Abstract
BackgroundLong non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. Emerging examples emphasize the biological importance of these RNA species but their regulation and functions remain poorly understood. In the filamentous fungus Neurospora crassa, the annotation and characterization of lncRNAs is incomplete.ResultsWe have performed a comprehensive transcriptome analysis of Neurospora crassa by using ChIP-seq, RNA-seq and polysome fractionation datasets. We have annotated and characterized 1478 long intergenic noncoding RNAs (lincRNAs) and 1056 natural antisense transcripts, indicating that 20% of the RNA Polymerase II transcripts of Neurospora are not coding for protein. Both classes of lncRNAs accumulate at lower levels than protein-coding mRNAs and they are considerably shorter. Our analysis showed that the vast majority of lincRNAs and antisense transcripts do not contain introns and carry less H3K4me2 modifications than similarly expressed protein coding genes. In contrast, H3K27me3 modifications inversely correlate with transcription of protein coding and lincRNA genes. We show furthermore most lincRNA sequences evolve rapidly, even between phylogenetically close species.ConclusionsOur transcriptome analyses revealed distinct features of Neurospora lincRNAs and antisense transcripts in comparison to mRNAs and showed that the prevalence of noncoding transcripts in this organism is higher than previously anticipated. The study provides a broad repertoire and a resource for further studies of lncRNAs.
Highlights
IntroductionLong non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types
Long non protein coding RNAs have been identified in many different organisms and cell types
ChIP-seq analyses of RNA polymerase II (RNAPII) [28] and a polyribosome fractionation analysis were included for the Neurospora transcriptome analysis
Summary
Long non protein coding RNAs (lncRNAs) have been identified in many different organisms and cell types. NcRNA species share common post-transcriptional modifications with protein-coding messenger-RNAs (mRNAs), including splicing and polyadenylation signals [6] but lack an open reading frame. These RNA types include ribosomal RNAs, transfer RNAs, microRNAs and long noncoding RNAs (lncRANs). One class of lncRNAs is natural antisense transcripts, which are transcribed from overlapping loci on the opposite strand of the DNA. They were found to regulate gene expression and provide an additional level of control by RNA-mediated mechanisms [14, 15]. The prevalence of lncRNAs has been reported in a wide range of eukaryotic organisms including plants [21], fungi [22, 23] and mammals [6, 14]
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