Integrative transcriptome sequencing reveals extensive alternative <i>trans</i>-splicing and <i>cis</i>-backsplicing in human cells

Chuang, Trees‐Juen; Chen, Yen–Ju; Chen, Chia-Ying; Mai, Te-Lun; Wang, Yi-Da; Yeh, Chung-Shu; Yang, Min-Yu; Hsiao, Yu‐Ting; Chang, Tang‐Hsien; Kuo, Tzu-Chien; Cho, Hsin-Hua; Shen, Chia-Ning; Kuo, Hung‐Chih; Lu, Mei-Yeh Jade; Chen, Yihua; Hsieh, Shan-Chi; Chiang, Tai-Wei

doi:10.1093/nar/gky032

Cited by 67 publications

(96 citation statements)

References 89 publications

(221 reference statements)

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“…Finally, northern blotting is a more stringent way based on the specific probe [134]. There are also some limitations, some linear RNAs with the same sequences as those through BSJ sites may be theoretically amplified by qRT-PCR, suggesting other existing mechanisms such as trans-splicing and template switching [135,136]. Otherwise, some studies demonstrated that some abundant linear RNAs were still detected while some cir-cRNA also were digested after prolonged RNase R treatment [26,109,136].…”

Section: Research Strategies and Identificationmentioning

confidence: 99%

Functions and clinical significance of circular RNAs in glioma

et al. 2020

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CircRNAs are a class of single-stranded RNA molecules with a covalently closed loop structure and have been characterized by high stability, abundance, conservation, and display tissue/developmental stage-specific expression, furthermore, based on the abundance in distinct body fluids or exosomes, circRNAs present novel biomarkers and targets for the diagnosis and prognosis of cancers. Recently, the regulatory mechanisms of biogenesis and molecular functions, including miRNAs and RBPs sponge, translation as well as transcriptional and splicing regulation, have been gradually uncovered, although various aspects remained to be elucidated in combination with deep-sequence and bioinformatics. Accumulating studies have indicated that circRNAs are more enriched in neuronal tissues partly due to the abundance of specific genes promoting circularization, suggesting dysregulation of circRNAs is closely related to diseases of the nervous system, including glioma. In this review, we elaborate on the biogenesis, functions, databases as well as novel advances especially involved in the molecular pathways, highlight its great value as diagnostic or therapeutic targets in glioma.

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Section: Research Strategies and Identificationmentioning

confidence: 99%

Functions and clinical significance of circular RNAs in glioma

et al. 2020

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“…Alu elements are primate specific and inverted Alu elements has been reported to affect the biogenesis of trans-splicing [37]. We wondered whether inverted Alu elements may be responsible for the formation of the six human-specific chimeric RNAs including PAX3-FOXO1.…”

Section: Discussionmentioning

confidence: 99%

PAX3-FOXO1 escapes miR-495 regulation during muscle differentiation

Xie

Tang

et al. 2019

RNA Biology

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Pax3 plays an essential role in myogenesis. Previously, we found a tumor-signature chimeric fusion RNA, PAX3-FOXO1 also present during muscle differentiation, raising the possibility of its physiological role. Here we demonstrated that the fusion is needed transiently for muscle lineage commitment. Interestingly, the fusion ortholog was not found in seven mouse muscle differentiation/regeneration systems, nor in other stem cell differentiation systems of another three mammal species. We noticed that Pax3 is expressed at a much lower level in human stem cells, and during muscle differentiation than in other mammals. Given the fact that the fusion and the parental Pax3 share common downstream targets, we reasoned that forming the fusion may be a mechanism for human cells to escape certain microRNA regulation on Pax3. By sequence comparison, we identified 16 candidate microRNAs that may specifically target the human PAX3 3ʹUTR. We used a luciferase reporter assay, examined the microRNAs expression, and conducted mutagenesis on the reporters, as well as a CRISPR/Cas9 mediated editing on the endogenous allele. Finally, we identified miR-495 as a microRNA that specifically targets human PAX3. Examining several other fusion RNAs revealed that the human-specificity is not limited to PAX3-FOXO1. Based on these observations, we conclude that PAX3-FOXO1 fusion RNA is absent in mouse, or other mammals we tested, the fusion RNA is a mechanism to escape microRNA, miR-495 regulation in humans, and that it is not the only human-specific fusion RNA.

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“…PacBio SMRT sequencing provides better completeness to the sequencing of both the 5’ and 3’ ends of cDNA molecules; thus, it is a superior strategy for the direct generation of a comprehensive transcriptome with precise AS isoforms and novel genes [36–37]. Yi et al identified 33,300 full-length transcripts (transcript N50 of 5234 bp) of Misgurnus anguillicaudatus based on SMRT sequencing, and constructed a transcriptome by performing functional annotations of the non-redundant transcripts with public databases [38].…”

Section: Discussionmentioning

confidence: 99%

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

Chen

Fan

et al. 2019

Preprint

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Ascosphaera apis is a widespread fungal pathogen of honeybee larvae that results in chalkbrood disease, leading to heavy losses for the beekeeping industry in China and many other countries. This work was aimed at generating a full-length transcriptome of A. apis using PacBio single-molecule real-time (SMRT) sequencing. Here, more than 23.97 Gb of clean reads was generated from long-read sequencing of A. apis mecylia, including 464,043 circular consensus sequences (CCS) and 394,142 full-length non-chimeric (FLNC) reads. In total, we identified 174,095 high-confidence transcripts covering 5141 known genes with an average length of 2728 bp. We also discovered 2405 genic loci and 11,623 isoforms that have not been annotated yet within the current reference genome. Additionally, 16,049, 10,682, 4520 and 7253 of the discovered transcripts have annotations in the Non-redundant protein (Nr), Clusters of Eukaryotic Orthologous Groups (KOG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Moreover, 1205 long non-coding RNAs (lncRNAs) were identified, which have less exons, shorter exon and intron lengths, shorter transcript lengths, lower GC percent, lower expression levels, and fewer alternative splicing (AS) evens, compared with protein-coding transcripts. A total of 253 members from 17 transcription factor (TF) families were identified from our transcript datasets. Finally, the expression of A. apis isoforms was validated using a molecular approach. Overall, this is the first report of a full-length transcriptome of entomogenous fungi including A. apis. Our data offer a comprehensive set of reference transcripts and hence contributes to improving the genome annotation and transcriptomic study of A. apis.

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Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

Cited by 67 publications

References 89 publications

Functions and clinical significance of circular RNAs in glioma

Functions and clinical significance of circular RNAs in glioma

PAX3-FOXO1 escapes miR-495 regulation during muscle differentiation

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

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