系统分析核下区室中的 circRNA。

IF 3.6 3区 生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY
Andre Brezski,Justin Murtagh,Marcel H Schulz,Kathi Zarnack
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引用次数: 0

摘要

CircRNA 是一类重要的 RNA,在人类生理和疾病中具有多种细胞功能。全面了解 circRNA(包括其生物发生和亚细胞分布)对于理解它们在各种过程中的作用非常重要。然而,从总 RNA 测序数据中分析 circRNAs 仍然具有挑战性。因此,我们开发了用于 circRNA 注释的多功能工作流程 Calcifer。利用 Calcifer,我们分析了 APEX-Seq 数据,比较了全细胞、细胞核和核下区室中 circRNA 的出现情况。我们普遍发现,与核样本相比,全细胞中的 circRNA 丰度更高,这与它们在细胞质中的积累一致。值得注意的例外是单外显子 circRNA circCANX(9),它意外地富集在细胞核中。此外,我们还观察到 circFIRRE 在细胞质和细胞核中都比线性 lncRNA FIRRE 占优势。放大到核下区室,我们发现circRNA在核斑点中被大量消耗,这表明该区室中过量的剪接因子抵消了反向剪接。因此,我们的研究结果为了解 circRNA 的核下分布提供了宝贵的信息。关于 circRNA 的功能,我们惊讶地发现,所有检测到的 circRNA 中,大多数都具有完整的开放阅读框,具有独立于帽子翻译的潜力。总之,我们发现 Calcifer 是一种易于使用、用途广泛且可持续的 circRNA 注释工作流程,它扩大了 circRNA 工具的范围,使我们对 circRNA 的分布和功能有了新的认识。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
A systematic analysis of circRNAs in subnuclear compartments.
CircRNAs are an important class of RNAs with diverse cellular functions in human physiology and disease. A thorough knowledge of circRNAs including their biogenesis and subcellular distribution is important to understand their roles in a wide variety of processes. However, the analysis of circRNAs from total RNA sequencing data remains challenging. Therefore, we developed Calcifer, a versatile workflow for circRNA annotation. Using Calcifer, we analysed APEX-Seq data to compare circRNA occurrence between whole cells, nucleus and subnuclear compartments. We generally find that circRNAs show higher abundance in whole cells compared to nuclear samples, consistent with their accumulation in the cytoplasm. The notable exception is the single-exon circRNA circCANX(9), which is unexpectedly enriched in the nucleus. In addition, we observe that circFIRRE prevails over the linear lncRNA FIRRE in both the cytoplasm and the nucleus. Zooming in on the subnuclear compartments, we show that circRNAs are strongly depleted from nuclear speckles, indicating that excess splicing factors in this compartment counteract back-splicing. Our results thereby provide valuable insights into the subnuclear distribution of circRNAs. Regarding circRNA function, we surprisingly find that the majority of all detected circRNAs possess complete open reading frames with potential for cap-independent translation. Overall, we show that Calcifer is an easy-to-use, versatile and sustainable workflow for the annotation of circRNAs which expands the repertoire of circRNA tools and allows to gain new insights into circRNA distribution and function.
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来源期刊
RNA Biology
RNA Biology 生物-生化与分子生物学
CiteScore
8.60
自引率
0.00%
发文量
82
审稿时长
1 months
期刊介绍: RNA has played a central role in all cellular processes since the beginning of life: decoding the genome, regulating gene expression, mediating molecular interactions, catalyzing chemical reactions. RNA Biology, as a leading journal in the field, provides a platform for presenting and discussing cutting-edge RNA research. RNA Biology brings together a multidisciplinary community of scientists working in the areas of: Transcription and splicing Post-transcriptional regulation of gene expression Non-coding RNAs RNA localization Translation and catalysis by RNA Structural biology Bioinformatics RNA in disease and therapy
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