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The coding and noncoding transcriptome of Neurospora crassa

Cemel, Ibrahim Avi ; Ha, Nati ; Schermann, Geza ; Yonekawa, Shusuke ; Brunner, Michael

In: BMC Genomics, 18 (2017), Nr. 978. pp. 1-11. ISSN 1471-2164

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Abstract

Background: Long 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.

Results: We 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.

Conclusions: Our 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.

Item Type: Article
Journal or Publication Title: BMC Genomics
Volume: 18
Number: 978
Publisher: BioMed Central ; Springer
Place of Publication: London ; Berlin ; Heidelberg
Date Deposited: 20 Apr 2018 09:06
Date: 2017
ISSN: 1471-2164
Page Range: pp. 1-11
Faculties / Institutes: Service facilities > Heidelberg University Biochemistry Center
Subjects: 570 Life sciences
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