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Giraudo P, Simonnot Q, Pflieger D, Peter J, Gagliardi D, Zuber H. Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing. Methods Mol Biol 2024; 2723:233-252. [PMID: 37824074 DOI: 10.1007/978-1-0716-3481-3_14] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
Deadenylation is a major process that regulates gene expression by shaping the length of mRNA poly(A) tails. Deadenylation is controlled by factors in trans that recruit or impede deadenylases, by the incorporation of non-adenosines during poly(A) tail synthesis, and by the posttranscriptional addition of 3' nucleotides to poly(A) tails. Deciphering the regulation of poly(A) tail shortening requires both transcriptome-wide approaches and more targeted methodologies, allowing deep analyses of specific mRNAs. In this chapter, we present Nano3'RACE, a nanopore-based cDNA sequencing method that allows in-depth analysis to precisely measure poly(A) tail length and detect 3' terminal nucleotide addition, such as uridylation, for mRNAs of interest.
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Affiliation(s)
- Pietro Giraudo
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Quentin Simonnot
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - David Pflieger
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Jackson Peter
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Dominique Gagliardi
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France
| | - Hélène Zuber
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, Strasbourg, France.
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2
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Barman SD, Frimand Z, De Morree A. Absolute Quantification of mRNA Isoforms in Adult Stem Cells Using Microfluidic Digital PCR. Bio Protoc 2023; 13:e4811. [PMID: 37719075 PMCID: PMC10501916 DOI: 10.21769/bioprotoc.4811] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 09/19/2023] Open
Abstract
Adult stem cells play key roles in homeostasis and tissue repair. These cells are regulated by a tight control of transcriptional programs. For example, muscle stem cells (MuSCs), located beneath the basal lamina, exist in the quiescent state but can transition to an activated, proliferative state upon injury. The control of MuSC state depends on the expression levels of myogenic transcription factors. Recent studies revealed the presence of different mRNA isoforms, with distinct biological regulation. Quantifying the exact expression levels of the mRNA isoforms encoding these myogenic transcription factors is therefore key to understanding how MuSCs switch between cell states. Previously, quantitative real-time polymerase chain reaction (qRT-PCR) has been used to quantify RNA expression levels. However, qRT-PCR depends on large amounts of RNA input and only measures relative abundance. Here, we present a protocol for the absolute quantification of mRNA isoforms using microfluidic digital PCR (mdPCR). Primary MuSCs isolated from individual skeletal muscles (gastrocnemius and masseter) are lysed, and their RNA is reverse-transcribed into cDNA and copied into double-stranded DNA. Following exonuclease I digestion to remove remaining single-stranded DNA, the samples are loaded onto a mdPCR chip with TaqMan probes targeting the mRNA isoforms of interest, whereupon target molecules are amplified in nanoliter chambers. We demonstrate that mdPCR can give exact molecule counts per cell for mRNA isoforms encoding the myogenic transcription factor Pax3. This protocol enables the absolute quantification of low abundant mRNA isoforms in a fast, precise, and reliable way.
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Affiliation(s)
| | - Zofija Frimand
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
| | - Antoine De Morree
- Department of Biomedicine, Aarhus University, Central Jutland, Denmark
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3
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Berry CW, Olivares GH, Gallicchio L, Ramaswami G, Glavic A, Olguín P, Li JB, Fuller MT. Developmentally regulated alternate 3' end cleavage of nascent transcripts controls dynamic changes in protein expression in an adult stem cell lineage. Genes Dev 2022; 36:916-935. [PMID: 36175033 PMCID: PMC9575692 DOI: 10.1101/gad.349689.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/06/2022] [Accepted: 09/12/2022] [Indexed: 02/03/2023]
Abstract
Alternative polyadenylation (APA) generates transcript isoforms that differ in the position of the 3' cleavage site, resulting in the production of mRNA isoforms with different length 3' UTRs. Although widespread, the role of APA in the biology of cells, tissues, and organisms has been controversial. We identified >500 Drosophila genes that express mRNA isoforms with a long 3' UTR in proliferating spermatogonia but a short 3' UTR in differentiating spermatocytes due to APA. We show that the stage-specific choice of the 3' end cleavage site can be regulated by the arrangement of a canonical polyadenylation signal (PAS) near the distal cleavage site but a variant or no recognizable PAS near the proximal cleavage site. The emergence of transcripts with shorter 3' UTRs in differentiating cells correlated with changes in expression of the encoded proteins, either from off in spermatogonia to on in spermatocytes or vice versa. Polysome gradient fractionation revealed >250 genes where the long 3' UTR versus short 3' UTR mRNA isoforms migrated differently, consistent with dramatic stage-specific changes in translation state. Thus, the developmentally regulated choice of an alternative site at which to make the 3' end cut that terminates nascent transcripts can profoundly affect the suite of proteins expressed as cells advance through sequential steps in a differentiation lineage.
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Affiliation(s)
- Cameron W Berry
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gonzalo H Olivares
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Escuela de Kinesiología, Facultad de Medicina y Ciencias de la Salud, Universidad Mayor, Huechuraba 8580745, Chile
- Center of Integrative Biology (CIB), Universidad Mayor, Huechuraba 8580745, Chile
| | - Lorenzo Gallicchio
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Alvaro Glavic
- Center for Genome Regulation (CRG), Universidad de Chile, Santiago 7810000, Chile
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Department of Biology, Faculty of Sciences, Universidad de Chile, Santiago 7810000, Chile
| | - Patricio Olguín
- Drosophila Ring in Developmental Adaptations to Nutritional Stress (DRiDANS), Universidad de Chile, Santiago 7810000, Chile
- Program of Human Genetics, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Department of Neuroscience, Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
- Biomedical Neuroscience Institute (BNI), Faculty of Medicine, Universidad de Chile, Santiago 8380453, Chile
| | - Jin Billy Li
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Margaret T Fuller
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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Abstract
BACKGROUND Nonsense-mediated mRNA decay (NMD) is a eukaryotic, translation-dependent degradation pathway that targets mRNAs with premature termination codons and also regulates the expression of some mRNAs that encode full-length proteins. Although many genes express NMD-sensitive transcripts, identifying them based on short-read sequencing data remains a challenge. RESULTS To identify and analyze endogenous targets of NMD, we apply cDNA Nanopore sequencing and short-read sequencing to human cells with varying expression levels of NMD factors. Our approach detects full-length NMD substrates that are highly unstable and increase in levels or even only appear when NMD is inhibited. Among the many new NMD-targeted isoforms that our analysis identifies, most derive from alternative exon usage. The isoform-aware analysis reveals many genes with significant changes in splicing but no significant changes in overall expression levels upon NMD knockdown. NMD-sensitive mRNAs have more exons in the 3΄UTR and, for those mRNAs with a termination codon in the last exon, the length of the 3΄UTR per se does not correlate with NMD sensitivity. Analysis of splicing signals reveals isoforms where NMD has been co-opted in the regulation of gene expression, though the main function of NMD seems to be ridding the transcriptome of isoforms resulting from spurious splicing events. CONCLUSIONS Long-read sequencing enables the identification of many novel NMD-sensitive mRNAs and reveals both known and unexpected features concerning their biogenesis and their biological role. Our data provide a highly valuable resource of human NMD transcript targets for future genomic and transcriptomic applications.
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Affiliation(s)
- Evangelos D Karousis
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Foivos Gypas
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058, Basel, Switzerland
| | - Mihaela Zavolan
- Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056, Basel, Switzerland
| | - Oliver Mühlemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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Schulz L, Torres-Diz M, Cortés-López M, Hayer KE, Asnani M, Tasian SK, Barash Y, Sotillo E, Zarnack K, König J, Thomas-Tikhonenko A. Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biol 2021; 22:190. [PMID: 34183059 PMCID: PMC8240250 DOI: 10.1186/s13059-021-02411-1] [Citation(s) in RCA: 12] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/16/2021] [Indexed: 11/24/2022] Open
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 2. While "exitrons" are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that the CD19 exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed "falsitrons," that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
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MESH Headings
- Alternative Splicing
- Antibodies, Bispecific/pharmacology
- Antineoplastic Agents, Immunological/pharmacology
- Artifacts
- B-Lymphocytes/drug effects
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Base Pairing
- Base Sequence
- Cell Line, Tumor
- Datasets as Topic
- Exons
- High-Throughput Nucleotide Sequencing
- Humans
- Immunotherapy/methods
- Introns
- Models, Biological
- Nucleic Acid Conformation
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- Protein Isoforms/chemistry
- Protein Isoforms/genetics
- Protein Isoforms/immunology
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/immunology
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/immunology
- Reverse Transcription
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Affiliation(s)
- Laura Schulz
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Manuel Torres-Diz
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | | | - Katharina E Hayer
- The Bioinformatics Group, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mukta Asnani
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Sarah K Tasian
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Yoseph Barash
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Elena Sotillo
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
- Present address: Stanford Cancer Institute, 265 Campus Dr., Stanford, CA, 94305, USA
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) and Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 15, 60438, Frankfurt, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
| | - Andrei Thomas-Tikhonenko
- Division of Cancer Pathobiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
- Department of Pathology & Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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6
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Kovalak C, Donovan S, Bicknell AA, Metkar M, Moore MJ. Deep sequencing of pre-translational mRNPs reveals hidden flux through evolutionarily conserved alternative splicing nonsense-mediated decay pathways. Genome Biol 2021; 22:132. [PMID: 33941243 PMCID: PMC8091538 DOI: 10.1186/s13059-021-02309-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 10/07/2019] [Accepted: 03/02/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Alternative splicing, which generates multiple mRNA isoforms from single genes, is crucial for the regulation of eukaryotic gene expression. The flux through competing splicing pathways cannot be determined by traditional RNA-Seq, however, because different mRNA isoforms can have widely differing decay rates. Indeed, some mRNA isoforms with extremely short half-lives, such as those subject to translation-dependent nonsense-mediated decay (AS-NMD), may be completely overlooked in even the most extensive RNA-Seq analyses. RESULTS RNA immunoprecipitation in tandem (RIPiT) of exon junction complex components allows for purification of post-splicing mRNA-protein particles (mRNPs) not yet subject to translation (pre-translational mRNPs) and, therefore, translation-dependent mRNA decay. Here we compare exon junction complex RIPiT-Seq to whole cell RNA-Seq data from HEK293 cells. Consistent with expectation, the flux through known AS-NMD pathways is substantially higher than that captured by RNA-Seq. Our RIPiT-Seq also definitively demonstrates that the splicing machinery itself has no ability to detect reading frame. We identify thousands of previously unannotated splicing events; while many can be attributed to splicing noise, others are evolutionarily conserved events that produce new AS-NMD isoforms likely involved in maintenance of protein homeostasis. Several of these occur in genes whose overexpression has been linked to poor cancer prognosis. CONCLUSIONS Deep sequencing of RNAs in post-splicing, pre-translational mRNPs provides a means to identify and quantify splicing events without the confounding influence of differential mRNA decay. For many known AS-NMD targets, the nonsense-mediated decay-linked alternative splicing pathway predominates. Exon junction complex RIPiT-Seq also revealed numerous conserved but previously unannotated AS-NMD events.
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Affiliation(s)
- Carrie Kovalak
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Scott Donovan
- Present Address: Moderna, 200 Technology Square, Cambridge, MA, 02139, USA
| | - Alicia A Bicknell
- Present Address: Moderna, 200 Technology Square, Cambridge, MA, 02139, USA
| | - Mihir Metkar
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Present Address: Moderna, 200 Technology Square, Cambridge, MA, 02139, USA
| | - Melissa J Moore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
- Present Address: Moderna, 200 Technology Square, Cambridge, MA, 02139, USA.
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7
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Taniguchi-Ponciano K, Peña-Martínez E, Silva-Román G, Vela-Patiño S, Guzman-Ortiz AL, Quezada H, Gomez-Apo E, Chavez-Macias L, Mercado-Medrez S, Vargas-Ortega G, Espinosa-de-los-Monteros AL, Gonzales-Virla B, Ferreira-Hermosillo A, Espinosa-Cardenas E, Ramirez-Renteria C, Sosa E, Lopez-Felix B, Guinto G, Marrero-Rodríguez D, Mercado M. Proteomic and Transcriptomic Analysis Identify Spliceosome as a Significant Component of the Molecular Machinery in the Pituitary Tumors Derived from POU1F1- and NR5A1-Cell Lineages. Genes (Basel) 2020; 11:genes11121422. [PMID: 33261069 PMCID: PMC7760979 DOI: 10.3390/genes11121422] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Pituitary adenomas (PA) are the second most common tumor in the central nervous system and have low counts of mutated genes. Splicing occurs in 95% of the coding RNA. There is scarce information about the spliceosome and mRNA-isoforms in PA, and therefore we carried out proteomic and transcriptomic analysis to identify spliceosome components and mRNA isoforms in PA. Methods: Proteomic profile analysis was carried out by nano-HPLC and mass spectrometry with a quadrupole time-of-flight mass spectrometer. The mRNA isoforms and transcriptomic profiles were carried out by microarray technology. With proteins and mRNA information we carried out Gene Ontology and exon level analysis to identify splicing-related events. Results: Approximately 2000 proteins were identified in pituitary tumors. Spliceosome proteins such as SRSF1, U2AF1 and RBM42 among others were found in PA. These results were validated at mRNA level, which showed up-regulation of spliceosome genes in PA. Spliceosome-related genes segregate and categorize PA tumor subtypes. The PA showed alterations in CDK18 and THY1 mRNA isoforms which could be tumor specific. Conclusions: Spliceosome components are significant constituents of the PA molecular machinery and could be used as molecular markers and therapeutic targets. Splicing-related genes and mRNA-isoforms profiles characterize tumor subtypes.
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Affiliation(s)
- Keiko Taniguchi-Ponciano
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Eduardo Peña-Martínez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Gloria Silva-Román
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Sandra Vela-Patiño
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Ana Laura Guzman-Ortiz
- Laboratorio de Investigacion en Inmunologia y Proteomica, Hospital Infantil de Mexico “Federico Gomez”, Mexico City 06720, Mexico; (A.L.G.-O.); (H.Q.)
| | - Hector Quezada
- Laboratorio de Investigacion en Inmunologia y Proteomica, Hospital Infantil de Mexico “Federico Gomez”, Mexico City 06720, Mexico; (A.L.G.-O.); (H.Q.)
| | - Erick Gomez-Apo
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de México 06720, Mexico; (E.G.-A.); (L.C.-M.)
| | - Laura Chavez-Macias
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de México 06720, Mexico; (E.G.-A.); (L.C.-M.)
- Facultad de Medicina, Universidad Nacional Autonoma de México, Mexico City 04510, Mexico
| | - Sophia Mercado-Medrez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Guadalupe Vargas-Ortega
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Ana Laura Espinosa-de-los-Monteros
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Baldomero Gonzales-Virla
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Aldo Ferreira-Hermosillo
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Etual Espinosa-Cardenas
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Claudia Ramirez-Renteria
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Ernesto Sosa
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Blas Lopez-Felix
- Servicio de Neurocirugia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (B.L.-F.); (G.G.)
| | - Gerardo Guinto
- Servicio de Neurocirugia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (B.L.-F.); (G.G.)
| | - Daniel Marrero-Rodríguez
- Catedra CONACyT-Laboratorio de Endocrinologia Experimental, Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico
- Correspondence: (D.M.-R.); (M.M.); Tel.: +54-401-021 (D.M.-R. & M.M.)
| | - Moises Mercado
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Correspondence: (D.M.-R.); (M.M.); Tel.: +54-401-021 (D.M.-R. & M.M.)
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8
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Zheng D, Cho H, Wang W, Rambout X, Tian B, Maquat LE. 3'READS + RIP defines differential Staufen1 binding to alternative 3'UTR isoforms and reveals structures and sequence motifs influencing binding and polysome association. RNA 2020; 26:1621-1636. [PMID: 32796083 PMCID: PMC7566578 DOI: 10.1261/rna.076133.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/15/2020] [Indexed: 06/11/2023]
Abstract
Staufen1 (STAU1) is an RNA-binding protein (RBP) that interacts with double-stranded RNA structures and has been implicated in regulating different aspects of mRNA metabolism. Previous studies have indicated that STAU1 interacts extensively with RNA structures in coding regions (CDSs) and 3'-untranslated regions (3'UTRs). In particular, duplex structures formed within 3'UTRs by inverted-repeat Alu elements (IRAlus) interact with STAU1 through its double-stranded RNA-binding domains (dsRBDs). Using 3' region extraction and deep sequencing coupled to ribonucleoprotein immunoprecipitation (3'READS + RIP), together with reanalyzing previous STAU1 binding and RNA structure data, we delineate STAU1 interactions transcriptome-wide, including binding differences between alternative polyadenylation (APA) isoforms. Consistent with previous reports, RNA structures are dominant features for STAU1 binding to CDSs and 3'UTRs. Overall, relative to short 3'UTR counterparts, longer 3'UTR isoforms of genes have stronger STAU1 binding, most likely due to a higher frequency of RNA structures, including specific IRAlus sequences. Nevertheless, a sizable fraction of genes express transcripts showing the opposite trend, attributable to AU-rich sequences in their alternative 3'UTRs that may recruit antagonistic RBPs and/or destabilize RNA structures. Using STAU1-knockout cells, we show that strong STAU1 binding to mRNA 3'UTRs generally enhances polysome association. However, IRAlus generally have little impact on STAU1-mediated polysome association despite having strong interactions with the protein. Taken together, our work reveals complex interactions of STAU1 with its cognate RNA substrates. Our data also shed light on distinct post-transcriptional fates for the widespread APA isoforms in mammalian cells.
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Affiliation(s)
- Dinghai Zheng
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Hana Cho
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Wei Wang
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry, and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Program in Gene Expression and Regulation, and Center for Systems and Computational Biology, Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA
- Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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9
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Mishra SK, Muthye V, Kandoi G. Computational Methods for Predicting Functions at the mRNA Isoform Level. Int J Mol Sci 2020; 21:ijms21165686. [PMID: 32784445 PMCID: PMC7460821 DOI: 10.3390/ijms21165686] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 07/13/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 11/16/2022] Open
Abstract
Multiple mRNA isoforms of the same gene are produced via alternative splicing, a biological mechanism that regulates protein diversity while maintaining genome size. Alternatively spliced mRNA isoforms of the same gene may sometimes have very similar sequence, but they can have significantly diverse effects on cellular function and regulation. The products of alternative splicing have important and diverse functional roles, such as response to environmental stress, regulation of gene expression, human heritable, and plant diseases. The mRNA isoforms of the same gene can have dramatically different functions. Despite the functional importance of mRNA isoforms, very little has been done to annotate their functions. The recent years have however seen the development of several computational methods aimed at predicting mRNA isoform level biological functions. These methods use a wide array of proteo-genomic data to develop machine learning-based mRNA isoform function prediction tools. In this review, we discuss the computational methods developed for predicting the biological function at the individual mRNA isoform level.
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10
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Patrick R, Humphreys DT, Janbandhu V, Oshlack A, Ho JW, Harvey RP, Lo KK. Sierra: discovery of differential transcript usage from polyA-captured single-cell RNA-seq data. Genome Biol 2020; 21:167. [PMID: 32641141 PMCID: PMC7341584 DOI: 10.1186/s13059-020-02071-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [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: 12/06/2019] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
High-throughput single-cell RNA-seq (scRNA-seq) is a powerful tool for studying gene expression in single cells. Most current scRNA-seq bioinformatics tools focus on analysing overall expression levels, largely ignoring alternative mRNA isoform expression. We present a computational pipeline, Sierra, that readily detects differential transcript usage from data generated by commonly used polyA-captured scRNA-seq technology. We validate Sierra by comparing cardiac scRNA-seq cell types to bulk RNA-seq of matched populations, finding significant overlap in differential transcripts. Sierra detects differential transcript usage across human peripheral blood mononuclear cells and the Tabula Muris, and 3 'UTR shortening in cardiac fibroblasts. Sierra is available at https://github.com/VCCRI/Sierra .
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Affiliation(s)
- Ralph Patrick
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - David T. Humphreys
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - Vaibhao Janbandhu
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
| | - Alicia Oshlack
- Murdoch Children’s Research Institute, Parkville, 3052 Victoria Australia
- Peter MacCallum Cancer Centre, Research Division, 305 Grattan Street, Melbourne, 3000 Victoria Australia
| | - Joshua W.K. Ho
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China
| | - Richard P. Harvey
- Victor Chang Cardiac Research Institute, 405 Liverpool St., Darlinghurst, 2010 Australia
- St. Vincent’s Clinical School, UNSW Sydney, Kensington, 2052 Australia
- School of Biotechnology and Biomolecular Science, UNSW Sydney, Kensington, 2052 Australia
| | - Kitty K. Lo
- School of Mathematics and Statistics, Faculty of Science, The University of Sydney, Camperdown, 2006 Australia
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11
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Assunto A, Ferrara U, De Luca A, Pivonello C, Lombardo L, Piscitelli A, Tortora C, Pinna V, Daniele P, Pivonello R, Russo MG, Limongelli G, Colao A, Tartaglia M, Strisciuglio P, Melis D. Isoform-specific NF1 mRNA levels correlate with disease severity in Neurofibromatosis type 1. Orphanet J Rare Dis 2019; 14:261. [PMID: 31730495 DOI: 10.1186/s13023-019-1223-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 06/08/2019] [Accepted: 10/09/2019] [Indexed: 12/29/2022] Open
Abstract
Background Neurofibromatosis type 1 (NF1) is characterized by an extreme clinical variability both within and between families that cannot be explained solely by the nature of the pathogenic NF1 gene mutations. A proposed model hypothesizes that variation in the levels of protein isoforms generated via alternative transcript processing acts as modifier and contributes to phenotypic variability. Results Here we used real-time quantitative PCR to investigate the levels of two major NF1 mRNA isoforms encoding proteins differing in their ability to control RAS signaling (isoforms I and II) in the peripheral blood leukocytes of 138 clinically well-characterized NF1 patients and 138 aged-matched healthy controls. As expected, expression analysis showed that NF1 isoforms I and II levels were significantly lower in patients than controls. Notably, these differences were more evident when patients were stratified according to the severity of phenotype. Moreover, a correlation was identified when comparing the levels of isoform I mRNA and the severity of NF1 features, with statistically significant lower levels associated with a severe phenotype (i.e., occurrence of learning disability/intellectual disability, optic gliomas and/or other neoplasias, and/or cerebrovascular disease) as well as in patients with cognitive impairment. Conclusions The present findings provide preliminary evidence for a role of circuits controlling NF1 transcript processing in modulating NF1 expressivity, and document an association between the levels of neurofibromin isoform I mRNA and the severity of phenotype and cognitive impairment in NF1.
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12
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Moqtaderi Z, Geisberg JV. Probing In Vivo Structure of Individual mRNA 3' Isoforms Using Dimethyl Sulfate. Curr Protoc Mol Biol 2019; 128:e99. [PMID: 31503415 PMCID: PMC6777956 DOI: 10.1002/cpmb.99] [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] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The DMS region extraction and deep sequencing (DREADS) procedure was designed to probe RNA structure in vivo and to link this structural information to specific 3' isoforms. Growing cells are treated with the alkylating agent dimethyl sulfate (DMS), which enters easily into cells and modifies RNA molecules at solvent-exposed A and C residues. RNA is isolated, and sequencing libraries are constructed in a manner that preserves the identities of individual mRNA isoforms arising from alternative cleavage/polyadenylation sites. During the cDNA synthesis step of library construction, the progress of reverse transcriptase (RT) is blocked when it encounters a DMS modification on the RNA, leading to disproportionate cDNA termination adjacent to DMS-modified positions. After paired-end deep sequencing, the downstream end of each sequenced fragment is mapped to a specific cleavage/poly(A) site representing an individual mRNA 3' isoform. The upstream mapped end of the sequenced fragment defines where the RT reaction stopped. Over the population of all sequenced fragments derived from a particular isoform, A and C positions that are overrepresented next to the upstream endpoints in the DMS sample (relative to a parallel untreated control) are inferred to have been DMS modified, and hence solvent exposed. This method thus allows in vivo structural information obtained using DMS to be linked to individual mRNA 3' isoforms. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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13
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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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14
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Lou H, Li H, Ho KJ, Cai LL, Huang AS, Shank TR, Verneris MR, Nickerson ML, Dean M, Anderson SK. The Human TET2 Gene Contains Three Distinct Promoter Regions With Differing Tissue and Developmental Specificities. Front Cell Dev Biol 2019; 7:99. [PMID: 31231651 PMCID: PMC6566030 DOI: 10.3389/fcell.2019.00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 02/21/2019] [Accepted: 05/23/2019] [Indexed: 12/13/2022] Open
Abstract
Tet methylcytosine dioxygenase 2 (TET2) is a tumor suppressor gene that is inactivated in a wide range of hematological cancers. TET2 enzymatic activity converts 5-methylcytosine (5-mC) into 5-hydroxymethylcytosine (5-hmC), an essential step in DNA demethylation. Human TET2 is highly expressed in pluripotent cells and down-regulated in differentiated cells: however, transcriptional regulation of the human TET2 gene has not been investigated in detail. Here we define three promoters within a 2.5 kb region located ∼ 87 kb upstream of the first TET2 coding exon. The three promoters, designated as Pro1, Pro2, and Pro3, generate three alternative first exons, and their presence in TET2 mRNAs varies with cell type and developmental stage. In general, all three TET2 transcripts are more highly expressed in human tissues rich in hematopoietic stem cells, such as spleen and bone marrow, compared to other tissues, such as brain and kidney. Transcripts from Pro2 are expressed by a broad range of tissues and at a significantly higher level than Pro1 or Pro3 transcripts. Pro3 transcripts were highly expressed by embryoid bodies generated from the H9 ES cell line, and the major Pro3 transcript is an alternatively spliced mRNA isoform that produces a truncated TET2 protein lacking the catalytic domain. Our study demonstrates distinct tissue-specific mechanisms of TET2 transcriptional regulation during early pluripotent states and in differentiated cell types.
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Affiliation(s)
- Hong Lou
- Laboratory of Translational Genomics, Frederick National Laboratory for Cancer Research, Gaithersburg, MD, United States
| | - Hongchuan Li
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States
| | - Kevin J Ho
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Luke L Cai
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Andy S Huang
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
| | - Tyler R Shank
- Department of Pediatrics, Center for Cancer and Blood Disorders, University of Colorado Denver, Denver, CO, United States
| | - Michael R Verneris
- Department of Pediatrics, Center for Cancer and Blood Disorders, University of Colorado Denver, Denver, CO, United States
| | - Michael L Nickerson
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD, United States
| | - Michael Dean
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Gaithersburg, MD, United States
| | - Stephen K Anderson
- Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, MD, United States.,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, United States
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15
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Chesnokova E, Zuzina A, Bal N, Vinarskaya A, Roshchin M, Artyuhov A, Dashinimaev E, Aseyev N, Balaban P, Kolosov P. Experiments with Snails Add to Our Knowledge about the Role of aPKC Subfamily Kinases in Learning. Int J Mol Sci 2019; 20:E2117. [PMID: 31035721 DOI: 10.3390/ijms20092117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 03/26/2019] [Revised: 04/26/2019] [Accepted: 04/26/2019] [Indexed: 12/28/2022] Open
Abstract
Protein kinase Mζ is considered important for memory formation and maintenance in different species, including invertebrates. PKMζ participates in multiple molecular pathways in neurons, regulating translation initiation rate, AMPA receptors turnover, synaptic scaffolding assembly, and other processes. Here, for the first time, we established the sequence of mRNA encoding PKMζ homolog in land snail Helix lucorum. We annotated important features of this mRNA: domains, putative capping sites, translation starts, and splicing sites. We discovered that this mRNA has at least two isoforms, and one of them lacks sequence encoding C1 domain. C1 deletion may be unique for snail because it has not been previously found in other species. We performed behavioral experiments with snails, measured expression levels of identified isoforms, and confirmed that their expression correlates with one type of learning.
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16
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Deslattes Mays A, Schmidt M, Graham G, Tseng E, Baybayan P, Sebra R, Sanda M, Mazarati JB, Riegel A, Wellstein A. Single-Molecule Real-Time (SMRT) Full-Length RNA-Sequencing Reveals Novel and Distinct mRNA Isoforms in Human Bone Marrow Cell Subpopulations. Genes (Basel) 2019; 10:genes10040253. [PMID: 30934798 PMCID: PMC6523297 DOI: 10.3390/genes10040253] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 02/19/2019] [Revised: 03/19/2019] [Accepted: 03/22/2019] [Indexed: 11/16/2022] Open
Abstract
Hematopoietic cells are continuously replenished from progenitor cells that reside in the bone marrow. To evaluate molecular changes during this process, we analyzed the transcriptomes of freshly harvested human bone marrow progenitor (lineage-negative) and differentiated (lineage-positive) cells by single-molecule real-time (SMRT) full-length RNA-sequencing. This analysis revealed a ~5-fold higher number of transcript isoforms than previously detected and showed a distinct composition of individual transcript isoforms characteristic for bone marrow subpopulations. A detailed analysis of messenger RNA (mRNA) isoforms transcribed from the ANXA1 and EEF1A1 loci confirmed their distinct composition. The expression of proteins predicted from the transcriptome analysis was evaluated by mass spectrometry and validated previously unknown protein isoforms predicted e.g., for EEF1A1. These protein isoforms distinguished the lineage negative cell population from the lineage positive cell population. Finally, transcript isoforms expressed from paralogous gene loci (e.g., CFD, GATA2, HLA-A, B, and C) also distinguished cell subpopulations but were only detectable by full-length RNA sequencing. Thus, qualitatively distinct transcript isoforms from individual genomic loci separate bone marrow cell subpopulations indicating complex transcriptional regulation and protein isoform generation during hematopoiesis.
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Affiliation(s)
- Anne Deslattes Mays
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
- The Jackson Laboratory, Farmington, CT 06032, USA.
| | - Marcel Schmidt
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
| | - Garrett Graham
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
| | | | | | - Robert Sebra
- Icahn School of Medicine at Mount Sinai, Institute for Genomics and Multi-scale Biology, New York, NY 10029, USA.
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
| | - Jean-Baptiste Mazarati
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
- Biomedical Center, National Reference Laboratory, Kigali, Rwanda.
| | - Anna Riegel
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA.
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17
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Mariotti FR, Petrini S, Ingegnere T, Tumino N, Besi F, Scordamaglia F, Munari E, Pesce S, Marcenaro E, Moretta A, Vacca P, Moretta L. PD-1 in human NK cells: evidence of cytoplasmic mRNA and protein expression. Oncoimmunology 2018; 8:1557030. [PMID: 30723590 PMCID: PMC6350684 DOI: 10.1080/2162402x.2018.1557030] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [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: 07/02/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 01/01/2023] Open
Abstract
Under physiological conditions, PD-1/PD-L1 interactions regulate unwanted over-reactions of immune cells and contribute to maintain peripheral tolerance. However, in tumor microenvironment, this interaction may greatly compromise the immune-mediated anti-tumor activity. PD-1+ NK cells have been detected in high percentage in peripheral blood and ascitic fluid of ovarian carcinoma patients. To acquire information on PD-1 expression and physiology in human NK cells, we analyzed whether PD-1 mRNA and protein are present in resting, surface PD-1−, NK cells from healthy donors. Both different splicing isoforms of PD-1 mRNA and a cytoplasmic pool of PD-1 protein were detected. Similar results were obtained also from both in vitro-activated and tumor-associated NK cells. PD-1 mRNA and protein were higher in CD56dim than in CD56bright NK cells. Confocal microscopy analyses revealed that PD-1 protein is present in virtually all NK cells analyzed. The present findings are compatible with a rapid surface expression of PD-1 in NK cells in response to appropriate, still undefined, stimuli.
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Affiliation(s)
| | - Stefania Petrini
- Confocal Microscopy Core Facility, Research Center, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
| | - Tiziano Ingegnere
- Department of Immunology, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
| | - Nicola Tumino
- Department of Immunology, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Besi
- Department of Immunology, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
| | | | - Enrico Munari
- Department of Pathology, Sacro Cuore Don Calabria Hospital, Negrar, Italy.,Department of Pathology AOUI, University of Verona, Verona, Italy
| | - Silvia Pesce
- Department of Experimental Medicine (DIMES), University of Genova, Genoa, Italy
| | - Emanuela Marcenaro
- Department of Experimental Medicine (DIMES), University of Genova, Genoa, Italy.,Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Alessandro Moretta
- Department of Experimental Medicine (DIMES), University of Genova, Genoa, Italy.,Center of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Paola Vacca
- Department of Immunology, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
| | - Lorenzo Moretta
- Department of Immunology, IRCSS Bambino Gesù Children's Hospital, Rome, Italy
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18
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Munkley J, Maia TM, Ibarluzea N, Livermore KE, Vodak D, Ehrmann I, James K, Rajan P, Barbosa-Morais NL, Elliott DJ. Androgen-dependent alternative mRNA isoform expression in prostate cancer cells. F1000Res 2018; 7:1189. [PMID: 30271587 PMCID: PMC6143958 DOI: 10.12688/f1000research.15604.1] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Background: Androgen steroid hormones are key drivers of prostate cancer. Previous work has shown that androgens can drive the expression of alternative mRNA isoforms as well as transcriptional changes in prostate cancer cells. Yet to what extent androgens control alternative mRNA isoforms and how these are expressed and differentially regulated in prostate tumours is unknown. Methods: Here we have used RNA-Seq data to globally identify alternative mRNA isoform expression under androgen control in prostate cancer cells, and profiled the expression of these mRNA isoforms in clinical tissue. Results: Our data indicate androgens primarily switch mRNA isoforms through alternative promoter selection. We detected 73 androgen regulated alternative transcription events, including utilisation of 56 androgen-dependent alternative promoters, 13 androgen-regulated alternative splicing events, and selection of 4 androgen-regulated alternative 3' mRNA ends. 64 of these events are novel to this study, and 26 involve previously unannotated isoforms. We validated androgen dependent regulation of 17 alternative isoforms by quantitative PCR in an independent sample set. Some of the identified mRNA isoforms are in genes already implicated in prostate cancer (including LIG4, FDFT1 and RELAXIN), or in genes important in other cancers (e.g. NUP93 and MAT2A). Importantly, analysis of transcriptome data from 497 tumour samples in the TGCA prostate adenocarcinoma (PRAD) cohort identified 13 mRNA isoforms (including TPD52, TACC2 and NDUFV3) that are differentially regulated in localised prostate cancer relative to normal tissue, and 3 ( OSBPL1A, CLK3 and TSC22D3) which change significantly with Gleason grade and tumour stage. Conclusions: Our findings dramatically increase the number of known androgen regulated isoforms in prostate cancer, and indicate a highly complex response to androgens in prostate cancer cells that could be clinically important.
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Affiliation(s)
- Jennifer Munkley
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Teresa M. Maia
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
- VIB Proteomics Core, Albert Baertsoenkaai 3, Ghent, 9000, Belgium
| | - Nekane Ibarluzea
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
- Biocruces Bizkaia Health Research Institute, Cruces University Hospital, Barakaldo, 48903, Spain
- Centre for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Valencia, 46010, Spain
| | - Karen E. Livermore
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Daniel Vodak
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Ingrid Ehrmann
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
| | - Katherine James
- Interdisciplinary Computing and Complex BioSystems Research Group, Newcastle University, Newcastle upon Tyne, NE4 5TG, UK
- Life and Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK
| | - Prabhakar Rajan
- Barts Cancer Institute, Queen Mary University of London, John Vane Science Centre, London, EC1M 6BQ, UK
| | - Nuno L. Barbosa-Morais
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, 1649-028, Portugal
| | - David J. Elliott
- Institute of Genetic Medicine, University of Newcastle, Newcastle upon Tyne, Newcastle, NE1 3BZ, UK
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19
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Lattimore VL, Pearson JF, Currie MJ, Spurdle AB, Robinson BA, Walker LC. Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants. Front Oncol 2018; 8:140. [PMID: 29774201 PMCID: PMC5943536 DOI: 10.3389/fonc.2018.00140] [Citation(s) in RCA: 6] [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: 11/27/2017] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess BRCA1 and BRCA2 mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 BRCA1 and 28 BRCA2 oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates (n > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across BRCA1 and BRCA2 can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of BRCA1 and BRCA2 mRNA aberrations associated with sequence variants of uncertain clinical significance.
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Affiliation(s)
- Vanessa L Lattimore
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - John F Pearson
- Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand.,Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Margaret J Currie
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | - Bridget A Robinson
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Canterbury Regional Cancer and Haematology Service, Canterbury District Health Board, Christchurch Hospital, Christchurch, New Zealand
| | - Logan C Walker
- Mackenzie Cancer Research Group, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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20
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Norman KL, Chen TC, Zeiner G, Sarnow P. Precursor microRNA-122 inhibits synthesis of Insig1 isoform mRNA by modulating polyadenylation site usage. RNA 2017; 23:1886-1893. [PMID: 28928276 PMCID: PMC5689008 DOI: 10.1261/rna.063099.117] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 09/09/2017] [Indexed: 06/07/2023]
Abstract
The insulin-induced gene 1 protein (Insig1) inhibits the cholesterol biosynthesis pathway by retaining transcription factor SREBP in the endoplasmic reticulum, and by causing the degradation of HMGCR, the rate-limiting enzyme in cholesterol biosynthesis. Liver-specific microRNA miR-122, on the other hand, enhances cholesterol biosynthesis by an unknown mechanism. We have found that Insig1 mRNAs are generated by alternative cleavage and polyadenylation, resulting in specific isoform mRNA species. During high cholesterol abundance, the short 1.4-kb Insig1 mRNA was found to be preferentially translated to yield Insig1 protein. Precursor molecules of miR-122 down-regulated the translation of the 1.4-kb Insig1 isoform mRNA by interfering with the usage of the promoter-proximal cleavage-polyadenylation site that gives rise to the 1.4-kb Insig1 mRNA. These findings argue that precursor miR-122 molecules modulate polyadenylation site usage in Insig1 mRNAs, resulting in down-regulation of Insig1 protein abundance. Thus, precursor microRNAs may have hitherto undetected novel functions in nuclear gene expression.
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Affiliation(s)
- Kara L Norman
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Tzu-Chun Chen
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Gusti Zeiner
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Peter Sarnow
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California 94305, USA
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21
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Pelechano V. From transcriptional complexity to cellular phenotypes: Lessons from yeast. Yeast 2017; 34:475-482. [PMID: 28866863 DOI: 10.1002/yea.3277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 07/10/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/12/2022] Open
Abstract
Pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves thousands of coding and non-coding RNAs. However, to date, the biological impact of transcriptome complexity is still poorly understood. Here I will review how subtle variations of the transcriptome can lead to divergent cellular phenotypes by fine-tuning both its coding potential and regulation. I will discuss strategies that can be used to link molecular variations with divergent biological outcomes. Finally, I will explore the implication of transcriptional complexity for our understanding of gene expression in the context of cell-to-cell phenotypic variability. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, P-Box 1031, 171 21, Solna, Sweden
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22
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Abstract
The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study.
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Affiliation(s)
- Luis P Iñiguez
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
| | - Georgina Hernández
- Programa de Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México Cuernavaca, México
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23
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López-Díez R, Rastrojo A, Villate O, Aguado B. Complex tissue-specific patterns and distribution of multiple RAGE splice variants in different mammals. Genome Biol Evol 2014; 5:2420-35. [PMID: 24273313 PMCID: PMC3879976 DOI: 10.1093/gbe/evt188] [Citation(s) in RCA: 30] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The receptor for advanced glycosylation end products (RAGE) is a multiligand receptor involved in diverse cell signaling pathways. Previous studies show that this gene expresses several splice variants in human, mouse, and dog. Alternative splicing (AS) plays an important role in expanding transcriptomic and proteomic diversity, and it has been related to disease. AS is also one of the main evolutionary mechanisms in mammalian genomes. However, limited information is available regarding the AS of RAGE in a wide context of mammalian tissues. In this study, we examined in detail the different RAGE mRNAs generated by AS from six mammals, including two primates (human and monkey), two artiodactyla (cow and pig), and two rodentia (mouse and rat) in 6–18 different tissues including fetal, adult, and tumor. By nested reverse transcription-polymerase chain reaction (RT-PCR) we identified a high number of splice variants including noncoding transcripts and predicted coding ones with different potential protein modifications affecting mainly the transmembrane and ligand-binding domains that could influence their biological function. However, analysis of RNA-seq data enabled detecting only the most abundant splice variants. More than 80% of the detected RT-PCR variants (87 of 101 transcripts) are novel (different exon/intron structure to the previously described ones), and interestingly, 20–60% of the total transcripts (depending on the species) are noncoding ones that present tissue specificity. Our results suggest that RAGE undergoes extensive AS in mammals, with different expression patterns among adult, fetal, and tumor tissues. Moreover, most splice variants seem to be species specific, especially the noncoding variants, with only two (canonical human Tv1-RAGE, and human N-truncated or Tv10-RAGE) conserved among the six different species. This could indicate a special evolution pattern of this gene at mRNA level.
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Affiliation(s)
- Raquel López-Díez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid (CSIC-UAM), Spain
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Moqtaderi Z, Geisberg JV, Struhl K. Secondary structures involving the poly(A) tail and other 3' sequences are major determinants of mRNA isoform stability in yeast. Microb Cell 2014; 1:137-139. [PMID: 25279376 PMCID: PMC4178928 DOI: 10.15698/mic2014.04.140] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In Saccharomyces cerevisiae, previous measurements of mRNA
stabilities have been determined on a per-gene basis. We and others have
recently shown that yeast genes give rise to a highly heterogeneous population
of mRNAs due to extensive alternative 3’ end formation. Typical genes can have
fifty or more distinct mRNA isoforms with 3’ endpoints differing by as little as
one and as many as hundreds of nucleotides. In our recent paper [Geisberg
et al. Cell (2014) 156: 812-824] we measured half-lives of
individual mRNA isoforms in Saccharomyces cerevisiae by using
the anchor away method for the rapid removal of Rpb1, the largest subunit of RNA
Polymerase II, from the nucleus, followed by direct RNA sequencing of the
cellular mRNA population over time. Combining these two methods allowed us to
determine half-lives for more than 20,000 individual mRNA isoforms originating
from nearly 5000 yeast genes. We discovered that different 3’ mRNA isoforms
arising from the same gene can have widely different stabilities, and that such
half-life variability across mRNA isoforms from a single gene is highly
prevalent in yeast cells. Determining half-lives for many different mRNA
isoforms from the same genes allowed us to identify hundreds of RNA sequence
elements involved in the stabilization and destabilization of individual
isoforms. In many cases, the poly(A) tail is likely to participate in the
formation of stability-enhancing secondary structures at mRNA 3’ ends. Our
results point to an important role for mRNA structure at 3’ termini in governing
transcript stability, likely by reducing the interaction of the mRNA with the
degradation apparatus.
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Affiliation(s)
- Zarmik Moqtaderi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Joseph V Geisberg
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
| | - Kevin Struhl
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
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25
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Pavlidou A, Dalamaga M, Kroupis C, Konstantoudakis G, Belimezi M, Athanasas G, Dimas K. Survivin isoforms and clinicopathological characteristics in colorectal adenocarcinomas using real-time qPCR. World J Gastroenterol 2011; 17:1614-21. [PMID: 21472129 PMCID: PMC3070134 DOI: 10.3748/wjg.v17.i12.1614] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/01/2010] [Accepted: 12/08/2010] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate three isoforms of survivin in colorectal adenocarcinomas.
METHODS: We used the LightCycler Technology (Roche), along with a common forward primer and reverse primers specific for the splice variants and two common hybridization probes labeled with fluorescein and LightCycler-Red fluorophore (LC-Red 640). Real time quantitative polymerase chain reaction (PCR) was performed on cDNAs from 52 tumor specimens from colorectal cancer patients and 10 unrelated normal colorectal tissues. In the patients group, carcinoembryonic antigen (CEA) and CA19-9 tumor markers were also measured immunochemically.
RESULTS: Wild type survivin mRNA isoform was expressed in 48% of the 52 tumor samples, survivin-2b in 38% and survivin-ΔΕx3 in 29%, while no expression was found in normal tissues. The mRNA expression of wild type survivin presented a significant correlation with the expression of the ratio of survivin-2b, survivin-ΔΕx3, survivin-2b/wild type survivin and survivin-ΔΕx3/wild type survivin (P < 0.001). The mRNA expression of wild-survivin and survivin-ΔΕx3 was related with tumor size and invasion (P = 0.006 and P < 0.005, respectively). A significant difference was found between survivin-2b and morphologic cancer type. Also, the ratio of survivin-ΔEx3/wild-survivin was significantly associated with prognosis. No association was observed between the three isoforms and grade, metastasis, Dukes stage and gender. The three isoforms were not correlated with CEA and CA19-9.
CONCLUSION: Survivin isoforms may play a role in cell apoptosis and their quantification could provide information about clinical management of patients suffering from colorectal cancer.
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