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Martin-Geary AC, Blakes AJM, Dawes R, Findlay SD, Lord J, Walker S, Talbot-Martin J, Wieder N, D’Souza EN, Fernandes M, Hilton S, Lahiri N, Campbell C, Jenkinson S, DeGoede CGEL, Anderson ER, Burge CB, Sanders SJ, Ellingford J, Baralle D, Banka S, Whiffin N. Systematic identification of disease-causing promoter and untranslated region variants in 8,040 undiagnosed individuals with rare disease. medRxiv 2023:2023.09.12.23295416. [PMID: 37745552 PMCID: PMC10516070 DOI: 10.1101/2023.09.12.23295416] [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] [Indexed: 09/26/2023]
Abstract
Background Both promoters and untranslated regions (UTRs) have critical regulatory roles, yet variants in these regions are largely excluded from clinical genetic testing due to difficulty in interpreting pathogenicity. The extent to which these regions may harbour diagnoses for individuals with rare disease is currently unknown. Methods We present a framework for the identification and annotation of potentially deleterious proximal promoter and UTR variants in known dominant disease genes. We use this framework to annotate de novo variants (DNVs) in 8,040 undiagnosed individuals in the Genomics England 100,000 genomes project, which were subject to strict region-based filtering, clinical review, and validation studies where possible. In addition, we performed region and variant annotation-based burden testing in 7,862 unrelated probands against matched unaffected controls. Results We prioritised eleven DNVs and identified an additional variant overlapping one of the eleven. Ten of these twelve variants (82%) are in genes that are a strong match to the individual's phenotype and six had not previously been identified. Through burden testing, we did not observe a significant enrichment of potentially deleterious promoter and/or UTR variants in individuals with rare disease collectively across any of our region or variant annotations. Conclusions Overall, we demonstrate the value of screening promoters and UTRs to uncover additional diagnoses for previously undiagnosed individuals with rare disease and provide a framework for doing so without dramatically increasing interpretation burden.
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Affiliation(s)
- Alexandra C Martin-Geary
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Alexander J M Blakes
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ruebena Dawes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Scott D Findlay
- Department of Biology, Massachusetts Institute of Technology, Cambridge, USA
| | | | | | | | - Nechama Wieder
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Elston N D’Souza
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Maria Fernandes
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
| | - Sarah Hilton
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nayana Lahiri
- St George’s, University of London & St George’s University Hospitals NHS Foundation Trust, Institute of Molecular and Clinical Sciences, London, SW17 0QT, UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Christian G E L DeGoede
- Department of Paediatric Neurology, Clinical research Facility, Lancashire Teaching Hospitals NHS Trust
- Manchester Metropolitan University
| | - Emily R Anderson
- Liverpool Centre for Genomic Medicine, Liverpool Women’s Hospital, Liverpool, UK
| | | | - Stephan J Sanders
- Institute of Developmental and Regenerative Medicine, Department of Paediatrics, University of Oxford, Oxford, OX3 7TY, UK
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
- New York Genome Center, New York, NY, USA
| | - Jamie Ellingford
- Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Diana Baralle
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Nicola Whiffin
- Big Data Institute, University of Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, UK
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
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Melo ARV, Raposo M, Ventura M, Martins S, Pavão S, Alonso I, Bettencourt C, Lima M. Genetic Variation in ATXN3 (Ataxin-3) 3'UTR: Insights into the Downstream Regulatory Elements of the Causative Gene of Machado-Joseph Disease/Spinocerebellar Ataxia Type 3. Cerebellum 2023; 22:37-45. [PMID: 35034258 DOI: 10.1007/s12311-021-01358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/09/2021] [Indexed: 02/01/2023]
Abstract
Untranslated regions are involved in the regulation of transcriptional and post-transcriptional processes. Characterization of these regions remains poorly explored for ATXN3, the causative gene of Machado-Joseph disease (MJD). Although a few genetic modifiers have been identified for MJD age at onset (AO), they only explain a small fraction of the AO variance. Our aim was to analyse variation at the 3'UTR of ATXN3 in MJD patients, analyse its impact on AO and attempt to build haplotypes that might discriminate between normal and expanded alleles.After assessing ATXN3 3'UTR variants in molecularly confirmed MJD patients, an in silico analysis was conducted to predict their functional impact (e.g. their effect on miRNA-binding sites). Alleles in cis with the expanded (CAG)n were inferred from family data, and haplotypes were built. The effect of the alternative alleles on the AO and on SARA and NESSCA ataxia scales was tested.Nine variants, all previously described, were found. For eight variants, in silico analyses predicted (a) deleterious effects (rs10151135; rs55966267); (b) changes on miRNA-binding sites (rs11628764; rs55966267; rs709930) and (c) alterations of RNA-binding protein (RBP)-binding sites (rs1055996; rs910369; rs709930; rs10151135; rs3092822; rs7158733). Patients harbouring the alternative allele at rs10151135 had significantly higher SARA Axial subscores (p = 0.023), comparatively with those homozygous for the reference allele. Ten different haplotypes were obtained, one of which was exclusively found in cis with the expanded and four with the normal allele. These findings, which are relevant for the design of allele-specific therapies, warrant further investigation in independent MJD cohorts.
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Meyer E, Chaung K, Dehghannasiri R, Salzman J. ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq. Genome Biol 2022; 23:226. [PMID: 36284317 PMCID: PMC9594907 DOI: 10.1186/s13059-022-02795-8] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/13/2022] [Indexed: 11/13/2022] Open
Abstract
RNA processing, including splicing and alternative polyadenylation, is crucial to gene function and regulation, but methods to detect RNA processing from single-cell RNA sequencing data are limited by reliance on pre-existing annotations, peak calling heuristics, and collapsing measurements by cell type. We introduce ReadZS, an annotation-free statistical approach to identify regulated RNA processing in single cells. ReadZS discovers cell type-specific RNA processing in human lung and conserved, developmentally regulated RNA processing in mammalian spermatogenesis-including global 3' UTR shortening in human spermatogenesis. ReadZS also discovers global 3' UTR lengthening in Arabidopsis development, highlighting the usefulness of this method in under-annotated transcriptomes.
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Affiliation(s)
- Elisabeth Meyer
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Kaitlin Chaung
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Roozbeh Dehghannasiri
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Julia Salzman
- Department of Biochemistry, Stanford University, Stanford, CA, 94305, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA.
- Department of Statistics (by courtesy), Stanford University, Stanford, CA, 94305, USA.
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Manzella C, Singhal M, Ackerman M, Alrefai WA, Saksena S, Dudeja PK, Gill RK. Serotonin transporter untranslated regions influence mRNA abundance and protein expression. Gene Rep 2020; 18. [PMID: 34113740 DOI: 10.1016/j.genrep.2019.100513] [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] [Indexed: 01/06/2023]
Abstract
The serotonin transporter (SERT, SLC6A4) is a Na+-dependent transporter that regulates the availability of serotonin (5-HT, 5-hydroxytryptamine), a key neurotransmitter and hormone in the brain and the intestine. The human SERT gene consists of two alternate promoters that drive expression of an identical SERT protein. However, there are different mRNA transcript variants derived from these two promoters that differ in their 5' untranslated region (5'UTR), which is the region of the mRNA upstream from the protein-coding region. Two of these transcripts contain exon-1a and are abundant in neuronal tissue, whereas the third transcript contains exon-1c and is abundant in the intestine. The 3'UTR is nearly identical among the transcripts. Current studies tested the hypothesis that the UTRs of SERT influence its expression in intestinal epithelial cells (IECs) by controlling mRNA or protein levels. The SERT UTRs were cloned into luciferase reporter plasmids and luciferase mRNA and activity were measured following transient transfection of the UTR constructs into the model IEC Caco-2. Luciferase activity and mRNA abundance were higher than the empty vector for two of the three 5'UTR variants. Calculation of translation index (luciferase activity divided by the relative luciferase mRNA level) revealed that the exon-1a containing 5'UTRs had enhanced translation when compared to the exon-1c containing 5'UTR which exhibited a low translation efficiency. Compared to the empty vector, the SERT 3'UTR markedly decreased luciferase activity. In silico analysis of the SERT 3'UTR revealed many conserved potential miRNA binding sites that may be responsible for this decrease. In conclusion, we have shown that the UTRs of SERT regulate mRNA abundance and protein expression. Delineating the molecular basis by which the UTRs of SERT influence its expression will lead to an increased understanding of post-transcriptional regulation of SERT in GI disorders associated with altered 5-HT availability.
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Affiliation(s)
- Christopher Manzella
- Department of Physiology & Biophysics, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Megha Singhal
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America
| | - Max Ackerman
- University of Illinois at Chicago, College of Liberal Arts and Sciences, United States of America
| | - Waddah A Alrefai
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America.,Jesse Brown VA Medical Center, Chicago, IL, United States of America
| | - Seema Saksena
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America.,Jesse Brown VA Medical Center, Chicago, IL, United States of America
| | - Pradeep K Dudeja
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America.,Jesse Brown VA Medical Center, Chicago, IL, United States of America
| | - Ravinder K Gill
- Division of Gastroenterology & Hepatology, University of Illinois at Chicago, Chicago, IL, United States of America.,Jesse Brown VA Medical Center, Chicago, IL, United States of America
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Zarghampoor F, Behzad-Behbahani A, Azarpira N, Khatami SR, Fanian M, Hossein Aghdaie M, Rafiei Dehbidi G. A Single Tube Overlap Extension PCR Method for Splicing of Multiple DNA Fragments. Avicenna J Med Biotechnol 2020; 12:37-43. [PMID: 32153737 PMCID: PMC7035467] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Despite the ease of conventional splicing by overlap-extension (SOEing) PCR technique in theory, when splicing more than two fragments, and especially if one of the complementary sequences is A-T rich, the attachment of the fragments would be challenging. A new rapid and highly efficient SOEing PCR assay was developed for simultaneous splicing of multiple DNA fragments and induction of site-directed mutagenesis in a single tube. METHODS The method was adapted for splicing human beta-globin UTRs to OCT4, SOX2, KLF4, C-MYC, LIN28A, and destabilized GFP for the construction of chimeric DNA fragments for in vitro transcription. In addition, the native Kozak sequence of beta-globin (K1) was replaced by the strongest Kozak sequence (K2) using site-directed mutagenesis to enhance the expression of target genes. RESULTS ChimericGFPd2/K1, GFPd2/K2, OCT4, and KLF4 were created by the optimized conventional SOEing PCR. The single tube method was able to create the chimeric SOX2, C-MYC, and LIN28A in high quality and quantity in comparison with the conventional SOEing PCR. Moreover, using single tube SOEing PCR, the reaction time and materials that are required in the conventional SOEing PCR were significantly reduced. Fluorescent microscopy and flow cytometry examinations indicated highly efficient translation of K2 sequence in comparison with the K1sequence. CONCLUSION Single tube SOEing PCR is a valuable method to construct more multiple fragments with high yield. The method can successfully be applied for construction of various kinds of complex chimeric genes.
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Affiliation(s)
- Farzaneh Zarghampoor
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Abbas Behzad-Behbahani
- Diagnostic Laboratory Sciences and Technology Research Centre, Faculty of Paramedical, Shiraz Sciences University of Medical Sciences, Shiraz, Iran,Corresponding authors: Abbas Behzad-Behbahani, Ph.D., Diagnostic Laboratory Sciences and Technology Research Centre, Faculty of Paramedical Sciences, Shiraz University of Medical, Shiraz, Iran, Negar Azarpira, Ph.D., Transplant Research Centre, Shiraz University of Medical Science, Shiraz, Iran, Tel: +98 71 32270301, Fax: +98 71 32270301, E-mail: , ,
| | - Negar Azarpira
- Transplant Research Centre, Shiraz University of Medical Science, Shiraz, Iran,Corresponding authors: Abbas Behzad-Behbahani, Ph.D., Diagnostic Laboratory Sciences and Technology Research Centre, Faculty of Paramedical Sciences, Shiraz University of Medical, Shiraz, Iran, Negar Azarpira, Ph.D., Transplant Research Centre, Shiraz University of Medical Science, Shiraz, Iran, Tel: +98 71 32270301, Fax: +98 71 32270301, E-mail: , ,
| | - Saeed Reza Khatami
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Maryam Fanian
- Transplant Research Centre, Shiraz University of Medical Science, Shiraz, Iran
| | | | - Gholamreza Rafiei Dehbidi
- Diagnostic Laboratory Sciences and Technology Research Centre, Faculty of Paramedical, Shiraz Sciences University of Medical Sciences, Shiraz, Iran
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Ntavatzikos A, Spathis A, Patapis P, Machairas N, Vourli G, Peros G, Papadopoulos I, Panayiotides I, Koumarianou A. TYMS/KRAS/BRAF molecular profiling predicts survival following adjuvant chemotherapy in colorectal cancer. World J Gastrointest Oncol 2019; 11:551-566. [PMID: 31367274 PMCID: PMC6657223 DOI: 10.4251/wjgo.v11.i7.551] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 04/30/2019] [Accepted: 06/12/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Patients with stage II-III colorectal cancer (CRC) treated with adjuvant chemotherapy, gain a 25% survival benefit. In the context of personalized medicine, there is a need to identify patients with CRC who may benefit from adjuvant chemotherapy. Molecular profiling could guide treatment decisions in these patients. Thymidylate synthase (TYMS) gene polymorphisms, KRAS and BRAF could be included in the molecular profile under consideration.
AIM To investigate the association of TYMS gene polymorphisms, KRAS and BRAF mutations with survival of CRC patients treated with chemotherapy.
METHODS A retrospective study studied formalin-fixed paraffin-embedded tissues (FFPEs) of consecutive patients treated with adjuvant chemotherapy during January/2005-January/2007. FFPEs were analysed with PCR for the detection of TYMS polymorphisms, mutated KRAS (mKRAS) and BRAF (mBRAF). Patients were classified into three groups (high, medium and low risk) according to 5’UTR TYMS polymorphisms Similarly, based on 3’UTR polymorphism ins/loss of heterozygosity (LOH) patients were allocated into two groups (high and low risk of relapse, respectively). Cox regression models examined the associated 5-year survival outcomes.
RESULTS One hundred and thirty patients with early stage CRC (stage I-II: 55 patients; stage III 75 patients; colon: 70 patients; rectal: 60 patients) were treated with surgery and chemotherapy. The 5-year disease free survival and overall survival rate was 61.6% and 73.9% respectively. 5’UTR polymorphisms of intermediate TYMS polymorphisms (2RG/3RG, 2RG/LOH, 3RC/LOH) were associated with lower risk for relapse [hazard ratio (HR) 0.320, P = 0.02 and HR 0.343, P = 0.013 respectively] and death (HR 0.368, P = 0.031 and HR 0.394, P = 0.029 respectively). The 3’UTR polymorphism ins/LOH was independently associated with increased risk for disease recurrence (P = 0.001) and death (P = 0.005). mBRAF (3.8% of patients) was associated with increased risk of death (HR 4.500, P = 0.022) whereas mKRAS (39% of patients) not.
CONCLUSION Prospective validating studies are required to confirm whether 2RG/3RG, 2RG/LOH, 3RC/LOH, absence of ins/LOH and wild type BRAF may indicate patients at lower risk of relapse following adjuvant chemotherapy.
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Affiliation(s)
- Anastasios Ntavatzikos
- Hematology-Oncology Unit, 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, Athens 12462, Greece
| | - Aris Spathis
- Department of Cytopathology, National and Kapodistrian University of Athens, Medical School, “ATTIKON” University Hospital, Athens 12462, Greece
| | - Paul Patapis
- 3rd Department of Surgery, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, Athens 12462, Greece
| | - Nikolaos Machairas
- 3rd Department of Surgery, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, Athens 12462, Greece
| | - Georgia Vourli
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece
| | - George Peros
- Department of Surgery, Medical School, National and Kapodistrian University of Athens, Evgenideio Therapeutirio S.A., “I AGIA TRIAS”, Athens 11528, Greece
| | - Iordanis Papadopoulos
- Department of Surgery, Medical School, National and Kapodistrian University of Athens, Evgenideio Therapeutirio S.A., “I AGIA TRIAS”, Athens 11528, Greece
| | - Ioannis Panayiotides
- 2nd Department of Pathology, University of Athens, Medical School, “ATTIKON” University Hospital, Athens 12462, Greece
| | - Anna Koumarianou
- Hematology-Oncology Unit, 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, “ATTIKON” University Hospital, Athens 12462, Greece
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Pereira-Patrón A, Solis-Pereira S, Lizama-Uc G, Ramírez-Prado JH, Pérez-Brito D, Tapia-Tussell R. Molecular characterization of laccase genes from the basidiomycete Trametes hirsuta Bm-2 and analysis of the 5' untranslated region (5'UTR). 3 Biotech 2019; 9:160. [PMID: 30944807 PMCID: PMC6441420 DOI: 10.1007/s13205-019-1691-y] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 03/21/2019] [Indexed: 11/25/2022] Open
Abstract
The aim of this study was to identify and characterize laccase genes produced by Trametes hirsuta Bm-2 in a liquid medium, both with and without induction. The amplification of 5'and 3'regions of laccase sequences was obtained by the RACE-PCR method, and these were assembled to obtain a cDNA of total length. Two new laccase genes were isolated from basal medium (lac-B) and lignocellulosic grapefruit substrate (lac-T), both encoding open reading frames of 2566 bp. Both laccase-predicted proteins consisted of 521 amino acids, four copper-binding regions, a signal peptide, and five potential glycosilation sites (Asn-Xaa-Ser/Tre). Moreover, the deduced amino acid sequences share about 76-85% identity with other laccases of WRF. Sequence comparison showed 47 synonymous point mutations between lac-B and lac-T. In addition, 5' untranslated regions (UTR) of laccase genes lac-B and lac-T showed differences in length and number of regulatory elements that may affect transcriptional or translational expression of these genes.
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Affiliation(s)
- Alejandrina Pereira-Patrón
- Depto. de Ingeniería Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Av. Tecnológico Km 4.5 S/N, 97118 Mérida, Yucatán Mexico
| | - Sara Solis-Pereira
- Depto. de Ingeniería Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Av. Tecnológico Km 4.5 S/N, 97118 Mérida, Yucatán Mexico
| | - Gabriel Lizama-Uc
- Depto. de Ingeniería Química y Bioquímica, Tecnológico Nacional de México, Instituto Tecnológico de Mérida, Av. Tecnológico Km 4.5 S/N, 97118 Mérida, Yucatán Mexico
| | - Jorge H. Ramírez-Prado
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán Mexico
| | - Daisy Pérez-Brito
- Laboratorio GeMBio, Centro de Investigación Científica de Yucatán, Calle 43 No. 130 x 32 y 34, Col. Chuburná de Hidalgo, 97205 Mérida, Yucatán Mexico
| | - Raul Tapia-Tussell
- Unidad de Energía Renovable, Centro de Investigación Científica de Yucatán, Carretera Sierra Papacal-Chuburná Puerto Km 5, 97302 Mérida, Yucatán Mexico
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Dong Z, Liu ZW, Chen R, Wen XJ, Ji J, Zheng XX, Zhao L, Wang ZY, Wen HL. The untranslated regions of EV-A71 contribute to its pathogenicity and virulence. Virus Res 2019; 263:55-63. [PMID: 30611822 DOI: 10.1016/j.virusres.2018.12.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/28/2018] [Accepted: 12/30/2018] [Indexed: 01/23/2023]
Abstract
Enterovirus A71 (EV-A71) is known for its manifestation as hand foot and mouth disease (HFMD), which has caused countless large-scale epidemic outbreaks throughout the world. However, the molecular pathogenesis of EV-A71 infection is still elusive. Previous studies found that the biological characteristics of a mild EV-A71 strain (SDLY1) and a severe EV-A71 strain (SDLY107) are significantly different, and sequence analysis showed that there are several differences in nucleotide sites of UTRs (88 nt, 123 nt, 143 nt, 154 nt, 187 nt, 241 nt, 243 nt, 253 nt, 291 nt, 438 nt, 440 nt, 571 nt, 579 nt, 602 nt, 658 nt, 664 nt, 690 nt, 696 nt, 7328 nt, 7335 nt, 7367 nt, and 7395 nt). The aim of this study was to determine whether these amino sites in UTRs are associated with the pathogenesis of EV-A71 and are responsible for different clinical manifestations. Based on the reverse genetics technology, we rescued two chimeric viruses SDLY107(1-5'UTR) and SDLY107(1-3'UTR) by replacing 5'UTR/3'UTR gene fragments of an infectious cDNA clone. Replication kinetics and cytotoxicity assays showed that the virulence of the two chimeric strains significantly changed in vitro. The viral loads of the two chimeric strains in infected ICR mice were reduced and pathological damage in the brains, lungs, intestinal tissues, and muscles were lightened. Our findings suggest that some nucleotide sites in UTRs may have a function in the pathogenicity and virulence of EV-A71.
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You M, Yang Y, Zhong C, Chen F, Wang X, Jia T, Chen Y, Zhou B, Mi Q, Zhao Q, An Z, Luo W, Xia N. Efficient mAb production in CHO cells with optimized signal peptide, codon, and UTR. Appl Microbiol Biotechnol 2018; 102:5953-64. [PMID: 29740673 DOI: 10.1007/s00253-018-8986-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 12/17/2022]
Abstract
Antibody drugs have been used to treat a number of diseases successfully. Producing antibodies with high yield and quality is necessary for clinical applications of antibodies. For a candidate molecule, optimization of a vector to produce sufficient yield and an accurate primary structure is indispensable in the early stage of the production process development. It is especially important to maintain the fidelity of N-terminal sequence. In order to produce antibodies with a high yield and accurate N-terminal, the expression vector was systematically optimized in this study. First, the heavy chain and light chain were co-expressed in Chinese hamster ovary (CHO) cells with different signal peptides. Mass spectrometry (MS) revealed that signal peptides Esp-K, Bsp-H, and 8Hsp-H were accurately deleted from mature antibodies. Further, the yield was doubled by codon optimization and increased by 50% with the presence of untranslated regions (UTR). The combination of UTR with optimal codon and signal peptide to form an expression vector resulted in yield improvement of 150% and correct N-terminal sequences. Moreover, the main product peak was above 98% as assessed by size-exclusion chromatography (SEC). Additionally, the bioactivity of products made from optimized transient gene expression (TGE) was almost identical to the standard sample. The production efficiency and product quality from the identified TGE optimization strategy was further demonstrated through application to two other antibodies. The expression level of SGE (stable gene expression) can also be improved effectively with this optimization strategy. In conclusion, vector optimization via combination of optimized signal peptide, codon, and UTR is an alternative approach for efficient antibody production with high fidelity N-terminal sequence in CHO cells.
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Woo HH, Lee SC, Gibson SJ, Chambers SK. Expression of the cytoplasmic nucleolin for post-transcriptional regulation of macrophage colony-stimulating factor mRNA in ovarian and breast cancer cells. Biochim Biophys Acta Gene Regul Mech 2017; 1860:337-348. [PMID: 28131007 DOI: 10.1016/j.bbagrm.2017.01.006] [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] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 01/08/2017] [Accepted: 01/08/2017] [Indexed: 01/21/2023]
Abstract
The formation of the mRNP complex is a critical component of translational regulation and mRNA decay. Both the 5' and 3'UTRs of CSF-1 mRNA are involved in post-transcriptional regulation. In CSF-1 mRNA, a small hairpin loop structure is predicted to form at the extreme 5' end (2-21nt) of the 5'UTR. Nucleolin binds the hairpin loop structure in the 5'UTR of CSF-1 mRNA and enhances translation, while removal of this hairpin loop nucleolin binding element dramatically represses translation. Thus in CSF-1 mRNA, the hairpin loop nucleolin binding element is critical for translational regulation. In addition, nucleolin interacts with the 3'UTR of CSF-1 mRNA and facilitates the miRISC formation which results in poly (A) tail shortening. The overexpression of nucleolin increases the association of CSF-1 mRNA containing short poly (A)n≤26, with polyribosomes. Nucleolin both forms an mRNP complex with the eIF4G and CSF-1 mRNA, and is co-localized with the eIF4G in the cytoplasm further supporting nucleolin's role in translational regulation. The distinct foci formation of nucleolin in the cytoplasm of ovarian and breast cancer cells implicates the translational promoting role of nucleolin in these cancers.
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Affiliation(s)
- Ho-Hyung Woo
- University of Arizona Cancer Center, Tucson, AZ 85724, USA.
| | - Sang C Lee
- University of Arizona Cancer Center, Tucson, AZ 85724, USA
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11
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Srivastava A, Gogoi P, Deka B, Goswami S, Kanaujia SP. In silico analysis of 5'-UTRs highlights the prevalence of Shine-Dalgarno and leaderless-dependent mechanisms of translation initiation in bacteria and archaea, respectively. J Theor Biol 2016; 402:54-61. [PMID: 27155047 DOI: 10.1016/j.jtbi.2016.05.005] [Citation(s) in RCA: 8] [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: 10/01/2015] [Revised: 04/29/2016] [Accepted: 05/02/2016] [Indexed: 11/26/2022]
Abstract
In prokaryotes, a heterogeneous set of protein translation initiation mechanisms such as Shine-Dalgarno (SD) sequence-dependent, SD sequence-independent or ribosomal protein S1 mediated and leaderless transcript-dependent exists. To estimate the distribution of coding sequences employing a particular translation initiation mechanism, a total of 107 prokaryotic genomes were analysed using in silico approaches. Analysis of 5'-untranslated regions (UTRs) of genes reveals the existence of three types of mRNAs described as transcripts with and without SD motif and leaderless transcripts. Our results indicate that although all the three types of translation initiation mechanisms are widespread among prokaryotes, the number of SD-dependent genes in bacteria is higher than that of archaea. In contrast, archaea contain a significantly higher number of leaderless genes than SD-led genes. The correlation analysis between genome size and SD-led & leaderless genes suggests that the SD-led genes are decreasing (increasing) with genome size in bacteria (archaea). However, the leaderless genes are increasing (decreasing) in bacteria (archaea) with genome size. Moreover, an analysis of the start-codon biasness confirms that among ATG, GTG and TTG codons, ATG is indeed the most preferred codon at the translation initiation site in most of the coding sequences. In leaderless genes, however, the codons GTG and TTG are also observed at the translation initiation site in some species contradicting earlier studies which suggested the usage of only ATG codon. Henceforth, the conventional mechanism of translation initiation cannot be generalized as an exclusive way of initiating the process of protein biosynthesis in prokaryotes.
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Affiliation(s)
- Ambuj Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Prerana Gogoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Bhagyashree Deka
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur 784028, Assam, India
| | - Shrayanti Goswami
- Department of Biotechnology, National Institute of Technology Durgapur, Durgapur 713205, West Bengal, India
| | - Shankar Prasad Kanaujia
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Abstract
Members of the Flaviviridae (e.g., Dengue virus, West Nile virus, and Hepatitis C virus) contain a positive-sense RNA genome that encodes a large polyprotein. It is now also clear most if not all of these viruses also produce an abundant subgenomic long non-coding RNA. These non-coding RNAs, which are called subgenomic flavivirus RNAs (sfRNAs) or Xrn1-resistant RNAs (xrRNAs), are stable decay intermediates generated from the viral genomic RNA through the stalling of the cellular exoribonuclease Xrn1 at highly structured regions. Several functions of these flavivirus long non-coding RNAs have been revealed in recent years. The generation of these sfRNAs/xrRNAs from viral transcripts results in the repression of Xrn1 and the dysregulation of cellular mRNA stability. The abundant sfRNAs also serve directly as a decoy for important cellular protein regulators of the interferon and RNA interference antiviral pathways. Thus the generation of long non-coding RNAs from flaviviruses, hepaciviruses and pestiviruses likely disrupts aspects of innate immunity and may directly contribute to viral replication, cytopathology and pathogenesis.
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Affiliation(s)
- Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80523, USA.
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Martínez-Salas E, Francisco-Velilla R, Fernandez-Chamorro J, Lozano G, Diaz-Toledano R. Picornavirus IRES elements: RNA structure and host protein interactions. Virus Res 2015; 206:62-73. [PMID: 25617758 DOI: 10.1016/j.virusres.2015.01.012] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [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: 10/16/2014] [Revised: 01/05/2015] [Accepted: 01/12/2015] [Indexed: 01/26/2023]
Abstract
Internal ribosome entry site (IRES) elements were discovered in picornaviruses. These elements are cis-acting RNA sequences that adopt diverse three-dimensional structures and recruit the translation machinery using a 5' end-independent mechanism assisted by a subset of translation initiation factors and various RNA binding proteins termed IRES transacting factors (ITAFs). Many of these factors suffer important modifications during infection including cleavage by picornavirus proteases, changes in the phosphorylation level and/or redistribution of the protein from the nuclear to the cytoplasm compartment. Picornavirus IRES are amongst the most potent elements described so far. However, given their large diversity and complexity, the mechanistic basis of its mode of action is not yet fully understood. This review is focused to describe recent advances on the studies of RNA structure and RNA-protein interactions modulating picornavirus IRES activity.
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Affiliation(s)
- Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Gloria Lozano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
| | - Rosa Diaz-Toledano
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Nicolas Cabrera 1, 28049 Madrid, Spain
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Taylor-Douglas DC, Basu A, Gardner RM, Aspelund S, Wen X, Yanovski JA. Evaluation of hypothalamic murine and human melanocortin 3 receptor transcript structure. Biochem Biophys Res Commun 2014; 454:234-8. [PMID: 25450386 DOI: 10.1016/j.bbrc.2014.10.072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 10/15/2014] [Indexed: 11/16/2022]
Abstract
The melanocortin 3 receptor (MC3R) is involved in regulation of energy homeostasis. However, its transcript structure is not well understood. We therefore studied initiation and termination sites for hypothalamic murine Mc3r and human MC3R transcripts. Rapid Amplification of cDNA Ends (RACE) was performed for the 5' and 3' ends of murine and human hypothalamic RNA. 5' RACE experiments using hypothalamic murine RNA indicated mouse hypothalamus expresses two major Mc3r transcription start sites: one with a 5' UTR approximately 368 bases in length and another previously unknown transcript with a 5' UTR approximately 440 bases in length. 5' RACE experiments using human hypothalamic RNA identified a 5' UTR beginning 533 bases upstream of the start codon with a 248 base splice. 3' RACE experiments using hypothalamic murine RNA indicated the 3' UTR terminates approximately 1286 bases after the translational stop codon, with a previously unknown 787 base splice between consensus splice donor and acceptor sites. 3' RACE experiments using human MC3R transcript indicated the 3' UTR terminates approximately 115-160 bases after the translational stop codon. These data provide insight into melanocortin 3 receptor transcript structure.
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Affiliation(s)
- Dezmond C Taylor-Douglas
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA; Howard University College of Medicine, Department of Physiology, 520 W Street N.W., Washington, DC 20059, USA
| | - Arunabha Basu
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Ryan M Gardner
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Sender Aspelund
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Xin Wen
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA
| | - Jack A Yanovski
- Section on Growth and Obesity, Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 10 Center Drive, Bethesda, MD 20892, USA.
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Garziera M, Toffoli G. Inhibition of host immune response in colorectal cancer: Human leukocyte antigen-G and beyond. World J Gastroenterol 2014; 20:3778-3794. [PMID: 24744572 PMCID: PMC3983436 DOI: 10.3748/wjg.v20.i14.3778] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/22/2014] [Accepted: 02/27/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most diffuse cancers worldwide and is still a clinical burden. Increasing evidences associate CRC clinical outcome to immune contexture represented by adaptive immune cells. Their type, density and location are summarized in the Immune Score that has been shown to improve prognostic prediction of CRC patients. The non-classical MHC class I human leukocyte antigen-G (HLA-G), is a crucial tumor-driven immune escape molecule involved in immune tolerance. HLA-G and soluble counterparts are able to exert inhibitory functions by direct interactions with inhibitory receptors present on both innate cells such as natural killer cells, and adaptive immune cells as cytotoxic T and B lymphocytes. HLA-G may play a prominent role in CRC strategies to avoid host immunosurveillance. This review highlights the current knowledge on HLA-G contribution in CRC, in related inflammatory diseases and in other type of cancers and disorders. HLA-G genetic setting (specific haplotypes, genotypes and alleles frequencies) and association with circulating/soluble profiles was highlighted. HLA G prognostic and predictive value in CRC was investigated in order to define a novel prognostic immune biomarker in CRC.
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Zhao J, Xia H, Zhang Y, Yin S, Zhang Z, Tang S, Kou Z, Yu J, Fan Z, Li T. Mini-genome rescue of Crimean-Congo hemorrhagic fever virus and research into the evolutionary patterns of its untranslated regions. Virus Res 2013; 177:22-34. [PMID: 23891575 DOI: 10.1016/j.virusres.2013.07.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 11/23/2022]
Abstract
Crimean-Congo hemorrhagic fever virus (CCHFV) is a member of genus Nairovirus, family Bunyaviridae, which are distributed widely in Africa, Europe and Asia with several genotypes. As a BSL-4 level pathogen, the requirement of high-level biosafety facilities severely constrains researches on live virus manipulation. In this study, we developed a helper-virus-independent mini-genome rescue system for the Chinese YL04057 strain. Based on the enhanced green fluorescent protein (EGFP)-derived mini-genome plasmids, this polymerase I driven system permits easy observation and quantification. Unlike previous report, gradually reduced levels of activity of the CCHFV L, M and S untranslated regions (UTRs) were observed in our system. We also demonstrated that the UTRs at both ends were indispensable for mini-genome background expression. In addition, we phylogentically analyzed all six UTRs of CCHFV and showed that L-UTRs were clustered together approximately corresponding to their original geographical continents. The UTRs of M segment showed a similar branch structure to its open reading frames (ORFs), and nearly an identical tree was generated with 5' UTRs of S segment compared with its ORFs. However, the 3' UTRs of S segment formed new divergent groups. Compatibility tests of YL04057 strain nucleocapsid protein and L protein expression plasmids with Nigerian strain IbAr10200 mini-genomes revealed lower compatibility of L-UTRs without an obvious effect on M-UTRs. Moreover, we demonstrated that the L-UTRs could tolerate certain nucleotide mutations. This system may provide a foundation for future studies of the viral replication cycle, pathogenic mechanisms and evolutionary patterns of CCHFV.
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Toffano-Nioche C, Luo Y, Kuchly C, Wallon C, Steinbach D, Zytnicki M, Jacq A, Gautheret D. Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline. Methods 2013; 63:60-5. [PMID: 23806640 DOI: 10.1016/j.ymeth.2013.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 03/24/2013] [Revised: 05/21/2013] [Accepted: 06/09/2013] [Indexed: 11/29/2022] Open
Abstract
RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.
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Affiliation(s)
- Claire Toffano-Nioche
- Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, Orsay F-91405, France
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Soñanez-Organis JG, Vázquez-Medina JP, Crocker DE, Ortiz RM. Prolonged fasting activates hypoxia inducible factors-1α, -2α and -3α in a tissue-specific manner in northern elephant seal pups. Gene 2013; 526:155-63. [PMID: 23707926 DOI: 10.1016/j.gene.2013.05.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/09/2013] [Accepted: 05/01/2013] [Indexed: 01/10/2023]
Abstract
Hypoxia inducible factors (HIFs) are important regulators of energy homeostasis and cellular adaptation to low oxygen conditions. Northern elephant seals are naturally adapted to prolonged periods (1-2 months) of food deprivation (fasting) which result in metabolic changes that may activate HIF-1. However, the effects of prolonged fasting on HIFs are not well defined. We obtained the full-length cDNAs of HIF-1α and HIF-2α, and partial cDNA of HIF-3α in northern elephant seal pups. We also measured mRNA and nuclear protein content of HIF-1α, -2α, -3α in muscle and adipose during prolonged fasting (1, 3, 5 & 7 weeks), along with mRNA expression of HIF-mediated genes, LDH and VEGF. HIF-1α, -2α and -3α are 2595, 2852 and 1842 bp and encode proteins of 823, 864 and 586 amino acid residues with conserved domains needed for their function (bHLH and PAS) and regulation (ODD and TAD). HIF-1α and -2α mRNA expression increased 3- to 5-fold after 7 weeks of fasting in adipose and muscle, whereas HIF-3α increased 5-fold after 7 weeks of fasting in adipose. HIF-2α protein expression was detected in nuclear fractions from adipose and muscle, increasing approximately 2-fold, respectively with fasting. Expression of VEGF increased 3-fold after 7 weeks in adipose and muscle, whereas LDH mRNA expression increased 12-fold after 7 weeks in adipose. While the 3 HIFα genes are expressed in muscle and adipose, only HIF-2α protein was detectable in the nucleus suggesting that HIF-2α may contribute more significantly in the up-regulation of genes involved in the metabolic adaptation during fasting in the elephant seal.
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