Circular RNAs (circRNAs) are a class of non-coding RNAs (ncRNAs) that are involved in transcriptional and posttranscriptional gene expression regulation. Typical circular RNA molecules comprise canonically spliced exonic sequences and are covalently closed. They have recently been shown to be expressed in eukaryotes (Salzman et al. 2012, Jeck et al. 2013, Memczak et al. 2013, Salzman et al. 2013), including plants (Wang et al. 2014, Ye et al. 2015, Lu et al. 2015).
In PlantcircBase (http://ibi.zju.edu.cn/plantcircbase/), we collected publicly available back-splice junction sequences and their full-length sequences of circRNAs identified in plants by us and other groups (Table 1). Based on the collected circRNAs, we further predicted those circRNAs putatively acting as miRNA sponges and their potential networks involving circRNA-miRNA-mRNA in the corresponding species. In the database, you can find plant circRNAs and their related information, such as their sequences, host genes, expression, experimental validation as well as bioinformatics tools such as BLASTcirc (Zhang et al. 2017) for searching and visualizing circRNAs.
Table 1 The number of circRNAs in PlantcircBase (Release 1)
|Organisms||Number of circRNAs||Full-length sequence of circRNAs||Acting as miRNA sponge*||Networks of circRNA-miRNA-mRNA*||Tissues||References|
|Total||Back-splicing site valided||Total||Sanger sequencing valided|
|Oryza sativa||12,037||10||0||0||405||251||Roots, shoots||Ye et al., 2015|
|2,354||30||0||0||73||49||Leaves||Lu et al., 2015|
|2,824||0||2,824||61||14||10||Roots||Ye et al., 2016|
|26,160||37||0||9||585||343||Leaves, anthers, pistils, seeds, shoots, roots||This study|
|Arabidopsis thaliana||6||6||0||0||0||0||Roots||Wang et al., 2014|
|6,012||0||0||0||231||188||Leaves||Ye et al., 2015|
|165||0||0||0||5||4||Siliques, seeds||Lu et al., 2015|
|970||6||0||0||10||6||NA||Sun et al., 2016|
|31,079||13||0||0||822||691||Inflorescences, roots, leaves, aerial||This study|
|Zea mays||496||0||0||0||1||1||Shoots||Lu et al., 2015|
|Hordeum vulgare||47||16||0||0||0||0||Leaves and seeds||Darbani et al. 2016|
|Solanum lycopersicum||854||0||0||0||4||3||Fruit||Zuo et al. 2016|
*miRNA sponges were predicted using eTM_finder (Ye et al., 2014); miRNA targets were predicted using psRNATarget (Dai and Zhao 2011) in our lab.
Table 2 Summary of circRNA entries in PlantcircBase (Release 1)
|Organisms||Total circRNAs||Back-splicing site validated||Full length sequence validated||Acting as miRNA sponge||Networks of circRNA-miRNA-mRNA|
In the Browse Page, all entries in PlanrcircBase are being listed. You can browse circRNAs by oaganisams, chromosomes, validation information or type of circRNAs.
You can search circRNAs in PlantcircBase by three methods. First is by keywords. ID, parent gene names or miRNA names are all available for searching corresponding circRNAs. Second is conditional search. You can search a set of circRNAs by submitting organism, chromosome or valided information. Third is sequences search. You can input a sequence or several sequences to find if it is/they are match to the circRNA genomic sequences in PlantcircBase. In this part, organisms could be chose and E-value could be reset by users.
For each entry in PlantcircBase, a list of items have been displayed. The table following describes the detail meaning of each item.
|circRNA ID||ID of circRNA in PlantcircBase. It is made up of three parts, species_RNA type_number of the circRNA. For the example of osa_circ_034078, "osa" is short for Oryza sativa; "circ" represents circRNA; "034078" represents the number of the circRNA in PlantcircBase.|
|Alias||Name of the circRNA used in other papers.|
|Organism||The organism from which the circRNA was identified.|
|Position||The exact genomic position of the circRNA, including chromosome, start site and end site (1-based).|
|Reference genome||The version of the reference genome used in PlantcircBase.|
|Type||Type of circRNA based on its genomic origin, e.g. exonic, intronic and intergenic.|
|Parent gene||The host gene from which the circRNA is derived.|
|Parent gene annotation||The annotation of the host gene based on the genome version used in PlantcircBase.|
|Strand||The strand on which the host gene resides.|
|Alternative splicing||In this study, circRNAs with overlapping sequences are considered as alternatively spliced isoforms. In Arabidopsis thaliana, if the length of circRNA is larger than 1000bp, alternative splicing circRNAs won't be presented here beause of the large number of alternative splicing circRNAs.|
|Splice junction sequence||Sequences showing in upper and lower cases represent the two sides of a back-splicing site.|
|Support reads||The total number of reads that support the junction of the circRNA. The supporting reads in different tissues (experiments) are separated by "/".|
|Tissues||Indicating the tissue from which the circRNA was identified. Tissues used in different experiments were separated by "/" based on the order of supporting reads showing in the previous item.|
|Exon boundary||It shows whether the splicing sites are on the boundary of exons or not. For example, "Yes-No" represents the donor splicing site is on the exon boundary and the accepter is not on the exon boundary.|
|Splicing signals||The splicing signals of the circRNA. For example, "AG-GT" represents that the donor and the accepter splicing signal is "AG" and "GT", respectively.|
|Evidence 1: Sanger sequencing||"Yes" represents Sanger sequencing has been performed to valid the back-splicing site, "No" represents the opposite, "NA" represents "not available".|
|Evidence 1: PCR primers||PCR primers (including convergent and divergent primers) used in back-splicing validation.|
|circRNA sequence (assembly)||The sequence of a circRNA based on assembly using circseq-cup (Ye et al., 2016) or Sanger sequencing.|
|Number of exons covered1||The number of exons that cover the assembly circRNA sequence.|
|Evidence 2: Sanger sequencing||"Yes" represents Sanger sequencing has been performed to valid the full length of circRNA, "No" represents the opposite.|
|Evidence 2: PCR primers||PCR primers used in validation of the full length circRNA.|
|Genomic sequence||Genomic sequence of the circRNA. If the length of genomic sequence is over than 20kb, the sequence won't be presented here.|
|Number of exons covered2||The number of exons that cover the genomic sequence of the circRNA.|
|Conserved circRNAs||Conserved circRNAs in other plants based on their back-splicing sequence similarity and parent genes.|
|Sponge-miRNA||miRNAs that are predicted to bind the circRNA (in other words, the circRNA acts as a potential miRNA sponge). Only the top three miRNAs of a circRNA are listed here if more than three are predicted.|
|Sponge-miRNA-mRNA||The target mRNAs of the miRNA listed in the item "Sponge-miRNA". Only the top three target mRNAs are shown if more than three are predicted.|
|Reference||The study in which the circRNA was first reported.|
There are still some pionts should be paid attention to:
(1) For the condition that we didn't collect or generate the exact information of some items listed above, "NA" will be used, which means "not available".
(2) Some genomic sequences of circRNA is quite long (over 20kb). For these circRNAs, genomic sequence are not presented.
(3) The genome version of each organism that used to predict target mRNAs of miRNAs are: transcript, MSU Rice Genome Annotation, version 7 (Oryza sativa), transcript, TAIR 10 (Arabidopsis thaliana), transcript, AGPv3.22 (Zea mays), transcript, v2.4 (Solanum lycopersicum ), unigene, DFCI Gene Index (HVGI), version 12 (Hordeum vulgare), respectively.
By inputing the organism, chromosome, start site and end site, all circRNAs in the database (as well as unknown circRNAs with poaition information) can be visualized in a "circular format" or a "linear format" based on the genomic sequences with annotation. Different genomic components (CDS, intron, exon and UTR) are color coded. In the left figure, the line with arrow represents the direction of transcripts. The vertical line with two numbers represents the back-splicing site of the circRNA. In the right figure, the grey area represents the exact position of the circRNA within its parent gene.
For the two pictures above, the left is in "circular format" and the right is in "linear format" of the circRNA whose position is from 3768053 to 3768717 on the 5th chromosome of Oryza sativa.
In PlantcircBase, the predicting tool can be used to predict whether or not a query sequence forms a circRNA. After submitting the query sequences, the datailed predict results will be displayed, including "Summary of BLASTN results", "Back-splicing sites information", and the visualization of the corresponding circRNA. Following is the result of an example prediction.
If you want to submit new circRNAs in plants to PlantcircBase, please contact us firstname.lastname@example.org
Institute of Crop Sciences / Institute of Bioinformatics, Zhejiang University. E-mail: email@example.com .
Dai X, Zhao PX. 2011. psRNATarget: a plant small RNA target analysis server. Nucleic Acids Res 39(Web Server issue): W155-159. [PubMed]
Darbani B, Noeparvar S, Borg S. 2016. Identification of circular RNAs from the parental genes involved in multiple aspects of cellular metabolism in barley. Front Plant Sci 7: 776. [PMC free article]
Jeck WR, Sorrentino JA, Wang K, Slevin MK, Burd CE, Liu JZ, Marzluff WF, Sharpless NE. 2013. Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19(3): 426-426. [Full text]
Lu T, Cui L, Zhou Y, Zhu C, Fan D, Gong H, Zhao Q, Zhou C, Zhao Y, Lu D, et al. 2015. Transcriptome-wide investigation of circular RNAs in rice. RNA 21(12): 2076-2087. [PubMed]
Memczak S, Jens M, Elefsinioti A, Torti F, Krueger J, Rybak A, Maier L, Mackowiak SD, Gregersen LH, Munschauer M, et al. 2013. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441): 333-338. [PubMed]
Salzman J, Chen RE, Olsen MN, Wang PL, Brown PO. 2013. Cell-type specific features of circular RNA expression. PLoS Genetics 9(9): e1003777. [Full text]
Salzman J, Gawad C, Wang PL, Lacayo N, Brown PO. 2012. Circular RNAs are the predominant transcript isoform from hundreds of human genes in diverse cell types. PloS One 7(2): e30733. [PMC free article]
Sun X, Wang L, Ding J, Wang Y, Wang J, Zhang X, Che Y, Liu Z, Zhang X, Ye J, et al. 2016. Integrative analysis of Arabidopsis thaliana transcriptomics reveals intuitive splicing mechanism for circular RNA. FEBS Lett 590(20): 3510-3516. [PubMed]
Wang PL, Bao Y, Yee MC, Barrett SP, Hogan GJ, Olsen MN, Dinneny JR, Brown PO, Salzman J. 2014. Circular RNA is expressed across the eukaryotic tree of life. PLoS One 9(6): e90859. [PubMed]
Ye CY, Chen L, Liu C, Zhu QH, Fan L. 2015. Widespread noncoding circular RNAs in plants. New Phytol 208(1): 88-95. [PubMed]
Ye CY, Xu H, Shen E, Liu Y, Wang Y, Shen Y, Qiu J, Zhu QH, Fan L. 2014. Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. Front Plant Sci 5: 743. [Full text]
Ye CY, Zhang X, Chu Q, Liu C, Yu Y, Jiang W, Zhu QH, Fan L, Guo L. 2016. Full-length sequence assembly reveals circular RNAs with diverse non-GT/AG splicing signals in rice. RNA Biol DOI: 10.1080/15476286.2016.1245268 [Full text]
Zuo J, Wang Q, Zhu B, Luo Y, Gao L. 2016. Deciphering the roles of circRNAs on chilling injury in tomato. Biochem Biophys Res Commun 479(2): 132-138. [Full Text]