151
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Towarnicki SG, Ballard JWO. Drosophila mitotypes determine developmental time in a diet and temperature dependent manner. JOURNAL OF INSECT PHYSIOLOGY 2017; 100:133-139. [PMID: 28619466 DOI: 10.1016/j.jinsphys.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
It is well known that specific mitochondrial (mt) DNA mutations can reduce organismal fitness and influence mitochondrial-nuclear interactions. However, determining specific mtDNA mutations that are beneficial has been elusive. In this study, we vary the diet and environmental temperature to study larval development time of two Drosophila melanogaster mitotypes (Alstonville and Dahomey), in two nuclear genetic backgrounds, and investigate developmental differences through weight, feeding rate, and movement. To manipulate the diet, we utilize the nutritional geometric framework to manipulate isocaloric diets of differing macronutrient ratios (1:2 and 1:16 protein: carbohydrate (P:C) ratios) and raise flies at three temperatures (19°C, 23°C and 27°C). Larvae with Dahomey mtDNA develop more slowly than Alstonville when fed the 1:2 P:C diet at all temperatures and developed more quickly when fed the 1:16 P:C diet at 23°C and 27°C. We determined that Dahomey larvae eat more, move less, and weigh more than Alstonville larvae when raised on the 1:16 P:C diet and that these physiological responses are modified by temperature. We suggest that 1 (or more) of 4 mtDNA changes is likely responsible for the observed effects and posit the mtDNA changes moderate a physiological trade-off between consumption and foraging.
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Affiliation(s)
- Samuel G Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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152
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Mining for Micropeptides. Trends Cell Biol 2017; 27:685-696. [PMID: 28528987 DOI: 10.1016/j.tcb.2017.04.006] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 11/23/2022]
Abstract
Advances in computational biology and large-scale transcriptome analyses have revealed that a much larger portion of the genome is transcribed than was previously recognized, resulting in the production of a diverse population of RNA molecules with both protein-coding and noncoding potential. Emerging evidence indicates that several RNA molecules have been mis-annotated as noncoding and in fact harbor short open reading frames (sORFs) that encode functional peptides and that have evaded detection until now due to their small size. sORF-encoded peptides (SEPs), or micropeptides, have been shown to have important roles in fundamental biological processes and in the maintenance of cellular homeostasis. These small proteins can act independently, for example as ligands or signaling molecules, or they can exert their biological functions by engaging with and modulating larger regulatory proteins. Given their small size, micropeptides may be uniquely suited to fine-tune complex biological systems.
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153
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Abstract
The elucidation of the genetic code remains among the most influential discoveries in biology. While innumerable studies have validated the general universality of the code and its value in predicting and analyzing protein coding sequences, established and emerging work has also suggested that full genome decryption may benefit from a greater consideration of a codon's neighborhood within an mRNA than has been broadly applied. This Review examines the evidence for context cues in translation, with a focus on several recent studies that reveal broad roles for mRNA context in programming translation start sites, the rate of translation elongation, and stop codon identity.
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154
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Pamudurti NR, Bartok O, Jens M, Ashwal-Fluss R, Stottmeister C, Ruhe L, Hanan M, Wyler E, Perez-Hernandez D, Ramberger E, Shenzis S, Samson M, Dittmar G, Landthaler M, Chekulaeva M, Rajewsky N, Kadener S. Translation of CircRNAs. Mol Cell 2017; 66:9-21.e7. [PMID: 28344080 PMCID: PMC5387669 DOI: 10.1016/j.molcel.2017.02.021] [Citation(s) in RCA: 1235] [Impact Index Per Article: 176.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 01/04/2017] [Accepted: 02/21/2017] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are abundant and evolutionarily conserved RNAs of largely unknown function. Here, we show that a subset of circRNAs is translated in vivo. By performing ribosome footprinting from fly heads, we demonstrate that a group of circRNAs is associated with translating ribosomes. Many of these ribo-circRNAs use the start codon of the hosting mRNA, are bound by membrane-associated ribosomes, and have evolutionarily conserved termination codons. In addition, we found that a circRNA generated from the muscleblind locus encodes a protein, which we detected in fly head extracts by mass spectrometry. Next, by performing in vivo and in vitro translation assays, we show that UTRs of ribo-circRNAs (cUTRs) allow cap-independent translation. Moreover, we found that starvation and FOXO likely regulate the translation of a circMbl isoform. Altogether, our study provides strong evidence for translation of circRNAs, revealing the existence of an unexplored layer of gene activity.
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Affiliation(s)
- Nagarjuna Reddy Pamudurti
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Osnat Bartok
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Marvin Jens
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Reut Ashwal-Fluss
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Christin Stottmeister
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Larissa Ruhe
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Mor Hanan
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Emanuel Wyler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Daniel Perez-Hernandez
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Evelyn Ramberger
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Shlomo Shenzis
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Moshe Samson
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gunnar Dittmar
- Mass Spectrometry Core Unit, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Markus Landthaler
- RNA Biology and Posttranscriptional Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Marina Chekulaeva
- Non Coding RNAs and Mechanisms of Cytoplasmic Gene Regulation, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene Regulatory Elements, Max-Delbrück-Center for Molecular Medicine, Berlin 13125, Germany
| | - Sebastian Kadener
- Biological Chemistry Department, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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155
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Andreev DE, O'Connor PBF, Loughran G, Dmitriev SE, Baranov PV, Shatsky IN. Insights into the mechanisms of eukaryotic translation gained with ribosome profiling. Nucleic Acids Res 2016; 45:513-526. [PMID: 27923997 PMCID: PMC5314775 DOI: 10.1093/nar/gkw1190] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/31/2016] [Accepted: 11/18/2016] [Indexed: 12/29/2022] Open
Abstract
The development of Ribosome Profiling (RiboSeq) has revolutionized functional genomics. RiboSeq is based on capturing and sequencing of the mRNA fragments enclosed within the translating ribosome and it thereby provides a ‘snapshot’ of ribosome positions at the transcriptome wide level. Although the method is predominantly used for analysis of differential gene expression and discovery of novel translated ORFs, the RiboSeq data can also be a rich source of information about molecular mechanisms of polypeptide synthesis and translational control. This review will focus on how recent findings made with RiboSeq have revealed important details of the molecular mechanisms of translation in eukaryotes. These include mRNA translation sensitivity to drugs affecting translation initiation and elongation, the roles of upstream ORFs in response to stress, the dynamics of elongation and termination as well as details of intrinsic ribosome behavior on the mRNA after translation termination. As the RiboSeq method is still at a relatively early stage we will also discuss the implications of RiboSeq artifacts on data interpretation.
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Affiliation(s)
- Dmitry E Andreev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | | | - Gary Loughran
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Pavel V Baranov
- School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Ivan N Shatsky
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
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156
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Dunn JG, Weissman JS. Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data. BMC Genomics 2016; 17:958. [PMID: 27875984 PMCID: PMC5120557 DOI: 10.1186/s12864-016-3278-x] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 11/09/2016] [Indexed: 12/28/2022] Open
Abstract
Background Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments ― for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length ― analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Results Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid’s data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Conclusions Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays. Examples, tutorials, and extensive documentation can be found at https://plastid.readthedocs.io.
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Affiliation(s)
- Joshua G Dunn
- California Institute of Quantitative Biosciences, San Francisco, USA. .,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA. .,Center for RNA Systems Biology, Berkeley, CA, USA.
| | - Jonathan S Weissman
- California Institute of Quantitative Biosciences, San Francisco, USA.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA.,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.,Center for RNA Systems Biology, Berkeley, CA, USA
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157
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DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo. Nat Methods 2016; 14:75-82. [PMID: 27819661 DOI: 10.1038/nmeth.4057] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/29/2016] [Indexed: 12/25/2022]
Abstract
Coupling of structure-specific in vivo chemical modification to next-generation sequencing is transforming RNA secondary structure studies in living cells. The dominant strategy for detecting in vivo chemical modifications uses reverse transcriptase truncation products, which introduce biases and necessitate population-average assessments of RNA structure. Here we present dimethyl sulfate (DMS) mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse transcriptase. DMS-MaPseq yields a high signal-to-noise ratio, can report multiple structural features per molecule, and allows both genome-wide studies and focused in vivo investigations of even low-abundance RNAs. We apply DMS-MaPseq for the first analysis of RNA structure within an animal tissue and to identify a functional structure involved in noncanonical translation initiation. Additionally, we use DMS-MaPseq to compare the in vivo structure of pre-mRNAs with their mature isoforms. These applications illustrate DMS-MaPseq's capacity to dramatically expand in vivo analysis of RNA structure.
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158
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Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci U S A 2016; 113:E7126-E7135. [PMID: 27791167 DOI: 10.1073/pnas.1614788113] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions. The resulting data not only support many annotated and predicted noncanonical translation events but also uncover small ORFs in annotated noncoding RNAs and pseudogenes. A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stable proteins. Thus, our study provides a valuable resource for plant genomics and an efficient optimization strategy for ribosome profiling in other organisms.
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159
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Gerashchenko MV, Gladyshev VN. Ribonuclease selection for ribosome profiling. Nucleic Acids Res 2016; 45:e6. [PMID: 27638886 PMCID: PMC5314788 DOI: 10.1093/nar/gkw822] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 08/14/2016] [Accepted: 09/06/2016] [Indexed: 11/14/2022] Open
Abstract
Ribosome profiling has emerged as a powerful method to assess global gene translation, but methodological and analytical challenges often lead to inconsistencies across labs and model organisms. A critical issue in ribosome profiling is nuclease treatment of ribosome-mRNA complexes, as it is important to ensure both stability of ribosomal particles and complete conversion of polysomes to monosomes. We performed comparative ribosome profiling in yeast and mice with various ribonucleases including I, A, S7 and T1, characterized their cutting preferences, trinucleotide periodicity patterns and coverage similarities across coding sequences, and showed that they yield comparable estimations of gene expression when ribosome integrity is not compromised. However, ribosome coverage patterns of individual transcripts had little in common between the ribonucleases. We further examined their potency at converting polysomes to monosomes across other commonly used model organisms, including bacteria, nematodes and fruit flies. In some cases, ribonuclease treatment completely degraded ribosome populations. Ribonuclease T1 was the only enzyme that preserved ribosomal integrity while thoroughly converting polysomes to monosomes in all examined species. This study provides a guide for ribonuclease selection in ribosome profiling experiments across most common model systems.
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Affiliation(s)
- Maxim V Gerashchenko
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
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160
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Abstract
Ribosome profiling has emerged as a technique for measuring translation comprehensively and quantitatively by deep sequencing of ribosome-protected mRNA fragments. By identifying the precise positions of ribosomes, footprinting experiments have unveiled key insights into the composition and regulation of the expressed proteome, including delineating potentially functional micropeptides, revealing pervasive translation on cytosolic RNAs, and identifying differences in elongation rates driven by codon usage or other factors. This Primer looks at important experimental and analytical concerns for executing ribosome profiling experiments and surveys recent examples where the approach was developed to explore protein biogenesis and homeostasis.
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161
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New Peptides Under the s(ORF)ace of the Genome. Trends Biochem Sci 2016; 41:665-678. [DOI: 10.1016/j.tibs.2016.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 01/30/2023]
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162
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Wang X, Hou J, Quedenau C, Chen W. Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals. Mol Syst Biol 2016; 12:875. [PMID: 27430939 PMCID: PMC4965872 DOI: 10.15252/msb.20166941] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 06/17/2016] [Accepted: 06/21/2016] [Indexed: 12/02/2022] Open
Abstract
Transcription initiated at alternative sites can produce mRNA isoforms with different 5'UTRs, which are potentially subjected to differential translational regulation. However, the prevalence of such isoform-specific translational control across mammalian genomes is currently unknown. By combining polysome profiling with high-throughput mRNA 5' end sequencing, we directly measured the translational status of mRNA isoforms with distinct start sites. Among 9,951 genes expressed in mouse fibroblasts, we identified 4,153 showed significant initiation at multiple sites, of which 745 genes exhibited significant isoform-divergent translation. Systematic analyses of the isoform-specific translation revealed that isoforms with longer 5'UTRs tended to translate less efficiently. Further investigation of cis-elements within 5'UTRs not only provided novel insights into the regulation by known sequence features, but also led to the discovery of novel regulatory sequence motifs. Quantitative models integrating all these features explained over half of the variance in the observed isoform-divergent translation. Overall, our study demonstrated the extensive translational regulation by usage of alternative transcription start sites and offered comprehensive understanding of translational regulation by diverse sequence features embedded in 5'UTRs.
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Affiliation(s)
- Xi Wang
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Jingyi Hou
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Claudia Quedenau
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Wei Chen
- Laboratory for Functional Genomics and Systems Biology, Berlin Institute for Medical Systems Biology, Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany Department of Biology, South University of Science and Technology of China, Shenzhen, Guangdong, China
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163
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Popa A, Lebrigand K, Paquet A, Nottet N, Robbe-Sermesant K, Waldmann R, Barbry P. RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing. F1000Res 2016; 5:1309. [PMID: 27347386 PMCID: PMC4918025 DOI: 10.12688/f1000research.8964.1] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 01/14/2023] Open
Abstract
The ribosome profiling technique (Ribo-seq) allows the selective sequencing of translated RNA regions. Recently, the analysis of genomic sequences associated to Ribo-seq reads has been widely employed to assess their coding potential. These analyses led to the identification of differentially translated transcripts under different experimental conditions, and/or ribosome pausing on codon motifs. In the context of the ever-growing need for tools analyzing Ribo-seq reads, we have developed 'RiboProfiling', a new Bioconductor open-source package. 'RiboProfiling' provides a full pipeline to cover all key steps for the analysis of ribosome footprints. This pipeline has been implemented in a single R workflow. The package takes an alignment (BAM) file as input and performs ribosome footprint quantification at a transcript level. It also identifies footprint accumulation on particular amino acids or multi amino-acids motifs. Report summary graphs and data quantification are generated automatically. The package facilitates quality assessment and quantification of Ribo-seq experiments. Its implementation in Bioconductor enables the modeling and statistical analysis of its output through the vast choice of packages available in R. This article illustrates how to identify codon-motifs accumulating ribosome footprints, based on data from Escherichia coli.
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Affiliation(s)
- Alexandra Popa
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Kevin Lebrigand
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Agnes Paquet
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Nicolas Nottet
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Karine Robbe-Sermesant
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Rainer Waldmann
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
| | - Pascal Barbry
- Institut de Pharmacologie Mol´eculaire et Cellulaire, University Nice Sophia Antipolis and CNRS, Sophia- Antipolis, 06560, France
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164
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Chew GL, Pauli A, Schier AF. Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish. Nat Commun 2016; 7:11663. [PMID: 27216465 PMCID: PMC4890304 DOI: 10.1038/ncomms11663] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Accepted: 04/18/2016] [Indexed: 02/07/2023] Open
Abstract
Upstream open reading frames (uORFs) are ubiquitous repressive genetic elements in vertebrate mRNAs. While much is known about the regulation of individual genes by their uORFs, the range of uORF-mediated translational repression in vertebrate genomes is largely unexplored. Moreover, it is unclear whether the repressive effects of uORFs are conserved across species. To address these questions, we analyse transcript sequences and ribosome profiling data from human, mouse and zebrafish. We find that uORFs are depleted near coding sequences (CDSes) and have initiation contexts that diminish their translation. Linear modelling reveals that sequence features at both uORFs and CDSes modulate the translation of CDSes. Moreover, the ratio of translation over 5′ leaders and CDSes is conserved between human and mouse, and correlates with the number of uORFs. These observations suggest that the prevalence of vertebrate uORFs may be explained by their conserved role in repressing CDS translation. Upstream open reading frames (uORFs) can repress gene expression. Here, Guo-Liang Chew and colleagues use bioinformatics approaches to show that conservation of uORF-mediated translational repression is mediated by sequence features in human, mouse and zebrafish genomes.
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Affiliation(s)
- Guo-Liang Chew
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Alexander F Schier
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA.,FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138, USA.,Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138, USA.,Harvard Stem Cell Institute, Harvard University, Cambridge, Massachusetts 02138, USA
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165
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Baranov PV, Michel AM. Illuminating translation with ribosome profiling spectra. Nat Methods 2016; 13:123-4. [DOI: 10.1038/nmeth.3738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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166
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Olexiouk V, Menschaert G. Identification of Small Novel Coding Sequences, a Proteogenomics Endeavor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 926:49-64. [PMID: 27686805 DOI: 10.1007/978-3-319-42316-6_4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The identification of small proteins and peptides has consistently proven to be challenging. However, technological advances as well as multi-omics endeavors facilitate the identification of novel small coding sequences, leading to new insights. Specifically, the application of next generation sequencing technologies (NGS), providing accurate and sample specific transcriptome / translatome information, into the proteomics field led to more comprehensive results and new discoveries. This book chapter focuses on the inclusion of RNA-Seq and RIBO-Seq also known as ribosome profiling, an RNA-Seq based technique sequencing the +/- 30 bp long fragments captured by translating ribosomes. We emphasize the identification of micropeptides and neo-antigens, two distinct classes of small translation products, triggering our current understanding of biology. RNA-Seq is capable of capturing sample specific genomic variations, enabling focused neo-antigen identification. RIBO-Seq can identify translation events in small open reading frames which are considered to be non-coding, leading to the discovery of micropeptides. The identification of small translation products requires the integration of multi-omics data, stressing the importance of proteogenomics in this novel research area.
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Affiliation(s)
- Volodimir Olexiouk
- Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Building A, Ghent, 9000, Belgium.
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics (BioBix), Faculty of Bioscience Engineering, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, Building A, Ghent, 9000, Belgium
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