title: Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters.
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.
authors.forename: Christopher
authors.initials: C
authors.lastname: Sibthorp
authors.forename: Huihai
authors.initials: H
authors.lastname: Wu
authors.forename: Gwendolyn
authors.initials: G
authors.lastname: Cowley
authors.forename: Prudence W H
authors.initials: PW
authors.lastname: Wong
authors.forename: Paulius
authors.initials: P
authors.lastname: Palaima
authors.forename: Igor Y
authors.initials: IY
authors.lastname: Morozov
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK. gweedall@liv.ac.uk.
authors.forename: Gareth D
authors.initials: GD
authors.lastname: Weedall
authors.forename: Mark X
authors.initials: MX
authors.lastname: Caddick
mesh_terms: D020121:5' Untranslated Regions; D017398:Alternative Splicing; D001233:Aspergillus nidulans / Q000235:genetics*; D001483:Base Sequence; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D059014:High-Throughput Nucleotide Sequencing; D007438:Introns; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D059372:Nucleotide Motifs; D016366:Open Reading Frames; D056510:Position-Specific Scoring Matrices; D011401:Promoter Regions, Genetic; D016372:RNA, Antisense; D022661:RNA, Untranslated / Q000235:genetics; D016415:Sequence Alignment; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D020121:5' Untranslated Regions; D016372:RNA, Antisense; D022661:RNA, Untranslated