Heidelberg University Biochemistry Center, 69120, Heidelberg, Germany.
present address: Cellzome GmbH, 69117, Heidelberg, Germany.
BMC Genomics. 2017 Dec 19;18(1):978. doi: 10.1186/s12864-017-4360-8.
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.
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.
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.
长非蛋白编码 RNA（lncRNA）已在许多不同的生物和细胞类型中被鉴定出来。新出现的例子强调了这些 RNA 种类的生物学重要性，但它们的调控和功能仍知之甚少。在丝状真菌粗糙脉孢菌中，lncRNA 的注释和特征描述并不完整。
我们通过使用 ChIP-seq、RNA-seq 和多核糖体馏分数据集，对粗糙脉孢菌进行了全面的转录组分析。我们注释和描述了 1478 个长基因间非编码 RNA（lincRNA）和 1056 个天然反义转录本，表明粗糙脉孢菌的 RNA 聚合酶 II 转录物中 20%不编码蛋白质。这两类 lncRNA 的积累水平均低于编码蛋白的 mRNA，且它们的长度要短得多。我们的分析表明，绝大多数 lincRNA 和反义转录本不含内含子，并且携带的 H3K4me2 修饰比表达相似的蛋白编码基因要少。相比之下，H3K27me3 修饰与蛋白编码和 lincRNA 基因的转录呈负相关。此外，我们还发现大多数 lincRNA 序列在进化上非常迅速，即使在亲缘关系较近的物种之间也是如此。
我们的转录组分析显示，与 mRNA 相比，粗糙脉孢菌的 lincRNA 和反义转录本具有明显的特征，并且表明该生物中非编码转录物的普遍性高于先前的预期。该研究提供了广泛的 repertoire，并为进一步研究 lncRNA 提供了资源。
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