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创新性构建首个可靠的牛环状 RNA 目录。

Innovative construction of the first reliable catalogue of bovine circular RNAs.

机构信息

GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France.

Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.

出版信息

RNA Biol. 2024 Jan;21(1):52-74. doi: 10.1080/15476286.2024.2375090. Epub 2024 Jul 11.

DOI:10.1080/15476286.2024.2375090
PMID:38989833
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11244336/
Abstract

The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated . CircRNA identification is mostly an process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.

摘要

本研究旨在比较不同组织的环状转录组，以了解：i）是否存在非外显子环状 RNA（circRNA），即来源于涉及已知外显子的反向剪接，以及 ii）人工环状 RNA（artif_circRNA）的起源，即未产生的环状 RNA。circRNA 的鉴定主要是一个过程，对 BovReg 项目（https://www.bovreg.eu/）的数据进行分析提供了探索识别可靠 circRNA 的新方法的机会。通过考虑 117 个组织样本，我们鉴定了 23926 个外显子 circRNA、来自 273 个内含子的 337 个 circRNA（191 个 ciRNA、146 个内含子环）、108 个来自小非编码基因的 circRNA 和近 36600 个被归类为其他 circRNA 的 circRNA。此外，对于其中 63 个样本，我们同时分析了核糖体 RNA 去除后进行文库制备（poly(A)-selected RNA）的总 RNAseq 平行数据和配对的 mRNAseq。在 mRNAseq 中检测到的 circRNA 数量很多，以及大量新的 circRNA，主要是其他 circRNA，这促使我们将在 mRNAseq 中检测到的所有 circRNA 都视为人工。本研究提供了在使用两个 circRNA 工具进行总 RNAseq/mRNAseq 比较时，在列表中外显子 circRNA 中有 189 个错误条目的确凿证据：103 个 artif_circRNAs 通过 circRNA 工具识别，26 个可能的 artif_circRNAs，以及 65 个通过深度注释分析识别。进行了广泛的基准测试（包括使用 CIRI2 和 CIRCexplorer-2 的分析），并确认了 23737 个可靠外显子 circRNA 中的 94%。此外，本研究证明了一组高度表达的外显子 circRNA（5-8%）在分析牛环状转录组的组织特异性方面的有效性。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/6c0000d7ff30/KRNB_A_2375090_F0010_OC.jpg
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https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/3b5a9dd78747/KRNB_A_2375090_F0004_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/32c4e0f601b6/KRNB_A_2375090_F0005_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/8ee2e307d005/KRNB_A_2375090_F0006_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/b4716ef4bbdb/KRNB_A_2375090_F0007_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/e5c9a580a8a7/KRNB_A_2375090_F0008_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/052040f6b1b0/KRNB_A_2375090_F0009_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9dfd/11244336/6c0000d7ff30/KRNB_A_2375090_F0010_OC.jpg

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Approaches and challenges in genome-wide circular RNA identification and quantification.全基因组环状 RNA 鉴定和定量的方法与挑战。
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Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer.
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Detecting intragenic trans-splicing events from non-co-linearly spliced junctions by hybrid sequencing.通过混合测序技术从非共线性拼接接头中检测基因内跨剪接事件。
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Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.大规模的环状 RNA 检测工具基准测试表明，在灵敏度方面存在很大差异，但在精确度方面没有差异。
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