- endogenous loop (ORCEL) in circular RNAs revealed through transcriptome. - Background: Emerging evidence indicates that Circular RNAs (circRNAs) exert post-transcriptional regulation of gene expression. - From this observation, supporting evidence of the competitive endogenous relationship of circRNAs and miRNAs targeting circRNA host genes can be observed. - Given the self-regulation and self-induction nature of these circRNAs, this kind of hypothetical phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs.. - Among this trend of digging into retroactive sourced experimental data, circular RNAs emerge on stump eventually.. - Circular RNAs (circRNAs) represent a type of regula- tory noncoding RNA whose head 3′ and tail 5′ ends covalently bond together to result in a circular form.. - Later, an improved version of the algorithm with exon splicing site AU/AC searching was applied to find the fact that. - 5 Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu, Taiwan Full list of author information is available at the end of the article. - 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - With the regulation potential of miRNAs, circRNAs became widely interested in the research field [11]. - In the following years, extended identification of cir- cRNAs in mouse [14], fly [15] and other animals [16]. - Aware of the significance of circRNAs research, in 2015, we constructed a database called CircNet [23] to not only collect the published data, but also extend the scope of reported circRNAs and provide resources to aid in field.. - Reported human back-spliced junction sites were also collected from 22 recent studies . - Circular RNA back-spliced junction sites were identi- fied within these samples. - To acquire the expression pat- terns of circRNAs within these samples, a pipeline was developed to annotate the sequence of the circRNAs.. - The calculated P-value of the circRNA and miRNA pairs are lower than 0.005. - Given the self-regulation and self-induction nature of these circRNAs, it was hereby named Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs.. - While on the other hand, the post- transcriptional roles of miRNAs to most of the genes has become a conventional knowledge [42]. - In the sequences of 909 circRNA transcripts from 728 human genes, we found enriched miRNA targeting sites. - Given the self-regulation and self-induction nature of these cir- cRNAs, the phenomenon was hereby named Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs. - Enrichment analysis of the ORCEL genes. - An enrichment analysis of the 728 ORCEL genes was conducted through DAVID [43]. - In the result of this. - In the 32 genes participated in the hsa05200: Pathways in cancer, 115 miRNAs and 45 circRNA transcripts were found participated in the ORCEL, as illustrated in the network of Fig. - 1, it can be no- ticed that among the 32 genes enriched in the pathways in cancer, only the ORCEL of HIA1 doesn’t involve miR- NAs targeting multiple other genes involved in the path- way. - A complete table of the enrichment can be found in Additional file 3. - In the network illustrated in Fig. - 2, for the 19 genes participated in the hsa04120: Ubiquitin mediated proteolysis, 52 miRNAs and 22 circRNA tran- scripts were found participated in the ORCEL. - It is also worth mentioned that 61 ORCEL genes were enriched in the GO term GO:0046907~intracellular transport and 121 ORCEL genes were enriched in GO:0031974~mem- brane-enclosed lumen. - Through statistical analysis of the abundance of the miRNA target seeds on circRNA se- quences, putative circRNA serving as miRNA sponges were identified. - The application of FPKM of the putative circRNA sequences, and SRPBM of the back spliced junction sites as thresholds should in- crease the prudence of the circRNA sequence prediction. - From these observations we hypothesize that genes targeted by miRNAs tend to be conserved with enriched miRNA targeting site in the coding region. - This phenomenon was hereby named Ouroboros Resembling Competitive En- dogenous Loop (ORCEL) in circular RNAs. - Given the self-regulation and self-induction nature of these circRNAs, this kind of phenomenon was hereby called Ouroboros Resembling Competitive Endogenous Loop (ORCEL) in circular RNAs.. - The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline adapting the scripts provided on circBase [7, 49], which was referred as find_circ [50]. - The annotated sequence were then ap- plied in the prediction of circRNA-miRNA interactions.. - Ex- pression profiling of the circRNAs within each of the samples collected from SRA was conducted in two different approaches: normalized counts of reads spanning the back spliced junction sites SRPBM [13]. - Detection of the back spliced junction sites. - Reported human back-spliced junction sites were collected from 22 recent studies . - The back-spliced junction sites in each RNA-seq sample were identified using a circRNA discovery pipeline referred as find_circ . - We apply the criteria defined in the pipeline hence the detected junction sites met same standards as those in the previous reports, as described in the Memczak et al. - miR-196a-3p miR-1233-5p. - miR-1273g-3p circ-RHOA-antisense.5 miR-124-3p. - miR-6512-3p miR-4789-5p. - miR-483-3p miR-508-5p. - circ-IGF1R.4 circ-SMAD4.17. - miR-590-3p miR-3674. - circ-PLCG2.5 circ-BRAF.48. - miR-4659b-3p miR-4659a-3p. - circ-TGFBR2.2 miR-216a-5p circ-TGFBR2.1. - circ-CBL.7 miR-150-5p. - circ-MAPK1.6 miR-190a-3p. - miR-5590-3p miR-142-5p. - circ-TGFBR2.9 miR-1296-3p. - circ-SPI1.6 miR-548an. - miR-579-3p miR-664b-3p. - let-7a-3p miR-346. - miR-381-3p miR-98-3p. - seq reads, back-spliced junction sites were compared with the hg19 human genome annotation as obtained from UCSC genome browser and RefSeq [51, 52].. - (1) For the back spliced junction sites locate on exact. - exons of the transcript were considered as part of the same circRNA.. - miR-4722-3p miR-498. - miR-6747-3p miR-6727-3p. - miR-548c-3p miR-139-3p. - circ-UBE2R2.5 circ-CUL4A.6. - let-7f-1-3p miR-302c-5p. - (3) For those circRNAs associated with these back- spliced junction sites having small misalignments to exon locations, flanked exons and a small portion of intron sequence locating in the head or tail. - locations were considered as parts of the isoforms.. - (4) For the junction sites that were found to be located in intergenic positions while others, despite overlapping with certain genes, localized to their antisense strands, the entire flanked sequence was considered as the sequence of the circRNA.. - To normalize the number of occurrences of these sites by the length of the transcripts, the following formula was used:. - ð 1 Þ Where the ‘N’ is the length of the seed. - 3 Overview of the data analysis process in this research. - The general view of the process of ORCEL discovery is illustrated in this figure. - We calculated all the frequency value of the circRNAs as well as the linear isoforms pairing to miRNAs, and then converted the Z-score of the normal distribution into one tail P-value through survival function.. - As previously described, the abundance of the circRNA within the collected samples were estimated through the transcript deconvolution algorithm of the Cufflinks pipe- line [41]. - The normalized count of reads on back spliced junctions To normalize the amount of the normalized sequence reads spanning the junction sites, a concept of spliced reads per billion mapping (SRPBM) was applied [13].. - With the forth-mentioned gtf file contain- ing annotated exon locus of circRNAs and mRNAs, and the bam files generated from STAR, we estimated the abundance within the sample of the annotated sequence through Cufflinks [41]. - From the result of recent year comparison study [50], we deducted that inconsistency between different cir- cRNA detection tools and false discovery of highly abun- dant circRNA could occur in the result of our analysis.. - The amount of previous peer review reports in which the back spliced junction sites were reported.. - The amount of samples among the 465 collected sam- ples in which the back spliced junction sites were found meeting the criteria defined in find_circ . - Only the circRNAs with the combined amount of these two values over 10 were considered in the analysis of this report.. - (XLSX 59 kb) Additional file 3: A complete table of the enrichment of ORCEL genes.. - This paper (work) is particularly supported by “ Aiming for the Top University Program ” of the National Chiao Tung University and Ministry of Education, Taiwan, R.O.C.. - All the analyzed data mentioned in this report is available in the additional files.. - The full contents of the supplement are available online at https://bmcgenomics.biomedcentral.com/. - Hsu M-T, Coca-Prados M: Electron microscopic evidence for the circular form of RNA in the cytoplasm of eukaryotic cells. - Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. - Circular RNAs are a large class of animal RNAs with regulatory potency. - Characterization of RNase R-digested cellular RNA source that consists of lariat and circular RNAs from pre-mRNA splicing. - Circular RNAs are abundant, conserved, and associated with ALU repeats. - Genome-wide analysis of drosophila circular RNAs reveals their structural and sequence properties and age-dependent neural accumulation. - Expanded identification and characterization of mammalian circular RNAs. - CircNet: a database of circular RNAs derived from transcriptome sequencing data. - Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood. - Specific identification and quantification of circular RNAs from sequencing data. - Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. - Tracing the expression of circular RNAs in human pre-implantation embryos.. - Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. - circBase: a database for circular RNAs.. - Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity
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