03/08/2020] [Indexed: 01/09/2023]
Abstract
The MDM2 oncogene is a negative regulator of the p53 tumour suppressor. This relationship appears to have originated over a billion years ago. The human MDM2 gene encodes a variety of mRNAs with exceptionally long 3'UTRs (up to 5.7 kb); however, it was unclear whether MDM2 3'UTRs from other species are similarly long or conserved at the sequence level. Here, we report that all but one of the primate species most closely related to humans (greater and lesser apes) have similarly long 3'UTRs with high sequence similarity across their entire length. More distantly related species (Old world monkeys and new world monkeys) tend to have shorter MDM2 3'UTRs homologous to the corresponding position of the human MDM2 3'UTR while non-primate species exhibit little similarity at all. Remarkably, DNA sequences downstream of the shorter primate 3'UTRs are syntenic with distal regions in the human and other ape MDM2 3'UTRs. These homologous non-transcribed intergenic and transcribed 3'UTR-encoding regions are comprised of a variety of transposable elements, an RLP24 pseudogene and a cluster of novel repeat sequences suggestive of another unknown transposable element. Our analysis suggests that the primary difference between long and short MDM2 3'UTRs is a switch in polyA site usage to include conserved transposable elements that remain intergenic in more distantly related primates. It will be important to determine the relative contribution of these elements to post-transcriptional and translational regulation of MDM2 and hence p53-mediated tumour suppression.
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Affiliation(s)
| | | | - Bruce C McKay
- Department of Biology and Institute of Biochemistry, Ottawa, ON, Canada.
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18
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Fischer JW, Busa VF, Shao Y, Leung AKL. Structure-Mediated RNA Decay by UPF1 and G3BP1. Mol Cell 2020; 78:70-84.e6. [PMID: 32017897 DOI: 10.1016/j.molcel.2020.01.021] [Citation(s) in RCA: 134] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 11/12/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Post-transcriptional mechanisms regulate the stability and, hence, expression of coding and noncoding RNAs. Sequence-specific features within the 3' untranslated region (3' UTR) often direct mRNAs for decay. Here, we characterize a genome-wide RNA decay pathway that reduces the half-lives of mRNAs based on overall 3' UTR structure formed by base pairing. The decay pathway is independent of specific single-stranded sequences, as regulation is maintained in both the original and reverse complement orientation. Regulation can be compromised by reducing the overall structure by fusing the 3' UTR with an unstructured sequence. Mutating base-paired RNA regions can also compromise this structure-mediated regulation, which can be restored by re-introducing base-paired structures of different sequences. The decay pathway requires the RNA-binding protein UPF1 and its associated protein G3BP1. Depletion of either protein increased steady-state levels of mRNAs with highly structured 3' UTRs as well as highly structured circular RNAs. This structure-dependent mechanism therefore enables cells to selectively regulate coding and noncoding RNAs.
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Affiliation(s)
- Joseph W Fischer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Veronica F Busa
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Yue Shao
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
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19
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Abstract
Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3′ end of RNA polymerase II transcripts from over 60% of human genes. APA is derived from the existence of multiple polyadenylation signals (PAS) within the same transcript, and results in the differential inclusion of sequence information at the 3′ end. While APA can occur between two PASs allowing for generation of transcripts with distinct coding potential from a single gene, most APA occurs within the untranslated region (3′UTR) and changes the length and content of these non-coding sequences. APA within the 3′UTR can have tremendous impact on its regulatory potential of the mRNA through a variety of mechanisms, and indeed this layer of gene expression regulation has profound impact on processes vital to cell growth and development. Recent studies have particularly highlighted the importance of APA dysregulation in cancer onset and progression. Here, we review the current knowledge of APA and its impacts on mRNA stability, translation, localization and protein localization. We also discuss the implications of APA dysregulation in cancer research and therapy.
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Affiliation(s)
- Fuwen Yuan
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - William Hankey
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Eric J Wagner
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA
| | - Qianben Wang
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.,Duke Cancer Institute Center for Prostate and Urologic Cancers, Duke University School of Medicine, Durham, NC, 27710, USA
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20
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Chen J, Zhang R, Lan J, Lin S, Li P, Gao J, Wang Y, Xie ZJ, Li FC, Jiang SJ. IGF2BP1 Significantly Enhances Translation Efficiency of Duck Hepatitis A Virus Type 1 without Affecting Viral Replication. Biomolecules 2019; 9:biom9100594. [PMID: 31658691 PMCID: PMC6843311 DOI: 10.3390/biom9100594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/06/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023] Open
Abstract
As a disease characterized by severe liver necrosis and hemorrhage, duck viral hepatitis (DVH) is mainly caused by duck hepatitis A virus (DHAV). The positive-strand RNA genome of DHAV type 1 (DHAV-1) contains an internal ribosome entry site (IRES) element within the 5′ untranslated region (UTR), structured sequence elements within the 3′ UTR, and a poly(A) tail at the 3′ terminus. In this study, we first examined that insulin-like growth factor-2 mRNA-binding protein-1 (IGF2BP1) specifically interacted with the DHAV-1 3′ UTR by RNA pull-down assay. The interaction between IGF2BP1 and DHAV-1 3′ UTR strongly enhanced IRES-mediated translation efficiency but failed to regulate DHAV-1 replication in a duck embryo epithelial (DEE) cell line. The viral propagation of DHAV-1 strongly enhanced IGF2BP1 expression level, and viral protein accumulation was identified as the key point to this increment. Collectively, our data demonstrated the positive role of IGF2BP1 in DHAV-1 viral proteins translation and provided data support for the replication mechanism of DHAV-1.
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Affiliation(s)
- Junhao Chen
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
- College of Public Health and Management, Weifang Medical University, Weifang 261042, Shandong, China.
| | - Ruihua Zhang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, Shandong, China.
| | - Jingjing Lan
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, Shandong, China.
| | - Shaoli Lin
- Molecular Virology Laboratory, VA-MD College of Veterinary Medicine and Maryland Pathogen Research Institute, University of Maryland, College Park, MD 20742, USA.
| | - Pengfei Li
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
| | - Jiming Gao
- Department of Basic Medical Sciences, Taishan Medical College, Taian 271000, Shandong, China.
| | - Yu Wang
- Department of Basic Medical Sciences, Taishan Medical College, Taian 271000, Shandong, China.
| | - Zhi-Jing Xie
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, Shandong, China.
| | - Fu-Chang Li
- College of Animal Science and Technology, Shandong Agricultural University, Taian 271000, Shandong, China.
| | - Shi-Jin Jiang
- College of Veterinary Medicine, Shandong Agricultural University, Taian 271000, Shandong, China.
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 271000, Shandong, China.
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21
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Kumar S, Karmakar R, Garg DK, Gupta I, Patel AK. Elucidating the functional aspects of different domains of bean common mosaic virus coat protein. Virus Res 2019; 273:197755. [PMID: 31525400 DOI: 10.1016/j.virusres.2019.197755] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 10/26/2022]
Abstract
The coat protein (CP) is the only structural protein present in the polyprotein of bean common mosaic virus. The well known characteristics of the CP are self-oligomerization and nucleic acid binding activity. The studies of the coat protein mutants revealed that the oligomeric property of CP solely depends on the amino-terminal residues and the nucleic acid binding domain present at the 194-202 residue position. The 3'UTR RNA of the virus showed high binding affinity with the RNA binding domain as compared to the 5'UTR RNA. Further, the intrinsic fluorescence study of the CP also suggested that the N- and C-terminal of CP contains a highly disordered region. The present study also illustrates that the coat protein contains a conserved RNA binding pocket among the potyviruses, but displays divergent oligomerization propensities due to the difference in residue at the N- and C-terminal.
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Affiliation(s)
- Sunil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ruma Karmakar
- Centre for Rural Development and Technology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Dushyant Kumar Garg
- School of Biotechnology, Jawaharlal Nehru University, New Mehrauli Road, New Delhi, 110067, India
| | - Ishu Gupta
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ashok Kumar Patel
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, 110016, India.
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22
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Cockman EM, Narayan V, Willard B, Shetty SP, Copeland PR, Driscoll DM. Identification of the Selenoprotein S Positive UGA Recoding (SPUR) element and its position-dependent activity. RNA Biol 2019; 16:1682-1696. [PMID: 31432740 PMCID: PMC6844570 DOI: 10.1080/15476286.2019.1653681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Selenoproteins are a unique class of proteins that contain the 21st amino acid, selenocysteine (Sec). Addition of Sec into a protein is achieved by recoding of the UGA stop codon. All 25 mammalian selenoprotein mRNAs possess a 3′ UTR stem-loop structure, the Selenocysteine Insertion Sequence (SECIS), which is required for Sec incorporation. It is widely believed that the SECIS is the major RNA element that controls Sec insertion, however recent findings in our lab suggest otherwise for Selenoprotein S (SelS). Here we report that the first 91 nucleotides of the SelS 3′ UTR contain a proximal stem loop (PSL) and a conserved sequence we have named the SelS Positive UGA Recoding (SPUR) element. We developed a SelS-V5/UGA surrogate assay for UGA recoding, which was validated by mass spectrometry to be an accurate measure of Sec incorporation in cells. Using this assay, we show that point mutations in the SPUR element greatly reduce recoding in the reporter; thus, the SPUR is required for readthrough of the UGA-Sec codon. In contrast, deletion of the PSL increased Sec incorporation. This effect was reversed when the PSL was replaced with other stem-loops or an unstructured sequence, suggesting that the PSL does not play an active role in Sec insertion. Additional studies revealed that the position of the SPUR relative to the UGA-Sec codon is important for optimal UGA recoding. Our identification of the SPUR element in the SelS 3′ UTR reveals a more complex regulation of Sec incorporation than previously realized.
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Affiliation(s)
- Eric M Cockman
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Vivek Narayan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Belinda Willard
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Sumangala P Shetty
- Department of Biochemistry and Molecular Biology, Rutgers University, New Brunswick, NJ, USA
| | - Paul R Copeland
- Department of Biochemistry and Molecular Biology, Rutgers University, New Brunswick, NJ, USA
| | - Donna M Driscoll
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA.,Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, The Cleveland Clinic Foundation, Cleveland, OH, USA
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23
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Doulazmi M, Cros C, Dusart I, Trembleau A, Dubacq C. Alternative polyadenylation produces multiple 3' untranslated regions of odorant receptor mRNAs in mouse olfactory sensory neurons. BMC Genomics 2019; 20:577. [PMID: 31299892 PMCID: PMC6624953 DOI: 10.1186/s12864-019-5927-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 06/23/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Odorant receptor genes constitute the largest gene family in mammalian genomes and this family has been extensively studied in several species, but to date far less attention has been paid to the characterization of their mRNA 3' untranslated regions (3'UTRs). Given the increasing importance of UTRs in the understanding of RNA metabolism, and the growing interest in alternative polyadenylation especially in the nervous system, we aimed at identifying the alternative isoforms of odorant receptor mRNAs generated through 3'UTR variation. RESULTS We implemented a dedicated pipeline using IsoSCM instead of Cufflinks to analyze RNA-Seq data from whole olfactory mucosa of adult mice and obtained an extensive description of the 3'UTR isoforms of odorant receptor mRNAs. To validate our bioinformatics approach, we exhaustively analyzed the 3'UTR isoforms produced from 2 pilot genes, using molecular approaches including northern blot and RNA ligation mediated polyadenylation test. Comparison between datasets further validated the pipeline and confirmed the alternative polyadenylation patterns of odorant receptors. Qualitative and quantitative analyses of the annotated 3' regions demonstrate that 1) Odorant receptor 3'UTRs are longer than previously described in the literature; 2) More than 77% of odorant receptor mRNAs are subject to alternative polyadenylation, hence generating at least 2 detectable 3'UTR isoforms; 3) Splicing events in 3'UTRs are restricted to a limited subset of odorant receptor genes; and 4) Comparison between male and female data shows no sex-specific differences in odorant receptor 3'UTR isoforms. CONCLUSIONS We demonstrated for the first time that odorant receptor genes are extensively subject to alternative polyadenylation. This ground-breaking change to the landscape of 3'UTR isoforms of Olfr mRNAs opens new avenues for investigating their respective functions, especially during the differentiation of olfactory sensory neurons.
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Affiliation(s)
- Mohamed Doulazmi
- CNRS, Institut de Biologie Paris Seine, Biological adaptation and ageing, B2A, Sorbonne Université, F-75005 Paris, France
| | - Cyril Cros
- CNRS, INSERM, Institut de Biologie Paris Seine, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
- Present Address: Columbia University, New York, NY 10027 USA
| | - Isabelle Dusart
- CNRS, INSERM, Institut de Biologie Paris Seine, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Alain Trembleau
- CNRS, INSERM, Institut de Biologie Paris Seine, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
| | - Caroline Dubacq
- CNRS, INSERM, Institut de Biologie Paris Seine, Neuroscience Paris Seine, NPS, Sorbonne Université, F-75005 Paris, France
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24
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Chen M, Ji G, Fu H, Lin Q, Ye C, Ye W, Su Y, Wu X. A survey on identification and quantification of alternative polyadenylation sites from RNA-seq data. Brief Bioinform 2019; 21:1261-1276. [PMID: 31267126 DOI: 10.1093/bib/bbz068] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/03/2019] [Accepted: 05/14/2019] [Indexed: 12/13/2022] Open
Abstract
Alternative polyadenylation (APA) has been implicated to play an important role in post-transcriptional regulation by regulating mRNA abundance, stability, localization and translation, which contributes considerably to transcriptome diversity and gene expression regulation. RNA-seq has become a routine approach for transcriptome profiling, generating unprecedented data that could be used to identify and quantify APA site usage. A number of computational approaches for identifying APA sites and/or dynamic APA events from RNA-seq data have emerged in the literature, which provide valuable yet preliminary results that should be refined to yield credible guidelines for the scientific community. In this review, we provided a comprehensive overview of the status of currently available computational approaches. We also conducted objective benchmarking analysis using RNA-seq data sets from different species (human, mouse and Arabidopsis) and simulated data sets to present a systematic evaluation of 11 representative methods. Our benchmarking study showed that the overall performance of all tools investigated is moderate, reflecting that there is still lot of scope to improve the prediction of APA site or dynamic APA events from RNA-seq data. Particularly, prediction results from individual tools differ considerably, and only a limited number of predicted APA sites or genes are common among different tools. Accordingly, we attempted to give some advice on how to assess the reliability of the obtained results. We also proposed practical recommendations on the appropriate method applicable to diverse scenarios and discussed implications and future directions relevant to profiling APA from RNA-seq data.
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Affiliation(s)
- Moliang Chen
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Qianmin Lin
- Xiang' an hospital of Xiamen university, Xiamen 361005, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China
| | - Wenbin Ye
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
| | - Yaru Su
- College of Mathematics and Computer Science, Fuzhou University, Fuzhou 350116, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen 361005, China.,Xiamen Research Institute of National Center of Healthcare Big Data, Xiamen 361005, China
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25
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Xiao Q, Sun Y, Liang X, Zhang L, Onxayvieng K, Li Z, Li D. Visualizing primordial germ cell migration in embryos of rice field eel (Monopterus albus) using fluorescent protein tagged 3' untranslated regions of nanos3, dead end and vasa. Comp Biochem Physiol B Biochem Mol Biol 2019; 235:62-69. [PMID: 31176867 DOI: 10.1016/j.cbpb.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/25/2019] [Accepted: 06/03/2019] [Indexed: 11/17/2022]
Abstract
In rice field eel (Monopterus albus), germ cell development in the developing gonad has been revealed in detail. However, it is unclear how primordial germ cells (PGCs) migrate to the somatic part of the gonad (genital ridge). This study visualized PGC migration by injecting a chimeric mRNA containing a fluorescent protein fused to the 3' untranslated region (3'UTR) of three different genes, nanos3 of zebrafish (Danio rerio) and dead end (dnd) and vasa of rice field eel. The mRNAs were injected either alone or in pairs into embryos at the one-cell stage. The results showed that mRNAs containing nanos3 and dnd 3'UTRs labeled PGCs over a wider time frame than those containing vasa 3'UTR, suggesting that nanos3 and dnd 3'UTRs are suitable for visualizing PGCs in rice field eel. Using this direct visualization method, the normal migration route of PGCs was observed from the 50%-epiboly stage to hatching stage for the first time, and the ectopic PGCs were also visualized during this period in rice field eel. These findings extend our knowledge of germ cell development, and lay a foundation for further research on the relationship between PGCs and sex differentiation, and on incubation conditions for embryos in rice field eel.
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Affiliation(s)
- Qing Xiao
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Yiqing Sun
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiao Liang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Lihan Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Kommaly Onxayvieng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhong Li
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan 430223, China.
| | - Dapeng Li
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
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26
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Kraft JJ, Peterson MS, Cho SK, Wang Z, Hui A, Rakotondrafara AM, Treder K, Miller CL, Miller WA. The 3' Untranslated Region of a Plant Viral RNA Directs Efficient Cap-Independent Translation in Plant and Mammalian Systems. Pathogens 2019; 8:E28. [PMID: 30823456 DOI: 10.3390/pathogens8010028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/03/2019] [Accepted: 02/23/2019] [Indexed: 11/29/2022] Open
Abstract
Many plant viral RNA genomes lack a 5′ cap, and instead are translated via a cap-independent translation element (CITE) in the 3′ untranslated region (UTR). The panicum mosaic virus-like CITE (PTE), found in many plant viral RNAs, binds and requires the cap-binding translation initiation factor eIF4E to facilitate translation. eIF4E is structurally conserved between plants and animals, so we tested cap-independent translation efficiency of PTEs of nine plant viruses in plant and mammalian systems. The PTE from thin paspalum asymptomatic virus (TPAV) facilitated efficient cap-independent translation in wheat germ extract, rabbit reticulocyte lysate, HeLa cell lysate, and in oat and mammalian (BHK) cells. Human eIF4E bound the TPAV PTE but not a PTE that did not stimulate cap-independent translation in mammalian extracts or cells. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) footprinting revealed that both human and wheat eIF4E protected the conserved guanosine (G)-rich domain in the TPAV PTE pseudoknot. The central G plays a key role, as it was found to be required for translation and protection from SHAPE modification by eIF4E. These results provide insight on how plant viruses gain access to the host’s translational machinery, an essential step in infection, and raise the possibility that similar PTE-like mechanisms may exist in mRNAs of mammals or their viruses.
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27
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Béthune J, Jansen RP, Feldbrügge M, Zarnack K. Membrane-Associated RNA-Binding Proteins Orchestrate Organelle-Coupled Translation. Trends Cell Biol 2018; 29:178-188. [PMID: 30455121 DOI: 10.1016/j.tcb.2018.10.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/28/2018] [Accepted: 10/29/2018] [Indexed: 02/02/2023]
Abstract
Proteins are positioned and act at defined subcellular locations. This is particularly important in eukaryotic cells that deliver proteins to membrane-bound organelles such as the endoplasmic reticulum (ER), mitochondria, or endosomes. It is axiomatic that organelle targeting depends mainly on polypeptide signals. However, recent results demonstrate that targeting elements within the encoding transcripts are essential for efficient protein localisation. Key readers of these elements are membrane-associated RNA-binding proteins (memRBPs) that orchestrate organelle-coupled translation. The translation products then either cross the membrane for organelle entry or hitchhike on organelle surfaces for complex assembly and co-transport. Understanding the interaction of protein- and RNA-based targeting signals is essential to decipher the molecular basis for mutant phenotypes in disease.
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Affiliation(s)
- Julien Béthune
- Heidelberg University, Biochemistry Center, Cluster of Excellence CellNetworks, 69120 Heidelberg, Germany
| | - Ralf-Peter Jansen
- Eberhard-Karls-University Tübingen, Interfaculty Institute of Biochemistry, Hoppe-Seyler-Straße 4, 72076 Tübingen, Germany
| | - Michael Feldbrügge
- Heinrich-Heine University Düsseldorf, Institute for Microbiology, Cluster of Excellence on Plant Sciences, 40204 Düsseldorf, Germany.
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.
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28
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Wang L, Hu X, Wang P, Shao ZM. Integrative 3' Untranslated Region-Based Model to Identify Patients with Low Risk of Axillary Lymph Node Metastasis in Operable Triple-Negative Breast Cancer. Oncologist 2018; 24:22-30. [PMID: 30082491 DOI: 10.1634/theoncologist.2017-0609] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/09/2018] [Accepted: 05/16/2018] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Sentinel lymph node biopsy is the standard surgical staging approach for operable triple-negative breast cancer (TNBC) with clinically negative axillae. In this study, we sought to develop a model to predict TNBC patients with negative nodal involvement, who would benefit from the exemption of the axillary staging surgery. MATERIALS AND METHODS We evaluated 3' untranslated region (3'UTR) profiles using microarray data of TNBC from two Gene Expression Omnibus datasets. Samples from GSE31519 were divided into training set (n = 164) and validation set (n = 163), and GSE76275 was used to construct testing set (n = 164). We built a six-member 3'UTR panel (ADD2, COL1A1, APOL2, IL21R, PKP2, and EIF4G3) using an elastic net model to estimate the risk of lymph node metastasis (LNM). Receiver operating characteristic and logistic analyses were used to assess the association between the panel and LNM status. RESULTS The six-member 3'UTR-panel showed a high distinguishing power with an area under the curve of 0.712, 0.729, and 0.708 in the training, validation, and testing sets, respectively. After adjustment by tumor size, the 3'UTR panel retained significant predictive power in the training, validation, and testing sets (odds ratio = 4.93, 4.58, and 3.59, respectively; p < .05 for all). A combinatorial analysis of the 3'UTR panel and tumor size yielded an accuracy of 97.2%, 100%, and 100% in training, validation, and testing set, respectively. CONCLUSION This study established an integrative 3'UTR-based model as a promising predictor for nodal negativity in operable TNBC. Although a prospective study is needed to validate the model, our results may permit a no axillary surgery option for selected patients. IMPLICATIONS FOR PRACTICE Currently, sentinel lymph node biopsy is the standard approach for surgical staging in breast cancer patients with negative axillae. Prediction estimation for lymph node metastasis of breast cancer relies on clinicopathological characteristics, which is unreliable, especially in triple-negative breast cancer (TNBC)-a highly heterogeneous disease. The authors developed and validated an effective prediction model for the lymph node status of patients with TNBC, which integrates 3'UTR markers and tumor size. This is the first 3'UTR-based model that will help identify TNBC patients with low risk of nodal involvement who are most likely to benefit from exemption axillary surgery.
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Affiliation(s)
- Lei Wang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Xin Hu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
| | - Peng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, People's Republic of China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, People's Republic of China
- Institutes of Biomedical Sciences, Fudan University, Shanghai, People's Republic of China
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29
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Wang L, Hu X, Wang P, Shao ZM. The 3'UTR signature defines a highly metastatic subgroup of triple-negative breast cancer. Oncotarget 2016; 7:59834-44. [PMID: 27494850 DOI: 10.18632/oncotarget.10975] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 07/18/2016] [Indexed: 01/13/2023] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly heterogeneous disease with an aggressive clinical course. Prognostic models are needed to chart potential patient outcomes. To address this, we used alternative 3′UTR patterns to improve postoperative risk stratification. We collected 327 publicly available microarrays and generated the 3′UTR landscape based on expression ratios of alternative 3′UTR. After initial feature filtering, we built a 17-3′UTR-based classifier using an elastic net model. Time-dependent ROC comparisons and Kaplan–Meier analyses confirmed an outstanding discriminating power of our prognostic model for TNBC patients. In the training cohort, 5-year event-free survival (EFS) was 78.6% (95% CI 71.2–86.0) for the low-risk group, and 16.3% (95% CI 2.3–30.4) for the high-risk group (log-rank p<0.0001; hazard ratio [HR] 8.29, 95% CI 4.78–14.4), In the validation set, 5-year EFS was 75.6% (95% CI 68.0–83.2) for the low-risk group, and 33.2% (95% CI 17.1–49.3) for the high-risk group (log-rank p<0.0001; HR 3.17, 95% CI 1.66–5.42). In conclusion, the 17-3′UTR-based classifier provides a superior prognostic performance for estimating disease recurrence and metastasis in TNBC patients and it may permit personalized management strategies.
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Abstract
Cellular mRNA levels are determined by the competing forces of transcription and decay. A wide array of cellular mRNA decay pathways carry out RNA turnover either on a constitutive basis or in response to changing cellular conditions. Here, we outline a method to investigate mRNA decay that employs RNAi knockdown of known or putative decay factors in commercially available Tet-off cell systems. Reporter mRNAs of interest are expressed under the control of a tetracycline-regulated promoter, allowing pulse-chase mRNA decay assays to be conducted. Levels of reporter and constitutively expressed control RNAs throughout the decay assay time course are detected by traditional northern blot analysis and used to calculate mRNA half-lives. We describe the utility of this approach to study nonsense-mediated mRNA decay substrates and factors, but it can be readily adapted to investigate key mechanistic features that dictate the specificity and functions of any mRNA decay pathway.
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Affiliation(s)
- Thomas D Baird
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - J Robert Hogg
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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31
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Kresoja-Rakic J, Sulemani M, Kirschner MB, Ronner M, Reid G, Kao S, Schwaller B, Weder W, Stahel RA, Felley-Bosco E. Posttranscriptional Regulation Controls Calretinin Expression in Malignant Pleural Mesothelioma. Front Genet 2017; 8:70. [PMID: 28611824 PMCID: PMC5447031 DOI: 10.3389/fgene.2017.00070] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/12/2017] [Indexed: 01/08/2023] Open
Abstract
Calretinin (CALB2) is a diagnostic and prognostic marker in malignant pleural mesothelioma (MPM). We previously reported that calretinin expression is regulated at the mRNA level. The presence of a medium-sized (573 nucleotide) 3' untranslated region (3'UTR) predicted to contain binding sites for miR-30a/b/c/d/e and miR-9 as well as an adenine/uridine-rich element (ARE) in all three transcripts arising from the CALB2 gene, suggests that calretinin expression is regulated via posttranscriptional mechanisms. Our aim was to investigate the role of the CALB2-3'UTR in the posttranscriptional regulation of calretinin expression in MPM. CALB2-3'UTR was inserted downstream of the luciferase reporter gene using pmiRGLO vector and reporter expression was determined after transfection into MPM cells. Targeted mutagenesis was used to generate variants harboring mutated miR-30 family and ARE binding sites. Electrophoretic mobility shift assay was used to test for the presence of ARE binding proteins. CALB2-3'UTR significantly decreased luciferase activity in MPM cells. Analysis of mutation in the ARE site revealed a further destabilization of the reporter and human antigen R (HuR) binding to the ARE sequence was detected. The mutation of two miR-30 binding sites abolished CALB2-3'UTR destabilization effect; a transient delivery of miR-30e-5p mimics or anti-miR into MPM cells resulted in a significant decrease/increase of the luciferase reporter expression and calretinin protein, respectively. Moreover, overexpression of CALB2-3'UTR quenched the effect of miR-30e-5p mimics on calretinin protein levels, possibly by sequestering the mimics, thereby suggesting a competitive endogenous RNA network. Finally, by data mining we observed that expression of miR-30e-5p was negatively correlated with the calretinin expression in a cohort of MPM patient samples. Our data show the role of (1) adenine-uridine (AU)-binding proteins in calretinin stabilization and (2) miR-30e-5p in the posttranscriptional negative regulation of calretinin expression via interaction with its 3'UTR. Furthermore, our study demonstrates a possible physiological role of calretinin's alternatively spliced transcripts.
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Affiliation(s)
- Jelena Kresoja-Rakic
- Laboratory of Molecular Oncology, Division of Thoracic SurgeryUniversity Hospital Zurich, Switzerland
| | - Merve Sulemani
- Laboratory of Molecular Oncology, Division of Thoracic SurgeryUniversity Hospital Zurich, Switzerland
| | | | - Manuel Ronner
- Laboratory of Molecular Oncology, Division of Thoracic SurgeryUniversity Hospital Zurich, Switzerland
| | - Glen Reid
- Asbestos Diseases Research Institute, SydneyNSW, Australia.,School of Medicine, The University of Sydney, SydneyNSW, Australia
| | - Steven Kao
- Asbestos Diseases Research Institute, SydneyNSW, Australia.,School of Medicine, The University of Sydney, SydneyNSW, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, SydneyNSW, Australia
| | - Beat Schwaller
- Department of Medicine, Anatomy, University of FribourgFribourg, Switzerland
| | - Walter Weder
- Division of Thoracic SurgeryUniversity Hospital Zurich, Switzerland
| | - Rolf A Stahel
- Clinic for OncologyUniversity Hospital Zurich, Zurich
| | - Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Division of Thoracic SurgeryUniversity Hospital Zurich, Switzerland
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32
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Tamburino AM, Kaymak E, Shrestha S, Holdorf AD, Ryder SP, Walhout AJM. PRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions. ACTA ACUST UNITED AC 2017; 5:e1295130. [PMID: 28702278 DOI: 10.1080/21690731.2017.1295130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 01/23/2017] [Accepted: 02/09/2017] [Indexed: 12/20/2022]
Abstract
Interactions between RNA binding proteins (RBPs) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest-in a 'gene-centered' manner-yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA 'bait' can be tested versus multiple RBP 'preys' in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-length Caenorhabditis elegans 3' UTRs. PRIMA faithfully recapitulated numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmed in vivo. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.
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Affiliation(s)
- Alex M Tamburino
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Ebru Kaymak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Shaleen Shrestha
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Amy D Holdorf
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Sean P Ryder
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Albertha J M Walhout
- Program in Systems Biology and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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Zambra FMB, Biolchi V, de Cerqueira CCS, Brum IS, Castelli EC, Chies JAB. Immunogenetics of prostate cancer and benign hyperplasia--the potential use of an HLA-G variant as a tag SNP for prostate cancer risk. HLA 2016; 87:79-88. [PMID: 26889902 DOI: 10.1111/tan.12741] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 01/06/2016] [Accepted: 01/13/2016] [Indexed: 12/14/2022]
Abstract
Human leukocyte antigen G (HLA-G) is an immunomodulatory molecule with important roles both physiologically as well as an escape mechanism of cancer cells. In this study, we evaluated the impact of eight polymorphisms at the 3' untranslated region (3'UTR) of the HLA-G gene in the development of prostate cancer (PCa) and benign prostatic hyperplasia (BPH). A total of 468 DNA samples of Brazilian men predominantly Euro-descendant with PCa (N = 187), BPH (N = 152) and healthy control individuals (N = 129) were evaluated. The HLA-G 3'UTR region was amplified by polymerase chain reaction (PCR), sequenced and genotyped to identify the 14 bp insertion/deletion (rs371194629), +3003T/C (rs1707), +3010C/G (rs1710), +3027A/C (rs17179101), +3035C/T (rs17179108), +3142G/C (rs1063320), +3187A/G (rs9380142) and +3196C/G (rs1610696) polymorphisms. Regression logistic and chi-square tests were performed to verify the influence of single nucleotide polymorphisms (SNPs) in PCa and/or BPH susceptibility, as well as in PCa progression (clinicopathological status). Our data showed the UTR-4 haplotype as a risk factor to PCa in comparison with control [odds ratio (OR) 2.35, 95% confidence interval (CI) 1.39-3.96, P adjusted = 0.003) and BPH groups (OR 1.82, 95% CI 1.15-2.86, P adjusted = 0.030). Further, the 'non-14bp Ins_ + 3142G_+3187A' haplotype (OR 1.56, 95% CI 1.10-2.20, P adjusted = 0.036), the +3003CT genotype (OR 4.44, 95% CI 1.33-4.50, P adjusted = 0.032) and the +3003C allele (OR 2.33, 95% CI 1.38-3.92, P adjusted = 0.016) also conferred susceptibility to PCa. Our data suggest an important influence of HLA-G 3'UTR polymorphisms in PCa susceptibility and support the use of the +3003 variant as a tag SNP for PCa risk.
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Affiliation(s)
- F M B Zambra
- Department of Genetics, Instituto de Biociências, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - V Biolchi
- Centro de Ciências Biológicas e da Saúde, Centro Universitário Univates, Lajeado, RS, Brazil
| | - C C S de Cerqueira
- Consejo Nacional de Investigaciones Científicas y Tecnicas, Centro Nacional Patagonico, Puerto Madryn, Chubut, Argentina
| | - I S Brum
- Department of Physiology, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - E C Castelli
- Department of Pathology, Faculdade de Medicina de Botucatu, Universidade Estadual Paulista - UNESP, Botucatu, SP, Brazil
| | - J A B Chies
- Department of Genetics, Instituto de Biociências, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
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Egeli U, Ak S, Cecener G, Tunca B, Tezcan G, Sevinc ED, Kaya E, Dundar HZ, Sarkut P, Ozen Y, Balcin O, Evrensel T, Yerci O, Ugras N. Impact of 3'UTR variation patterns of the KRAS gene on the aggressiveness of pancreatobiliary tumors with the KRAS G13D mutation in a Turkish population. Pancreatology 2016; 16:677-86. [PMID: 27256640 DOI: 10.1016/j.pan.2016.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/26/2016] [Accepted: 05/20/2016] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Several studies have demonstrated the importance of mutations in codons 12, 13 and 61 and variations in the 3' untranslated region (3'UTR) of the KRAS gene, frequently observed genetic events in the progression of pancreatobiliary tumors (PBT). However, limited data exist on the clinical effect of these alterations. The aim of the current study was to clarify the frequency of relevant alterations of the 3'UTR regions of the KRAS gene and the effect of KRAS 3'UTR polymorphisms on the prognosis of patients with codon 12, 13 and 61 mutations in a Turkish population with PBT. METHODS Codons 12, 13, and 61 and 3'UTRs of the KRAS gene were screened by single-strand conformation polymorphism (SSCP) analysis and DNA sequencing in 43 patients and 10 controls. Chi-squared and independent sample T tests were used to evaluate the results of the mutation analysis and clinical features of the patients. RESULTS We defined the c.38G > A (rs112445441, p.G13D) (39.54%) mutation and two 3'UTR variations, c.*4066delA (rs560890523) (23.26%) and c.*4065_*4066delAA (rs57698689) (6.98%), in the KRAS gene of Turkish patients. There was a statistically significant relationship between the c.*4066delA (rs560890523) and c.*4065_*4066delAA (rs57698689) variations and invasion and lymph node metastasis status of the patients (p < 0.001). Compared to patients with c.38G > A (rs112445441, p.G13D), patients with c.*4066delA (rs560890523) and c.38G > A (rs112445441, p.G13D) presented more aggressive tumors with highly invasive features. The present study contributes findings regarding the clinical effects of KRAS alterations in PBT. Based on our study, further investigations are required.
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Affiliation(s)
- Unal Egeli
- Department of Medical Biology, Medical Faculty, Uludag University, Bursa, Turkey.
| | - Secil Ak
- Department of Medical Biology, Medical Faculty, Uludag University, Bursa, Turkey
| | - Gulsah Cecener
- Department of Medical Biology, Medical Faculty, Uludag University, Bursa, Turkey
| | - Berrin Tunca
- Department of Medical Biology, Medical Faculty, Uludag University, Bursa, Turkey
| | - Gulcin Tezcan
- Department of Medical Biology, Medical Faculty, Uludag University, Bursa, Turkey
| | | | - Ekrem Kaya
- Department of General Surgery, Medical Faculty, Uludag University, Bursa, Turkey
| | - Halit Ziya Dundar
- Department of General Surgery, Medical Faculty, Uludag University, Bursa, Turkey
| | - Pinar Sarkut
- Department of General Surgery, Medical Faculty, Uludag University, Bursa, Turkey
| | - Yilmaz Ozen
- Department of General Surgery, Medical Faculty, Uludag University, Bursa, Turkey
| | - Ozkan Balcin
- Department of General Surgery, Medical Faculty, Uludag University, Bursa, Turkey
| | - Turkkan Evrensel
- Department of Medical Oncology, Medical Faculty, Uludag University, Bursa, Turkey
| | - Omer Yerci
- Department of Pathology, Medical Faculty, Uludag University, Bursa, Turkey
| | - Nesrin Ugras
- Department of Pathology, Medical Faculty, Uludag University, Bursa, Turkey
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Caminsky NG, Mucaki EJ, Perri AM, Lu R, Knoll JHM, Rogan PK. Prioritizing Variants in Complete Hereditary Breast and Ovarian Cancer Genes in Patients Lacking Known BRCA Mutations. Hum Mutat 2016; 37:640-52. [PMID: 26898890 DOI: 10.1002/humu.22972] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 01/22/2016] [Accepted: 02/16/2016] [Indexed: 12/11/2022]
Abstract
BRCA1 and BRCA2 testing for hereditary breast and ovarian cancer (HBOC) does not identify all pathogenic variants. Sequencing of 20 complete genes in HBOC patients with uninformative test results (N = 287), including noncoding and flanking sequences of ATM, BARD1, BRCA1, BRCA2, CDH1, CHEK2, EPCAM, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD51B, STK11, TP53, and XRCC2, identified 38,372 unique variants. We apply information theory (IT) to predict and prioritize noncoding variants of uncertain significance in regulatory, coding, and intronic regions based on changes in binding sites in these genes. Besides mRNA splicing, IT provides a common framework to evaluate potential affinity changes in transcription factor (TFBSs), splicing regulatory (SRBSs), and RNA-binding protein (RBBSs) binding sites following mutation. We prioritized variants affecting the strengths of 10 splice sites (four natural, six cryptic), 148 SRBS, 36 TFBS, and 31 RBBS. Three variants were also prioritized based on their predicted effects on mRNA secondary (2°) structure and 17 for pseudoexon activation. Additionally, four frameshift, two in-frame deletions, and five stop-gain mutations were identified. When combined with pedigree information, complete gene sequence analysis can focus attention on a limited set of variants in a wide spectrum of functional mutation types for downstream functional and co-segregation analysis.
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Affiliation(s)
- Natasha G Caminsky
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Eliseos J Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ami M Perri
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Ruipeng Lu
- Department of Computer Science, Faculty of Science, Western University, London, Ontario, Canada
| | - Joan H M Knoll
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Cytognomix Inc, London, Ontario, Canada
| | - Peter K Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada.,Department of Computer Science, Faculty of Science, Western University, London, Ontario, Canada.,Cytognomix Inc, London, Ontario, Canada.,Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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Abstract
High levels of the pro-inflammatory cytokine tumour necrosis factor (TNF) have been associated with many diseases including rheumatoid arthritis (RA), ankylosing spondylitis (AS), inflammatory bowel disease (IBD) and psoriasis. Although it has been clear for twenty-five years that TNF plays a major role in RA and AS, two major questions remain unanswered: (1) What mechanism underlies the loss of control of TNF levels in patients? (2) How does TNF exert its detrimental effects? Nonetheless, biological anti-TNF drugs have become the most successful treatment of these conditions with a third of patients entering remission, and the global market for biological TNF inhibitors is now estimated at around US$35 billions. However, their use is limited by their cost, the fact that they need to be injected, non-negligible side effects and the development of resistance due to the protein (thus antigenic) nature of these TNF inhibitors. It looks inevitable that new approaches to lower the amount of TNF should be considered. To do this, a better understanding of the regulation of TNF expression is necessary.
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Affiliation(s)
- Derek Lacey
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Philippe Bouillet
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3052, Australia.
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Chen HH, Keyhanian K, Zhou X, Vilmundarson RO, Almontashiri NAM, Cruz SA, Pandey NR, Lerma Yap N, Ho T, Stewart CA, Huang H, Hari A, Geoffrion M, McPherson R, Rayner KJ, Stewart AFR. IRF2BP2 Reduces Macrophage Inflammation and Susceptibility to Atherosclerosis. Circ Res 2015. [PMID: 26195219 DOI: 10.1161/circresaha.114.305777] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RATIONALE Inflammation impairs macrophage cholesterol clearance from vascular tissues and promotes atherosclerosis. Inflammatory macrophages suppress expression of the transcription cofactor interferon regulatory factor 2-binding protein 2 (IRF2BP2), and genetic variants near IRF2BP2 associate with ischemic heart disease progression in humans. OBJECTIVES To test whether IRF2BP2 in macrophages affects atherosclerosis in mice and humans. METHODS AND RESULTS We generated mice that delete IRF2BP2 in macrophages. IRF2BP2-deficient macrophages worsened atherosclerosis in irradiated low-density lipoprotein receptor null-recipient mice and in apolipoprotein E null mice. IRF2BP2-deficient macrophages were inflammatory and had impaired cholesterol efflux because of their inability to activate the cholesterol transporter ABCA1 in response to cholesterol loading. Their expression of the anti-inflammatory transcription factor Krüppel-like factor 2 was markedly reduced. Promoter studies revealed that IRF2BP2 is required for MEF2-dependent activation of Krüppel-like factor 2. Importantly, restoring Krüppel-like factor 2 in IRF2BP2-deficient macrophages attenuated M1 inflammatory and rescued M2 anti-inflammatory gene activation and improved the cholesterol efflux deficit by restoring ABCA1 activation in response to cholesterol loading. In a cohort of 1066 angiographic cases and 1011 controls, homozygous carriers of a deletion polymorphism (rs3045215) in the 3' untranslated region sequence of human IRF2BP2 mRNA had a higher risk of coronary artery disease (recessive model, odds ratio [95% confidence interval]=1.560 [1.179-2.065], P=1.73E-03) and had lower IRF2BP2 (and Krüppel-like factor 2) protein levels in peripheral blood mononuclear cells. The effect of this deletion polymorphism to suppress protein expression was confirmed in luciferase reporter studies. CONCLUSION Ablation of IRF2BP2 in macrophages worsens atherosclerosis in mice, and a deletion variant that lowers IRF2BP2 expression predisposes to coronary artery disease in humans.
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Affiliation(s)
- Hsiao-Huei Chen
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.).
| | - Kianoosh Keyhanian
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Xun Zhou
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Ragnar O Vilmundarson
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Naif A M Almontashiri
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Shelly A Cruz
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Nihar R Pandey
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Nida Lerma Yap
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Tiffany Ho
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Chloe A Stewart
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Hua Huang
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Aswin Hari
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Michele Geoffrion
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Ruth McPherson
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Katey J Rayner
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.)
| | - Alexandre F R Stewart
- From the Department of Cellular and Molecular Medicine, University of Ottawa, and the Ottawa Hospital Research Institute, Ottawa, Ontario, Canada (H.-H.C., K.K., X.Z., S.A.C., N.R.P., C.A.S., H.H., A.H.); the Department of Biochemistry, Microbiology and Immunology, University of Ottawa, and the University of Ottawa Heart Institute, Ottawa, Ontario, Canada (R.O.V., N.A.M.A., N.L.Y., T.H., M.G., R.M., K.J.R., A.F.R.S.); and Department of Medicine, University of Ottawa, Ottawa, Ontario, Canada (H.H.C., R.M., A.F.R.S.).
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Clarke BD, Roby JA, Slonchak A, Khromykh AA. Functional non-coding RNAs derived from the flavivirus 3' untranslated region. Virus Res 2015; 206:53-61. [PMID: 25660582 DOI: 10.1016/j.virusres.2015.01.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/28/2015] [Accepted: 01/29/2015] [Indexed: 12/25/2022]
Abstract
Flaviviruses are single-stranded positive sense RNA enveloped viruses. The flavivirus genus includes important human pathogens such as dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), Japanese encephalitis virus (JEV), tick-borne encephalitis virus (TBEV), and Murray Valley encephalitis virus (MVEV). In addition to the viral proteins and viral genomic RNA, flaviviruses produce at least two functional non-coding RNAs derived from the 3' untranslated region (3'UTR), the subgenomic flavivirus RNA (sfRNA) and a putative WNV miRNA (KUN-miR-1). In this review we summarize published data from studies with WNV, YFV, DENV, JEV, and MVEV on sfRNA production following incomplete degradation of the viral genomic RNA by the cellular 5'-3' exoribonuclease 1 (XRN1), RNA structural elements involved in stalling XRN1 to generate sfRNA, and functions of sfRNA in modulating cellular mRNA decay and RNAi pathways as well as in modulating anti-viral type I interferon response. In addition, we also summarize data on the mechanisms of biogenesis of 3'UTR-derived KUN-miR-1 and its function in WNV replication in mosquito host, along with recent findings on a discovery of a second potential flaviviral miRNA vsRNA5, derived from the 3'UTR of DENV. This review thus summarizes the known mechanisms of generation and the functions of flaviviral 3'UTR-derived non-coding RNAs.
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Affiliation(s)
- B D Clarke
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - J A Roby
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - A Slonchak
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - A A Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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Abstract
Polyadenylation is the RNA processing step that completes the maturation of nearly all eukaryotic mRNAs. It is a two-step nuclear process that involves an endonucleolytic cleavage of the pre-mRNA at the 3'-end and the polymerization of a polyadenosine (polyA) tail, which is fundamental for mRNA stability, nuclear export and efficient translation during development. The core molecular machinery responsible for the definition of a polyA site includes several recognition, cleavage and polyadenylation factors that identify and act on a given polyA signal present in a pre-mRNA, usually an AAUAAA hexamer or similar sequence. This mechanism is tightly regulated by other cis-acting elements and trans-acting factors, and its misregulation can cause inefficient gene expression and may ultimately lead to disease. The majority of genes generate multiple mRNAs as a result of alternative polyadenylation in the 3'-untranslated region. The variable lengths of the 3' untranslated regions created by alternative polyadenylation are a recognizable target for differential regulation and clearly affect the fate of the transcript, ultimately modulating the expression of the gene. Over the past few years, several studies have highlighted the importance of polyadenylation and alternative polyadenylation in gene expression and their impact in a variety of physiological conditions, as well as in several illnesses. Abnormalities in the 3'-end processing mechanisms thus represent a common feature among many oncological, immunological, neurological and hematological disorders, but slight imbalances can lead to the natural establishment of a specific cellular state. This review addresses the key steps of polyadenylation and alternative polyadenylation in different cellular conditions and diseases focusing on the molecular effectors that ensure a faultless pre-mRNA 3' end formation.
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Key Words
- 3′ untranslated region
- 3′READS, 3′ Region Extraction and Deep Sequencing
- AD, Alzheimer disease
- APA, Alternative polyadenylation
- AREs, Au-rich elements
- BPV, bovine papilloma virus
- CAH, congenital adrenal hyperplasia
- CFIm25, Cleavage Factor Im 25 kDa
- COX-2, cyclooxygenase 2
- CPSF, Cleavage and Polyadenylation Specificity Factor
- CSTF2, cleavage stimulatory factor-64kDa
- DMKN, dermokine
- DSE, downstream sequence element
- ESC, embryonic stem cells
- FMR1, Fragil X mental retardation 1
- FOXP3, forkhead box P3
- FXPOI, fragile X-associated immature ovarian insufficiency
- FXS, Fragile X syndrome
- FXTAS, fragile X-associated tremor/ataxia syndrome
- HGRG-14, high-glucose-regulated gene
- IMP-1, Insulin-like growth factor 2 mRNA binding protein 1
- IPEX, immune dysfunction, polyendocrinopathy, enteropathy, X-linked
- LPS, lipopolysaccharide
- OPMD, oculopharyngeal muscular dystrophy
- PABPN1, poly(A) binding protein
- PAP, polyA polymerase
- PAS, polyA site
- PD, Parkinson disease
- PDXK, pyridoxal kinase
- PPIE, peptidylpropylisomerase E
- RBP, RNA-binding protein
- RNA Pol II, RNA polymerase II
- SLE, systemic lupus erythematosus
- SMA, Spinal Muscular Atrophy
- SMN, Survival Motor Neuron
- SNP, single nucleotide polymorphism
- StAR, steroigogenic acute regulatory
- TCF/LEF, T cell factor/lymphoid enhancer factor.
- TCF7L2, transcription factor 7-like 2
- TCR, T cell receptor
- TLI, tandem UTR length index
- TNF-α, tumor necrosis factor-α
- USE, upstream sequence element
- UTR, untranslated region
- WAS, Wiskott-Aldrich syndrome
- WASP, Wiskott-Aldrich syndrome protein
- aSyn, α-Synuclein
- aSynL, longest aSyn isoform
- alternative polyadenylation
- cell state
- disease
- gene expression
- miRNA, microRNA
- nuclear 1
- pA signal, polyA signal
- pA tail, polyA tail
- polyadenylation
- siRNAs, small interfering RNAs
- snRNPs, spliceosomal small nuclear ribonucleoproteins
- α-GalA, α-galactosidase A
- μ, IgM heavy-chain mRNA
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Affiliation(s)
- Ana Curinha
- a Gene Regulation Group; IBMC-Instituto de Biologia Molecular e Celular ; Universidade do Porto ; Porto , Portugal
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Grindheim AK, Hollås H, Ramirez J, Saraste J, Travé G, Vedeler A. Effect of serine phosphorylation and Ser25 phospho-mimicking mutations on nuclear localisation and ligand interactions of annexin A2. J Mol Biol 2014; 426:2486-99. [PMID: 24780253 DOI: 10.1016/j.jmb.2014.04.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 04/09/2014] [Accepted: 04/19/2014] [Indexed: 11/19/2022]
Abstract
Annexin A2 (AnxA2) interacts with numerous ligands, including calcium, lipids, mRNAs and intracellular and extracellular proteins. Different post-translational modifications participate in the discrimination of the functions of AnxA2 by modulating its ligand interactions. Here, phospho-mimicking mutants (AnxA2-S25E and AnxA2-S25D) were employed to investigate the effects of Ser25 phosphorylation on the structure and function of AnxA2 by using AnxA2-S25A as a control. The overall α-helical structure of AnxA2 is not affected by the mutations, since the thermal stabilities and aggregation tendencies of the mutants differ only slightly from the wild-type (wt) protein. Unlike wt AnxA2, all mutants bind the anxA2 3' untranslated region and β-γ-G-actin with high affinity in a Ca(2+)-independent manner. AnxA2-S25E is not targeted to the nucleus in transfected PC12 cells. In vitro phosphorylation of AnxA2 by protein kinase C increases its affinity to mRNA and inhibits its nuclear localisation, in accordance with the data obtained with the phospho-mimicking mutants. Ca(2+)-dependent binding of wt AnxA2 to phosphatidylinositol, phosphatidylinositol-3-phosphate, phosphatidylinositol-4-phosphate and phosphatidylinositol-5-phosphate, as well as weaker but still Ca(2+)-dependent binding to phosphatidylserine and phosphatidylinositol-3,5-bisphosphate, was demonstrated by a protein-lipid overlay assay, whereas binding of AnxA2 to these lipids, as well as its binding to liposomes, is inhibited by the Ser25 mutations. Thus, introduction of a modification (mutation or phosphorylation) at Ser25 appears to induce a conformational change leading to increased accessibility of the mRNA- and G-actin-binding sites in domain IV independent of Ca(2+) levels, while the Ca(2+)-dependent binding of AnxA2 to phospholipids is attenuated.
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Affiliation(s)
- Ann Kari Grindheim
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; Molecular Imaging Center (MIC), University of Bergen, N-5009 Bergen, Norway
| | - Hanne Hollås
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway
| | - Juan Ramirez
- Biotechnologie et Signalisation Cellulaire UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France
| | - Jaakko Saraste
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway; Molecular Imaging Center (MIC), University of Bergen, N-5009 Bergen, Norway
| | - Gilles Travé
- Biotechnologie et Signalisation Cellulaire UMR 7242, Ecole Supérieure de Biotechnologie de Strasbourg, F-67412 Illkirch, France
| | - Anni Vedeler
- Department of Biomedicine, University of Bergen, N-5009 Bergen, Norway.
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Abstract
The 3' UTR of insulin has been identified as a critical region that confers mRNA stability, which is crucial for promoting transcription in response to glucose challenge. miRNAs are endogenously encoded non-coding RNAs that function as regulators of gene expression. This regulatory function is generally mediated by complementary binding to the 3'UTR of its mRNA targets that affects subsequent translational process. Genes involved in the regulation of glucose homeostasis, particularly in insulin production, have been found as targets of several miRNAs. Yet, no direct miRNA-based regulators of insulin biosynthesis have been identified. In this study, identification of possible miRNA-based regulators of insulin production is explored. Members of a miRNA family, miR-25 and miR-92a, are found as direct modulators of insulin expression. Overexpression of miR-25 or miR-92a reduced insulin expression while inhibition of miR-25 and miR-92a expression using corresponding antagomiRs promoted insulin expression and ultimately enhanced glucose-induced insulin secretion. Furthermore, suppression of insulin secretion by pre miR-9 could be attenuated by treatment with anti-miR-25 or miR-92a. Interestingly, we found the binding site of miR-25 and miR-92a to overlap with that of PTBP1, an important RNA binding molecule that stabilizes insulin mRNA for translation. Despite the increase in PTBP1 protein in the pancreas of diabetic rats, we observed insulin expression to be reduced alongside upregulation of miR-25 and miR-92a, suggesting an intricate regulation of insulin (bio)synthesis at its mRNA level.
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Affiliation(s)
- Dwi Setyowati Karolina
- Department of Biochemistry; Yong Loo Lin School of Medicine; National University Health System; Singapore
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Abstract
OBJECTIVE Brown adipose tissue (BAT) produces heat using chemical energy of lipids and glucose, a function induced by cold exposure or diet. The brown adipogenesis is tightly controlled in a coordinated interplay between several transcriptional factors. It is not known what enables and coordinates this robust program of concerted cooperation between the transcriptional factors and co-regulators necessary for the brown adipogenesis. MATERIALS/METHODS A. In vivo studies--we investigated the expression levels of miR-27a and b in mice after cold exposure. B. Using gene expression and functional studies together with high throughput imaging in primary preadipocytes, and cell culture models, we investigated the role of miR-27 in beige and brown adipogenesis. C. Using gene silencing and rescue experiments we dissected the molecular mechanisms of the miR-27 action. RESULTS After cold exposure, miR-27 is downregulated in BAT and subcutaneous white adipose tissue (SAT). MiR-27 is also downregulated during brown adipogenesis of primary preadipocytes in vitro, and it directly targets and negatively regulates the essential components of the brown transcriptional network: Prdm16, Pparα, Creb, and in part Pgc1β. Together with its direct effect on Pparγ, and indirect on Pgc1α, mir-27 decreases brown differentiation of cultured cells and of primary SAT preadipocytes. CONCLUSIONS Our results point to miR-27 as a central upstream regulator of the transcriptional network involved in beige and brown adipogenesis after cold exposure, and suggest miR-27 inhibition as a novel therapeutic approach for metabolic diseases aiming at increasing the beige/brown fat mass.
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Affiliation(s)
- Lei Sun
- Duke-NUS Medical School Singapore, 8 College Rd, 169857, Singapore; Institute of Molecular and Cell Biology (IMCB), Agency for Science,Technology and Research, 61 Biopolis Drive, 138673, Singapore
| | - Mirko Trajkovski
- University of Geneva, Medical Faculty, Department of Cell Physiology and Metabolism, Centre Médical Universitaire (CMU), 1211 Geneva 4, Switzerland; University College London (UCL), Division of Biosciences, School of Life and Medical Sciences, Institute of Structural and Molecular Biology, Darwin Building, Gower Street, WC1E 6BT, London, UK.
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Crowley EH, Arena S, Lamba S, Di Nicolantonio F, Bardelli A. Targeted knock-in of the polymorphism rs61764370 does not affect KRAS expression but reduces let-7 levels. Hum Mutat 2013; 35:208-14. [PMID: 24282149 DOI: 10.1002/humu.22487] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 11/21/2013] [Indexed: 01/02/2023]
Abstract
Understanding the role of single-nucleotide polymorphisms (SNPs) in the pathological process represents a unique experimental challenge especially when the variants occur outside of coding regions. The noncoding SNP rs61764370 located in the 3'-untranslated region of Kirsten rat sarcoma viral oncogene homolog (KRAS) has been implicated as a risk factor for the development of cancer and the response to targeted therapies. This cancer-associated variant is thought to affect the binding of the microRNA let-7, which allegedly modulates KRAS expression. Using site-specific homologous recombination, we inserted the rs61764370:T>G KRAS gene variant in the colorectal cancer cell line SW48 (SW48 +SNP) and assessed the cellular and biochemical phenotype. We observed a significant increase in cellular proliferation, as well as a reduction in the levels of the microRNA let-7a, let-7b, and let-7c. Transcriptional and biochemical analysis showed no concomitant change in the KRAS protein expression or modulation of the downstream mitogen activated kinase or PI3K/AKT signaling. These results suggest that the cancer-associated rs61764370 variant exerts a biological effect not through transcriptional modulation of KRAS but rather by tuning the expression of the microRNA let-7.
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Zhang Y, Yang L, Gao YF, Fan ZM, Cai XY, Liu MY, Guo XR, Gao CL, Xia ZK. MicroRNA-106b induces mitochondrial dysfunction and insulin resistance in C2C12 myotubes by targeting mitofusin-2. Mol Cell Endocrinol 2013; 381:230-40. [PMID: 23954742 DOI: 10.1016/j.mce.2013.08.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 08/01/2013] [Accepted: 08/05/2013] [Indexed: 11/16/2022]
Abstract
MicroRNA-106b (miR-106b) is reported to correlate closely with skeletal muscle insulin resistance and type 2 diabetes. The aim of this study was to identify an mRNA targeted by miR-106b which regulates skeletal muscle insulin sensitivity. MiR-106b was found to target the 3' untranslated region (3' UTR) of mitofusin-2 (Mfn2) through miR-106b binding sites and to downregulate Mfn2 protein abundance at the post-transcriptional level by luciferase activity assay combined with mutational analysis and immunoblotting. Overexpression of miR-106b resulted in mitochondrial dysfunction and insulin resistance in C2C12 myotubes. MiR-106b was increased in insulin-resistant cultured C2C12 myotubes induced by TNF-α, and accompanied by increasing Mfn2 level, miR-106b loss of function improved mitochondrial function and insulin sensitivity impaired by TNF-α in C2C12 myotubes. In addition, both overexpression and downregulation of miR-106b upregulated peroxisome proliferator-activated receptor gamma coactivator (PGC)-1α and estrogen-related receptor (ERR)-α expression. MiR-106b targeted Mfn2 and regulated skeletal muscle mitochondrial function and insulin sensitivity. Therefor, Inhibition of miR-106b may be a potential new strategy for treating insulin resistance and type 2 diabetes.
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Affiliation(s)
- Ying Zhang
- Department of Pediatrics, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, People's Republic of China
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Epstein I, Tushev G, Will TJ, Vlatkovic I, Cajigas IJ, Schuman EM. Alternative polyadenylation and differential expression of Shank mRNAs in the synaptic neuropil. Philos Trans R Soc Lond B Biol Sci 2013; 369:20130137. [PMID: 24298140 DOI: 10.1098/rstb.2013.0137] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The stability and dynamics of synapses rely on tight regulation of the synaptic proteome. Shank proteins, encoded by the three genes Shank1, Shank2 and Shank3 are scaffold molecules in the postsynaptic density of excitatory neurons that contribute to activity-dependent neuronal signalling. Mutations in the Shank genes are associated with neurological diseases. Using state-of-the-art technologies, we investigated the levels of expression of the Shank family messenger RNAs (mRNAs) within the synaptic neuropil of the rat hippocampus. We detected all three Shank transcripts in the neuropil of CA1 pyramidal neurons. We found Shank1 to be the most abundantly expressed among the three Shank mRNA homologues. We also examined the turnover of Shank mRNAs and predict the half-lives of Shank1, Shank2 and Shank3 mRNAs to be 18-28 h. Using 3'-end sequencing, we identified novel 3' ends for the Shank1 and Shank2 3' untranslated regions (3' UTRs) that may contribute to the diversity of alternative polyadenylation (APA) for the Shank transcripts. Our findings consolidate the view that the Shank molecules play a central role at the postsynaptic density. This study may shed light on synaptopathologies associated with disruption of local protein synthesis, perhaps linked to mutations in mRNA 3' UTRs or inappropriate 3' end processing.
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Affiliation(s)
- Irina Epstein
- Max Planck Institute for Brain Research, , Max-von-Laue Strasse 4, Frankfurt am Main 60438, Germany
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Zhen J, Wang D, He L, Zou H, Xu Y, Gao S, Yang B, Deng Z. Genetic profile of KIR and HLA in southern Chinese Han population. Hum Immunol 2013; 75:59-64. [PMID: 24055695 DOI: 10.1016/j.humimm.2013.09.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 09/04/2013] [Accepted: 09/11/2013] [Indexed: 12/26/2022]
Abstract
KIR and their HLA ligands are encoded by two of the most diverse gene families in the human genome. The function of KIR on the NK cell is highly dependent on the normal expression of class I HLA on the target cell. Previous population studies in southern Chinese have been focused on the KIR framework genes and genotypes but little is known about the compound profiles of KIR/HLA. The present study examined 503 unrelated individuals from southern Chinese Han population for the polymorphism of KIR and class I HLA genes. All 16 KIR genes were detected in the study population and the four framework genes KIR3DL2, 3DL3, 3DP1, and 2DL4 were present in all individuals. Thirty unique KIR gene profiles were found reflecting a rather limited number of KIR haplotypes in this population. KIRAA1 was the most common profile observed in 54.7% of the samples. Among the AA1 individuals, 15.6% were homozygous for the deleted KIR2DS4. Haplotype A (74.8%) was more common than haplotype B (25.2%). HLA-C1 was a much more common ligand for 2D KIRs than C2. Bw4-80I, Bw4-80T, and the Bw4-bearing HLA-A alleles were detected at similar frequencies. The matched KIR+HLA pairs 2DL2/3+C1 (98.1%), 3DL1+Bw4 (73.3%), 3DL2+A3/11 (60.0%) were the most common ones whereas 3DS1+Bw4-80I was the least common (9.4%). A total of 193 unique compound profiles of KIR-HLA were identified in 480 informative individuals, 130 of the profiles being detected only once. The study provided a comprehensive analysis of the KIR/HLA profiles in southern Chinese in regards of the presence/absence of KIR genes, HLA ligands, matched KIR+HLA pairs, and KIR/HLA compound profiles. The results could help to better understand the role played by KIR/HLA interaction in associated diseases and clinical transplantation in southern Chinese.
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Affiliation(s)
- Jianxin Zhen
- Southern Medical University, Guangzhou, Guangdong 510515, China; Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Daming Wang
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Liumei He
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Hongyan Zou
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Yunping Xu
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Suqing Gao
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Baocheng Yang
- Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China
| | - Zhihui Deng
- Southern Medical University, Guangzhou, Guangdong 510515, China; Immunogenetics Laboratory, Shenzhen Blood Center, Shenzhen, Guangdong 518035, China.
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Baglìo SR, Devescovi V, Granchi D, Baldini N. MicroRNA expression profiling of human bone marrow mesenchymal stem cells during osteogenic differentiation reveals Osterix regulation by miR-31. Gene 2013; 527:321-31. [PMID: 23827457 DOI: 10.1016/j.gene.2013.06.021] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 06/09/2013] [Indexed: 01/13/2023]
Abstract
Osteogenesis is the result of a complex sequence of events that involve the differentiation of mesenchymal stem cells (MSC) into osteoblasts. MSCs are multipotent adult stem cells that can give rise to different cell types of the mesenchymal germ layer. The differentiation fate of MSCs depends on the microenvironmental signals received by these cells and is tightly regulated by multiple pathways that lead to the activation of specific transcription factors. Among the transcription factors involved in osteogenic differentiation Osterix (Sp7) plays a key role and has been shown to be fundamental for bone homeostasis. However, the molecular events governing the expression of this transcription factor are not fully understood. In this study we set out to investigate the changes in the microRNA (miRNA) expression that occur during the osteogenic differentiation of bone marrow-derived MSCs. To this purpose, we analyzed the miRNA expression profile of MSCs deriving from 3 donors during the differentiation and mineralization processes by microarray. 29 miRNAs were significantly and consistently modulated during the osteogenic differentiation and 5 during the mineralization process. Interestingly, most of the differentially expressed miRNAs have been reported to be implicated in stemness maintenance, differentiation and/or oncogenesis. Subsequently, we focused our attention on the regulation of Osterix by miRNAs and demonstrated that one of the miRNAs differentially modulated during osteogenic differentiation, miR-31, controls Osterix expression through association to the 3' untranslated region of this transcription factor. By analyzing miR-31 and Osterix expression levels we found an inverse miRNA-target expression trend during osteogenic differentiation and in osteosarcoma cell lines. Moreover, the inhibition of the microRNA activity led to an increase in the endogenous expression of Osterix. Our results define a miRNA signature characterizing the osteogenic differentiation of MSCs and provide evidence for the involvement of miR-31 in the regulation of the bone-specific transcription factor Osterix.
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Affiliation(s)
- Serena Rubina Baglìo
- Laboratory for Orthopedic Pathophysiology and Regenerative Medicine, Istituto Ortopedico Rizzoli, via di Barbiano 1/10, 40136, Bologna Italy.
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Jiang K, Ren C, Nair VD. MicroRNA-137 represses Klf4 and Tbx3 during differentiation of mouse embryonic stem cells. Stem Cell Res 2013; 11:1299-313. [PMID: 24084696 DOI: 10.1016/j.scr.2013.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 09/05/2013] [Accepted: 09/05/2013] [Indexed: 02/01/2023] Open
Abstract
MicroRNA-137 (miR-137) has been shown to play an important role in the differentiation of neural stem cells. Embryonic stem (ES) cells have the potential to differentiate into different cell types including neurons; however, the contribution of miR-137 in the maintenance and differentiation of ES cells remains unknown. Here, we show that miR-137 is mainly expressed in ES cells at the mitotic phase of the cell cycle and highly upregulated during differentiation. We identify that ES cell transcription factors, Klf4 and Tbx3, are downstream targets of miR-137, and we show that endogenous miR-137 represses the 3' untranslated regions of Klf4 and Tbx3. Transfection of ES cells with mature miR-137 RNA duplexes led to a significant reduction in cell proliferation and the expression of Klf4, Tbx3, and other self-renewal genes. Furthermore, we demonstrate that increased miR-137 expression accelerates differentiation of ES cells in vitro. Loss of miR-137 during ES cell differentiation significantly impeded neuronal gene expression and morphogenesis. Taken together, our results suggest that miR-137 regulates ES cell proliferation and differentiation by repressing the expression of downstream targets, including Klf4 and Tbx3.
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Affiliation(s)
- Ke Jiang
- Department of Neurology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Ling S, Birnbaum Y, Nanhwan MK, Thomas B, Bajaj M, Ye Y. MicroRNA-dependent cross-talk between VEGF and HIF1α in the diabetic retina. Cell Signal 2013; 25:2840-7. [PMID: 24018047 DOI: 10.1016/j.cellsig.2013.08.039] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 08/30/2013] [Indexed: 12/13/2022]
Abstract
Both HIF1α (hypoxia-inducible factor alpha) and VEGF (vascular endothelial growth factor) are implicated in the pathogenesis of diabetic retinopathy (DR). Competitive endogenous RNAs (ceRNAs) are messenger RNA (mRNA) molecules that affect each other expression through competition for their shared microRNAs (miRNA). However, little is known about the role of ceRNAs in DR. We assess whether the expression of HIF1α and VEGF in DR is interdependent through sequestration of common miRNAs. We used bioinformatics to identify potential miRNAs that affect both genes and validated the interdependence of the genes by silencing or overexpression of the genes and assessed the luciferase-HIF1α 3'UTR activity. We found that HIF1α and VEGF are targeted by 12 common miRNAs. Silencing either HIF1α or VEGF increased the availabilities of the shared miRNAs, therefore suppressed the luciferase-HIF1α 3'UTR activity, whereas over-expressing HIF1α or VEGF increased the luciferase activity. HIF1α was co-expressed with VEGF in-vivo and in-vitro in DR models. Silencing HIF1α transcripts resulted in a significant reduction in VEGF protein levels and vice versa. This interdependence was miRNA- and 3'UTR-dependent, as silencing Dicer abolished the interdependence. Over-expression of a common miRNA (miR-106a) significantly reduced the expression of HIF1α and VEGF and prevented high glucose-induced increased permeability. There is a cross-talk between HIF1α and VEGF through interactions with their common miRNAs. miRNA based therapy can affect the expression of both HIF1α and VEGF and may represent a therapeutic potential for the treatment of DR.
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Affiliation(s)
- Shukuan Ling
- The Department of Biochemistry and Molecular Biology, University of Texas Medical Branch; Galveston, TX, USA; School of Life Science and Technology, Harbin Institute of Technology, Harbin, China; State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, China
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Abstract
Hypoxia, or low oxygen tension, is a unique environmental stress that induces global changes in a complex regulatory network of transcription factors and signaling proteins to coordinate cellular adaptations in metabolism, proliferation, DNA repair, and apoptosis. Several lines of evidence now establish microRNAs (miRNAs), which are short noncoding RNAs that regulate gene expression through posttranscriptional mechanisms, as key elements in this response to hypoxia. Oxygen deprivation induces a distinct shift in the expression of a specific group of miRNAs, termed hypoxamirs, and emerging evidence indicates that hypoxia regulates several facets of hypoxamir transcription, maturation, and function. Transcription factors such as hypoxia-inducible factor are upregulated under conditions of low oxygen availability and directly activate the transcription of a subset of hypoxamirs. Conversely, hypoxia selectively represses other hypoxamirs through less well characterized mechanisms. In addition, oxygen deprivation has been directly implicated in epigenetic modifications such as DNA demethylation that control specific miRNA transcription. Finally, hypoxia also modulates the activity of key proteins that control posttranscriptional events in the maturation and activity of miRNAs. Collectively, these findings establish hypoxia as an important proximal regulator of miRNA biogenesis and function. It will be important for future studies to address the relative contributions of transcriptional and posttranscriptional events in the regulation of specific hypoxamirs and how such miRNAs are coordinated in order to integrate into the complex hierarchical regulatory network induced by hypoxia.
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Affiliation(s)
- Shriram Nallamshetty
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Stephen Y. Chan
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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