2 Bhartiya et al.miRNA into a ribonucleoprotein complex which regulates gene expression by binding to 3’ UTR or 5’ UTR ofcoding transcripts (Du and Zamore, 2005; Bartel, 2004; Meyers et al., 2010; Cai et al., 2009; Kim et al., 2005). The availability of high-throughput DNA sequencing technology has enabled large-scale sequencing of humansand other model organisms revealing a wealth of information on human variability. The functional role of thesevariations has been studied mostly in the context of protein-coding genes (Frazer et al., 2009) whereas thefunctional consequences of variations in noncoding RNAs are just beginning to be reported and understood at themolecular level. Recently, it was shown that genetic variations in the loci encoding for precursor of hsa-mir-146areduces the cellular level of mature miRNA and thereby confers genetic predisposition to papillary thyroidcarcinoma (Jazdzewski et al., 2008). Later, the group also found an association between variations in the passengerstrand of hsa-mir-146a and thyroid cancer (Jazdzewski et al., 2009). Similarly other studies have suggested that asingle nucleotide variant rs11614913 in hsa-mir-196a-2 might be associated with survival of patients with non-small cell lung cancer and affect mature miRNA expression (Tian et al., 2009; Hu et al., 2009; Hu et al., 2008).Likewise rs895819 in hsa-mir-27a, an oncogenic miRNA, was showed to have association with a reduced risk offamilial breast cancer (Yang et al., 2009). Mencia et al., 2009 showed that a point mutation in seed region of hsa-miR-96 result in significant reduction of mRNA targeting causing autosomal dominant, progressive hearing loss.These evidences suggest a greater role of genomic variations in modulating miRNA function and regulationmanifesting as phenotypic correlates (Sun et al., 2009). It is thus imperative to catalog the genomic variations in an interactive, web-based database along withnecessary tools to mine the information to identify and study their potential pathogenic effects. This wouldnecessitate not only a well-annotated and continuously updated set of variant information at these loci in terms ofstandard notations, phenotypes or disease associations along with features for the community to actively contributevariations that may be tagged with the clinical phenotypes. In addition, the resource should supportinteroperability with other tools and resources. To this end, we have used the Leiden Open (source) VariationDatabase (LOVD) Software (Fokkema et al., 2005) for creating a catalog of variations in miRNA loci, throughmanual curation of data from literature and from public databases available at http://genome.igib.res.in/mirlovd.With just a few studies on variations in miRNA, there is no standard ontology and format for them which makeintegration of data on a single platform strenuous. Thus we also propose a nomenclature standard for miRNAvariations which fall in line with the already existing standards for variations in protein coding genes. To the bestof our knowledge this is the first comprehensive collection and systematic genome-wide analysis of genomicvariations in miRNA loci. DATA COLLECTION AND ANALYSESData Collection We collected and manually curated variations from public resources and published literature. The database ofSingle Nucleotide Polymorphisms (dbSNP build 130 on March 2006 assembly of the human genome) (Smigielskiet al., 2000) was used to collect data for genetic variations in human genome which have been reported asvalidated by one or more methods. This data was mapped to human precursor miRNA (pre-miRNA) loci andsequence information was downloaded from hg18 version of human genome from UCSC genome browser (Kent etal., 2002). The data comparison including standardization of positions and analysis was performed using in-housePerl scripts available freely at http://genome.igib.res.in/mirvar/pipeline.html and the dataset was further manuallycurated to check for any possible error. We also manually curated variation information from published literature which reported variations in miRNAloci. These include variations in 17 X-linked miRNAs from male patients diagnosed with autism or schizophrenia(Sun et al., 2009). In addition six post-transcriptionally modified miRNAs with adenosine to inosine RNA editingwere also included (Blow et al., 2006). The information about the hairpin structure of pre-miRNAs was collectedfrom miRNA registry (miRBase, release 13) (Griffiths-Jones et al., 2008; Griffiths-Jones et al., 2006) and wasused for the analysis of structure and effects of variations on mature miRNAs.
Analysis of Genomic Variations in microRNAs 3Nomenclature We standardized the nomenclature for reporting miRNAs, keeping in mind the standards laid down by theHuman Genome Variation Society (HGVS) (http://www.hgvs.org/mutnomen/). We followed the HUGO GeneNomenclature Committee (HGNC) (Bruford et al., 2008) nomenclature for miRNAs along with the miRBasenomenclature.The Database The database, miRvar, is based on Leiden Open (source) Variation Database (LOVD) system which is web-based and user- interactive. LOVD provides individual home pages for all the genes and contains a list ofvariations for each gene. miRvar contains gene pages for each of the miRNAs found to harbor variations and the variant information wasconverted following the guidelines described in the previous section. We have considered the pre-miRNAsequences as described in miRNA registry as the reference sequence because the transcriptional start sites ofmiRNAs are poorly understood. All variations were mapped to their respective reference sequences. The HGNCnomenclature of miRNAs was used and miRNA names were converted accordingly. The database is based onMySQL and additional links have been provided to enable easy access of related information in other databaseslike UCSC genome browser, miRBase (Griffiths-Jones et al., 2008; Griffiths-Jones et al., 2006), miR2Diseases(Jiang et al., 2009), miRecords (Xiao et al., 2009), and 1000 Genome Project (http://www.1000genomes.org). Inaddition, export of data in tab delimited formats and feeds for aggregation have been enabled for interoperabilitywith other resources.Data Analysis and Pipeline A computational pipeline was established to predict potential effects of variations on miRNA biogenesis and itsfunctions (Figure 1). This pipeline includes PHDcleav (http://imtech.res.in/raghava/phdcleav/submission.html)which predicts dicer processing sites using Support Vector Machine (SVM) models. We have used defaultparameters which is zero for positive dicer processing site predictions. The dicer cleavage site changes werepredicted both for wild type pre-miRNAs and pre-miRNAs with variations. In addition, RISCbinder (Ahmed et al., 2009) was used to predict the guide strand of miRNAs. We have usedsequence based approach in RISCbinder with default cutoff. The strand with score more than the cutoff score(which was set zero) was predicted as positive (miRNA) else as negative (miRNA*). Guide strand of miRNAswere predicted both for wild type mature miRNAs and mature miRNAs with variations. Input files used for boththe methods are in fasta format. Further, we have analyzed the allele frequencies data of SNPs from the HapMap populations(http://hapmap.ncbi.nlm.nih.gov/biomart/martview) in order to evaluate the possible effect of the variations in themiRNA and its penetrance in the population. RESULTS AND DISCUSSIONMapping A systematic mapping of validated SNP from dbSNP (build 130) from UCSC genome browser on genomiclocations of pre-miRNA revealed 106 SNPs positions mapping to 85 miRNAs (Supp. Table S1). We mapped theposition of genetic variants on pre-miRNA structure (Table 1) and found that 67 map to stem region of pre-miRNAs, six mapped to the terminal loop and 10 to the overhang (5’ or 3’), while 23 mapped to the maturemiRNA loci of which five mapped to the 5 eight nucleotides or the seed region of the miRNAs (Table 2).
4 Bhartiya et al. Figure 1. Workflow depicting analysis of variations in miRNA loci.Table 1. Location of genetic variation on hairpin structure of precursor miRNAs from the mapped data from dbSNP Location in precursor Genetic variations (SNP) miRNA mapped from dbSNP Terminal loop 6 Stem and Secondary Loop 67 (excluding mature region) Mature 23 (5 in seed region) Overhang (5’ or 3’) 10
Analysis of Genomic Variations in microRNAs 5Table 2. miRNAs with variations in seed region miRNAs HGNC ID Variation dbSNP ID hsa-mir-1977 37065 g.5A>G rs2854138 hsa-mir-146a 31533 g.60C>G rs2910164 hsa-mir-938 33681 g.16C>T rs12416605 hsa-mir-518d 32121 g.59A>G rs73602910 hsa-mir-499 32133 g.73C>T rs7267163According to miRBase, release 13, hsa-mir-1977 have been found to be present in chromosome 1 and Mitochondria (MT)which overlaps with Mt tRNA sequence so it has been removed from the current release of miRBase. The SNP was mapped onthe same position on hsa-mir-1977 in both the chromosomes.Functional consequences of variations To investigate the potential functional effects of variants in the stem region in the biogenesis of miRNA, weestablished a protocol by using algorithms that predict functional features in a set of input miRNA sequences.PHDcleav predicted two miRNAs (Table 3) from the entire dataset having altered dicer processing sites as a resultof variation suggesting the potential effect of variations on the processing of miRNAs. RISCbinder predicted hsa-mir-608 (Table 3) from the 23 miRNAs having SNPs in mature sequence to have adifferent guide strand with the incorporation of variation in its sequence. The alteration in the selection of guidestrand for RISC might hamper the target mRNA translation inhibition. All the variants, methods and potentialfunctional effects are summarized in Table 3. Of all the miRNA variations we tested, these three variations inmiRNAs could have potential impact in the biogenesis process and function. In order to evaluate the possible effects of the variations in the miRNA sequences in the mapped data fromUCSC, we have analyzed the allele frequencies of the 41 SNPs from the HapMap database, and found the medianallele frequency to be less than 0.1. In addition, for 23 SNPs the minor allele was absent in at least one of thepopulations. Both these facts point towards a possible negative selection for the minor allele implicating that theremight be functional consequences for the variant allele (Supp. Fig. S1).Table 3. Functional analysis using PHDcleav and RISCbinder HGNC miRBase ID ID Variation Effect of variation hsa-mir-608 32864 g.37C>G Might alter incorporation in RISC(RI) hsa-mir-449b 32794 g.27A>G Might alter Dicer Cleavage Site(D) hsa-mir-1324 35377 g.31C>G Might alter Dicer Cleavage Site(D)(RI): RISCbinder used to predict guide strand of miRNA. (D): PHDcleav used to predict Dicer cleavage sites in pre-miRNAFor the details about the scores of both the tools used, see Supp. Table S2.
6 Bhartiya et al.miRvar The data was then uploaded on miRvar, a community curation resource for genomic variation in miRNA loci.miRvar provides a user friendly interface to search variants in different miRNAs and has information about thevariant position and the allele change in the respective miRNA, in addition to making it easy to browse forinformation through linkouts like miRBase, UCSC Genome Browser, miR2Disease, 1000 Genomes Project andmiRecords. The database comprises of a total 108 unique entries including 85 miRNAs from UCSC-dbSNPmapping and 25 from published literature (Supp. Table S1). The 25 miRNAs from literature include 19 X-linkedmiRNAs having variations (Sun et al., 2009) and 6 post-transcriptionally modified miRNAs with adenosine toinosine RNA editing (Blow et al., 2006). Eight of the systematic mapped genetic variations have been previouslyreported to be associated with diseases (Supp. Table S3). The variant files can be downloaded from the database instandard meta-tagged format to enable interoperability with other resources. We have also enabled the data forvisualization on genome browser including the UCSC genome browser. The database also provides a search pageto search for miRNAs using their names, disease associations, location of SNP on the hairpin structure andchromosome. The database is open for curation and data suggestions from the community. FUTURE PERSPECTIVES miRvar is a starting point for systematic curation and analysis of genetic variants in miRNA loci. Since theunderstanding of miRNAs and their effects in biological processes, including diseases are just emerging and so isthe understanding on the potential functional role of the genomic variations in these loci, we foresee this databaseto be enriched with new variations and information on disease associations. Though there have been a paucity oftools for predicting functional impact of variations in miRNAs, a curated and up-to-date dataset, as we foreseewould also enable researchers to create and test newer methodologies to predict pathogenic effects of geneticvariation in miRNAs. In support to the community effort towards creating high-quality annotations and standardsfor data exchange, we have enabled a standardized format for collection and reporting of variations in these loci. We feel the database would be immensely enriched by data generated through the ongoing efforts internationallyto understand variations in human populations, including disease associations. In addition to the existing data, wehave already started porting variation data from high-throughput small-RNA sequencing experiments using next-generation sequencing technology. We would work towards making the resource compatible and linked with othermajor resources and tools in the field. We also feel the standards and methods laid forward in developing theresource would be widely used by the community in the future and would be a guide to curation of variations inother noncoding RNA loci. ACKNOWLEDGMENTS The authors acknowledge group members of RNA@IGIB for stimulating discussions and Dr. Anshu Bhardwajfor reviewing the manuscript. We thank Mr. Anupam Kumar Mondal and Ms. Saakshi Jalali for evaluating thedatabase and Mr. Hemant Suryawanshi for his valuable inputs. The work was supported by funding from theCouncil of Scientific and Industrial Research (CSIR), India through project NWP0036” (Comparative genomicsof non-coding RNAs). The authors also acknowledge Dr. Debasis Dash and the Gen2Phen project (FP7/2007-2013) for considerable support and inputs in the terms of designing and standardizing the data and annotations. REFERENCESAhmed F, Ansari HR, Raghava GP. 2009. Prediction of guide strand of microRNAs from its sequence and secondary structure. BMC Bioinformatics 10:105.Bartel DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281-297.Blow MJ, Grocock RJ, van DS, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR. 2006. RNA editing of human microRNAs. Genome Biol 7:R27.
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Analysis of Genomic Variations in microRNAs 9 SUPPORTING INFORMATION Supp. Figure S1. Minor Allele Frequencies of the Variations in HapMap Populations.
Analysis of Genomic Variations in microRNAs 17 Location SNP miRBase dbSNP on hairpin Validation StrategyChr ID*** HGNC ID Variation* ID** structure status Used UCSC- by-cluster, dbSNPMT* hsa-mir-1977 37065 g.53C>T rs9701099 Stem by-2hit-2allele Mapping UCSC- dbSNPMT* hsa-mir-1978 37066 g.44A>G rs3937039 Mature by-cluster Mapping Blow et al.,chr1 hsa-mir-197 31569 r.14a>i - Stem RNA Editing 2006 Blow et al.,chr8 hsa-mir-151 31762 r.49a>i - Seed RNA Editing 2006 Blow et al.,chr14 hsa-mir-376a-1 31869 r.9a>i - Seed RNA Editing 2006 Blow et al.,chr14 hsa-mir-376a-1 31869 r.49a>i - Seed RNA Editing 2006 Blow et al.,chr14 hsa-mir-379 31872 r.10a>i - Seed RNA Editing 2006 Blow et al.,chr21 hsa-mir-99a 31650 r.13a>i - Mature RNA Editing 2006 Sun et al.,chrX hsa-let-7f-2 31484 g.11G>A - Stem X linked 2009 Sun et al.,chrX hsa-mir-188 31559 g.60C>T - Seed X linked 2009 Sun et al.,chrX hsa-mir-18b 32025 g.32A>G - Stem X linked 2009 Blow et al.,chrX hsa-mir-223 31603 r.20A>I - Stem RNA Editing 2006 Terminal Sun et al.,chrX hsa-mir-224 31604 g.41G>A - loop X linked 2009 Sun et al.,chrX hsa-mir-325 31768 g.66G>A - Stem X linked 2009 Sun et al.,chrX hsa-mir-421 32793 g.73G>A - Stem X linked 2009 4 nt down from 3 end of Sun et al.,chrX hsa-mir-421 32793 the stem - 3’ Overhang X linked 2009 Sun et al.,chrX hsa-mir-450a-2 32137 g.4T>C - Seed X linked 2009 Sun et al.,chrX hsa-mir-502 32136 g.13C>G - Stem X linked 2009 Sun et al.,chrX hsa-mir-505 32140 g.8C>T - Stem X linked 2009 Sun et al.,chrX hsa-mir-509-1 32146 g.54insTGA - Stem X linked 2009 Sun et al.,chrX hsa-mir-509-2 33641 g.9G>T - Stem X linked 2009 Sun et al.,chrX hsa-mir-509-2 33641 g.11->A - Mature X linked 2009 Sun et al.,chrX hsa-mir-509-3 33675 g.22G>A - Mature X linked 2009
18 Bhartiya et al. Location SNP miRBase dbSNP on hairpin Validation StrategyChr ID*** HGNC ID Variation* ID** structure status Used Sun et al.,chrX hsa-mir-509-3 33675 g.19C>G - Mature X linked 2009 Sun et al.,chrX hsa-mir-509-3 33675 g.13C>T - Seed X linked 2009 Sun et al.,chrX hsa-mir-510 32147 g.48T>C - Stem X linked 2009 Sun et al.,chrX hsa-mir-510 32147 g.6G>A - Stem X linked 2009 Sun et al.,chrX hsa-mir-660 32916 g.15C>T - Mature X linked 2009 Sun et al.,chrX hsa-mir-888 33648 g.77A>C - 3’ Overhang X linked 2009 Sun et al.,chrX hsa-mir-890 33644 g.66G>C - Stem X linked 2009 Terminal Sun et al.,chrX hsa-mir-891b 33645 g.35C>G - loop X linked 2009 Sun et al.,chrX hsa-mir-892b 33649 g.15T>C - Stem X linked 2009 Sun et al.,chrX hsa-mir-934 33677 g.1T>G - Mature X linked 2009 *Genomic positions are from build hg18 (UCSC) **All rsIDs are based on dbSNP (build130) *** All miRNA names (ID) are from miRBase. · MT*= Mitochondria Dead Entry in miRBase new release: • According to miRBase, release 13, hsa-mir-1977 have been found to be present in chromosome 1 and Mitochondria (MT) which overlaps with Mt tRNA sequence so it has been removed from the current release of miRBase. Supp. Table S2. Functional analysis using PHDcleav and RISCbinder Wild Variant miRBase HGNC miRNA miRNA Effect of ID ID Variation Score Score Variation Method Strategy Altered UCSC- hsa-mir- incorporation dbSNP 608 32864 g.37C>G 0.183 -0.132 in RISC RISCbinder mapping Altered Dicer UCSC- hsa-mir- No site Cleavage dbSNP 449b 32794 g.27A>G 0.8014721 predicted Site PHDcleav mapping Altered Dicer UCSC- hsa-mir- No site Cleavage dbSNP 1324 35377 g.31C>T 1.513702 predicted Site PHDcleav mapping
Analysis of Genomic Variations in microRNAs 19Supp. Table S3. Systematic mapped genetic variations previously reported in diseases HGNC Disease Chr miRbase ID ID dbSNP ID Associations References chr2 hsa-mir-149 31536 rs2292832 Breast cancer Hu et al., 2008 chr2 hsa-mir-149 31536 rs2292832 Lung cancer Tian et al., 2009 Pneumoconiosis chr2 hsa-mir-149 31536 rs2292832 (Lung) Wang et al., 2010 Papillary thyroid Jazdzewski et al., chr5 hsa-mir-146a 31533 rs2910164 carcinoma 2008 Hepatocellular chr5 hsa-mir-146a 31533 rs2910164 carcinoma Hu T et al., 2008 Chatzikyriakidou et chr5 hsa-mir-146a 31533 rs2910164 Psoriasic arthritis al., 2010 chr5 hsa-mir-146a 31533 rs2910164 Prostate cancer Xu et al., 2010 chr5 hsa-mir-146a 31533 rs2910164 Breast cancer Shen et al., 2008 chr5 hsa-mir-146a 31533 rs2910164 Ovarian cancer Shen et al., 2008 chr12 hsa-mir-196a-2 31568 rs11614913 Lung cancer Tian et al., 2009 chr12 hsa-mir-196a-2 31568 rs11614913 Oesophageal cancer Ye et al., 2008 chr12 hsa-mir-196a-2 31568 rs11614913 Breast cancer Hoffman et al., 2009 chr12 hsa-mir-196a-2 31568 rs11614913 Gastric cancer Peng et al., 2009 Hepatocellular chr12 hsa-mir-196a-2 31568 rs11614913 carcinoma Qi et al., 2010 chr12 hsa-mir-196a-2 31568 rs11614913 Glioma Dou et al., 2010 Dilated chr12 hsa-mir-196a-2 31568 rs11614913 cardiomyopathy (Heart) Zhou et al., 2010 Head and neck Christensen et al., chr12 hsa-mir-196a-2 31568 rs11614913 squamous cell carcinoma 2010 chr12 hsa-mir-492 32081 rs2289030 Bladder cancer Yang et al., 2008 chr15 hsa-mir-631 32887 rs5745925 Esophageal cancer Ye et al., 2008 chr17 hsa-mir-423 31880 rs6505162 Bladder cancer Yang et al., 2008 Kontorovich et al., chr17 hsa-mir-423 31880 rs6505162 Breast Cancer 2010 chr17 hsa-mir-423 31880 rs6505162 Oesophageal cancer Ye et al., 2008 Kontorovich et al., chr19 hsa-mir-27a 31613 rs895819 Breast cancer 2009; Yang et al., 2009 chr20 hsa-mir-499 32133 rs3746444 Breast cancer Hu et al., 2008
20 Bhartiya et al. HGNC Disease Chr miRbase ID ID dbSNP ID Associations References chr20 hsa-mir-499 32133 rs3746444 Lung cancer Tian et al., 2009 Dilated chr20 hsa-mir-499 32133 rs3746444 cardiomyopathy (Heart) Zhou et al., 2010