Natural antisense transcripts and long non-coding RNA in Neurospora crassa

The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at t...

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Bibliographic Details
Published in:PloS one 2014-03, Vol.9 (3), p.e91353-e91353
Main Authors: Arthanari, Yamini, Heintzen, Christian, Griffiths-Jones, Sam, Crosthwaite, Susan K
Format: Article
Language:English
Subjects:
Acids
Antisense RNA
Bioinformatics
Biology
Circadian rhythm
Coding
Darkness
DNA methylation
Environmental effects
Fungi
Gene expression
Gene Expression Regulation, Fungal - radiation effects
Gene sequencing
Genes
Genetic aspects
Genomes
Genomics
Introns
Life sciences
Light levels
Molecular Sequence Annotation
Mutation
Neurospora
Neurospora crassa
Neurospora crassa - genetics
Neurospora crassa - growth & development
Neurospora crassa - radiation effects
Non-coding RNA
Post-transcription
Proteins
Ribonucleic acid
RNA
RNA polymerase
RNA sequencing
RNA, Antisense - genetics
RNA, Long Noncoding - genetics
RNA, Messenger - genetics
Sequence Analysis, RNA
Stimuli
Temperature
Transcription (Genetics)
Transfer RNA
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Summary:The prevalence of long non-coding RNAs (lncRNA) and natural antisense transcripts (NATs) has been reported in a variety of organisms. While a consensus has yet to be reached on their global importance, an increasing number of examples have been shown to be functional, regulating gene expression at the transcriptional and post-transcriptional level. Here, we use RNA sequencing data from the ABI SOLiD platform to identify lncRNA and NATs obtained from samples of the filamentous fungus Neurospora crassa grown under different light and temperature conditions. We identify 939 novel lncRNAs, of which 477 are antisense to annotated genes. Across the whole dataset, the extent of overlap between sense and antisense transcripts is large: 371 sense/antisense transcripts are complementary over 500 nts or more and 236 overlap by more than 1000 nts. Most prevalent are 3' end overlaps between convergently transcribed sense/antisense pairs, but examples of divergently transcribed pairs and nested transcripts are also present. We confirm the expression of a subset of sense/antisense transcript pairs by qPCR. We examine the size, types of overlap and expression levels under the different environmental stimuli of light and temperature, and identify 11 lncRNAs that are up-regulated in response to light. We also find differences in transcript length and the position of introns between protein-coding transcripts that have antisense expression and transcripts with no antisense expression. These results demonstrate the ability of N. crassa lncRNAs and NATs to be regulated by different environmental stimuli and provide the scope for further investigation into the function of NATs.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0091353