1
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Volegova MP, Brown LE, Banerjee U, Dries R, Sharma B, Kennedy A, Porco JA, George RE. The MYCN 5' UTR as a therapeutic target in neuroblastoma. Cell Rep 2024; 43:114134. [PMID: 38662542 PMCID: PMC11284644 DOI: 10.1016/j.celrep.2024.114134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/07/2024] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Tumor MYCN amplification is seen in high-risk neuroblastoma, yet direct targeting of this oncogenic transcription factor has been challenging. Here, we take advantage of the dependence of MYCN-amplified neuroblastoma cells on increased protein synthesis to inhibit the activity of eukaryotic translation initiation factor 4A1 (eIF4A1) using an amidino-rocaglate, CMLD012824. Consistent with the role of this RNA helicase in resolving structural barriers in 5' untranslated regions (UTRs), CMLD012824 increased eIF4A1 affinity for polypurine-rich 5' UTRs, including that of the MYCN and associated transcripts with critical roles in cell proliferation. CMLD012824-mediated clamping of eIF4A1 spanned the full lengths of mRNAs, while translational inhibition was mediated through 5' UTR binding in a cap-dependent and -independent manner. Finally, CMLD012824 led to growth inhibition in MYCN-amplified neuroblastoma models without generalized toxicity. Our studies highlight the key role of eIF4A1 in MYCN-amplified neuroblastoma and demonstrate the therapeutic potential of disrupting its function.
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Affiliation(s)
- Marina P Volegova
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Lauren E Brown
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Ushashi Banerjee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Ruben Dries
- Boston University School of Medicine, Computational Biomedicine, Boston, MA, USA
| | - Bandana Sharma
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alyssa Kennedy
- Boston Children's Cancer and Blood Disorders Center, Pediatric Hematology/Oncology, Boston, MA, USA
| | - John A Porco
- Boston University, Center for Molecular Discovery (BU-CMD), Boston, MA, USA; Boston University, Department of Chemistry, Boston, MA, USA
| | - Rani E George
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
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2
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O’Connor PBF, Mahony J, Casey E, Baranov PV, van Sinderen D, Yordanova MM. Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection. Microbiol Spectr 2024; 12:e0398923. [PMID: 38451091 PMCID: PMC10986495 DOI: 10.1128/spectrum.03989-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacteria have evolved diverse defense mechanisms to counter bacteriophage attacks. Genetic programs activated upon infection characterize phage-host molecular interactions and ultimately determine the outcome of the infection. In this study, we applied ribosome profiling to monitor protein synthesis during the early stages of sk1 bacteriophage infection in Lactococcus cremoris. Our analysis revealed major changes in gene expression within 5 minutes of sk1 infection. Notably, we observed a specific and severe downregulation of several pyr operons which encode enzymes required for uridine monophosphate biosynthesis. Consistent with previous findings, this is likely an attempt of the host to starve the phage of nucleotides it requires for propagation. We also observed a gene expression response that we expect to benefit the phage. This included the upregulation of 40 ribosome proteins that likely increased the host's translational capacity, concurrent with a downregulation of genes that promote translational fidelity (lepA and raiA). In addition to the characterization of host-phage gene expression responses, the obtained ribosome profiling data enabled us to identify two putative recoding events as well as dozens of loci currently annotated as pseudogenes that are actively translated. Furthermore, our study elucidated alterations in the dynamics of the translation process, as indicated by time-dependent changes in the metagene profile, suggesting global shifts in translation rates upon infection. Additionally, we observed consistent modifications in the ribosome profiles of individual genes, which were apparent as early as 2 minutes post-infection. The study emphasizes our ability to capture rapid alterations of gene expression during phage infection through ribosome profiling. IMPORTANCE The ribosome profiling technology has provided invaluable insights for understanding cellular translation and eukaryotic viral infections. However, its potential for investigating host-phage interactions remains largely untapped. Here, we applied ribosome profiling to Lactococcus cremoris cultures infected with sk1, a major infectious agent in dairy fermentation processes. This revealed a profound downregulation of genes involved in pyrimidine nucleotide synthesis at an early stage of phage infection, suggesting an anti-phage program aimed at restricting nucleotide availability and, consequently, phage propagation. This is consistent with recent findings and contributes to our growing appreciation for the role of nucleotide limitation as an anti-viral strategy. In addition to capturing rapid alterations in gene expression levels, we identified translation occurring outside annotated regions, as well as signatures of non-standard translation mechanisms. The gene profiles revealed specific changes in ribosomal densities upon infection, reflecting alterations in the dynamics of the translation process.
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Affiliation(s)
- Patrick B. F. O’Connor
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
- EIRNA Bio, Bioinnovation Hub, Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Eoghan Casey
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Pavel V. Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
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3
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Sokabe M, Fraser CS. It's a competitive business. eLife 2024; 13:e96304. [PMID: 38393777 PMCID: PMC10890784 DOI: 10.7554/elife.96304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
A new in vitro system called Rec-Seq sheds light on how mRNA molecules compete for the machinery that translates their genetic sequence into proteins.
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Affiliation(s)
- Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
| | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, Davis, United States
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4
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Soto I, Couvillion M, Hansen KG, McShane E, Moran JC, Barrientos A, Churchman LS. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes. Genome Biol 2022; 23:170. [PMID: 35945592 PMCID: PMC9361522 DOI: 10.1186/s13059-022-02732-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 07/18/2022] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome. RESULTS We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways. CONCLUSIONS Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.
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Affiliation(s)
- Iliana Soto
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Mary Couvillion
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Katja G Hansen
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Erik McShane
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - J Conor Moran
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - L Stirling Churchman
- Blavatnik Institute, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
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5
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Liu X, Huang H, Karbstein K. Using DMS-MaPseq to Uncover the Roles of DEAD-box Proteins in Ribosome Assembly. Methods 2022; 204:249-257. [PMID: 35550176 PMCID: PMC10152975 DOI: 10.1016/j.ymeth.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/27/2022] [Accepted: 05/05/2022] [Indexed: 12/20/2022] Open
Abstract
DMS (dimethylsulfate) is a time-tested chemical probe for nucleic acid secondary structure that has recently re-emerged as a powerful tool to study RNA structure and structural changes, by coupling it to high throughput sequencing techniques. This variant, termed DMS-MaPseq, allows for mapping of all RNAs in a cell at the same time. However, if an RNA adopts different structures, for example during the assembly of an RNA-protein complex, or as part of its functional cycle, then DMS-MaPseq cannot differentiate between these structures, and an ensemble average will be produced. This is especially challenging for long-lived RNAs, such as ribosomes, whose steady-state abundance far exceeds that of any assembly intermediates, rendering those inaccessible to DMS-MaPseq on total RNAs. These challenges can be overcome by purification of assembly intermediates stalled at specific assembly steps (or steps in the functional cycle), via a combination of affinity tags and mutants stalled at defined steps, and subsequent DMS probing of these intermediates. Interpretation of the differences in DMS accessibility is facilitated by additional structural information, e.g. from cryo-EM experiments, available for many functional RNAs. While this approach is generally useful for studying RNA folding or conformational changes within RNA-protein complexes, it can be particularly valuable for studying the role(s) of DEAD-box proteins, as these tend to lead to larger conformational rearrangements, often resulting from the release of an RNA-binding protein from a bound RNA. Here we provide an adaptation of the DMS-MaPseq protocol to study RNA conformational transitions during ribosome assembly, which addresses the challenges arising from the presence of many assembly intermediates, all at concentrations far below that of mature ribosomes. While this protocol was developed for the yeast S. cerevisiae, we anticipate that it should be readily transferable to other model organisms for which affinity purification has been established.
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6
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Douka K, Agapiou M, Birds I, Aspden JL. Optimization of Ribosome Footprinting Conditions for Ribo-Seq in Human and Drosophila melanogaster Tissue Culture Cells. Front Mol Biosci 2022; 8:791455. [PMID: 35145996 PMCID: PMC8822167 DOI: 10.3389/fmolb.2021.791455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/03/2021] [Indexed: 11/22/2022] Open
Abstract
Our understanding of mRNA translation and its regulation has been transformed by the development of ribosome profiling. This approach relies upon RNase footprinting of translating ribosomes in a precise manner to generate an accurate snapshot of ribosome positions with nucleotide resolution. Here we tested a variety of conditions, which contribute to the preciseness of ribosome footprinting and therefore the success of ribosome profiling. We found that NaCl concentration, RNaseI source, RNaseI amount, and temperature of footprinting all contributed to the quality of ribosome footprinting in human neuroblastoma SH-SY5Y cells. These ideal conditions for footprinting also improved footprint quality when used with Drosophila melanogaster S2 cells. Footprinting under the same conditions generated different footprints sizes and framing patterns in human and D. melanogaster cells. We also found that treatment of S2 cells with cycloheximide prior to footprinting impacted the distribution of footprints across ORFs, without affecting overall read length distribution and framing pattern, as previously found in other organisms. Together our results indicate that a variety of factors affect ribosome footprint quality and the nature of precise footprinting varies across species.
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Affiliation(s)
- Katerina Douka
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Michaela Agapiou
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Isabel Birds
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Julie L. Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
- LeedsOmics, University of Leeds, Leeds, United Kingdom
- *Correspondence: Julie L. Aspden,
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7
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Shirokikh NE. Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells. Crit Rev Biochem Mol Biol 2021; 57:261-304. [PMID: 34852690 DOI: 10.1080/10409238.2021.2006599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.
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Affiliation(s)
- Nikolay E Shirokikh
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
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8
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Douka K, Birds I, Wang D, Kosteletos A, Clayton S, Byford A, Vasconcelos EJR, O'Connell MJ, Deuchars J, Whitehouse A, Aspden JL. Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation. RNA (NEW YORK, N.Y.) 2021; 27:1082-1101. [PMID: 34193551 PMCID: PMC8370745 DOI: 10.1261/rna.078782.121] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/22/2021] [Indexed: 06/10/2023]
Abstract
The expression of long noncoding RNAs is highly enriched in the human nervous system. However, the function of neuronal lncRNAs in the cytoplasm and their potential translation remains poorly understood. Here we performed Poly-Ribo-Seq to understand the interaction of lncRNAs with the translation machinery and the functional consequences during neuronal differentiation of human SH-SY5Y cells. We discovered 237 cytoplasmic lncRNAs up-regulated during early neuronal differentiation, 58%-70% of which are associated with polysome translation complexes. Among these polysome-associated lncRNAs, we find 45 small ORFs to be actively translated, 17 specifically upon differentiation. Fifteen of 45 of the translated lncRNA-smORFs exhibit sequence conservation within Hominidea, suggesting they are under strong selective constraint in this clade. The profiling of publicly available data sets revealed that 8/45 of the translated lncRNAs are dynamically expressed during human brain development, and 22/45 are associated with cancers of the central nervous system. One translated lncRNA we discovered is LINC01116, which is induced upon differentiation and contains an 87 codon smORF exhibiting increased ribosome profiling signal upon differentiation. The resulting LINC01116 peptide localizes to neurites. Knockdown of LINC01116 results in a significant reduction of neurite length in differentiated cells, indicating it contributes to neuronal differentiation. Our findings indicate cytoplasmic lncRNAs interact with translation complexes, are a noncanonical source of novel peptides, and contribute to neuronal function and disease. Specifically, we demonstrate a novel functional role for LINC01116 during human neuronal differentiation.
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Affiliation(s)
- Katerina Douka
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Isabel Birds
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Andreas Kosteletos
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Sophie Clayton
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Abigail Byford
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | | | - Mary J O'Connell
- School of Life Sciences, Faculty of Medicine and Health Sciences, The University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jim Deuchars
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Adrian Whitehouse
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Julie L Aspden
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom
- LeedsOmics, University of Leeds, Leeds LS2 9JT, United Kingdom
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9
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Schneider K, Nelson GM, Watson JL, Morf J, Dalglish M, Luh LM, Weber A, Bertolotti A. Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation. Cell Rep 2020; 32:108154. [PMID: 32937139 PMCID: PMC7495045 DOI: 10.1016/j.celrep.2020.108154] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/25/2020] [Accepted: 08/25/2020] [Indexed: 01/28/2023] Open
Abstract
Phosphorylation of the translation initiation factor eIF2α is a rapid and vital response to many forms of stress, including protein-misfolding stress in the endoplasmic reticulum (ER stress). It is believed to cause a general reduction in protein synthesis while enabling translation of few transcripts. Such a reduction of protein synthesis comes with the threat of depleting essential proteins, a risk thought to be mitigated by its transient nature. Here, we find that translation attenuation is not uniform, with cytosolic and mitochondrial ribosomal subunits being prominently downregulated. Translation attenuation of these targets persists after translation recovery. Surprisingly, this occurs without a measurable decrease in ribosomal proteins. Explaining this conundrum, translation attenuation preferentially targets long-lived proteins, a finding not only demonstrated by ribosomal proteins but also observed at a global level. This shows that protein stability buffers the cost of translational attenuation, establishing an evolutionary principle of cellular robustness.
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Affiliation(s)
- Kim Schneider
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
| | - Geoffrey Michael Nelson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Joseph Luke Watson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Jörg Morf
- Wellcome - MRC Cambridge Stem Cell Institute, Puddicombe Way, Cambridge CB2 0AW, United Kingdom
| | - Maximillian Dalglish
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Laura Martina Luh
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Annika Weber
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom
| | - Anne Bertolotti
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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10
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Chothani S, Adami E, Ouyang JF, Viswanathan S, Hubner N, Cook SA, Schafer S, Rackham OJL. deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo-seq and RNA-seq Data. ACTA ACUST UNITED AC 2020; 129:e108. [PMID: 31763789 PMCID: PMC9285699 DOI: 10.1002/cpmb.108] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Ribosome profiling quantifies the genome‐wide ribosome occupancy of transcripts. With the integration of matched RNA sequencing data, the translation efficiency (TE) of genes can be calculated to reveal translational regulation. This layer of gene‐expression regulation is otherwise difficult to assess on a global scale and generally not well understood in the context of human disease. Current statistical methods to calculate differences in TE have low accuracy, cannot accommodate complex experimental designs or confounding factors, and do not categorize genes into buffered, intensified, or exclusively translationally regulated genes. This article outlines a method [referred to as deltaTE (ΔTE), standing for change in TE] to identify translationally regulated genes, which addresses the shortcomings of previous methods. In an extensive benchmarking analysis, ΔTE outperforms all methods tested. Furthermore, applying ΔTE on data from human primary cells allows detection of substantially more translationally regulated genes, providing a clearer understanding of translational regulation in pathogenic processes. In this article, we describe protocols for data preparation, normalization, analysis, and visualization, starting from raw sequencing files. © 2019 The Authors. Basic Protocol: One‐step detection and classification of differential translation efficiency genes using DTEG.R Alternate Protocol: Step‐wise detection and classification of differential translation efficiency genes using R Support Protocol: Workflow from raw data to read counts
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany.,DZHK (German Centre for Cardiovascular Research), partner site Berlin, Germany.,Charité-Universitätsmedizin, Berlin, Germany
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,National Heart Centre Singapore, Singapore.,National Heart and Lung Institute, Imperial College London, London, U.K.,MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London, U.K
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore.,National Heart Centre Singapore, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore
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11
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Myers DR, Norlin E, Vercoulen Y, Roose JP. Active Tonic mTORC1 Signals Shape Baseline Translation in Naive T Cells. Cell Rep 2020; 27:1858-1874.e6. [PMID: 31067469 PMCID: PMC6593126 DOI: 10.1016/j.celrep.2019.04.037] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 01/25/2019] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Naive CD4+ T cells are an example of dynamic cell homeostasis: T cells need to avoid autoreactivity while constantly seeing self-peptides, yet they must be primed to react to foreign antigens during infection. The instructive signals that balance this primed yet quiescent state are unknown. Interactions with self-peptides result in membrane-proximal, tonic signals in resting T cells. Here we reveal selective and robust tonic mTORC1 signals in CD4+ T cells that influence T cell fate decisions. We find that the Ras exchange factor Rasgrp1 is necessary to generate tonic mTORC1 signals. Genome-wide ribosome profiling of resting, primary CD4+ T cells uncovers a baseline translational landscape rich in mTOR targets linked to mitochondria, oxidative phosphorylation, and splicing. Aberrantly increased tonic mTORC1 signals from a Rasgrp1Anaef allele result in immunopathology with spontaneous appearance of T peripheral helper cells, follicular helper T cells, and anti-nuclear antibodies that are preceded by subtle alterations in the translational landscape. Myers et al. evaluate a mouse model of autoimmunity, Rasgrp1Anaef. They find that T cells with the Rasgrp1Anaef allele exhibit altered signaling from Rasgrp1 to the mTORC1 pathway in the basal state. They show that increased basal Rasgrp1Anaef-mTORC1 signals lead to an altered translational landscape in T cells and immunopathology.
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Affiliation(s)
- Darienne R Myers
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emilia Norlin
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yvonne Vercoulen
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA 94143, USA.
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12
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Myers DR, Wheeler B, Roose JP. mTOR and other effector kinase signals that impact T cell function and activity. Immunol Rev 2020; 291:134-153. [PMID: 31402496 DOI: 10.1111/imr.12796] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 07/11/2019] [Indexed: 12/27/2022]
Abstract
T cells play important roles in autoimmune diseases and cancer. Following the cloning of the T cell receptor (TCR), the race was on to map signaling proteins that contributed to T cell activation downstream of the TCR as well as co-stimulatory molecules such as CD28. We term this "canonical TCR signaling" here. More recently, it has been appreciated that T cells need to accommodate increased metabolic needs that stem from T cell activation in order to function properly. A central role herein has emerged for mechanistic/mammalian target of rapamycin (mTOR). In this review we briefly cover canonical TCR signaling to set the stage for discussion on mTOR signaling, mRNA translation, and metabolic adaptation in T cells. We also discuss the role of mTOR in follicular helper T cells, regulatory T cells, and other T cell subsets. Our lab recently uncovered that "tonic signals", which pass through proximal TCR signaling components, are robustly and selectively transduced to mTOR to promote baseline translation of various mRNA targets. We discuss insights on (tonic) mTOR signaling in the context of T cell function in autoimmune diseases such as lupus as well as in cancer immunotherapy through CAR-T cell or checkpoint blockade approaches.
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Affiliation(s)
- Darienne R Myers
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Benjamin Wheeler
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, San Francisco, CA, USA
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13
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Ham AS, Chojnowska K, Tintignac LA, Lin S, Schmidt A, Ham DJ, Sinnreich M, Rüegg MA. mTORC1 signalling is not essential for the maintenance of muscle mass and function in adult sedentary mice. J Cachexia Sarcopenia Muscle 2020; 11:259-273. [PMID: 31697050 PMCID: PMC7015237 DOI: 10.1002/jcsm.12505] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The balance between protein synthesis and degradation (proteostasis) is a determining factor for muscle size and function. Signalling via the mammalian target of rapamycin complex 1 (mTORC1) regulates proteostasis in skeletal muscle by affecting protein synthesis and autophagosomal protein degradation. Indeed, genetic inactivation of mTORC1 in developing and growing muscle causes atrophy resulting in a lethal myopathy. However, systemic dampening of mTORC1 signalling by its allosteric inhibitor rapamycin is beneficial at the organismal level and increases lifespan. Whether the beneficial effect of rapamycin comes at the expense of muscle mass and function is yet to be established. METHODS We conditionally ablated the gene coding for the mTORC1-essential component raptor in muscle fibres of adult mice [inducible raptor muscle-specific knockout (iRAmKO)]. We performed detailed phenotypic and biochemical analyses of iRAmKO mice and compared them with muscle-specific raptor knockout (RAmKO) mice, which lack raptor in developing muscle fibres. We also used polysome profiling and proteomics to assess protein translation and associated signalling in skeletal muscle of iRAmKO mice. RESULTS Analysis at different time points reveal that, as in RAmKO mice, the proportion of oxidative fibres decreases, but slow-type fibres increase in iRAmKO mice. Nevertheless, no significant decrease in body and muscle mass or muscle fibre area was detected up to 5 months post-raptor depletion. Similarly, ex vivo muscle force was not significantly reduced in iRAmKO mice. Despite stable muscle size and function, inducible raptor depletion significantly reduced the expression of key components of the translation machinery and overall translation rates. CONCLUSIONS Raptor depletion and hence complete inhibition of mTORC1 signalling in fully grown muscle leads to metabolic and morphological changes without inducing muscle atrophy even after 5 months. Together, our data indicate that maintenance of muscle size does not require mTORC1 signalling, suggesting that rapamycin treatment is unlikely to negatively affect muscle mass and function.
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Affiliation(s)
| | | | - Lionel A Tintignac
- Department of Biomedicine, Pharmazentrum, University of Basel, Basel, Switzerland
| | - Shuo Lin
- Biozentrum, University of Basel, Basel, Switzerland
| | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Daniel J Ham
- Biozentrum, University of Basel, Basel, Switzerland
| | - Michael Sinnreich
- Department of Biomedicine, Pharmazentrum, University of Basel, Basel, Switzerland
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14
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Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol 2019; 16:458-468. [PMID: 31819274 PMCID: PMC7085969 DOI: 10.1038/s41589-019-0425-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 11/01/2019] [Indexed: 12/13/2022]
Abstract
Functional protein-coding small open reading frames (smORFs) are emerging as an important class of genes. However, the number of translated smORFs in the human genome is unclear because proteogenomic methods are not sensitive enough, and, as we show, Ribo-Seq strategies require additional measures to ensure comprehensive and accurate smORF annotation. Here, we integrate de novo transcriptome assembly and Ribo-Seq into an improved workflow that overcomes obstacles with previous methods to more confidently annotate thousands of smORFs. Evolutionary conservation analyses suggest that hundreds of smORF-encoded microproteins are likely functional. Additionally, many smORFs are regulated during fundamental biological processes, such as cell stress. Peptides derived from smORFs are also detectable on human leukocyte antigen complexes, revealing smORFs as a source of antigens. Thus, by including additional validation into our smORF annotation workflow, we accurately identify thousands of unannotated translated smORFs that will provide a rich pool of unexplored, functional human genes.
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Affiliation(s)
- Thomas F Martinez
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Qian Chu
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Cynthia Donaldson
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Dan Tan
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Maxim N Shokhirev
- Razavi Newman Integrative Genomics Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, Salk Institute for Biological Studies, La Jolla, CA, USA.
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15
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Zhang H, Alsaleh G, Feltham J, Sun Y, Napolitano G, Riffelmacher T, Charles P, Frau L, Hublitz P, Yu Z, Mohammed S, Ballabio A, Balabanov S, Mellor J, Simon AK. Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence. Mol Cell 2019; 76:110-125.e9. [PMID: 31474573 PMCID: PMC6863385 DOI: 10.1016/j.molcel.2019.08.005] [Citation(s) in RCA: 192] [Impact Index Per Article: 38.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 02/08/2023]
Abstract
Failure to make adaptive immune responses is a hallmark of aging. Reduced B cell function leads to poor vaccination efficacy and a high prevalence of infections in the elderly. Here we show that reduced autophagy is a central molecular mechanism underlying immune senescence. Autophagy levels are specifically reduced in mature lymphocytes, leading to compromised memory B cell responses in old individuals. Spermidine, an endogenous polyamine metabolite, induces autophagy in vivo and rejuvenates memory B cell responses. Mechanistically, spermidine post-translationally modifies the translation factor eIF5A, which is essential for the synthesis of the autophagy transcription factor TFEB. Spermidine is depleted in the elderly, leading to reduced TFEB expression and autophagy. Spermidine supplementation restored this pathway and improved the responses of old human B cells. Taken together, our results reveal an unexpected autophagy regulatory mechanism mediated by eIF5A at the translational level, which can be harnessed to reverse immune senescence in humans.
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Affiliation(s)
- Hanlin Zhang
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Ghada Alsaleh
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Jack Feltham
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Yizhe Sun
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131, Naples, Italy
| | - Thomas Riffelmacher
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Philip Charles
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Lisa Frau
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Philip Hublitz
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131, Naples, Italy; Department of Molecular and Human Genetics and Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stefan Balabanov
- Division of Haematology, University Hospital and University of Zürich, 8091, Zürich, Switzerland
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anna Katharina Simon
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.
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16
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Li S, Cha SW, Heffner K, Hizal DB, Bowen MA, Chaerkady R, Cole RN, Tejwani V, Kaushik P, Henry M, Meleady P, Sharfstein ST, Betenbaugh MJ, Bafna V, Lewis NE. Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements. J Proteome Res 2019; 18:2433-2445. [PMID: 31020842 DOI: 10.1021/acs.jproteome.8b00935] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A high-quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely on de novo gene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrect predictions of translated sequence, inaccurate splice isoforms, and missing genes. Here, we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 3529 new proteins compared to the hamster RefSeq protein annotation and 2256 novel translational events (e.g., alternative splices, mutations, and novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 119 type-C retroviruses, thus enabling future efforts to eliminate retroviruses to reduce the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate resource for CHO cell line engineering, by facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.
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Affiliation(s)
| | | | | | - Deniz Baycin Hizal
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | - Michael A Bowen
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | - Raghothama Chaerkady
- Antibody Discovery and Protein Engineering , AstraZeneca , Gaithersburg , Maryland , United States
| | | | - Vijay Tejwani
- Colleges of Nanoscale Science and Engineering , SUNY Polytechnic Institute , Albany , New York 12203 , United States
| | - Prashant Kaushik
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular Biotechnology , Dublin City University , Dublin 9, Ireland
| | - Susan T Sharfstein
- Colleges of Nanoscale Science and Engineering , SUNY Polytechnic Institute , Albany , New York 12203 , United States
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17
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Parham LR, Williams PA, Chatterji P, Whelan KA, Hamilton KE. RNA regulons are essential in intestinal homeostasis. Am J Physiol Gastrointest Liver Physiol 2019; 316:G197-G204. [PMID: 30520692 PMCID: PMC6383383 DOI: 10.1152/ajpgi.00403.2017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intestinal epithelial cells are among the most rapidly proliferating cell types in the human body. There are several different subtypes of epithelial cells, each with unique functional roles in responding to the ever-changing environment. The epithelium's ability for rapid and customized responses to environmental changes requires multitiered levels of gene regulation. An emerging paradigm in gastrointestinal epithelial cells is the regulation of functionally related mRNA families, or regulons, via RNA-binding proteins (RBPs). RBPs represent a rapid and efficient mechanism to regulate gene expression and cell function. In this review, we will provide an overview of intestinal epithelial RBPs and how they contribute specifically to intestinal epithelial stem cell dynamics. In addition, we will highlight key gaps in knowledge in the global understanding of RBPs in gastrointestinal physiology as an opportunity for future studies.
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Affiliation(s)
- Louis R. Parham
- 1Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Patrick A. Williams
- 1Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Priya Chatterji
- 2Division of Gastroenterology, Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kelly A. Whelan
- 3Department of Pathology and Laboratory Medicine, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania,4Fels Institute for Cancer Research and Molecular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Kathryn E. Hamilton
- 1Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
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18
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Ji Z. RibORF: Identifying Genome-Wide Translated Open Reading Frames Using Ribosome Profiling. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018; 124:e67. [PMID: 30178897 PMCID: PMC6168376 DOI: 10.1002/cpmb.67] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Ribosome profiling identifies RNA fragments associated with translating ribosomes. The technology provides an opportunity to examine genome-wide translation events at single-nucleotide resolution and in an unbiased manner. Here I present a computational pipeline named RibORF to systematically identify translated open reading frames (ORFs), based on read distribution features representing active translation, including 3-nt periodicity and uniformness across codons. Analyses using the computational tool revealed pervasive translation in putative 'noncoding' regions, such as lncRNAs, pseudogenes, and 5'UTRs. The computational tool is useful for studying functional roles of non-canonical translation events in various biological processes. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
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19
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Ji Z. Rfoot: Transcriptome-Scale Identification of RNA-Protein Complexes from Ribosome Profiling Data. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2018; 124:e66. [PMID: 30168907 PMCID: PMC6168344 DOI: 10.1002/cpmb.66] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ribosome profiling was developed to identify genome-wide RNA fragments associated with translating ribosomes. However, no experimental procedure was developed to effectively purify ribosome-RNA complexes. Actually, ribosome profiling is a transcriptomic RNase footprinting assay, which can identify both ribosomal and non-ribosomal protein-RNA complexes. Many sequencing reads represent functional RNA footprints associated with non-ribosomal proteins. Here I present a computational pipeline named Rfoot to systematically identify genome-wide non-ribosomal RNA footprints, based on the highly localized read distribution feature. Analyses have revealed native functional protein-RNA complexes in lncRNAs, 3'UTRs of mRNAs, and all types of small noncoding RNAs. This computational tool is useful for discovering novel noncoding functions of RNAs. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Zhe Ji
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA. Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, IL 60208, USA
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20
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Gerst JE. Pimp My Ribosome: Ribosomal Protein Paralogs Specify Translational Control. Trends Genet 2018; 34:832-845. [PMID: 30195580 DOI: 10.1016/j.tig.2018.08.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 08/06/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
The ability of cells to grow and divide, differentiate and function, and even senesce is dependent on the fine-tuning of both gene and protein expression. Protein concentration in the cell is regulated not only at the transcriptional and post-translational levels, but also at the level of translation. Ribosomes, the molecular machines behind translation, were once considered to be an invariant driving force behind protein expression. However, studies over the past decade paint a rather different picture; namely, that ribosomes constitute an additional layer of regulatory control that might define which subsets of mRNAs are translated, to what extent, and to what purpose. Recent works summarized herein directly implicate ribosome heterogeneity and, in particular, ribosomal protein (RP) paralog specificity in regulating mRNA translation and control of the cellular translatome.
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Affiliation(s)
- Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
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21
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Novel insights into global translational regulation through Pumilio family RNA-binding protein Puf3p revealed by ribosomal profiling. Curr Genet 2018; 65:201-212. [PMID: 29951697 DOI: 10.1007/s00294-018-0862-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/16/2018] [Accepted: 06/19/2018] [Indexed: 01/13/2023]
Abstract
RNA binding proteins (RBPs) can regulate the stability, localization, and translation of their target mRNAs. Among them, Puf3p is a well-known Pumilio family RBP whose biology has been intensively studied. Nevertheless, the impact of Puf3p on the translational regulation of its downstream genes still remains to be investigated at the genome-wide level. In this study, we combined ribosome profiling and RNA-Seq in budding yeast (Saccharomyces cerevisiae) to investigate Puf3p's functions in translational regulation. Comparison of translational efficiency (TE) between wild-type and puf3Δ strains demonstrates extensive translational modulation in the absence of Puf3p (over 27% genes are affected at the genome level). Besides confirming its known role in regulating mitochondrial metabolism, our data demonstrate that Puf3p serves as a key post-transcriptional regulator of downstream RBPs by regulating their translational efficiencies, indicating a network of interactions among RBPs at the post-transcriptional level. Furthermore, Puf3p switches the balance of translational flux between mitochondrial and cytosolic ribosome biogenesis to adapt to changes in cellular metabolism. In summary, our results indicate that TE can be utilized as an informative index to interrogate the mechanism underlying RBP functions, and provide novel insights into Puf3p's mode-of-action.
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22
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Lim CS, T. Wardell SJ, Kleffmann T, Brown CM. The exon-intron gene structure upstream of the initiation codon predicts translation efficiency. Nucleic Acids Res 2018; 46:4575-4591. [PMID: 29684192 PMCID: PMC5961209 DOI: 10.1093/nar/gky282] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 03/28/2018] [Accepted: 04/06/2018] [Indexed: 12/16/2022] Open
Abstract
Introns in mRNA leaders are common in complex eukaryotes, but often overlooked. These introns are spliced out before translation, leaving exon-exon junctions in the mRNA leaders (leader EEJs). Our multi-omic approach shows that the number of leader EEJs inversely correlates with the main protein translation, as does the number of upstream open reading frames (uORFs). Across the five species studied, the lowest levels of translation were observed for mRNAs with both leader EEJs and uORFs (29%). This class of mRNAs also have ribosome footprints on uORFs, with strong triplet periodicity indicating uORF translation. Furthermore, the positions of both leader EEJ and uORF are conserved between human and mouse. Thus, the uORF, in combination with leader EEJ predicts lower expression for nearly one-third of eukaryotic proteins.
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Affiliation(s)
- Chun Shen Lim
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Samuel J T. Wardell
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Torsten Kleffmann
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Chris M Brown
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
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23
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The impact of ribosomal interference, codon usage, and exit tunnel interactions on translation elongation rate variation. PLoS Genet 2018; 14:e1007166. [PMID: 29337993 PMCID: PMC5786338 DOI: 10.1371/journal.pgen.1007166] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/26/2018] [Accepted: 12/25/2017] [Indexed: 11/19/2022] Open
Abstract
Previous studies have shown that translation elongation is regulated by multiple factors, but the observed heterogeneity remains only partially explained. To dissect quantitatively the different determinants of elongation speed, we use probabilistic modeling to estimate initiation and local elongation rates from ribosome profiling data. This model-based approach allows us to quantify the extent of interference between ribosomes on the same transcript. We show that neither interference nor the distribution of slow codons is sufficient to explain the observed heterogeneity. Instead, we find that electrostatic interactions between the ribosomal exit tunnel and specific parts of the nascent polypeptide govern the elongation rate variation as the polypeptide makes its initial pass through the tunnel. Once the N-terminus has escaped the tunnel, the hydropathy of the nascent polypeptide within the ribosome plays a major role in modulating the speed. We show that our results are consistent with the biophysical properties of the tunnel.
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24
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Vučićević D, Gehre M, Dhamija S, Friis-Hansen L, Meierhofer D, Sauer S, Ørom UA. The long non-coding RNA PARROT is an upstream regulator of c-Myc and affects proliferation and translation. Oncotarget 2017; 7:33934-47. [PMID: 27129154 PMCID: PMC5085129 DOI: 10.18632/oncotarget.8985] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 04/16/2016] [Indexed: 12/26/2022] Open
Abstract
Long non-coding RNAs are important regulators of gene expression and signaling pathways. The expression of long ncRNAs is dysregulated in cancer and other diseases. The identification and characterization of long ncRNAs is often challenging due to their low expression level and localization to chromatin. Here, we identify a functional long ncRNA, PARROT (Proliferation Associated RNA and Regulator Of Translation) transcribed by RNA polymerase II and expressed at a relatively high level in a number of cell lines. The PARROT long ncRNA is associated with proliferation in both transformed and normal cell lines. We characterize the long ncRNA PARROT as an upstream regulator of c-Myc affecting cellular proliferation and translation using RNA sequencing and mass spectrometry following depletion of the long ncRNA. PARROT is repressed during senescence of human mammary epithelial cells and overexpressed in some cancers, suggesting an important association with proliferation through regulation of c-Myc. With this study, we add to the knowledge of cytoplasmic functional long ncRNAs and extent the long ncRNA-Myc regulatory network in transformed and normal cells.
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Affiliation(s)
- Dubravka Vučićević
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Maja Gehre
- Max Planck Institute for Molecular Genetics, Berlin, Germany.,EMBL, Heidelberg, Germany
| | - Sonam Dhamija
- Medizinische Hochschule Hannover Institute of Biochemistry, Hannover, Germany.,RNA Biology and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
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25
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Mayer A, Churchman LS. A Detailed Protocol for Subcellular RNA Sequencing (subRNA-seq). ACTA ACUST UNITED AC 2017; 120:4.29.1-4.29.18. [PMID: 28967997 DOI: 10.1002/cpmb.44] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In eukaryotic cells, RNAs at various maturation and processing levels are distributed across cellular compartments. The standard approach to determine transcript abundance and identity in vivo is RNA sequencing (RNA-seq). RNA-seq relies on RNA isolation from whole-cell lysates and thus mainly captures fully processed, stable, and more abundant cytoplasmic RNAs over nascent, unstable, and nuclear RNAs. Here, we provide a step-by-step protocol for subcellular RNA-seq (subRNA-seq). subRNA-seq allows the quantitative measurement of RNA polymerase II-generated RNAs from the chromatin, nucleoplasm, and cytoplasm of mammalian cells. This approach relies on cell fractionation prior to RNA isolation and sequencing library preparation. High-throughput sequencing of the subcellular RNAs can then be used to reveal the identity, abundance, and subcellular distribution of transcripts, thus providing insights into RNA processing and maturation. Deep sequencing of the chromatin-associated RNAs further offers the opportunity to study nascent RNAs. Subcellular RNA-seq libraries are obtained within 5 days. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Andreas Mayer
- Max Planck Institute for Molecular Genetics, Berlin, Germany
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26
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Liu CL, Place AR, Jagus R. Use of Antibiotics for Maintenance of Axenic Cultures of Amphidinium carterae for the Analysis of Translation. Mar Drugs 2017; 15:E242. [PMID: 28763019 PMCID: PMC5577597 DOI: 10.3390/md15080242] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 07/17/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022] Open
Abstract
Most dinoflagellates in culture are bacterized, complicating the quantification of protein synthesis, as well as the analysis of its regulation. In bacterized cultures of Amphidinium carterae Hulbert, up to 80% of protein synthetic activity appears to be predominantly bacterial based on responses to inhibitors of protein synthesis. To circumvent this, axenic cultures of A. carterae were obtained and shown to respond to inhibitors of protein synthesis in a manner characteristic of eukaryotes. However, these responses changed with time in culture correlating with the reappearance of bacteria. Here we show that culture with kanamycin (50 μg/mL), carbenicillin (100 μg/mL), and streptomycin sulfate (50 μg/mL) (KCS), but not 100 units/mL of penicillin and streptomycin (PS), prevents the reappearance of bacteria and allows A. carterae protein synthesis to be quantified without the contribution of an associated bacterial community. We demonstrate that A. carterae can grow in the absence of a bacterial community. Furthermore, maintenance in KCS does not inhibit the growth of A. carterae cultures but slightly extends the growth phase and allows accumulation to somewhat higher saturation densities. We also show that cultures of A. carterae maintained in KCS respond to the eukaryotic protein synthesis inhibitors cycloheximide, emetine, and harringtonine. Establishment of these culture conditions will facilitate our ability to use polysome fractionation and ribosome profiling to study mRNA recruitment. Furthermore, this study shows that a simple and fast appraisal of the presence of a bacterial community in A. carterae cultures can be made by comparing responses to cycloheximide and chloramphenicol rather than depending on lengthier culture-based assessments.
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Affiliation(s)
- Chieh-Lun Liu
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
| | - Allen R Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
| | - Rosemary Jagus
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, 701 E. Pratt Street, Baltimore, MD 21202, USA.
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27
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Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLoS Biol 2017; 15:e2001882. [PMID: 28323820 PMCID: PMC5360235 DOI: 10.1371/journal.pbio.2001882] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 02/22/2017] [Indexed: 01/12/2023] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) plays a key role in regulating the levels of plasma low-density lipoprotein cholesterol (LDL-C). Here, we demonstrate that the compound PF-06446846 inhibits translation of PCSK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain within the exit tunnel. We further show that PF-06446846 reduces plasma PCSK9 and total cholesterol levels in rats following oral dosing. Using ribosome profiling, we demonstrate that PF-06446846 is highly selective for the inhibition of PCSK9 translation. The mechanism of action employed by PF-06446846 reveals a previously unexpected tunability of the human ribosome that allows small molecules to specifically block translation of individual transcripts. Many disease-mediating proteins have proven difficult to target with traditional small-molecule pharmaceuticals. In this paper, we report that a small molecule, PF-06446846, directly inhibits translation of one such protein, proprotein convertase subtilisin/kexin type 9 (PCSK9), by acting on the translating human ribosome. PF-06446846 causes the translating ribosome to stall soon after translating the PCSK9 signal sequence. We further show that PF-06446846 activity is dependent on the amino acid sequence of the nascent chain inside the ribosome exit tunnel. In a rat safety study, we observe decreases in plasma PCSK9, total cholesterol, and low-density lipoprotein (LDL) cholesterol. Using mass spectrometry in cell culture and ribosome profiling, we demonstrate that despite acting on the ribosome, which synthesizes every protein in the cell, PF-06446846 displays a high level of selectivity for PCSK9. This unexpected potential for small molecules to selectively inhibit the human ribosome opens the possibility for future development of small molecules targeting disease-mediating proteins that were previously thought to be undruggable.
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Vrettos N, Maragkakis M, Alexiou P, Mourelatos Z. Kc167, a widely used Drosophila cell line, contains an active primary piRNA pathway. RNA (NEW YORK, N.Y.) 2017; 23:108-118. [PMID: 27789612 PMCID: PMC5159643 DOI: 10.1261/rna.059139.116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 10/22/2016] [Indexed: 06/02/2023]
Abstract
PIWI family proteins bind to small RNAs known as PIWI-interacting RNAs (piRNAs) and play essential roles in the germline by silencing transposons and by promoting germ cell specification and function. Here we report that the widely used Kc167 cell line, derived from Drosophila melanogaster embryos, expresses piRNAs that are loaded to Aub and Piwi. Kc167 piRNAs are produced by a canonical, primary piRNA biogenesis pathway, from phased processing of precursor transcripts by the Zuc endonuclease, Armi helicase, and dGasz mitochondrial scaffold protein. Kc167 piRNAs derive from cytoplasmic transcripts, notably tRNAs and mRNAs, and their abundance correlates with that of parent transcripts. The expression of Aub is robust in Kc167, that of Piwi is modest, while Ago3 is undetectable, explaining the lack of transposon-related piRNA amplification by the Aub-Ago3, ping-pong mechanism. We propose that the default state of the primary piRNA biogenesis machinery is random transcript sampling to allow generation of piRNAs from any transcript, including newly acquired retrotransposons. This state is unmasked in Kc167, likely because they do not express piRNA cluster transcripts in sufficient amounts and do not amplify transposon piRNAs. We use Kc167 to characterize an inactive isoform of Aub protein. Since most Kc167 piRNAs are genic, they can be mapped uniquely to the genome, facilitating computational analyses. Furthermore, because Kc167 is a widely used and well-characterized cell line that is easily amenable to experimental manipulations, we expect that it will serve as an excellent system to study piRNA biogenesis and piRNA-related factors.
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Affiliation(s)
- Nicholas Vrettos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Manolis Maragkakis
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Panagiotis Alexiou
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Zissimos Mourelatos
- Department of Pathology and Laboratory Medicine, Division of Neuropathology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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29
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Adjibade P, Grenier St-Sauveur V, Droit A, Khandjian EW, Toren P, Mazroui R. Analysis of the translatome in solid tumors using polyribosome profiling/RNA-Seq. J Biol Methods 2016; 3:e59. [PMID: 31453221 PMCID: PMC6706116 DOI: 10.14440/jbm.2016.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/22/2016] [Accepted: 10/18/2016] [Indexed: 01/25/2023] Open
Abstract
Gene expression involves multiple steps from the transcription of a mRNA in the nucleus to the production of the encoded protein in the cytoplasm. This final step occurs through a highly regulated process of mRNA translation on ribosomes that is required to maintain cell homeostasis. Alterations in the control of mRNA translation may lead to cell's transformation, a hallmark of cancer development. Indeed, recent advances indicated that increased translation of mRNAs encoding tumor-promoting proteins may be a key mechanism of tumor resistance in several cancers. Moreover, it was found that proteins whose encoding mRNAs are translated at higher efficiencies may be effective biomarkers. Evaluation of global changes in translation efficiency in human tumors has thus the potential of better understanding what can be used as biomarkers and therapeutic targets. Investigating changes in translation efficiency in human cancer cells has been made possible through the development and use of the polyribosome profiling combined with DNA microarray or deep RNA sequencing (RNA-Seq). While helpful, the use of cancer cell lines has many limitations and it is essential to define translational changes in human tumor samples in order to properly prioritize genes implicated in cancer phenotype. We present an optimized polyribosome RNA-Seq protocol suitable for quantitative analysis of mRNA translation that occurs in human tumor samples and murine xenografts. Applying this innovative approach to human tumors, which requires a complementary bioinformatics analysis, unlocks the potential to identify key mRNA which are preferentially translated in tumor tissue compared to benign tissue as well as translational changes which occur following treatment. These technical advances will be of interest to those researching all solid tumors, opening possibilities for understanding what may be therapeutic Achilles heels' or relevant biomarkers.
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Affiliation(s)
- Pauline Adjibade
- Centre de Recherche en Cancérologie. Centre de Recherche du CHU de Québec. Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, PQ, Canada
| | - Valérie Grenier St-Sauveur
- Centre de Recherche en Cancérologie. Centre de Recherche du CHU de Québec. Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, PQ, Canada
| | - Arnaud Droit
- Centre de Recherche du CHU de Québec. Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, PQ, Canada
| | - Edouard W. Khandjian
- Centre de Recherche, Institut Universitaire en Santé Mentale de Québec. Département de Psychiatrie et de Neurosciences, Faculté de Médecine, Université Laval, Québec, PQ, Canada
| | - Paul Toren
- Centre de Recherche du CHU de Québec. Département de Chirurgie, Faculté de Médecine, Université Laval, Québec, PQ, Canada
| | - Rachid Mazroui
- Centre de Recherche en Cancérologie. Centre de Recherche du CHU de Québec. Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, PQ, Canada
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30
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Blin J, Ricci EP. [An intimate look at the viral replication cycle through ribosome profiling]. Med Sci (Paris) 2016; 32:849-860. [PMID: 27758749 DOI: 10.1051/medsci/20163210018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Next Generation Sequencing (NGS) techniques have revolutionized most biomedical research fields over the past decade by allowing a broader vision on biological processes that occur at the molecular level. Among these, ribosome profiling or footprinting is a powerful tool to study mRNA translation in a transcriptome-wide manner. Ribosome profiling has been used to study the impact of translational control of gene expression under many different cellular conditions including viral infections. Indeed, translation is a critical step during the viral replication cycle in which the infected cell is embezzled to produce viral proteins. Ribosome profiling tools can provide new insights on viral translation by monitoring ribosome binding to viral and cellular RNAs with a high definition during the time course of an infection. Here, we describe the potential uses of ribosome profiling for the understanding of viral translational control and the impact of viral infection on host gene expression. We also discuss the main limitations and biases related to the technique that need to be taken into account for its use.
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Affiliation(s)
- Juliana Blin
- CIRI, international center for infectiology research, université de Lyon, 46, allée d'Italie, Lyon, France
| | - Emiliano P Ricci
- CIRI, international center for infectiology research, université de Lyon, 46, allée d'Italie, Lyon, France - Inserm, U1111, Lyon, France - École normale supérieure de Lyon, 46, allée d'Italie, 69007 Lyon, France - Université Claude Bernard Lyon 1, centre international de recherche en infectiologie, Lyon, France - CNRS, UMR5308, Lyon, France
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31
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Anthony TG. Mechanisms of protein balance in skeletal muscle. Domest Anim Endocrinol 2016; 56 Suppl:S23-32. [PMID: 27345321 PMCID: PMC4926040 DOI: 10.1016/j.domaniend.2016.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 01/07/2023]
Abstract
Increased global demand for adequate protein nutrition against a backdrop of climate change and concern for animal agriculture sustainability necessitates new and more efficient approaches to livestock growth and production. Anabolic growth is achieved when rates of new synthesis exceed turnover, producing a positive net protein balance. Conversely, deterioration or atrophy of lean mass is a consequence of a net negative protein balance. During early life and periods of growth, muscle mass is driven by increases in protein synthesis at the level of mRNA translation. Throughout life, muscle mass is further influenced by degradative processes such as autophagy and the ubiquitin proteasome pathway. Multiple signal transduction networks guide and coordinate these processes alongside quality control mechanisms to maintain protein homeostasis (proteostasis). Genetics, hormones, and environmental stimuli each influence proteostasis control, altering capacity and/or efficiency of muscle growth. An overview of recent findings and current methods to assess muscle protein balance and proteostasis is presented. Current efforts to identify novel control points have the potential through selective breeding design or development of hormetic strategies to better promote growth and health span during environmental stress.
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Affiliation(s)
- T G Anthony
- Department of Nutritional Sciences, Rutgers University, New Brunswick, NJ 08901, USA.
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32
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Zanet J, Chanut-Delalande H, Plaza S, Payre F. Small Peptides as Newcomers in the Control of Drosophila Development. Curr Top Dev Biol 2016; 117:199-219. [PMID: 26969979 DOI: 10.1016/bs.ctdb.2015.11.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Throughout the last century, studies using the fruit fly have contributed to the discovery of many key genetic elements that control animal development. Recent work has shed light on an unexpectedly large number of RNAs that lack the classical hallmarks of protein-coding genes and are thus referred to as noncoding RNAs. However, there is mounting evidence that both mRNA and noncoding RNAs often contain small open reading frames (sORFs/smORFs), which can be translated into peptides. While genome-wide profiling supports a pervasive translation of these noncanonical sORF/smORF/SEP peptides, their functions remain poorly understood. Here, we review recent data obtained in Drosophila demonstrating the overlooked role of smORF peptides in the control of development and adult life. Focusing on a few smORF peptides whose functions have been elucidated recently, we discuss the importance of these newly identified regulatory molecules and how they act to regulate the building and function of the whole organism.
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Affiliation(s)
- J Zanet
- Centre de Biologie du Développement, Université de Toulouse, UPS, Toulouse, France; Centre de Biologie du Développement, CNRS, UMR5547, Toulouse, France
| | - H Chanut-Delalande
- Centre de Biologie du Développement, Université de Toulouse, UPS, Toulouse, France; Centre de Biologie du Développement, CNRS, UMR5547, Toulouse, France
| | - Serge Plaza
- Centre de Biologie du Développement, Université de Toulouse, UPS, Toulouse, France; Centre de Biologie du Développement, CNRS, UMR5547, Toulouse, France.
| | - Francios Payre
- Centre de Biologie du Développement, Université de Toulouse, UPS, Toulouse, France; Centre de Biologie du Développement, CNRS, UMR5547, Toulouse, France.
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33
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Spealman P, Wang H, May G, Kingsford C, McManus CJ. Exploring Ribosome Positioning on Translating Transcripts with Ribosome Profiling. Methods Mol Biol 2016; 1358:71-97. [PMID: 26463378 DOI: 10.1007/978-1-4939-3067-8_5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Recent technological advances (e.g., microarrays and massively parallel sequencing) have facilitated genome-wide measurement of many aspects of gene regulation. Ribosome profiling is a high-throughput sequencing method used to measure gene expression at the level of translation. This is accomplished by quantifying both the number of translating ribosomes and their locations on mRNA transcripts. The inventors of this approach have published several methods papers detailing its implementation and addressing the basics of ribosome profiling data analysis. Here we describe our lab's procedure, which differs in some respects from those published previously. In addition, we describe a data analysis pipeline, Ribomap, for ribosome profiling data. Ribomap allocates sequence reads to alternative mRNA isoforms, normalizes sequencing bias along transcripts using RNA-seq data, and outputs count vectors of per-codon ribosome occupancy for each transcript.
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Affiliation(s)
- Pieter Spealman
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Hao Wang
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Gemma May
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA
| | - Carl Kingsford
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
| | - C Joel McManus
- Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Ave, Pittsburgh, PA, 15213, USA.
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34
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Merchante C, Hu Q, Heber S, Alonso J, Stepanova A. A Ribosome Footprinting Protocol for Plants. Bio Protoc 2016. [DOI: 10.21769/bioprotoc.1985] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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Abstract
BACKGROUND During protein synthesis, the nascent peptide chain emerges from the ribosome through the ribosomal exit tunnel. Biochemical interactions between the nascent peptide and the tunnel may stall the ribosome movement and thus affect the expression level of the protein being synthesized. Earlier studies focused on one model organism (S. cerevisiae), have suggested that certain amino acid sequences may be responsible for ribosome stalling; however, the stalling effect at the individual amino acid level across many organisms has not yet been quantified. RESULTS By analyzing multiple ribosome profiling datasets from different organisms (including prokaryotes and eukaryotes), we report for the first time the organism-specific amino acids that significantly lead to ribosome stalling. We show that the identity of the stalling amino acids vary across the tree of life. In agreement with previous studies, we observed a remarkable stalling signal of proline and arginine in S. cerevisiae. In addition, our analysis supports the conjecture that the stalling effect of positively charged amino acids is not universal and that in certain conditions, negative charge may also induce ribosome stalling. Finally, we show that the beginning part of the tunnel tends to undergo more interactions with the translated amino acids than other positions along the tunnel. CONCLUSIONS The reported results support the conjecture that the ribosomal exit tunnel interacts with various amino acids and that the nature of these interactions varies among different organisms. Our findings should contribute towards better understanding of transcript and proteomic evolution and translation elongation regulation.
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Affiliation(s)
- Renana Sabi
- Department of Biomedical Engineering, Tel Aviv University (TAU), Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University (TAU), Tel Aviv, Israel
- The Sagol School of Neuroscience, Tel-Aviv University (TAU), Tel-Aviv, Israel
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36
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Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I. The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis. RNA (NEW YORK, N.Y.) 2015; 21:1731-45. [PMID: 26286745 PMCID: PMC4574750 DOI: 10.1261/rna.052548.115] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/23/2015] [Indexed: 05/19/2023]
Abstract
Ribosome profiling is a technique that permits genome-wide, quantitative analysis of translation and has found broad application in recent years. Here we describe a modified profiling protocol and software package designed to benefit more broadly the translation community in terms of simplicity and utility. The protocol, applicable to diverse organisms, including organelles, is based largely on previously published profiling methodologies, but uses duplex-specific nuclease (DSN) as a convenient, species-independent way to reduce rRNA contamination. We show that DSN-based depletion compares favorably with other commonly used rRNA depletion strategies and introduces little bias. The profiling protocol typically produces high levels of triplet periodicity, facilitating the detection of coding sequences, including upstream, downstream, and overlapping open reading frames (ORFs) and an alternative ribosome conformation evident during termination of protein synthesis. In addition, we provide a software package that presents a set of methods for parsing ribosomal profiling data from multiple samples, aligning reads to coding sequences, inferring alternative ORFs, and plotting average and transcript-specific aspects of the data. Methods are also provided for extracting the data in a form suitable for differential analysis of translation and translational efficiency.
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Affiliation(s)
- Betty Y Chung
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Thomas J Hardcastle
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Joshua D Jones
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Nerea Irigoyen
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - Andrew E Firth
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
| | - David C Baulcombe
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom
| | - Ian Brierley
- Division of Virology, Department of Pathology, University of Cambridge, Cambridge CB2 1QP, United Kingdom
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37
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Mascarenhas R, Pietrzak M, Smith RM, Webb A, Wang D, Papp AC, Pinsonneault JK, Seweryn M, Rempala G, Sadee W. Allele-Selective Transcriptome Recruitment to Polysomes Primed for Translation: Protein-Coding and Noncoding RNAs, and RNA Isoforms. PLoS One 2015; 10:e0136798. [PMID: 26331722 PMCID: PMC4558023 DOI: 10.1371/journal.pone.0136798] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 08/07/2015] [Indexed: 11/19/2022] Open
Abstract
mRNA translation into proteins is highly regulated, but the role of mRNA isoforms, noncoding RNAs (ncRNAs), and genetic variants remains poorly understood. mRNA levels on polysomes have been shown to correlate well with expressed protein levels, pointing to polysomal loading as a critical factor. To study regulation and genetic factors of protein translation we measured levels and allelic ratios of mRNAs and ncRNAs (including microRNAs) in lymphoblast cell lines (LCL) and in polysomal fractions. We first used targeted assays to measure polysomal loading of mRNA alleles, confirming reported genetic effects on translation of OPRM1 and NAT1, and detecting no effect of rs1045642 (3435C>T) in ABCB1 (MDR1) on polysomal loading while supporting previous results showing increased mRNA turnover of the 3435T allele. Use of high-throughput sequencing of complete transcript profiles (RNA-Seq) in three LCLs revealed significant differences in polysomal loading of individual RNA classes and isoforms. Correlated polysomal distribution between protein-coding and non-coding RNAs suggests interactions between them. Allele-selective polysome recruitment revealed strong genetic influence for multiple RNAs, attributable either to differential expression of RNA isoforms or to differential loading onto polysomes, the latter defining a direct genetic effect on translation. Genes identified by different allelic RNA ratios between cytosol and polysomes were enriched with published expression quantitative trait loci (eQTLs) affecting RNA functions, and associations with clinical phenotypes. Polysomal RNA-Seq combined with allelic ratio analysis provides a powerful approach to study polysomal RNA recruitment and regulatory variants affecting protein translation.
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Affiliation(s)
- Roshan Mascarenhas
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Maciej Pietrzak
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
| | - Ryan M. Smith
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Amy Webb
- Department of Biomedical Informatics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Danxin Wang
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Audrey C. Papp
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Julia K. Pinsonneault
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
| | - Michal Seweryn
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Department of Mathematics and Computer Science, University of Lodz, Lodz, Poland
- Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Grzegorz Rempala
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, Ohio, United States of America
- Mathematical Biosciences Institute, The Ohio State University, Columbus, Ohio, United States of America
| | - Wolfgang Sadee
- Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Medical Genetics, College of Medicine, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- * E-mail:
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38
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Martens AT, Taylor J, Hilser VJ. Ribosome A and P sites revealed by length analysis of ribosome profiling data. Nucleic Acids Res 2015; 43:3680-7. [PMID: 25805170 PMCID: PMC4402525 DOI: 10.1093/nar/gkv200] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 02/25/2015] [Indexed: 01/10/2023] Open
Abstract
The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and has furthered investigations into the connections between codon biases and translation rates. Yet the location of the codon being decoded in ribosome footprints is still unknown, and has been complicated by the recent observation of footprints with non-canonical lengths. Here we show how taking into account the variations in ribosome footprint lengths can reveal the ribosome aminoacyl (A) and peptidyl (P) site locations. These location assignments are in agreement with the proposed mechanisms for various ribosome pauses and further enhance the resolution of the profiling data. We also show that GC-rich motifs at the 5' ends of footprints are found in yeast, calling into question the anti-Shine-Dalgarno effect's role in ribosome pausing.
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Affiliation(s)
- Andrew T Martens
- Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA
| | - James Taylor
- Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400 N. Charles St Baltimore, MD 21218, USA
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39
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Juntawong P, Hummel M, Bazin J, Bailey-Serres J. Ribosome profiling: a tool for quantitative evaluation of dynamics in mRNA translation. Methods Mol Biol 2015; 1284:139-73. [PMID: 25757771 DOI: 10.1007/978-1-4939-2444-8_7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Translational regulation is important for plant growth, metabolism, and acclimation to environmental challenges. Ribosome profiling involves the nuclease digestion of mRNAs associated with ribosomes and mapping of the generated ribosome-protected footprints to transcripts. This is useful for investigation of translational regulation. Here we present a detailed method to generate, purify, and high-throughput-sequence ribosome footprints from Arabidopsis thaliana using two different isolation methods, namely, conventional differential centrifugation and the translating ribosome affinity purification (TRAP) technology. These methodologies provide researchers with an opportunity to quantitatively assess with high-resolution the translational activity of individual mRNAs by determination of the position and number of ribosomes in the corresponding mRNA. The results can provide insights into the translation of upstream open reading frames, alternatively spliced transcripts, short open reading frames, and other aspects of translation.
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Affiliation(s)
- Piyada Juntawong
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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40
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Heyer EE, Ozadam H, Ricci EP, Cenik C, Moore MJ. An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. Nucleic Acids Res 2014; 43:e2. [PMID: 25505164 PMCID: PMC4288154 DOI: 10.1093/nar/gku1235] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Deep sequencing of strand-specific cDNA libraries is now a ubiquitous tool for identifying and quantifying RNAs in diverse sample types. The accuracy of conclusions drawn from these analyses depends on precise and quantitative conversion of the RNA sample into a DNA library suitable for sequencing. Here, we describe an optimized method of preparing strand-specific RNA deep sequencing libraries from small RNAs and variably sized RNA fragments obtained from ribonucleoprotein particle footprinting experiments or fragmentation of long RNAs. Our approach works across a wide range of input amounts (400 pg to 200 ng), is easy to follow and produces a library in 2–3 days at relatively low reagent cost, all while giving the user complete control over every step. Because all enzymatic reactions were optimized and driven to apparent completion, sequence diversity and species abundance in the input sample are well preserved.
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Affiliation(s)
- Erin E Heyer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Hakan Ozadam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Emiliano P Ricci
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Can Cenik
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Melissa J Moore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
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41
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Brosius J. The persistent contributions of RNA to eukaryotic gen(om)e architecture and cellular function. Cold Spring Harb Perspect Biol 2014; 6:a016089. [PMID: 25081515 DOI: 10.1101/cshperspect.a016089] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Currently, the best scenario for earliest forms of life is based on RNA molecules as they have the proven ability to catalyze enzymatic reactions and harbor genetic information. Evolutionary principles valid today become apparent in such models already. Furthermore, many features of eukaryotic genome architecture might have their origins in an RNA or RNA/protein (RNP) world, including the onset of a further transition, when DNA replaced RNA as the genetic bookkeeper of the cell. Chromosome maintenance, splicing, and regulatory function via RNA may be deeply rooted in the RNA/RNP worlds. Mostly in eukaryotes, conversion from RNA to DNA is still ongoing, which greatly impacts the plasticity of extant genomes. Raw material for novel genes encoding protein or RNA, or parts of genes including regulatory elements that selection can act on, continues to enter the evolutionary lottery.
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Affiliation(s)
- Jürgen Brosius
- Institute of Experimental Pathology (ZMBE), University of Münster, D-48149 Münster, Germany
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42
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Sharma CM, Vogel J. Differential RNA-seq: the approach behind and the biological insight gained. Curr Opin Microbiol 2014; 19:97-105. [PMID: 25024085 DOI: 10.1016/j.mib.2014.06.010] [Citation(s) in RCA: 142] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 06/15/2014] [Accepted: 06/19/2014] [Indexed: 01/14/2023]
Abstract
RNA-sequencing has revolutionized the quantitative and qualitative analysis of transcriptomes in both prokaryotes and eukaryotes. It provides a generic approach for gene expression profiling, annotation of transcript boundaries and operons, as well as identifying novel transcripts including small noncoding RNA molecules and antisense RNAs. We recently developed a differential RNA-seq (dRNA-seq) method which in addition to the above, yields information as to whether a given RNA is a primary or processed transcript. Originally applied to describe the primary transcriptome of the gastric pathogen Helicobacter pylori, dRNA-seq has since provided global maps of transcriptional start sites in diverse species, informed new biology in the CRISPR-Cas9 system, advanced to a tool for comparative transcriptomics, and inspired simultaneous RNA-seq of pathogen and host.
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Affiliation(s)
- Cynthia M Sharma
- University of Würzburg, Institute for Molecular Infection Biology & Research Center for Infectious Diseases, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.
| | - Jörg Vogel
- University of Würzburg, Institute for Molecular Infection Biology & Research Center for Infectious Diseases, Josef-Schneider-Straße 2/D15, D-97080 Würzburg, Germany.
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43
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Brubaker SW, Gauthier AE, Mills EW, Ingolia NT, Kagan JC. A bicistronic MAVS transcript highlights a class of truncated variants in antiviral immunity. Cell 2014; 156:800-11. [PMID: 24529381 PMCID: PMC3959641 DOI: 10.1016/j.cell.2014.01.021] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 12/05/2013] [Accepted: 01/09/2014] [Indexed: 11/29/2022]
Abstract
Bacterial and viral mRNAs are often polycistronic. Akin to alternative splicing, alternative translation of polycistronic messages is a mechanism to generate protein diversity and regulate gene function. Although a few examples exist, the use of polycistronic messages in mammalian cells is not widely appreciated. Here we report an example of alternative translation as a means of regulating innate immune signaling. MAVS, a regulator of antiviral innate immunity, is expressed from a bicistronic mRNA encoding a second protein, miniMAVS. This truncated variant interferes with interferon production induced by full-length MAVS, whereas both proteins positively regulate cell death. To identify other polycistronic messages, we carried out genome-wide ribosomal profiling and identified a class of antiviral truncated variants. This study therefore reveals the existence of a functionally important bicistronic antiviral mRNA and suggests a widespread role for polycistronic mRNAs in the innate immune system.
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Affiliation(s)
- Sky W Brubaker
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Anna E Gauthier
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
| | - Eric W Mills
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218, USA; Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
| | - Nicholas T Ingolia
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Jonathan C Kagan
- Division of Gastroenterology, Boston Children's Hospital and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA.
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44
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Head SR, Komori HK, LaMere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P. Library construction for next-generation sequencing: overviews and challenges. Biotechniques 2014; 56:61-4, 66, 68, passim. [PMID: 24502796 DOI: 10.2144/000114133] [Citation(s) in RCA: 345] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 01/21/2014] [Indexed: 01/03/2023] Open
Abstract
High-throughput sequencing, also known as next-generation sequencing (NGS), has revolutionized genomic research. In recent years, NGS technology has steadily improved, with costs dropping and the number and range of sequencing applications increasing exponentially. Here, we examine the critical role of sequencing library quality and consider important challenges when preparing NGS libraries from DNA and RNA sources. Factors such as the quantity and physical characteristics of the RNA or DNA source material as well as the desired application (i.e., genome sequencing, targeted sequencing, RNA-seq, ChIP-seq, RIP-seq, and methylation) are addressed in the context of preparing high quality sequencing libraries. In addition, the current methods for preparing NGS libraries from single cells are also discussed.
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Affiliation(s)
- Steven R Head
- NGS and Microarray Core Facility, The Scripps Research Institute, La Jolla, CA
| | - H Kiyomi Komori
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Sarah A LaMere
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Thomas Whisenant
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Daniel R Salomon
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
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45
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Hingorani KS, Gierasch LM. Comparing protein folding in vitro and in vivo: foldability meets the fitness challenge. Curr Opin Struct Biol 2014; 24:81-90. [PMID: 24434632 DOI: 10.1016/j.sbi.2013.11.007] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/21/2013] [Accepted: 11/21/2013] [Indexed: 01/09/2023]
Abstract
In this review, we compare and contrast current knowledge about in vitro and in vivo protein folding. Major advances in understanding fundamental principles underlying protein folding in optimized in vitro conditions have yielded detailed physicochemical principles of folding landscapes for small, single domain proteins. In addition, there has been increased research focusing on the key features of protein folding in the cell that differentiate it from in vitro folding, such as co-translational folding, chaperone-facilitated folding, and folding in crowded conditions with many weak interactions. Yet these two research areas have not been bridged effectively in research carried out to date. This review points to gaps between the two that are ripe for future research. Moreover, we emphasize the biological selection pressures that impact protein folding in vivo and how fitness drives the evolution of protein sequences in ways that may place foldability in tension with other requirements on a given protein. We suggest that viewing the physicochemical process of protein folding through the lens of evolution will unveil new insights and pose novel challenges about in-cell folding landscapes.
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Affiliation(s)
- Karan S Hingorani
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States
| | - Lila M Gierasch
- Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Biochemistry & Molecular Biology, University of Massachusetts, Amherst, Amherst, MA 01003, United States; Department of Chemistry, University of Massachusetts, Amherst, Amherst, MA 01003, United States.
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46
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van Heesch S, van Iterson M, Jacobi J, Boymans S, Essers PB, de Bruijn E, Hao W, MacInnes AW, Cuppen E, Simonis M. Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol 2014; 15:R6. [PMID: 24393600 PMCID: PMC4053777 DOI: 10.1186/gb-2014-15-1-r6] [Citation(s) in RCA: 276] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 01/07/2014] [Indexed: 02/04/2023] Open
Abstract
Background Long noncoding RNAs (lncRNAs) form an abundant class of transcripts, but the function of the majority of them remains elusive. While it has been shown that some lncRNAs are bound by ribosomes, it has also been convincingly demonstrated that these transcripts do not code for proteins. To obtain a comprehensive understanding of the extent to which lncRNAs bind ribosomes, we performed systematic RNA sequencing on ribosome-associated RNA pools obtained through ribosomal fractionation and compared the RNA content with nuclear and (non-ribosome bound) cytosolic RNA pools. Results The RNA composition of the subcellular fractions differs significantly from each other, but lncRNAs are found in all locations. A subset of specific lncRNAs is enriched in the nucleus but surprisingly the majority is enriched in the cytosol and in ribosomal fractions. The ribosomal enriched lncRNAs include H19 and TUG1. Conclusions Most studies on lncRNAs have focused on the regulatory function of these transcripts in the nucleus. We demonstrate that only a minority of all lncRNAs are nuclear enriched. Our findings suggest that many lncRNAs may have a function in cytoplasmic processes, and in particular in ribosome complexes.
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Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG. The Vertebrate Genome Annotation browser 10 years on. Nucleic Acids Res 2013; 42:D771-9. [PMID: 24316575 PMCID: PMC3964964 DOI: 10.1093/nar/gkt1241] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Vertebrate Genome Annotation (VEGA) database (http://vega.sanger.ac.uk), initially designed as a community resource for browsing manual annotation of the human genome project, now contains five reference genomes (human, mouse, zebrafish, pig and rat). Its introduction pages have been redesigned to enable the user to easily navigate between whole genomes and smaller multi-species haplotypic regions of interest such as the major histocompatibility complex. The VEGA browser is unique in that annotation is updated via the Human And Vertebrate Analysis aNd Annotation (HAVANA) update track every 2 weeks, allowing single gene updates to be made publicly available to the research community quickly. The user can now access different haplotypic subregions more easily, such as those from the non-obese diabetic mouse, and display them in a more intuitive way using the comparative tools. We also highlight how the user can browse manually annotated updated patches from the Genome Reference Consortium (GRC).
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Affiliation(s)
- Jennifer L Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1HH, UK
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48
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Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res 2013; 42:D756-63. [PMID: 24259432 PMCID: PMC3965018 DOI: 10.1093/nar/gkt1114] [Citation(s) in RCA: 715] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The National Center for Biotechnology Information (NCBI) Reference Sequence (RefSeq) database is a collection of annotated genomic, transcript and protein sequence records derived from data in public sequence archives and from computation, curation and collaboration (http://www.ncbi.nlm.nih.gov/refseq/). We report here on growth of the mammalian and human subsets, changes to NCBI’s eukaryotic annotation pipeline and modifications affecting transcript and protein records. Recent changes to NCBI’s eukaryotic genome annotation pipeline provide higher throughput, and the addition of RNAseq data to the pipeline results in a significant expansion of the number of transcripts and novel exons annotated on mammalian RefSeq genomes. Recent annotation changes include reporting supporting evidence for transcript records, modification of exon feature annotation and the addition of a structured report of gene and sequence attributes of biological interest. We also describe a revised protein annotation policy for alternatively spliced transcripts with more divergent predicted proteins and we summarize the current status of the RefSeqGene project.
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Affiliation(s)
- Kim D Pruitt
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
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49
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Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SMJ, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JGR, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD. Current status and new features of the Consensus Coding Sequence database. Nucleic Acids Res 2013; 42:D865-72. [PMID: 24217909 PMCID: PMC3965069 DOI: 10.1093/nar/gkt1059] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the Wellcome Trust Sanger Institute and the University of California Santa Cruz, provide coordinated and continuous review of the dataset to ensure high-quality CCDS representations. We describe here the current status and recent growth in the CCDS dataset, as well as recent changes to the CCDS web and FTP sites. These changes include more explicit reporting about the NCBI and Ensembl annotation releases being compared, new search and display options, the addition of biologically descriptive information and our approach to representing genes for which support evidence is incomplete. We also present a summary of recent and future curation targets.
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Affiliation(s)
- Catherine M Farrell
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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