Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters

C. Sibthorp, H. Wu, G. Cowley, P.W.H. Wong, P. Palaima, Igor Morozov, G.D. Weedall, M.X. Caddick

    Research output: Contribution to journalArticle

    29 Citations (Scopus)
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    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.
    Original languageEnglish
    Article number847
    JournalBMC Genomics
    Volume14
    DOIs
    Publication statusPublished - 2013

    Fingerprint

    Aspergillus nidulans
    Gene Expression Profiling
    Fungi
    Transcriptome
    Genes
    Genome
    Molecular Sequence Annotation
    Chromosome Mapping
    5' Untranslated Regions
    Transcription Initiation Site
    Genetic Models
    Alternative Splicing
    Aspergillus
    Cell Biology
    Exons

    Bibliographical note

    Additional supplemental material is available from the publisher's website at http://www.biomedcentral.com/1471-2164/14/847/additional.
    This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

    Keywords

    • Aspergillus nidulans
    • transcriptome
    • RNA-seq
    • gene annotation
    • alternative splicing
    • natural antisense transcripts
    • transcription start sites
    • transcription factor binding sites

    Cite this

    Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. / Sibthorp, C.; Wu, H.; Cowley, G.; Wong, P.W.H.; Palaima, P.; Morozov, Igor; Weedall, G.D.; Caddick, M.X.

    In: BMC Genomics, Vol. 14, 847, 2013.

    Research output: Contribution to journalArticle

    Sibthorp, C. ; Wu, H. ; Cowley, G. ; Wong, P.W.H. ; Palaima, P. ; Morozov, Igor ; Weedall, G.D. ; Caddick, M.X. / Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters. In: BMC Genomics. 2013 ; Vol. 14.
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    AU - Wu, H.

    AU - Cowley, G.

    AU - Wong, P.W.H.

    AU - Palaima, P.

    AU - Morozov, Igor

    AU - Weedall, G.D.

    AU - Caddick, M.X.

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    N2 - 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.

    AB - 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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