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Canzler S, Stadler PF, Schor J. The fungal snoRNAome. RNA (NEW YORK, N.Y.) 2018; 24:342-360. [PMID: 29196413 PMCID: PMC5824354 DOI: 10.1261/rna.062778.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/19/2017] [Indexed: 06/07/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are essential players in the rRNA biogenesis due to their involvement in the nucleolytic processing of the precursor and the subsequent guidance of nucleoside modifications. Within the kingdom Fungi, merely a few species-specific surveys have explored their snoRNA repertoire. However, the wide range of the snoRNA landscape spanning all major fungal lineages has not been mapped so far, mainly because of missing tools for automatized snoRNA detection and functional analysis. For the first time, we report here a comprehensive inventory of fungal snoRNAs together with a functional analysis and an in-depth investigation of their evolutionary history including innovations, deletions, and target switches. This large-scale analysis, incorporating more than 120 snoRNA families with more than 7700 individual snoRNA sequences, catalogs and clarifies the landscape of fungal snoRNA families, assigns functions to previously orphan snoRNAs, and increases the number of sequences by 450%. We also show that the snoRNAome is subject to ongoing rearrangements and adaptations, e.g., through lineage-specific targets and redundant guiding functions.
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Affiliation(s)
- Sebastian Canzler
- Bioinformatics Group, Department of Computer Science, Leipzig University, D-04107 Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Leipzig University, D-04107 Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Leipzig University, D-04103 Leipzig, Germany
- Department of Diagnostics, Fraunhofer Institute for Cell Therapy and Immunology - IZI, D-04103 Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, D-04103 Leipzig, Germany
- Department of Theoretical Chemistry, University of Vienna, A-1090 Wien, Austria
- Center for non-coding RNA in Technology and Health, University of Copenhagen, DK-1870 Frederiksberg C, Denmark
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA
| | - Jana Schor
- Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics, Helmholtz Centre for Environmental Research - UFZ, D-04318 Leipzig, Germany
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2
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Li S, Breaker RR. Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics. BMC Genomics 2017; 18:785. [PMID: 29029611 PMCID: PMC5640933 DOI: 10.1186/s12864-017-4171-y] [Citation(s) in RCA: 11] [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: 02/06/2017] [Accepted: 10/05/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies. RESULTS We have adapted a bioinformatics pipeline for discovering bacterial ncRNAs to systematically analyze many fungal genomes. This comparative genomics pipeline integrates information on conserved RNA sequence and structural features with alternative splicing information to reveal fungal RNA motifs that are candidate regulatory domains, or that might have other possible functions. A total of 15 prominent classes of structured ncRNA candidates were identified, including variant HDV self-cleaving ribozyme representatives, atypical snoRNA candidates, and possible structured antisense RNA motifs. Candidate regulatory motifs were also found associated with genes for ribosomal proteins, S-adenosylmethionine decarboxylase (SDC), amidase, and HexA protein involved in Woronin body formation. We experimentally confirm that the variant HDV ribozymes undergo rapid self-cleavage, and we demonstrate that the SDC RNA motif reduces the expression of SAM decarboxylase by translational repression. Furthermore, we provide evidence that several other motifs discovered in this study are likely to be functional ncRNA elements. CONCLUSIONS Systematic screening of fungal genomes using a computational discovery pipeline has revealed the existence of a variety of novel structured ncRNAs. Genome contexts and similarities to known ncRNA motifs provide strong evidence for the biological and biochemical functions of some newly found ncRNA motifs. Although initial examinations of several motifs provide evidence for their likely functions, other motifs will require more in-depth analysis to reveal their functions.
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Affiliation(s)
- Sanshu Li
- Institute of Genomics, School of Biomedical Sciences, Huaqiao University, 668 Jimei Road, Xiamen, 361021 China
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103 USA
| | - Ronald R. Breaker
- Howard Hughes Medical Institute, Yale University, Box 208103, New Haven, CT 06520-8103 USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, Box 208103, New Haven, CT 06520-8103 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, Box 208103, New Haven, CT 06520-8103 USA
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Patra Bhattacharya D, Canzler S, Kehr S, Hertel J, Grosse I, Stadler PF. Phylogenetic distribution of plant snoRNA families. BMC Genomics 2016; 17:969. [PMID: 27881081 PMCID: PMC5122169 DOI: 10.1186/s12864-016-3301-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022] Open
Abstract
Background Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. Results In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. Conclusions The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3301-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deblina Patra Bhattacharya
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.,Institut für Informatik, Halle (Saale), D-06120, Germany
| | - Sebastian Canzler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Stephanie Kehr
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany
| | - Jana Hertel
- Young Investigators Group Bioinformatics & Transcriptomics, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, Leipzig, D-04318, Germany
| | - Ivo Grosse
- Institut für Informatik, Halle (Saale), D-06120, Germany.,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany. .,Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, Leipzig, D-04103, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, Leipzig, D-04103, Germany. .,Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, Leipzig, A-1090, Germany. .,Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Copenhagen, Denmark. .,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA. .,German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Leipzig, Germany.
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Donovan PD, Schröder MS, Higgins DG, Butler G. Identification of Non-Coding RNAs in the Candida parapsilosis Species Group. PLoS One 2016; 11:e0163235. [PMID: 27658249 PMCID: PMC5033589 DOI: 10.1371/journal.pone.0163235] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 09/06/2016] [Indexed: 01/08/2023] Open
Abstract
The Candida CTG clade is a monophyletic group of fungal species that translates CTG as serine, and includes the pathogens Candida albicans and Candida parapsilosis. Research has typically focused on identifying protein-coding genes in these species. Here, we use bioinformatic and experimental approaches to annotate known classes of non-coding RNAs in three CTG-clade species, Candida parapsilosis, Candida orthopsilosis and Lodderomyces elongisporus. We also update the annotation of ncRNAs in the C. albicans genome. The majority of ncRNAs identified were snoRNAs. Approximately 50% of snoRNAs (including most of the C/D box class) are encoded in introns. Most are within mono- and polycistronic transcripts with no protein coding potential. Five polycistronic clusters of snoRNAs are highly conserved in fungi. In polycistronic regions, splicing occurs via the classical pathway, as well as by nested and recursive splicing. We identified spliceosomal small nuclear RNAs, the telomerase RNA component, signal recognition particle, RNase P RNA component and the related RNase MRP RNA component in all three genomes. Stem loop IV of the U2 spliceosomal RNA and the associated binding proteins were lost from the ancestor of C. parapsilosis and C. orthopsilosis, following the divergence from L. elongisporus. The RNA component of the MRP is longer in C. parapsilosis, C. orthopsilosis and L. elongisporus than in S. cerevisiae, but is substantially shorter than in C. albicans.
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Affiliation(s)
- Paul D. Donovan
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Markus S. Schröder
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Desmond G. Higgins
- School of Medicine and UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Geraldine Butler
- School of Biomedical and Biomolecular Science and UCD Conway Institute of Biomolecular and Biomedical Research, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
- * E-mail:
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Qu J, Zhao M, Hsiang T, Feng X, Zhang J, Huang C. Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus. BIOMED RESEARCH INTERNATIONAL 2016; 2016:2503023. [PMID: 27703969 PMCID: PMC5040776 DOI: 10.1155/2016/2503023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/21/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
Abstract
Noncoding RNAs (ncRNAs) have been identified in many fungi. However, no genome-scale identification of ncRNAs has been inventoried for basidiomycetes. In this research, we detected 254 small noncoding RNAs (sncRNAs) in a genome assembly of an isolate (CCEF00389) of Pleurotus ostreatus, which is a widely cultivated edible basidiomycetous fungus worldwide. The identified sncRNAs include snRNAs, snoRNAs, tRNAs, and miRNAs. SnRNA U1 was not found in CCEF00389 genome assembly and some other basidiomycetous genomes by BLASTn. This implies that if snRNA U1 of basidiomycetes exists, it has a sequence that varies significantly from other organisms. By analyzing the distribution of sncRNA loci, we found that snRNAs and most tRNAs (88.6%) were located in pseudo-UTR regions, while miRNAs are commonly found in introns. To analyze the evolutionary conservation of the sncRNAs in P. ostreatus, we aligned all 254 sncRNAs to the genome assemblies of some other Agaricomycotina fungi. The results suggest that most sncRNAs (77.56%) were highly conserved in P. ostreatus, and 20% were conserved in Agaricomycotina fungi. These findings indicate that most sncRNAs of P. ostreatus were not conserved across Agaricomycotina fungi.
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Affiliation(s)
- Jibin Qu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Mengran Zhao
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Xiaoxing Feng
- College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, Guangdong, China
- Shenzhen Micro & Nano Research Institute of IC and System Applications, Shenzhen, Guangdong, China
| | - Jinxia Zhang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
| | - Chenyang Huang
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
- Key Laboratory of Microbial Resources, Ministry of Agriculture, Beijing, China
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Abstract
Genome defense likely evolved to curtail the spread of transposable elements and invading viruses. A combination of effective defense mechanisms has been shown to limit colonization of the Neurospora crassa genome by transposable elements. A novel DNA transposon named Sly1-1 was discovered in the genome of the most widely used laboratory "wild-type" strain FGSC 2489 (OR74A). Meiotic silencing by unpaired DNA, also simply called meiotic silencing, prevents the expression of regions of the genome that are unpaired during karyogamy. This mechanism is posttranscriptional and is proposed to involve the production of small RNA, so-called masiRNAs, by proteins homologous to those involved in RNA interference-silencing pathways in animals, fungi, and plants. Here, we demonstrate production of small RNAs when Sly1-1 was unpaired in a cross between two wild-type strains. These small RNAs are dependent on SAD-1, an RNA-dependent RNA polymerase necessary for meiotic silencing. We present the first case of endogenously produced masiRNA from a novel N. crassa DNA transposable element.
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7
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Diao LT, Xiao ZD, Leng XM, Li B, Li JH, Luo YP, Li SG, Yu CH, Zhou H, Qu LH. Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. RNA (NEW YORK, N.Y.) 2014; 20:1376-1385. [PMID: 25002674 PMCID: PMC4138321 DOI: 10.1261/rna.042309.113] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 05/05/2014] [Indexed: 06/03/2023]
Abstract
Coordinated assembly of the ribosome is essential for proper translational activity in eukaryotic cells. It is therefore critical to coordinate the expression of components of ribosomal programs with the cell's nutritional status. However, coordinating expression of these components is poorly understood. Here, by combining experimental and computational approaches, we systematically identified box C/D snoRNAs in four fission yeasts and found that the expression of box C/D snoRNA and ribosomal protein (RP) genes were orchestrated by a common Homol-D box, thereby ensuring a constant balance of these two genetic components. Interestingly, such transcriptional coregulations could be observed in most Ascomycota species and were mediated by different cis-regulatory elements. Via the reservation of cis elements, changes in spatial configuration, the substitution of cis elements, and gain or loss of cis elements, the regulatory networks of box C/D snoRNAs evolved to correspond with those of the RP genes, maintaining transcriptional coregulation between box C/D snoRNAs and RP genes. Our results indicate that coregulation via common cis elements is an important mechanism to coordinate expression of the RP and snoRNA genes, which ensures a constant balance of these two components.
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Affiliation(s)
- Li-Ting Diao
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Zhen-Dong Xiao
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Xiao-Min Leng
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Bin Li
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Jun-Hao Li
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Yu-Ping Luo
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Si-Guang Li
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Chuan-He Yu
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Hui Zhou
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
| | - Liang-Hu Qu
- State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China
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8
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Identification and characterisation of non-coding small RNAs in the pathogenic filamentous fungus Trichophyton rubrum. BMC Genomics 2013; 14:931. [PMID: 24377353 PMCID: PMC3890542 DOI: 10.1186/1471-2164-14-931] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 12/20/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Accumulating evidence demonstrates that non-coding RNAs (ncRNAs) are indispensable components of many organisms and play important roles in cellular events, regulation, and development. RESULTS Here, we analysed the small non-coding RNA (ncRNA) transcriptome of Trichophyton rubrum by constructing and sequencing a cDNA library from conidia and mycelia. We identified 352 ncRNAs and their corresponding genomic loci. These ncRNA candidates included 198 entirely novel ncRNAs and 154 known ncRNAs classified as snRNAs, snoRNAs and other known ncRNAs. Further bioinformatic analysis detected 96 snoRNAs, including 56 snoRNAs that had been annotated in other organisms and 40 novel snoRNAs. All snoRNAs belonged to two major classes--C/D box snoRNAs and H/ACA snoRNAs--and their potential target sites in rRNAs and snRNAs were predicted. To analyse the evolutionary conservation of the ncRNAs in T. rubrum, we aligned all 352 ncRNAs to the genomes of six dermatophytes and to the NCBI non-redundant nucleotide database (NT). The results showed that most of the identified snRNAs were conserved in dermatophytes. Of the 352 ncRNAs, 102 also had genomic loci in other dermatophytes, and 27 were dermatophyte-specific. CONCLUSIONS Our systematic analysis may provide important clues to the function and evolution of ncRNAs in T. rubrum. These results also provide important information to complement the current annotation of the T. rubrum genome, which primarily comprises protein-coding genes.
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Sibthorp C, Wu H, Cowley G, Wong PWH, Palaima P, Morozov IY, Weedall GD, Caddick MX. Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. BMC Genomics 2013; 14:847. [PMID: 24299161 PMCID: PMC4046813 DOI: 10.1186/1471-2164-14-847] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/15/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of A. nidulans with a focus on 5' end analysis. RESULTS Strand-specific whole transcriptome sequencing showed that 80-95% of annotated genes appear to be expressed across the conditions tested. We estimate that the total gene number should be increased by approximately 1000, to 11,800. With respect to splicing 8.3% of genes had multiple alternative transcripts, but alternative splicing by exon-skipping was very rare. 75% of annotated genes showed some level of antisense transcription and for one gene, meaB, we demonstrated the antisense transcript has a regulatory role. Specific sequencing of the 5' ends of transcripts was used for genome wide mapping of transcription start sites, allowing us to interrogate over 7000 promoters and 5' untranslated regions. CONCLUSIONS Our data has revealed the complexity of the A. nidulans transcriptome and contributed to improved genome annotation. The data can be viewed on the AspGD genome browser.
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Affiliation(s)
- Christopher Sibthorp
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Huihai Wu
- />Department of Computer Science, University of Liverpool, Ashton Building, Ashton Street, Liverpool, L69 3BX UK
| | - Gwendolyn Cowley
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Prudence W H Wong
- />Department of Computer Science, University of Liverpool, Ashton Building, Ashton Street, Liverpool, L69 3BX UK
| | - Paulius Palaima
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Igor Y Morozov
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
- />Department of Biomolecular and Sports Sciences, Faculty of Health and Life Sciences, Coventry University, James Starley Building, Coventry, CV1 5FB UK
| | - Gareth D Weedall
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
| | - Mark X Caddick
- />Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool, L69 7ZB UK
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10
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Liu N, Xiao B, Ren HY, Tang ZL, Li K. Systematic identification and characterization of porcine snoRNAs: structural, functional and developmental insights. Anim Genet 2012; 44:24-33. [DOI: 10.1111/j.1365-2052.2012.02363.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Nan Liu
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Bang Xiao
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Hong-Yan Ren
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Zhong-Lin Tang
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
| | - Kui Li
- State Key Laboratory for Animal Nutrition; Institute of Animal Science; Chinese Academy of Agricultural Sciences; Beijing; 100193; China
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11
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Tripathy S, Jiang RHY. Massively parallel sequencing technology in pathogenic microbes. Methods Mol Biol 2012; 835:271-94. [PMID: 22183660 DOI: 10.1007/978-1-61779-501-5_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Next-Generation Sequencing (NGS) methods have revolutionized various aspects of genomics including transcriptome analysis. Digital expression analysis is all set to replace analog expression analysis that uses microarray chips through their cost-effectiveness, reproducibility, accuracy, and speed. The last 2 years have seen a surge in the development of statistical methods and software tools for analysis and visualization of NGS data. Large amounts of NGS data are available for pathogenic fungi and oomycetes. As the analysis results start pouring in, it brings about a paradigm shift in the understanding of host pathogen interactions with discovery of new transcripts, splice variants, mutations, regulatory elements, and epigenetic controls. Here we describe the core technology of the new sequencing platforms, the methodology of data analysis, and different aspects of applications.
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Affiliation(s)
- Sucheta Tripathy
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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12
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van Nues RW, Granneman S, Kudla G, Sloan KE, Chicken M, Tollervey D, Watkins NJ. Box C/D snoRNP catalysed methylation is aided by additional pre-rRNA base-pairing. EMBO J 2011; 30:2420-30. [PMID: 21556049 PMCID: PMC3116282 DOI: 10.1038/emboj.2011.148] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/07/2011] [Indexed: 11/09/2022] Open
Abstract
2'-O-methylation of eukaryotic ribosomal RNA (r)RNA, essential for ribosome function, is catalysed by box C/D small nucleolar (sno)RNPs. The RNA components of these complexes (snoRNAs) contain one or two guide sequences, which, through base-pairing, select the rRNA modification site. Adjacent to the guide sequences are protein-binding sites (the C/D or C'/D' motifs). Analysis of >2000 yeast box C/D snoRNAs identified additional conserved sequences in many snoRNAs that are complementary to regions adjacent to the rRNA methylation site. This 'extra base-pairing' was also found in many human box C/D snoRNAs and can stimulate methylation by up to five-fold. Sequence analysis, combined with RNA-protein crosslinking in Saccharomyces cerevisiae, identified highly divergent box C'/D' motifs that are bound by snoRNP proteins. In vivo rRNA methylation assays showed these to be active. Our data suggest roles for non-catalytic subunits (Nop56 and Nop58) in rRNA binding and support an asymmetric model for box C/D snoRNP organization. The study provides novel insights into the extent of the snoRNA-rRNA interactions required for efficient methylation and the structural organization of the snoRNPs.
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Affiliation(s)
- Robert Willem van Nues
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK
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Mitrovich QM, Tuch BB, De La Vega FM, Guthrie C, Johnson AD. Evolution of yeast noncoding RNAs reveals an alternative mechanism for widespread intron loss. Science 2010; 330:838-41. [PMID: 21051641 PMCID: PMC3496775 DOI: 10.1126/science.1194554] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The evolutionary forces responsible for intron loss are unresolved. Whereas research has focused on protein-coding genes, here we analyze noncoding small nucleolar RNA (snoRNA) genes in which introns, rather than exons, are typically the functional elements. Within the yeast lineage exemplified by the human pathogen Candida albicans, we find--through deep RNA sequencing and genome-wide annotation of splice junctions--extreme compaction and loss of associated exons, but retention of snoRNAs within introns. In the Saccharomyces yeast lineage, however, we find it is the introns that have been lost through widespread degeneration of splicing signals. This intron loss, perhaps facilitated by innovations in snoRNA processing, is distinct from that observed in protein-coding genes with respect to both mechanism and evolutionary timing.
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Affiliation(s)
- Quinn M. Mitrovich
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143-2200, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143-2200, USA
| | - Brian B. Tuch
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143-2200, USA
- Genetic Systems Division, Research and Development, Life Technologies, Foster City, CA 94404, USA
| | - Francisco M. De La Vega
- Genetic Systems Division, Research and Development, Life Technologies, Foster City, CA 94404, USA
| | - Christine Guthrie
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143-2200, USA
| | - Alexander D. Johnson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143-2200, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143-2200, USA
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Abstract
Small nucleolar RNAs (snoRNAs) are among the most evolutionarily ancient classes of small RNA. Two experimental screens published in BMC Genomics expand the eukaryotic snoRNA catalog, but many more snoRNAs remain to be found. See research articles http://www.biomedcentral.com/1471-2164/10/515 and http://www.biomedcentral.com/1471-2164/11/61.
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Affiliation(s)
- Paul P Gardner
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB101SA, UK.
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