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Briefings in functional genomics & proteomics最新文献

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The role of RNA molecules in cellular biology. Editorial. RNA分子在细胞生物学中的作用。社论。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 DOI: 10.1093/bfgp/elp044
Sam Griffiths-Jones
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引用次数: 2
Deciphering the diversity of small RNAs in plants: the long and short of it. 解读植物中小rna的多样性：长与短。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 Epub Date: 2009-07-29 DOI: 10.1093/bfgp/elp024
Frank Schwach, Simon Moxon, Vincent Moulton, Tamas Dalmay
{"title":"Deciphering the diversity of small RNAs in plants: the long and short of it.","authors":"Frank Schwach, Simon Moxon, Vincent Moulton, Tamas Dalmay","doi":"10.1093/bfgp/elp024","DOIUrl":"10.1093/bfgp/elp024","url":null,"abstract":"<p><p>RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in such diverse processes as development, pathogen control, genome maintenance and response to environmental changes. Since its recent discovery, RNA silencing has become a fast moving key area of research in plant and animal molecular biology. Research in this field has greatly profited from recent developments in novel sequencing technologies that allow massive parallel sequencing of small RNA (sRNA) molecules, the key players of all RNA silencing phenomena. As researchers are beginning to decipher the complexity of RNA silencing, novel methodologies have to be developed to make sense of the large amounts of data that are currently being generated. In this review we present an overview of RNA silencing pathways in plants and the current challenges in analysing sRNA data, with a special focus on computational approaches.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"472-81"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28409383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Annotating non-coding transcription using functional genomics strategies. 使用功能基因组学策略注释非编码转录。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 DOI: 10.1093/bfgp/elp041
Alistair R R Forrest, Rehab F Abdelhamid, Piero Carninci
{"title":"Annotating non-coding transcription using functional genomics strategies.","authors":"Alistair R R Forrest,&nbsp;Rehab F Abdelhamid,&nbsp;Piero Carninci","doi":"10.1093/bfgp/elp041","DOIUrl":"https://doi.org/10.1093/bfgp/elp041","url":null,"abstract":"<p><p>Non-coding RNA (ncRNA) transcripts are RNA molecules that do not code for proteins, but elicit function by other mechanisms. The vast majority of RNA produced in a cell is non-coding ribosomal RNA, produced from relatively few loci, however more recently complementary DNA (cDNA) cloning, tag sequencing, and genome tiling array studies suggest that ncRNAs also account for the majority of RNA species produced by a cell. ncRNA based regulation has been referred to as a 'hidden layer' of signals or 'dark matter' that control gene expression in cellular processes by poorly described mechanisms. These terms have appeared as ncRNAs until recently have been ignored by expression profiling and cDNA annotation projects and their mode of action is diverse (e.g. influencing chromatin structure and epigenetics, translational silencing, transcriptional silencing). Here, we highlight recent functional genomics strategies toward identifying and assigning function to ncRNA transcription.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"437-43"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp041","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28439447","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Transcription attenuation in bacteria: theme and variations. 细菌的转录衰减:主题和变异。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 Epub Date: 2009-08-03 DOI: 10.1093/bfgp/elp025
Magali Naville, Daniel Gautheret
{"title":"Transcription attenuation in bacteria: theme and variations.","authors":"Magali Naville,&nbsp;Daniel Gautheret","doi":"10.1093/bfgp/elp025","DOIUrl":"https://doi.org/10.1093/bfgp/elp025","url":null,"abstract":"<p><p>Premature termination of transcription, or attenuation, is an efficient RNA-based regulatory strategy that is commonly used in bacterial organisms. Attenuators are generally located in the 5' untranslated regions of genes or operons and combine a Rho-independent terminator, controlling transcription, with an RNA element that senses specific environmental signals. A striking diversity of sensing elements enable regulation of gene expression in response to multiple environmental conditions, including temperature changes, availability of small metabolites (such as ions, amino acids, nucleobases or vitamins), or availability of macromolecules such as tRNAs and regulatory proteins. The wide distribution of attenuators suggests an early emergence among bacteria. However, attenuators also display a great mobility and lability, illustrated by a multiplicity of recent horizontal transfers and duplications. For these reasons, attenuation systems are of high interest both from a fundamental evolutionary perspective and for possible biotechnological applications.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":" ","pages":"482-92"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp025","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40007659","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 63
Customized strategies for discovering distant ncRNA homologs. 发现远端ncRNA同源物的定制策略。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 Epub Date: 2009-09-24 DOI: 10.1093/bfgp/elp035
Axel Mosig, Liang Zhu, Peter F Stadler
{"title":"Customized strategies for discovering distant ncRNA homologs.","authors":"Axel Mosig,&nbsp;Liang Zhu,&nbsp;Peter F Stadler","doi":"10.1093/bfgp/elp035","DOIUrl":"https://doi.org/10.1093/bfgp/elp035","url":null,"abstract":"<p><p>A large fraction of non-coding RNAs is short and/or poorly conserved in sequence. Most of the longer examples, furthermore, consist of a collection of conserved structural motifs rather than a coherent globally conserved secondary structure. As a consequence, the conceptually simple problem of homology search becomes a complex and technically demanding task. Despite the best efforts of databases such as Rfam, the situation is complicated further by the sparsity of information in many--in particular prokaryotic--RNA families. In this contribution, we review recent efforts to customize sequence-based search tools for ncRNA applications. In particular, semi-global alignments and the development of methods for fragmented pattern search have brought significant practical advances. Current developments in this area focus on the integration of fragmented sequence pattern search with search algorithms for secondary structure patterns. We focus here, in particular, on strategies that can be successful in the 'twilight zone' where generic approaches from blast to infernal to start to fail.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":" ","pages":"451-60"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp035","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40034218","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 26
Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. 真核生物基因组的普遍转录:功能指标和概念含义。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 Epub Date: 2009-09-21 DOI: 10.1093/bfgp/elp038
Marcel E Dinger, Paulo P Amaral, Timothy R Mercer, John S Mattick
{"title":"Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications.","authors":"Marcel E Dinger,&nbsp;Paulo P Amaral,&nbsp;Timothy R Mercer,&nbsp;John S Mattick","doi":"10.1093/bfgp/elp038","DOIUrl":"https://doi.org/10.1093/bfgp/elp038","url":null,"abstract":"<p><p>Genome-wide analyses of the eukaryotic transcriptome have revealed that the majority of the genome is transcribed, producing large numbers of non-protein-coding RNAs (ncRNAs). This surprising observation challenges many assumptions about the genetic programming of higher organisms and how information is stored and organized within the genome. Moreover, the rapid advances in genomics have given little opportunity for biologists to integrate these emerging findings into their intellectual and experimental frameworks. This problem has been compounded by the perception that genome-wide studies often generate more questions than answers, which in turn has led to confusion and controversy. In this article, we address common questions associated with the phenomenon of pervasive transcription and consider the indices that can be used to evaluate the function (or lack thereof) of the resulting ncRNAs. We suggest that many lines of evidence, including expression profiles, conservation signatures, chromatin modification patterns and examination of increasing numbers of individual cases, argue in favour of the widespread functionality of non-coding transcription. We also discuss how informatic and experimental approaches used to analyse protein-coding genes may not be applicable to ncRNAs and how the general perception that protein-coding genes form the main informational output of the genome has resulted in much of the misunderstanding surrounding pervasive transcription and its potential significance. Finally, we present the conceptual implications of the majority of the eukaryotic genome being functional and describe how appreciating this perspective will provide considerable opportunity to further understand the molecular basis of development and complex diseases.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"407-23"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp038","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28414967","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 157
Retrotransposons and non-protein coding RNAs. 反转录转座子和非蛋白编码rna。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 Epub Date: 2009-09-03 DOI: 10.1093/bfgp/elp036
Tobias Mourier, Eske Willerslev
{"title":"Retrotransposons and non-protein coding RNAs.","authors":"Tobias Mourier,&nbsp;Eske Willerslev","doi":"10.1093/bfgp/elp036","DOIUrl":"https://doi.org/10.1093/bfgp/elp036","url":null,"abstract":"<p><p>Retrotransposons constitute a significant fraction of mammalian genomes. Considering the finding of widespread transcriptional activity across entire genomes, it is not surprising that retrotransposons contribute to the collective RNA pool. However, the transcriptional output from retrotransposons does not merely represent spurious transcription. We review examples of functional RNAs transcribed from retrotransposons, and address the collection of non-protein coding RNAs derived from transposable element sequences, including numerous human microRNAs and the neuronal BC RNAs. Finally, we review the emerging understanding of how retrotransposons themselves are regulated by small RNAs.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"493-501"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp036","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28380169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 22
The use of covariance models to annotate RNAs in whole genomes. 利用协方差模型对全基因组中的rna进行注释。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 DOI: 10.1093/bfgp/elp042
Paul P Gardner
{"title":"The use of covariance models to annotate RNAs in whole genomes.","authors":"Paul P Gardner","doi":"10.1093/bfgp/elp042","DOIUrl":"https://doi.org/10.1093/bfgp/elp042","url":null,"abstract":"<p><p>In this review we discuss bioinformatic issues in non-coding RNA analysis, in particular the annotation of genome sequences using covariance models. Some recent innovations for improving the speed and accuracy of covariance models is discussed.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"444-50"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp042","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28439448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 24
Establishing legitimacy and function in the new transcriptome. 在新的转录组中建立合法性和功能。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 DOI: 10.1093/bfgp/elp037
Harm van Bakel, Timothy R Hughes
{"title":"Establishing legitimacy and function in the new transcriptome.","authors":"Harm van Bakel,&nbsp;Timothy R Hughes","doi":"10.1093/bfgp/elp037","DOIUrl":"https://doi.org/10.1093/bfgp/elp037","url":null,"abstract":"<p><p>The last decade has seen an explosion of interest in new classes of non-coding RNA. While some are now firmly established as new categories of legitimate functional RNAs, the purpose and even existence of others remain to be solidified. Here, we discuss the challenges associated with discovery and characterization of non-traditional categories of non-coding RNA.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"424-36"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp037","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28441729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 70
From consensus structure prediction to RNA gene finding. 从共识结构预测到RNA基因发现。
Briefings in functional genomics & proteomics Pub Date : 2009-11-01 DOI: 10.1093/bfgp/elp043
Stephan H Bernhart, Ivo L Hofacker
{"title":"From consensus structure prediction to RNA gene finding.","authors":"Stephan H Bernhart,&nbsp;Ivo L Hofacker","doi":"10.1093/bfgp/elp043","DOIUrl":"https://doi.org/10.1093/bfgp/elp043","url":null,"abstract":"<p><p>Reliable structure prediction is a prerequisite for most types of bioinformatical analysis of RNA. Since the accuracy of structure prediction from single sequences is limited, one often resorts to computing the consensus structure for a set of related RNA sequences. Since functionally important RNA structures are expected to evolve much more slowly than the underlying sequences, the pattern of sequence (co-)variation can be exploited to dramatically improve structure prediction. Since a conserved common structure is only expected when the RNA structure is under selective pressure, consensus structure prediction also provides an ideal starting point for the de novo detection of structured non-coding RNAs. Here, we review different strategies for the prediction of consensus secondary structures, and show how these approaches can be used to predict non-coding RNA genes.</p>","PeriodicalId":87063,"journal":{"name":"Briefings in functional genomics & proteomics","volume":"8 6","pages":"461-71"},"PeriodicalIF":0.0,"publicationDate":"2009-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1093/bfgp/elp043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"28439449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
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