51
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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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52
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Granados-Riveron JT, Aquino-Jarquin G. The complexity of the translation ability of circRNAs. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1245-51. [PMID: 27449861 DOI: 10.1016/j.bbagrm.2016.07.009] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/21/2016] [Accepted: 07/15/2016] [Indexed: 12/12/2022]
Abstract
Circular RNAs (circRNAs) are a new class of long non-coding RNAs that play a potential role in gene expression regulation, acting as efficient microRNAs sponges. The latest surprise concerning circRNAs is that we now know that they can serve as transcriptional activators in human cells, indicating that circRNAs are involved in important regulatory tasks. Recently, new insight has been gained about the coding potential of circular viroid RNAs, as well as the presence of Internal Ribosomal Entry Sites (IRES) allowing the formation of peptides or proteins from circular RNA. Here, we discuss the current state of our knowledge regarding evidence supporting the hypothesis that circRNAs serve as protein-coding sequences in vitro and in vivo. Also, we remark on the difficulties of their identification and highlight some tools currently available for exploring the coding potential of circRNA.
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Affiliation(s)
- Javier T Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, 4to Piso, Sección 2, Hospital Infantil de México, Federico Gómez, Mexico.
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53
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Nam JW, Choi SW, You BH. Incredible RNA: Dual Functions of Coding and Noncoding. Mol Cells 2016; 39:367-74. [PMID: 27137091 PMCID: PMC4870183 DOI: 10.14348/molcells.2016.0039] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/20/2016] [Accepted: 03/29/2016] [Indexed: 11/27/2022] Open
Abstract
Since the RNA world hypothesis was proposed, a large number of regulatory noncoding RNAs (ncRNAs) have been identified in many species, ranging from microorganisms to mammals. During the characterization of these newly discovered RNAs, RNAs having both coding and noncoding functions were discovered, and these were considered bifunctional RNAs. The recent use of computational and high-throughput experimental approaches has revealed increasing evidence of various sources of bifunctional RNAs, such as protein-coding mRNAs with a noncoding isoform and long ncRNAs bearing a small open reading frame. Therefore, the genomic diversity of Janus-faced RNA molecules that have dual characteristics of coding and noncoding indicates that the functional roles of RNAs have to be revisited in cells on a genome-wide scale. Such studies would allow us to further understand the complex gene-regulatory network in cells. In this review, we discuss three major genomic sources of bifunctional RNAs and present a handful of examples of bifunctional RNA along with their functional roles.
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Affiliation(s)
- Jin-Wu Nam
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Seo-Won Choi
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
| | - Bo-Hyun You
- Department of Life Science, College of Natural Sciences, Hanyang University, Seoul 04763,
Korea
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Hellens RP, Brown CM, Chisnall MAW, Waterhouse PM, Macknight RC. The Emerging World of Small ORFs. TRENDS IN PLANT SCIENCE 2016; 21:317-328. [PMID: 26684391 DOI: 10.1016/j.tplants.2015.11.005] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 10/23/2015] [Accepted: 11/05/2015] [Indexed: 05/10/2023]
Abstract
Small open reading frames (sORFs) are an often overlooked feature of plant genomes. Initially found in plant viral RNAs and considered an interesting curiosity, an increasing number of these sORFs have been shown to encode functional peptides or play a regulatory role. The recent discovery that many of these sORFs initiate with start codons other than AUG, together with the identification of functional small peptides encoded in supposedly noncoding primary miRNA transcripts (pri-miRs), has drastically increased the number of potentially functional sORFs within the genome. Here we review how advances in technology, notably ribosome profiling (RP) assays, are complementing bioinformatics and proteogenomic methods to provide powerful ways to identify these elusive features of plant genomes, and highlight the regulatory roles sORFs can play.
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Affiliation(s)
- Roger P Hellens
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Chris M Brown
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Matthew A W Chisnall
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter M Waterhouse
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, GPO Box 2434, Brisbane, QLD 4001, Australia
| | - Richard C Macknight
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand; New Zealand Institute for Plant and Food Research Ltd.
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55
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Pueyo JI, Magny EG, Sampson CJ, Amin U, Evans IR, Bishop SA, Couso JP. Hemotin, a Regulator of Phagocytosis Encoded by a Small ORF and Conserved across Metazoans. PLoS Biol 2016; 14:e1002395. [PMID: 27015288 PMCID: PMC4807881 DOI: 10.1371/journal.pbio.1002395] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 01/29/2016] [Indexed: 12/12/2022] Open
Abstract
Translation of hundreds of small ORFs (smORFs) of less than 100 amino acids has recently been revealed in vertebrates and Drosophila. Some of these peptides have essential and conserved cellular functions. In Drosophila, we have predicted a particular smORF class encoding ~80 aa hydrophobic peptides, which may function in membranes and cell organelles. Here, we characterise hemotin, a gene encoding an 88aa transmembrane smORF peptide localised to early endosomes in Drosophila macrophages. hemotin regulates endosomal maturation during phagocytosis by repressing the cooperation of 14-3-3ζ with specific phosphatidylinositol (PI) enzymes. hemotin mutants accumulate undigested phagocytic material inside enlarged endo-lysosomes and as a result, hemotin mutants have reduced ability to fight bacteria, and hence, have severely reduced life span and resistance to infections. We identify Stannin, a peptide involved in organometallic toxicity, as the Hemotin functional homologue in vertebrates, showing that this novel regulator of phagocytic processing is widely conserved, emphasizing the significance of smORF peptides in cell biology and disease.
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Affiliation(s)
- José I. Pueyo
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Emile G. Magny
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | | | - Unum Amin
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Iwan R. Evans
- Department of Infection and Immunity and the Bateson Centre, University of Sheffield, Sheffield, South Yorkshire, United Kingdom
| | - Sarah A. Bishop
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
| | - Juan P. Couso
- Brighton and Sussex Medical School, University of Sussex, Brighton, United Kingdom
- * E-mail:
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56
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Sheshukova EV, Shindyapina AV, Komarova TV, Dorokhov YL. “Matreshka” genes with alternative reading frames. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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57
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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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58
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Wan Y, Tang K, Zhang D, Xie S, Zhu X, Wang Z, Lang Z. Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana. Genome Biol 2015; 16:272. [PMID: 26667818 PMCID: PMC4714525 DOI: 10.1186/s13059-015-0839-2] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 11/18/2015] [Indexed: 12/25/2022] Open
Abstract
Background m6A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m6A patterns in Arabidopsis have been assayed recently. However, differential m6A patterns between organs have not been well characterized. Results Over two-third of the transcripts in Arabidopsis are modified by m6A. In contrast to a recent observation of m6A enrichment in 5′ mRNA, we find that m6A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m6A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m6A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m6A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m6A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m6A methylation in the cells. Conclusions This is the first study to comprehensively analyze m6A patterns in a variety of RNAs, the relationship between transcript level and m6A methylation extent, and differential m6A patterns across organs in Arabidopsis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0839-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yizhen Wan
- State Key Lab Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. .,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Dayong Zhang
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Shaojun Xie
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xiaohong Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zegang Wang
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, China
| | - Zhaobo Lang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA. .,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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59
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Abstract
For many decades, the major function of mRNA was thought to be to provide protein-coding information embedded in the genome. The advent of high-throughput sequencing has led to the discovery of pervasive transcription of eukaryotic genomes and opened the world of RNA-mediated gene regulation. Many regulatory RNAs have been found to be incapable of protein coding and are hence termed as non-coding RNAs (ncRNAs). However, studies in recent years have shown that several previously annotated non-coding RNAs have the potential to encode proteins, and conversely, some coding RNAs have regulatory functions independent of the protein they encode. Such bi-functional RNAs, with both protein coding and non-coding functions, which we term as 'cncRNAs', have emerged as new players in cellular systems. Here, we describe the functions of some cncRNAs identified from bacteria to humans. Because the functions of many RNAs across genomes remains unclear, we propose that RNAs be classified as coding, non-coding or both only after careful analysis of their functions.
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Affiliation(s)
- Pooja Kumari
- Division of Biomedical Cell Biology, Warwick Medical School, The University of Warwick, Gibbet Hill Road, Coventry CV47AJ, United Kingdom
| | - Karuna Sampath
- Division of Biomedical Cell Biology, Warwick Medical School, The University of Warwick, Gibbet Hill Road, Coventry CV47AJ, United Kingdom.
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60
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Mohammadin S, Edger PP, Pires JC, Schranz ME. Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae. BMC PLANT BIOLOGY 2015; 15:217. [PMID: 26362138 PMCID: PMC4566204 DOI: 10.1186/s12870-015-0603-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 09/04/2015] [Indexed: 05/04/2023]
Abstract
BACKGROUND Long non-coding RNAs (LncRNAs) have been identified as gene regulatory elements that influence the transcription of their neighbouring protein-coding genes. The discovery of LncRNAs in animals has stimulated genome-wide scans for these elements across plant genomes. Recently, 6480 LincRNAs were putatively identified in Arabidopsis thaliana (Brassicaceae), however there is limited information on their conservation. RESULTS Using a phylogenomics approach, we assessed the positional and sequence conservation of these LncRNAs by analyzing the genomes of the basal Brassicaceae species Aethionema arabicum and Tarenaya hassleriana of the sister-family Cleomaceae. Furthermore, we generated transcriptomes for another three Aethionema species and one other Cleomaceae species to validate their transcriptional activity. We show that a subset of LncRNAs are highly diverged at the nucleotide level, but conserved by position (syntenic). Positionally conserved LncRNAs that are expressed neighbour important developmental and physiological genes. Interestingly, >65 % of the positionally conserved LncRNAs are located within 2.5 Mb of telomeres in Arabidopsis thaliana chromosomes. CONCLUSION These results highlight the importance of analysing not only sequence conservation, but also positional conservation of non-coding genetic elements in plants including LncRNAs.
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Affiliation(s)
- Setareh Mohammadin
- Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
| | - Patrick P Edger
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Michael Eric Schranz
- Biosystematics, Plant Science Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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61
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Tavormina P, De Coninck B, Nikonorova N, De Smet I, Cammue BPA. The Plant Peptidome: An Expanding Repertoire of Structural Features and Biological Functions. THE PLANT CELL 2015; 27:2095-118. [PMID: 26276833 PMCID: PMC4568509 DOI: 10.1105/tpc.15.00440] [Citation(s) in RCA: 218] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/08/2015] [Accepted: 07/25/2015] [Indexed: 05/18/2023]
Abstract
Peptides fulfill a plethora of functions in plant growth, development, and stress responses. They act as key components of cell-to-cell communication, interfere with signaling and response pathways, or display antimicrobial activity. Strikingly, both the diversity and amount of plant peptides have been largely underestimated. Most characterized plant peptides to date acting as small signaling peptides or antimicrobial peptides are derived from nonfunctional precursor proteins. However, evidence is emerging on peptides derived from a functional protein, directly translated from small open reading frames (without the involvement of a precursor) or even encoded by primary transcripts of microRNAs. These novel types of peptides further add to the complexity of the plant peptidome, even though their number is still limited and functional characterization as well as translational evidence are often controversial. Here, we provide a comprehensive overview of the reported types of plant peptides, including their described functional and structural properties. We propose a novel, unifying peptide classification system to emphasize the enormous diversity in peptide synthesis and consequent complexity of the still expanding knowledge on the plant peptidome.
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Affiliation(s)
- Patrizia Tavormina
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Barbara De Coninck
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium
| | - Ive De Smet
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Genetics, Ghent University, B-9052 Ghent, Belgium Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Leicestershire LE12 5RD, United Kingdom Centre for Plant Integrative Biology, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom
| | - Bruno P A Cammue
- Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, University of Leuven (KU Leuven), B-3000 Leuven, Belgium Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
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62
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Wu X, Zeng Y, Guan J, Ji G, Huang R, Li QQ. Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana. BMC Genomics 2015; 16:511. [PMID: 26155789 PMCID: PMC4568572 DOI: 10.1186/s12864-015-1691-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 06/05/2015] [Indexed: 12/22/2022] Open
Abstract
Background Messenger RNA polyadenylation is an essential step for the maturation of most eukaryotic mRNAs. Accurate determination of poly(A) sites helps define the 3’-ends of genes, which is important for genome annotation and gene function research. Genomic studies have revealed the presence of poly(A) sites in intergenic regions, which may be attributed to 3’-UTR extensions and novel transcript units. However, there is no systematically evaluation of intergenic poly(A) sites in plants. Results Approximately 16,000 intergenic poly(A) site clusters (IPAC) in Arabidopsis thaliana were discovered and evaluated at the whole genome level. Based on the distributions of distance from IPACs to nearby sense and antisense genes, these IPACs were classified into three categories. About 70 % of them were from previously unannotated 3’-UTR extensions to known genes, which would extend 6985 transcripts of TAIR10 genome annotation beyond their 3’-ends, with a mean extension of 134 nucleotides. 1317 IPACs were originated from novel intergenic transcripts, 37 of which were likely to be associated with protein coding transcripts. 2957 IPACs corresponded to antisense transcripts for genes on the reverse strand, which might affect 2265 protein coding genes and 39 non-protein-coding genes, including long non-coding RNA genes. The rest of IPACs could be originated from transcriptional read-through or gene mis-annotations. Conclusions The identified IPACs corresponding to novel transcripts, 3’-UTR extensions, and antisense transcription should be incorporated into current Arabidopsis genome annotation. Comprehensive characterization of IPACs from this study provides insights of alternative polyadenylation and antisense transcription in plants. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1691-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Yong Zeng
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Jinting Guan
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, Fujian, China. .,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, China.
| | - Rongting Huang
- Department of Automation, Xiamen University, Xiamen, Fujian, China.
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education on Costal Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China. .,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, USA. .,Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China.
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63
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Patel M, Milla-Lewis S, Zhang W, Templeton K, Reynolds WC, Richardson K, Biswas M, Zuleta MC, Dewey RE, Qu R, Sathish P. Overexpression of ubiquitin-like LpHUB1 gene confers drought tolerance in perennial ryegrass. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:689-699. [PMID: 25487628 DOI: 10.1111/pbi.12291] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 10/08/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
HUB1, also known as Ubl5, is a member of the subfamily of ubiquitin-like post-translational modifiers. HUB1 exerts its role by conjugating with protein targets. The function of this protein has not been studied in plants. A HUB1 gene, LpHUB1, was identified from serial analysis of gene expression data and cloned from perennial ryegrass. The expression of this gene was reported previously to be elevated in pastures during the summer and by drought stress in climate-controlled growth chambers. Here, pasture-type and turf-type transgenic perennial ryegrass plants overexpressing LpHUB1 showed improved drought tolerance, as evidenced by improved turf quality, maintenance of turgor and increased growth. Additional analyses revealed that the transgenic plants generally displayed higher relative water content, leaf water potential, and chlorophyll content and increased photosynthetic rate when subjected to drought stress. These results suggest HUB1 may play an important role in the tolerance of perennial ryegrass to abiotic stresses.
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Affiliation(s)
- Minesh Patel
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Susana Milla-Lewis
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Wanjun Zhang
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Kerry Templeton
- Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd/Fonterra, Auckland, New Zealand
| | - William C Reynolds
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Kim Richardson
- AgResearch Ltd, Grasslands Research Centre, Palmerston North, New Zealand
| | - Margaret Biswas
- Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd/Fonterra, Auckland, New Zealand
| | - Maria C Zuleta
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Ralph E Dewey
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Rongda Qu
- Department of Crop Science, North Carolina State University, Raleigh, NC, USA
| | - Puthigae Sathish
- Pastoral Genomics, c/o ViaLactia Biosciences (NZ) Ltd/Fonterra, Auckland, New Zealand
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64
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Abstract
AbstractPeptides of great number and diversity occur in all domains of life and exhibit a range of pharmaceutically relevant bioactivities. The complexity of biological samples including human cells or tissues, plant extracts or animal venom cocktails, often impedes the discovery of novel bioactive peptides using mass spectrometrybased peptidomics analysis. An increasing number of publicly available genome and transcriptome datasets, together with refined bioinformatics analysis, allows for rapid identification of novel peptides which may have been previously unrecognized. Moreover, a combination of information extracted from
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65
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Abstract
Over the past decade, high-throughput studies have identified many novel transcripts. While their existence is undisputed, their coding potential and functionality have remained controversial. Recent computational approaches guided by ribosome profiling have indicated that translation is far more pervasive than anticipated and takes place on many transcripts previously assumed to be non-coding. Some of these newly discovered translated transcripts encode short, functional proteins that had been missed in prior screens. Other transcripts are translated, but it might be the process of translation rather than the resulting peptides that serves a function. Here, we review annotation studies in zebrafish to discuss the challenges of placing RNAs onto the continuum that ranges from functional protein-encoding mRNAs to potentially non-functional peptide-producing RNAs to non-coding RNAs. As highlighted by the discovery of the novel signaling peptide Apela/ELABELA/Toddler, accurate annotations can give rise to exciting opportunities to identify the functions of previously uncharacterized transcripts.
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Affiliation(s)
- Andrea Pauli
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Eivind Valen
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
| | - Alexander F. Schier
- Department of Molecular and Cellular Biology, Harvard University, MA, USA
- The Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- FAS Center for Systems Biology, Harvard University, Cambridge, MA, USA
- Center for Brain Science, Harvard University, Cambridge, MA, USA
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66
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Bashir K, Hanada K, Shimizu M, Seki M, Nakanishi H, Nishizawa NK. Transcriptomic analysis of rice in response to iron deficiency and excess. RICE (NEW YORK, N.Y.) 2014; 7:18. [PMID: 26224551 PMCID: PMC4884027 DOI: 10.1186/s12284-014-0018-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/23/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Iron (Fe) is essential micronutrient for plants and its deficiency as well as toxicity is a serious agricultural problem. The mechanisms of Fe deficiency are reasonably understood, however our knowledge about plants response to excess Fe is limited. Moreover, the regulation of small open reading frames (sORFs) in response to abiotic stress has not been reported in rice. Understanding the regulation of rice transcriptome in response to Fe deficiency and excess could provide bases for developing strategies to breed plants tolerant to Fe deficiency as well as excess Fe. RESULTS We used a novel rice 110 K microarray harbouring ~48,620 sORFs to understand the transcriptomic changes that occur in response to Fe deficiency and excess. In roots, 36 genes were upregulated by excess Fe, of which three were sORFs. In contrast, 1509 genes were upregulated by Fe deficiency, of which 90 (6%) were sORFs. Co-expression analysis revealed that the expression of some sORFs was positively correlated with the genes upregulated by Fe deficiency. In shoots, 50 (19%) of the genes upregulated by Fe deficiency and 1076 out of 2480 (43%) genes upregulated by excess Fe were sORFs. These results suggest that excess Fe may significantly alter metabolism, particularly in shoots. CONCLUSION These data not only reveal the genes regulated by excess Fe, but also suggest that sORFs might play an important role in the response of plants to Fe deficiency and excess.
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Affiliation(s)
- Khurram Bashir
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
| | - Kousuke Hanada
- />Gene Discovery Research Group, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
- />Frontier Research Academy for Young Researchers, Department of Bioscience and Bioinformatics, Kyusyu Institute of Technology, Iizuka, 820-8502 Fukuoka, Japan
| | - Minami Shimizu
- />Frontier Research Academy for Young Researchers, Department of Bioscience and Bioinformatics, Kyusyu Institute of Technology, Iizuka, 820-8502 Fukuoka, Japan
| | - Motoaki Seki
- />Plant Genomics Network Research Team, Center for Sustainable Resource Science, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, 230-0045 Kanagawa, Japan
- />Kihara Institute for Biological Research, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, 236-0027 Japan
| | - Hiromi Nakanishi
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
| | - Naoko K Nishizawa
- />Laboratory of Plant Biotechnology, Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657 Japan
- />Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 1-308 Suematsu, Nonoichi-shi, 921-8836 Ishikawa, Japan
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67
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Gawron D, Gevaert K, Van Damme P. The proteome under translational control. Proteomics 2014; 14:2647-62. [PMID: 25263132 DOI: 10.1002/pmic.201400165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 08/21/2014] [Accepted: 09/23/2014] [Indexed: 02/02/2023]
Abstract
A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multilevel regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. MS-enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customized and sample-specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA- and/or RNA-oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re-)annotation of genomes.
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Affiliation(s)
- Daria Gawron
- Department of Medical Protein Research, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium
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68
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Li YL, Dai XR, Yue X, Gao XQ, Zhang XS. Identification of small secreted peptides (SSPs) in maize and expression analysis of partial SSP genes in reproductive tissues. PLANTA 2014; 240:713-28. [PMID: 25048445 DOI: 10.1007/s00425-014-2123-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 07/03/2014] [Indexed: 05/14/2023]
Abstract
Maize 1,491 small secreted peptides were identified, which were classified according to the character of peptide sequences. Partial SSP gene expressions in reproductive tissues were determined by qRT-PCR. Small secreted peptides (SSPs) are important cell-cell communication messengers in plants. Most information on plant SSPs come from Arabidopsis thaliana and Oryza sativa, while little is known about the SSPs of other grass species such as maize (Zea mays). In this study, we identified 1,491 SSP genes from maize genomic sequences. These putative SSP genes were distributed throughout the ten maize chromosomes. Among them, 611 SSPs were classified into 198 superfamilies according to their conserved domains, and 725 SSPs with four or more cysteines at their C-termini shared similar cysteine arrangements with their counterparts in other plant species. Moreover, the SSPs requiring post-translational modification, as well as defensin-like (DEFL) proteins, were identified. Further, the expression levels of 110 SSP genes were analyzed in reproductive tissues, including male flower, pollen, silk, and ovary. Most of the genes encoding basal-layer antifungal peptide-like, small coat proteins-like, thioredoxin-like proteins, γ-thionins-like, and DEFL proteins showed high expression levels in the ovary and male flower compared with their levels in silk and mature pollen. The rapid alkalinization factor-like genes were highly expressed only in the mature ovary and mature pollen, and pollen Ole e 1-like genes showed low expression in silk. The results of this study provide basic information for further analysis of SSP functions in the reproductive process of maize.
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Affiliation(s)
- Ye Long Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, China
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69
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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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70
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Crappé J, Van Criekinge W, Menschaert G. Little things make big things happen: A summary of micropeptide encoding genes. EUPA OPEN PROTEOMICS 2014. [DOI: 10.1016/j.euprot.2014.02.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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71
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Ericson M, Janes MA, Butter F, Mann M, Ullu E, Tschudi C. On the extent and role of the small proteome in the parasitic eukaryote Trypanosoma brucei. BMC Biol 2014; 12:14. [PMID: 24552149 PMCID: PMC3942054 DOI: 10.1186/1741-7007-12-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 02/06/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Although technical advances in genomics and proteomics research have yielded a better understanding of the coding capacity of a genome, one major challenge remaining is the identification of all expressed proteins, especially those less than 100 amino acids in length. Such information can be particularly relevant to human pathogens, such as Trypanosoma brucei, the causative agent of African trypanosomiasis, since it will provide further insight into the parasite biology and life cycle. RESULTS Starting with 993 T. brucei transcripts, previously shown by RNA-Sequencing not to coincide with annotated coding sequences (CDS), homology searches revealed that 173 predicted short open reading frames in these transcripts are conserved across kinetoplastids with 13 also conserved in representative eukaryotes. Mining mass spectrometry data sets revealed 42 transcripts encoding at least one matching peptide. RNAi-induced down-regulation of these 42 transcripts revealed seven to be essential in insect-form trypanosomes with two also required for the bloodstream life cycle stage. To validate the specificity of the RNAi results, each lethal phenotype was rescued by co-expressing an RNAi-resistant construct of each corresponding CDS. These previously non-annotated essential small proteins localized to a variety of cell compartments, including the cell surface, mitochondria, nucleus and cytoplasm, inferring the diverse biological roles they are likely to play in T. brucei. We also provide evidence that one of these small proteins is required for replicating the kinetoplast (mitochondrial) DNA. CONCLUSIONS Our studies highlight the presence and significance of small proteins in a protist and expose potential new targets to block the survival of trypanosomes in the insect vector and/or the mammalian host.
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Affiliation(s)
- Megan Ericson
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Michael A Janes
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
- Current address: San Francisco General Hospital, Pulmonary & Critical Care, San Francisco, CA, USA
| | - Falk Butter
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Current address: Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Elisabetta Ullu
- Department of Cell Biology and Internal Medicine, School of Medicine, Yale University, New Haven, CT, USA
| | - Christian Tschudi
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
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72
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Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 2014; 15:193-204. [PMID: 24514441 DOI: 10.1038/nrg3520] [Citation(s) in RCA: 385] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Short open reading frames (sORFs) are a common feature of all genomes, but their coding potential has mostly been disregarded, partly because of the difficulty in determining whether these sequences are translated. Recent innovations in computing, proteomics and high-throughput analyses of translation start sites have begun to address this challenge and have identified hundreds of putative coding sORFs. The translation of some of these has been confirmed, although the contribution of their peptide products to cellular functions remains largely unknown. This Review examines this hitherto overlooked component of the proteome and considers potential roles for sORF-encoded peptides.
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73
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Campbell MS, Law M, Holt C, Stein JC, Moghe GD, Hufnagel DE, Lei J, Achawanantakun R, Jiao D, Lawrence CJ, Ware D, Shiu SH, Childs KL, Sun Y, Jiang N, Yandell M. MAKER-P: a tool kit for the rapid creation, management, and quality control of plant genome annotations. PLANT PHYSIOLOGY 2014; 164:513-24. [PMID: 24306534 PMCID: PMC3912085 DOI: 10.1104/pp.113.230144] [Citation(s) in RCA: 286] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Accepted: 11/26/2013] [Indexed: 05/18/2023]
Abstract
We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better parallelization for large repeat-rich plant genomes, noncoding RNA annotation capabilities, and support for pseudogene identification. We have benchmarked the resulting software tool kit, MAKER-P, using the Arabidopsis (Arabidopsis thaliana) and maize (Zea mays) genomes. Here, we demonstrate the ability of the MAKER-P tool kit to automatically update, extend, and revise the Arabidopsis annotations in light of newly available data and to annotate pseudogenes and noncoding RNAs absent from The Arabidopsis Informatics Resource 10 build. Our results demonstrate that MAKER-P can be used to manage and improve the annotations of even Arabidopsis, perhaps the best-annotated plant genome. We have also installed and benchmarked MAKER-P on the Texas Advanced Computing Center. We show that this public resource can de novo annotate the entire Arabidopsis and maize genomes in less than 3 h and produce annotations of comparable quality to those of the current The Arabidopsis Information Resource 10 and maize V2 annotation builds.
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74
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Okamoto M, Higuchi-Takeuchi M, Shimizu M, Shinozaki K, Hanada K. Substantial expression of novel small open reading frames in Oryza sativa. PLANT SIGNALING & BEHAVIOR 2014; 9:e27848. [PMID: 24526015 PMCID: PMC4091330 DOI: 10.4161/psb.27848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In our previous integrated study combining informatics and molecular biology analyses, we revealed that Arabidopsis small open reading frames (sORFs) predicted by computational analysis have biological functions in morphogenesis. Here, we report that sequences homologous to Arabidopsis sORFs are abundant in intergenic regions of the rice genome. These sequences represent a subset of non-protein-coding DNA, and some are transcribed into mRNA. These results indicate that many sORFs associated with morphogenesis are hidden in the genomes of crop species.
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Affiliation(s)
- Masanori Okamoto
- Arid Land Research Center; Tottori University; Tottori, Japan
- RIKEN Center for Sustainable Resource Science; Yokohama, Japan
| | | | - Minami Shimizu
- RIKEN Center for Sustainable Resource Science; Yokohama, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science; Yokohama, Japan
| | - Kousuke Hanada
- RIKEN Center for Sustainable Resource Science; Yokohama, Japan
- Frontier Research Academy for Young Researchers; Kyushu Institute of Technology; Fukuoka, Japan
- Correspondence to: Kousuke Hanada,
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75
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Su M, Ling Y, Yu J, Wu J, Xiao J. Small proteins: untapped area of potential biological importance. Front Genet 2013; 4:286. [PMID: 24379829 PMCID: PMC3864261 DOI: 10.3389/fgene.2013.00286] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/27/2013] [Indexed: 01/13/2023] Open
Abstract
Polypeptides containing ≤100 amino acid residues (AAs) are generally considered to be small proteins (SPs). Many studies have shown that some SPs are involved in important biological processes, including cell signaling, metabolism, and growth. SP generally has a simple domain and has an advantage to be used as model system to overcome folding speed limits in protein folding simulation and drug design. But SPs were once thought to be trivial molecules in biological processes compared to large proteins. Because of the constraints of experimental methods and bioinformatics analysis, many genome projects have used a length threshold of 100 amino acid residues to minimize erroneous predictions and SPs are relatively under-represented in earlier studies. The general protein discovery methods have potential problems to predict and validate SPs, and very few effective tools and algorithms were developed specially for SPs identification. In this review, we mainly consider the diverse strategies applied to SPs prediction and discuss the challenge for differentiate SP coding genes from artifacts. We also summarize current large-scale discovery of SPs in species at the genome level. In addition, we present an overview of SPs with regard to biological significance, structural application, and evolution characterization in an effort to gain insight into the significance of SPs.
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Affiliation(s)
- Mingming Su
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Yunchao Ling
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China ; Graduate University of Chinese Academy of Sciences Beijing, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences Beijing, China
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76
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Zhou P, Silverstein KAT, Gao L, Walton JD, Nallu S, Guhlin J, Young ND. Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application). BMC Bioinformatics 2013; 14:335. [PMID: 24256031 PMCID: PMC3924332 DOI: 10.1186/1471-2105-14-335] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/15/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Small peptides encoded as one- or two-exon genes in plants have recently been shown to affect multiple aspects of plant development, reproduction and defense responses. However, popular similarity search tools and gene prediction techniques generally fail to identify most members belonging to this class of genes. This is largely due to the high sequence divergence among family members and the limited availability of experimentally verified small peptides to use as training sets for homology search and ab initio prediction. Consequently, there is an urgent need for both experimental and computational studies in order to further advance the accurate prediction of small peptides. RESULTS We present here a homology-based gene prediction program to accurately predict small peptides at the genome level. Given a high-quality profile alignment, SPADA identifies and annotates nearly all family members in tested genomes with better performance than all general-purpose gene prediction programs surveyed. We find numerous mis-annotations in the current Arabidopsis thaliana and Medicago truncatula genome databases using SPADA, most of which have RNA-Seq expression support. We also show that SPADA works well on other classes of small secreted peptides in plants (e.g., self-incompatibility protein homologues) as well as non-secreted peptides outside the plant kingdom (e.g., the alpha-amanitin toxin gene family in the mushroom, Amanita bisporigera). CONCLUSIONS SPADA is a free software tool that accurately identifies and predicts the gene structure for short peptides with one or two exons. SPADA is able to incorporate information from profile alignments into the model prediction process and makes use of it to score different candidate models. SPADA achieves high sensitivity and specificity in predicting small plant peptides such as the cysteine-rich peptide families. A systematic application of SPADA to other classes of small peptides by research communities will greatly improve the genome annotation of different protein families in public genome databases.
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Affiliation(s)
- Peng Zhou
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Kevin AT Silverstein
- Supercomputing Institute for Advanced Computational Research, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Liangliang Gao
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Jonathan D Walton
- Department of Plant Biology and U.S. Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, USA
| | - Sumitha Nallu
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
| | - Joseph Guhlin
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, USA
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, Minnesota 55108, USA
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108, USA
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Combining in silico prediction and ribosome profiling in a genome-wide search for novel putatively coding sORFs. BMC Genomics 2013; 14:648. [PMID: 24059539 PMCID: PMC3852105 DOI: 10.1186/1471-2164-14-648] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 09/13/2013] [Indexed: 11/23/2022] Open
Abstract
Background It was long assumed that proteins are at least 100 amino acids (AAs) long. Moreover, the detection of short translation products (e.g. coded from small Open Reading Frames, sORFs) is very difficult as the short length makes it hard to distinguish true coding ORFs from ORFs occurring by chance. Nevertheless, over the past few years many such non-canonical genes (with ORFs < 100 AAs) have been discovered in different organisms like Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster. Thanks to advances in sequencing, bioinformatics and computing power, it is now possible to scan the genome in unprecedented scrutiny, for example in a search of this type of small ORFs. Results Using bioinformatics methods, we performed a systematic search for putatively functional sORFs in the Mus musculus genome. A genome-wide scan detected all sORFs which were subsequently analyzed for their coding potential, based on evolutionary conservation at the AA level, and ranked using a Support Vector Machine (SVM) learning model. The ranked sORFs are finally overlapped with ribosome profiling data, hinting to sORF translation. All candidates are visually inspected using an in-house developed genome browser. In this way dozens of highly conserved sORFs, targeted by ribosomes were identified in the mouse genome, putatively encoding micropeptides. Conclusion Our combined genome-wide approach leads to the prediction of a comprehensive but manageable set of putatively coding sORFs, a very important first step towards the identification of a new class of bioactive peptides, called micropeptides.
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Targeting of Painting of fourth to roX1 and roX2 proximal sites suggests evolutionary links between dosage compensation and the regulation of the fourth chromosome in Drosophila melanogaster. G3-GENES GENOMES GENETICS 2013; 3:1325-34. [PMID: 23733888 PMCID: PMC3737172 DOI: 10.1534/g3.113.006866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In Drosophila melanogaster, two chromosome-specific targeting and regulatory systems have been described. The male-specific lethal (MSL) complex supports dosage compensation by stimulating gene expression from the male X-chromosome, and the protein Painting of fourth (POF) specifically targets and stimulates expression from the heterochromatic 4(th) chromosome. The targeting sites of both systems are well characterized, but the principles underlying the targeting mechanisms have remained elusive. Here we present an original observation, namely that POF specifically targets two loci on the X-chromosome, PoX1 and PoX2 (POF-on-X). PoX1 and PoX2 are located close to the roX1 and roX2 genes, which encode noncoding RNAs important for the correct targeting and spreading of the MSL-complex. We also found that the targeting of POF to PoX1 and PoX2 is largely dependent on roX expression and identified a high-affinity target region that ectopically recruits POF. The results presented support a model linking the MSL-complex to POF and dosage compensation to regulation of heterochromatin.
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Tong J, Yang H, Yang H, Eom SH, Im YJ. Structure of Osh3 reveals a conserved mode of phosphoinositide binding in oxysterol-binding proteins. Structure 2013; 21:1203-13. [PMID: 23791945 DOI: 10.1016/j.str.2013.05.007] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/25/2013] [Accepted: 05/08/2013] [Indexed: 11/27/2022]
Abstract
The oxysterol-binding protein (OSBP)-related proteins (ORPs) are conserved from yeast to humans, and implicated in the regulation of lipid homeostasis and in signaling pathways. Saccharomyces cerevisiae has seven ORPs (Osh1-Osh7) that share one unknown essential function. Here, we report the 1.5-2.3 Å structures of the PH domain and ORD (OSBP-related domain) of yeast Osh3 in apo-form or in complex with phosphatidylinositol 4-phosphate (PI[4]P). Osh3 recognizes PI(4)P by the highly conserved residues in the tunnel of ORD whereas it lacks sterol binding due to the narrow hydrophobic tunnel. Yeast complementation tests suggest that PI(4)P binding to PH and ORD is essential for function. This study suggests that the unifying feature in all ORP homologs is the binding of PI(4)P to ORD and sterol binding is additional to certain homologs. Structural modeling of full-length Osh3 is consistent with the concept that Osh3 is a lipid transfer protein or regulator in membrane contact sites.
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Affiliation(s)
- Junsen Tong
- College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea
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The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14. Nat Commun 2013; 4:1566. [PMID: 23463009 PMCID: PMC3615354 DOI: 10.1038/ncomms2542] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 01/24/2013] [Indexed: 01/11/2023] Open
Abstract
Rice tillering is a multigenic trait that influences grain yield, but its regulation molecular module is poorly understood. Here we report that OsMADS57 interacts with OsTB1 (TEOSINTE BRANCHED1) and targets D14 (Dwarf14) to control the outgrowth of axillary buds in rice. An activation-tagged mutant osmads57-1 and OsMADS57-overexpression lines showed increased tillers, whereas OsMADS57 antisense lines had fewer tillers. OsMIR444a-overexpressing lines exhibited suppressed OsMADS57 expression and tillering. Furthermore, osmads57-1 was insensitive to strigolactone treatment to inhibit axillary bud outgrowth, and OsMADS57’s function in tillering was dependent on D14. D14 expression was downregulated in osmads57-1, but upregulated in antisense and OsMIR444a-overexpressing lines. OsMADS57 bound to the CArG motif [C(A/T)TTAAAAAG] in the promoter and directly suppressed D14 expression. Interaction of OsMADS57 with OsTB1 reduced OsMADS57 inhibition of D14 transcription. Therefore, OsMIR444a-regulated OsMADS57, together with OsTB1, target D14 to control tillering. This regulation mechanism could have important application in rice molecular breeding programs focused on high grain yield. Tillering is a multigenic complex trait that influences grain yield in cereal; however, the molecular network for its regulation remains unclear. Guo et al. show that OsMADS57, a transcription factor controlled by miR444a, interacts with OsTEOSINTE BRANCHED1 and targets DWARF14 to control tillering in rice.
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81
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Small open reading frames associated with morphogenesis are hidden in plant genomes. Proc Natl Acad Sci U S A 2013; 110:2395-400. [PMID: 23341627 DOI: 10.1073/pnas.1213958110] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
It is likely that many small ORFs (sORFs; 30-100 amino acids) are missed when genomes are annotated. To overcome this limitation, we identified ∼8,000 sORFs with high coding potential in intergenic regions of the Arabidopsis thaliana genome. However, the question remains as to whether these coding sORFs play functional roles. Using a designed array, we generated an expression atlas for 16 organs and 17 environmental conditions among 7,901 identified coding sORFs. A total of 2,099 coding sORFs were highly expressed under at least one experimental condition, and 571 were significantly conserved in other land plants. A total of 473 coding sORFs were overexpressed; ∼10% (49/473) induced visible phenotypic effects, a proportion that is approximately seven times higher than that of randomly chosen known genes. These results indicate that many coding sORFs hidden in plant genomes are associated with morphogenesis. We believe that the expression atlas will contribute to further study of the roles of sORFs in plants.
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82
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Moghe GD, Lehti-Shiu MD, Seddon AE, Yin S, Chen Y, Juntawong P, Brandizzi F, Bailey-Serres J, Shiu SH. Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis. PLANT PHYSIOLOGY 2013; 161:210-24. [PMID: 23132786 PMCID: PMC3532253 DOI: 10.1104/pp.112.205245] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 10/21/2012] [Indexed: 05/23/2023]
Abstract
The Arabidopsis (Arabidopsis thaliana) genome is the most well-annotated plant genome. However, transcriptome sequencing in Arabidopsis continues to suggest the presence of polyadenylated (polyA) transcripts originating from presumed intergenic regions. It is not clear whether these transcripts represent novel noncoding or protein-coding genes. To understand the nature of intergenic polyA transcription, we first assessed its abundance using multiple messenger RNA sequencing data sets. We found 6,545 intergenic transcribed fragments (ITFs) occupying 3.6% of Arabidopsis intergenic space. In contrast to transcribed fragments that map to protein-coding and RNA genes, most ITFs are significantly shorter, are expressed at significantly lower levels, and tend to be more data set specific. A surprisingly large number of ITFs (32.1%) may be protein coding based on evidence of translation. However, our results indicate that these "translated" ITFs tend to be close to and are likely associated with known genes. To investigate if ITFs are under selection and are functional, we assessed ITF conservation through cross-species as well as within-species comparisons. Our analysis reveals that 237 ITFs, including 49 with translation evidence, are under strong selective constraint and relatively distant from annotated features. These ITFs are likely parts of novel genes. However, the selective pressure imposed on most ITFs is similar to that of randomly selected, untranscribed intergenic sequences. Our findings indicate that despite the prevalence of ITFs, apart from the possibility of genomic contamination, many may be background or noisy transcripts derived from "junk" DNA, whose production may be inherent to the process of transcription and which, on rare occasions, may act as catalysts for the creation of novel genes.
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MESH Headings
- Arabidopsis/genetics
- Arabidopsis/metabolism
- Base Sequence
- Conserved Sequence
- DNA, Intergenic/genetics
- DNA, Intergenic/metabolism
- DNA, Plant/genetics
- DNA, Plant/metabolism
- Evolution, Molecular
- Gene Expression Regulation, Plant
- Genes, Plant
- Molecular Sequence Annotation
- Plants, Genetically Modified/genetics
- Plants, Genetically Modified/metabolism
- Protein Biosynthesis
- Pseudogenes
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Ribosomes/genetics
- Ribosomes/metabolism
- Selection, Genetic
- Sequence Analysis, RNA
- Transcription, Genetic
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Affiliation(s)
- Gaurav D. Moghe
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Melissa D. Lehti-Shiu
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Alex E. Seddon
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Shan Yin
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Yani Chen
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Piyada Juntawong
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Federica Brandizzi
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Julia Bailey-Serres
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
| | - Shin-Han Shiu
- Department of Plant Biology (G.D.M., M.D.L.-S., A.E.S., S.Y., Y.C., F.B., S.-H.S.), Programs in Genetics and Quantitative Biology (G.D.M., S.-H.S.), and Plant Research Laboratory (Y.C., F.B.), Michigan State University, East Lansing, Michigan 48824; and Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521 (P.J., J.B.-S.)
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83
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Coman D, Gruissem W, Hennig L. Transcript profiling in Arabidopsis with genome tiling microarrays. Methods Mol Biol 2013; 1067:35-49. [PMID: 23975784 DOI: 10.1007/978-1-62703-607-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Microarray technology is at present a standardized workflow for genome-wide expression analysis. Whole-genome tiling microarrays have emerged as an important platform for flexible and comprehensive expression profiling. In this chapter we describe a detailed standardized workflow for experiments assessing the transcriptome of Arabidopsis using tiling arrays and provide useful hints for critical steps from experimental design to data analysis. Although the protocol is optimized for AGRONOMICS1 arrays, it can readily be adapted to other tiling arrays. AGRONOMICS1 is the first platform that enables strand-specific expression analysis of the Arabidopsis genome with a single array. Moreover, it includes all perfect match probes from the original ATH1 array, allowing readily integration with the large existing ATH1 knowledge base. This workflow is designed for the analysis of raw data for any number of samples and it does not pose any particular hardware requirements.
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Affiliation(s)
- Diana Coman
- Plant Biotechnology, Department of Biology, ETH Zurich, Zurich, Switzerland
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84
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Hotto AM, Germain A, Stern DB. Plastid non-coding RNAs: emerging candidates for gene regulation. TRENDS IN PLANT SCIENCE 2012; 17:737-44. [PMID: 22981395 DOI: 10.1016/j.tplants.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 07/27/2012] [Accepted: 08/05/2012] [Indexed: 05/08/2023]
Abstract
Recent advances in transcriptomics and bioinformatics, specifically strand-specific RNA sequencing, have allowed high-throughput, comprehensive detection of low-abundance transcripts typical of the non-coding RNAs studied in bacteria and eukaryotes. Before this, few plastid non-coding RNAs (pncRNAs) had been identified, and even fewer had been investigated for any functional role in gene regulation. Relaxed plastid transcription initiation and termination result in full transcription of both chloroplast DNA strands. Following this, post-transcriptional processing produces a pool of metastable RNA species, including distinct pncRNAs. Here we review pncRNA biogenesis and possible functionality, and speculate that this RNA class may have an underappreciated role in plastid gene regulation.
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Affiliation(s)
- Amber M Hotto
- Boyce Thompson Institute for Plant Research, Tower Road, Ithaca, NY 14853, USA
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85
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Pan B, Sheng J, Sun W, Zhao Y, Hao P, Li X. OrysPSSP: a comparative platform for small secreted proteins from rice and other plants. Nucleic Acids Res 2012. [PMID: 23203890 PMCID: PMC3531210 DOI: 10.1093/nar/gks1090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had not been any effort to systematically analyze rice SSPs. Here, we constructed a comparative platform, OrysPSSP (http://www.genoportal.org/PSSP/index.do), involving >100 000 SSPs from rice and 25 plant species. OrysPSSP is composed of a core SSP database and a dynamic web interface that integrates a variety of user tools and resources. The current release (v0530) of core SSP database contains a total of 101 048 predicted SSPs, which were generated through a rigid computation/curation pipeline. The web interface consists of eight different modules, providing users with rich resources/functions, e.g. browsing SSP by chromosome, searching and filtering SSP, validating SSP with omics data, comparing SSP among multiple species and querying core SSP database with BLAST. Some cases of application are discussed to demonstrate the utility of OrysPSSP. OrysPSSP serves as a comprehensive resource to explore SSP on the genome scale and across the phylogeny of plant species.
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Affiliation(s)
- Bohu Pan
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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86
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An Integrated Analysis of Lineage-specific Small Proteins Across Eight Eukaryotes Reveals Functional and Evolutionary Significance*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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87
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Cheng H, Chan WS, Li Z, Wang D, Liu S, Zhou Y. Small open reading frames: current prediction techniques and future prospect. Curr Protein Pept Sci 2012; 12:503-7. [PMID: 21787300 DOI: 10.2174/138920311796957667] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 04/01/2011] [Accepted: 05/04/2011] [Indexed: 11/22/2022]
Abstract
Evidence is accumulating that small open reading frames (sORF, <100 codons) play key roles in many important biological processes. Yet, they are generally ignored in gene annotation despite they are far more abundant than the genes with more than 100 codons. Here, we demonstrate that popular homolog search and codon-index techniques perform poorly for small genes relative to that for larger genes, while a method dedicated to sORF discovery has a similar level of accuracy as homology search. The result is largely due to the small dataset of experimentally verified sORF available for homology search and for training ab initio techniques. It highlights the urgent need for both experimental and computational studies in order to further advance the accuracy of sORF prediction.
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Affiliation(s)
- Haoyu Cheng
- Indiana University School of Informatics, Indiana University-Purdue University and Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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88
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Abstract
It is clear that RNA has a diverse set of functions and is more than just a messenger between gene and protein. The mammalian genome is extensively transcribed, giving rise to thousands of non-coding transcripts. Whether all of these transcripts are functional is debated, but it is evident that there are many functional large non-coding RNAs (ncRNAs). Recent studies have begun to explore the functional diversity and mechanistic role of these large ncRNAs. Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions.
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Affiliation(s)
- Mitchell Guttman
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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89
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Meng L. Roles of secreted peptides in intercellular communication and root development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 183:106-114. [PMID: 22195583 DOI: 10.1016/j.plantsci.2011.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 10/24/2011] [Accepted: 10/26/2011] [Indexed: 05/31/2023]
Abstract
Intercellular signaling networks control cell identity and activity in all multicellular organisms. Secreted peptides that function as extracellular ligands play essential roles in local communication between adjacent plant cells. The extracellular domain of receptor kinases bind to secreted peptides and initiate downstream cellular responses, resulting in cell proliferation, growth, or differentiation in multicellular organisms. Root growth and development are highly organized processes involving cell division, expansion, and differentiation; these processes depend on the establishment and maintenance of root apical meristem. The regulatory networks controlling root growth and development are tightly controlled by various signal transduction pathways, feedback loops, and crosstalk among signaling pathways. This review demonstrates the remarkable diversity and importance of secreted peptides in cell signaling and summarizes the current understanding of the molecular mechanisms underlying the peptide signaling cascades with particular emphasis on pathways involved in regulating root apical meristem and vascular tissue development and those involved in rhizobium-legume symbiosis. Furthermore, this review provides an integrated view of the regulatory networks that control root development, including transcription factors, phytohormones and peptide signalings. Future perspectives in peptide signaling are also discussed.
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Affiliation(s)
- Ling Meng
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA 94720-3102, USA.
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90
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Abstract
Vast tracts of noncoding DNA contain elements that regulate gene expression in higher eukaryotes. Describing these regulatory elements and understanding how they evolve represent major challenges for biologists. Advances in the ability to survey genome-scale DNA sequence data are providing unprecedented opportunities to use evolutionary models and computational tools to identify functionally important elements and the mode of selection acting on them in multiple species. This chapter reviews some of the current methods that have been developed and applied on noncoding DNA, what they have shown us, and how they are limited. Results of several recent studies reveal that a significantly larger fraction of noncoding DNA in eukaryotic organisms is likely to be functional than previously believed, implying that the functional annotation of most noncoding DNA in these organisms is largely incomplete. In Drosophila, recent studies have further suggested that a large fraction of noncoding DNA divergence observed between species may be the product of recurrent adaptive substitution. Similar studies in humans have revealed a more complex pattern, with signatures of recurrent positive selection being largely concentrated in conserved noncoding DNA elements. Understanding these patterns and the extent to which they generalize to other organisms awaits the analysis of forthcoming genome-scale polymorphism and divergence data from more species.
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Affiliation(s)
- Ying Zhen
- Department of Ecology and Evolutionary Biology, The Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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91
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Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 2011; 40:D1202-10. [PMID: 22140109 PMCID: PMC3245047 DOI: 10.1093/nar/gkr1090] [Citation(s) in RCA: 1457] [Impact Index Per Article: 112.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is a genome database for Arabidopsis thaliana, an important reference organism for many fundamental aspects of biology as well as basic and applied plant biology research. TAIR serves as a central access point for Arabidopsis data, annotates gene function and expression patterns using controlled vocabulary terms, and maintains and updates the A. thaliana genome assembly and annotation. TAIR also provides researchers with an extensive set of visualization and analysis tools. Recent developments include several new genome releases (TAIR8, TAIR9 and TAIR10) in which the A. thaliana assembly was updated, pseudogenes and transposon genes were re-annotated, and new data from proteomics and next generation transcriptome sequencing were incorporated into gene models and splice variants. Other highlights include progress on functional annotation of the genome and the release of several new tools including Textpresso for Arabidopsis which provides the capability to carry out full text searches on a large body of research literature.
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Affiliation(s)
- Philippe Lamesch
- Department of Plant Biology, Carnegie Institution, 260 Panama St, Stanford, CA 94305, USA
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92
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Ladoukakis E, Pereira V, Magny EG, Eyre-Walker A, Couso JP. Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol 2011; 12:R118. [PMID: 22118156 PMCID: PMC3334604 DOI: 10.1186/gb-2011-12-11-r118] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 11/04/2011] [Accepted: 11/25/2011] [Indexed: 12/22/2022] Open
Abstract
Background The relationship between DNA sequence and encoded information is still an unsolved puzzle. The number of protein-coding genes in higher eukaryotes identified by genome projects is lower than was expected, while a considerable amount of putatively non-coding transcription has been detected. Functional small open reading frames (smORFs) are known to exist in several organisms. However, coding sequence detection methods are biased against detecting such very short open reading frames. Thus, a substantial number of non-canonical coding regions encoding short peptides might await characterization. Results Using bio-informatics methods, we have searched for smORFs of less than 100 amino acids in the putatively non-coding euchromatic DNA of Drosophila melanogaster, and initially identified nearly 600,000 of them. We have studied the pattern of conservation of these smORFs as coding entities between D. melanogaster and Drosophila pseudoobscura, their presence in syntenic and in transcribed regions of the genome, and their ratio of conservative versus non-conservative nucleotide changes. For negative controls, we compared the results with those obtained using random short sequences, while a positive control was provided by smORFs validated by proteomics data. Conclusions The combination of these analyses led us to postulate the existence of at least 401 functional smORFs in Drosophila, with the possibility that as many as 4,561 such functional smORFs may exist.
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93
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Seo PJ, Hong SY, Kim SG, Park CM. Competitive inhibition of transcription factors by small interfering peptides. TRENDS IN PLANT SCIENCE 2011; 16:541-9. [PMID: 21723179 DOI: 10.1016/j.tplants.2011.06.001] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Revised: 06/01/2011] [Accepted: 06/06/2011] [Indexed: 05/04/2023]
Abstract
Combinatorial assortment by dynamic dimer formation diversifies gene transcriptional specificities of transcription factors. A similar but biochemically distinct mechanism is competitive inhibition in which small proteins act as negative regulators by competitively forming nonfunctional heterodimers with specific transcription factors. The most extensively studied is the negative regulation of auxin response factors by AUXIN/INDOLE-3-ACETIC ACID repressors. Similarly, Arabidopsis thaliana (Arabidopsis) little zipper and mini finger proteins act as competitive inhibitors of target transcription factors. Competitive inhibitors are also generated by alternative splicing and controlled proteolytic processing. Because they provide a way of attenuating transcription factors we propose to call them small interfering peptides (siPEPs). The siPEP-mediated strategy could be applied to deactivate specific transcription factors in crop plants.
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Affiliation(s)
- Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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94
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Nanjo Y, Maruyama K, Yasue H, Yamaguchi-Shinozaki K, Shinozaki K, Komatsu S. Transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings. PLANT MOLECULAR BIOLOGY 2011; 77:129-44. [PMID: 21656040 DOI: 10.1007/s11103-011-9799-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Accepted: 05/27/2011] [Indexed: 05/25/2023]
Abstract
To understand the transcriptional responses to flooding stress in roots including hypocotyl of soybean seedlings, genome-wide changes in gene expression were analyzed using a soybean microarray chip containing 42,034 60-mer oligonucleotide probes. More than 6,000 of flooding-responsive genes in the roots including hypocotyl of soybean seedlings were identified. The transcriptional analysis showed that genes related to photosynthesis, glycolysis, Ser-Gly-Cys group amino acid synthesis, regulation of transcription, ubiquitin-mediated protein degradation and cell death were significantly up-regulated by flooding. Meanwhile, genes related to cell wall synthesis, secondary metabolism, metabolite transport, cell organization, chromatin structure synthesis, and degradation of aspartate family amino acid were significantly down-regulated. Comparison of the responses with other plants showed that genes encoding pyrophosphate dependent phosphofructokinase were down-regulated in flooded soybean seedlings, however, those in tolerant plants were up-regulated. Additionally, genes related to RNA processing and initiation of protein synthesis were not up-regulated in soybean, however, those in tolerant plants were up-regulated. Furthermore, we found that flooding-specific up-regulation of genes encoding small proteins which might have roles in acclimation to flooding. These results suggest that functional disorder of acclimative responses to flooding through transcriptional and post-transcriptional regulations is involved in occurring flooding injury to soybean seedlings.
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Affiliation(s)
- Yohei Nanjo
- National Institute of Crop Science, Tsukuba 305-8518, Japan
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95
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Bardou F, Merchan F, Ariel F, Crespi M. Dual RNAs in plants. Biochimie 2011; 93:1950-4. [PMID: 21824505 DOI: 10.1016/j.biochi.2011.07.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Accepted: 07/25/2011] [Indexed: 01/08/2023]
Abstract
Plants have remarkable developmental plasticity, and the same genotype can result in different phenotypes depending on environmental variation. Indeed, abiotic stresses or biotic interactions affect organogenesis and post-embryonic growth and significantly affect gene regulation. The large diversity of non-protein-coding RNAs (npcRNAs) and genes containing only short open reading frames that are expressed during plant growth and development, contribute to the regulation of gene expression. Certain npcRNAs code for oligopeptides and may possess additional biological activity linked to the RNA moiety. The ENOD40 gene is a dual RNA that is activated during a symbiotic interaction leading to root nodule organogenesis. Both the oligopeptides encoded by ENOD40 and the structured regions of the ENOD40 RNA have been shown to interact with different proteins in the cell to control enzymatic activities or induce the relocalisation of ribonucleoproteins, respectively. Other npcRNAs encode for small signalling peptides or are the precursors of small RNAs involved in post-transcriptional or transcriptional gene silencing. They may have RNA-related activities or encode peptides (or even larger proteins), and therefore act as dual RNAs. In addition, long natural antisense RNAs with a coding function and a regulatory RNA-mediated action that are expressed in response to abiotic stress in plants have been identified. In certain cases, these RNAs lead to the synthesis of nat-siRNAs, that are small RNAs derived from the overlapping double-stranded RNA region of natural antisense RNAs, which facilitates the silencing of complementary mRNAs. Finally, the advent of deep sequencing technologies has identified a large number of non-protein-coding RNAs in plants, which could be a large reservoir for dual RNAs.
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Affiliation(s)
- Florian Bardou
- Institut des Sciences du Végétal, Centre National de la Recherche Scientifique, 91198 Gif sur Yvette, France
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96
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Kageyama Y, Kondo T, Hashimoto Y. Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts. Biochimie 2011; 93:1981-6. [PMID: 21729735 DOI: 10.1016/j.biochi.2011.06.024] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Accepted: 06/20/2011] [Indexed: 01/13/2023]
Abstract
Genome analysis has identified a number of putative non-protein-coding transcripts that do not contain ORFs longer than 100 codons. Although evidence strongly suggests that non-coding RNAs are important in a variety of biological phenomena, the discovery of small peptide-coding mRNAs confirms that some transcripts that have been assumed to be non-coding actually have coding potential. Their abundance and importance in biological phenomena makes the sorting of non-coding RNAs from small peptide-coding mRNAs a key issue in functional genomics. However, validating the coding potential of small peptide-coding RNAs is complicated, because their ORF sequences are usually too short for computational analysis. In this review, we discuss computational and experimental methods for validating the translatability of these non-coding RNAs.
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Affiliation(s)
- Yuji Kageyama
- Okazaki Institute for Integrated Biosciences, National Institutes of Natural Sciences, 5-1 Myodaiji-Higashiyama, Okazaki, Aichi 444-8787, Japan.
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97
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Yang X, Tschaplinski TJ, Hurst GB, Jawdy S, Abraham PE, Lankford PK, Adams RM, Shah MB, Hettich RL, Lindquist E, Kalluri UC, Gunter LE, Pennacchio C, Tuskan GA. Discovery and annotation of small proteins using genomics, proteomics, and computational approaches. Genome Res 2011; 21:634-41. [PMID: 21367939 DOI: 10.1101/gr.109280.110] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Small proteins (10-200 amino acids [aa] in length) encoded by short open reading frames (sORF) play important regulatory roles in various biological processes, including tumor progression, stress response, flowering, and hormone signaling. However, ab initio discovery of small proteins has been relatively overlooked. Recent advances in deep transcriptome sequencing make it possible to efficiently identify sORFs at the genome level. In this study, we obtained ~2.6 million expressed sequence tag (EST) reads from Populus deltoides leaf transcriptome and reconstructed full-length transcripts from the EST sequences. We identified an initial set of 12,852 sORFs encoding proteins of 10-200 aa in length. Three computational approaches were then used to enrich for bona fide protein-coding sORFs from the initial sORF set: (1) coding-potential prediction, (2) evolutionary conservation between P. deltoides and other plant species, and (3) gene family clustering within P. deltoides. As a result, a high-confidence sORF candidate set containing 1469 genes was obtained. Analysis of the protein domains, non-protein-coding RNA motifs, sequence length distribution, and protein mass spectrometry data supported this high-confidence sORF set. In the high-confidence sORF candidate set, known protein domains were identified in 1282 genes (higher-confidence sORF candidate set), out of which 611 genes, designated as highest-confidence candidate sORF set, were supported by proteomics data. Of the 611 highest-confidence candidate sORF genes, 56 were new to the current Populus genome annotation. This study not only demonstrates that there are potential sORF candidates to be annotated in sequenced genomes, but also presents an efficient strategy for discovery of sORFs in species with no genome annotation yet available.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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98
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Plett JM, Martin F. Blurred boundaries: lifestyle lessons from ectomycorrhizal fungal genomes. Trends Genet 2011; 27:14-22. [DOI: 10.1016/j.tig.2010.10.005] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Revised: 10/18/2010] [Accepted: 10/25/2010] [Indexed: 11/29/2022]
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99
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Hong SY, Kim OK, Kim SG, Yang MS, Park CM. Nuclear import and DNA binding of the ZHD5 transcription factor is modulated by a competitive peptide inhibitor in Arabidopsis. J Biol Chem 2010; 286:1659-68. [PMID: 21059647 PMCID: PMC3020774 DOI: 10.1074/jbc.m110.167692] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Competitive inhibition of transcription factors by small proteins is an intriguing component of gene regulatory networks in both animals and plants. The small interfering proteins possess limited sequence homologies to specific transcription factors but lack one or more protein motifs required for transcription factor activities. They interfere with the activities of transcription factors, such as DNA binding and transcriptional activation, by forming nonfunctional heterodimers. A potential example is the Arabidopsis MIF1 (mini zinc finger 1) protein consisting of 101 residues. It has a zinc finger domain but lacks other protein motifs normally present in transcription factors. In this work, we show that MIF1 and its functional homologues physically interact with a group of zinc finger homeodomain (ZHD) transcription factors, such as ZHD5, that regulate floral architecture and leaf development. Gel mobility shift assays revealed that MIF1 blocks the DNA binding activity of ZHD5 homodimers by competitively forming MIF1-ZHD5 heterodimers. Accordingly, the transcriptional activation activity of ZHD5 was significantly suppressed by MIF1 coexpressed transiently in Arabidopsis protoplasts. Notably, MIF1 also prevents ZHD5 from nuclear localization. Although ZHD5 was localized exclusively in the nucleus, it was scattered throughout the cytoplasm when MIF1 was coexpressed. Transgenic plants overexpressing the ZHD5 gene (35S:ZHD5) exhibited accelerated growth with larger leaves. Consistent with the negative regulation of ZHD5 by MIF1, the 35S:ZHD5 phenotypes were diminished by MIF1 coexpression. These observations indicate that MIF1 regulates the ZHD5 activities in a dual step manner: nuclear import and DNA binding.
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Affiliation(s)
- Shin-Young Hong
- Department of Chemistry, Seoul National University, Seoul 151-742, Korea
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100
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Abstract
A sequence analysis-oriented binary search-like algorithm was transformed to a sensitive and accurate analysis tool for processing whole-genome data. The advantage of the algorithm over previous methods is its ability to detect the margins of both short and long genome fragments, enriched by up-regulated signals, at equal accuracy. The score of an enriched genome fragment reflects the difference between the actual concentration of up-regulated signals in the fragment and the chromosome signal baseline. The "divide-and-conquer"-type algorithm detects a series of nonintersecting fragments of various lengths with locally optimal scores. The procedure is applied to detected fragments in a nested manner by recalculating the lower-than-baseline signals in the chromosome. The algorithm was applied to simulated whole-genome data, and its sensitivity/specificity were compared with those of several alternative algorithms. The algorithm was also tested with four biological tiling array datasets comprising Arabidopsis (i) expression and (ii) histone 3 lysine 27 trimethylation CHIP-on-chip datasets; Saccharomyces cerevisiae (iii) spliced intron data and (iv) chromatin remodeling factor binding sites. The analyses' results demonstrate the power of the algorithm in identifying both the short up-regulated fragments (such as exons and transcription factor binding sites) and the long--even moderately up-regulated zones--at their precise genome margins. The algorithm generates an accurate whole-genome landscape that could be used for cross-comparison of signals across the same genome in evolutionary and general genomic studies.
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