miRBase: Explained – Bioinformatics Review (2023)

Micro RNAs (miRNAs) are short (~22 nucleotides) endogenous RNAs and are derived from non-coding RNAs [1] produced in unicellular eukaryotes, viruses, plants, and animals [2]. miRNAs can control homeostasis [2] and play important roles in several biological processes, such as mRNA degradation and post-translational inhibition through complementary base pairing [3].Several miRNA databases exist that provide detailed information on miRNA sequences, annotations, functions, and their predicted targets, including miRBase, a leading online database of mature miRNA sequences and annotations [4-6]. This article explains the detailed structure and algorithm of miRBase.

miRBase is an online database available atwww.mirbase.org[4-6]. Data can be downloaded from an FTP site (ftp://mirbase.org/pub/mirbase/CURRENT/) in various formats, including FASTA and MySQL dumps for relational databases [7]. It provides a user-friendly interface for miRNA sequence data, its intended gene targets, and annotations [6]. miRBase Release 10.1 consists of 5071 miRNA loci from 58 species expressing 5922 mature miRNA sequences [7]. miRBase has three main functions:

1. miRBase registration:

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It is a confidential source for assigning independent names to new miRNA genes even before they are published in a peer-reviewed journal [7]. This service is used by more than 70 publications. According to them, miRNAs are assigned sequential numerical identifiers that use 3- or 4-letter abbreviations to designate the species. Example: hsa-miR-101 (ina wise man) [8].

2. miRBase sequences:

It acts as the main online repository for miRNA sequences and annotations. Provides miRNA information, notes, references, and links to other resources for all published and validated miRNAs [5,7]. This database consists of more than 5000 sequences from 58 species.

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3. miRBase objectives:

It is the database of predicted miRNA target genes. It predicts the targets of all published animal miRNAs [5,7]. Version 5 of this database predicts targets for more than 500,000 mRNAs for all miRNAs in 24 different species. All individual target miRNA binding sites, several species-conserved binding sites, and several binding sites in UTRs are assigned a P value [9], helping the user to determine confidence in the predicted results.

miRBase has a naming scheme for all predicted targets, its main features are described below [7]:

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  • the name of the predicted miRNA, composed of three or four letters of the species name as a prefix and a number as a suffix. Example: has-me-212.
  • A predicted mature miRNA sequence expressed from one or more hairpin parental loci and composed of other numerical suffixes. Example: dme-mir-6-1 and dme-mir-6-2
  • The related mature miRNA sequences expressed from the related hairpin loci consist of additional alphabets in their suffixes. For example mmu-mir-181a and mmu-mir-181b.
  • The plant miRNA genes are designated ath-MIR166a, where the letters in the suffixes indicate the different loci that express all the related mature miRNAs and numbers are not used in the suffixes.
  • The names of viral miRNAs consist of the locus from which they are derived. For example, ebv-mirBART1 from the Epstein-Barr virus BART locus.

miRBase data

The latest version of miRBase (version 20) updated the database with 24,521 hairpin sequences from 206 species and 30,424 mature sequences [10]. In many cases, the 5' and 3' arms of the hairpin parent express the mature miRNAs, suggesting that both might be functional or that insufficient data is available to determine the predominant product [7]. These miRNAs are represented as has-miR-140-5p and has-miR-140-3p. The Evidence panel provides information about the provenance of each sequence available in the database.

The miRBase:Targets database predicts targets in the UTRs of 37 different Ensembl animal genomes [5,7]. miRBase provides a list of overlapping mRNAs in each miRNA, defining its type (intron, UTR, or exon) and direction (forward or backward) [7]. miRNAs are often clustered within a genome, so miRBase provides a list of such miRNAs that can be retrieved for each organism. miRBase also shows the distribution of genomic properties of miRNAs, showing CpG islands, poly-A site, EST, cDNA, TSS, and DITAG. TSS are predicted using the Eponine TSS software.

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How does it work?

miRBase uses the miRANDA algorithm [7,11] to identify all available miRNA sequences for a given genome against the 3' UTR of that genome obtained from Ensembl [12]. The algorithm is based on dynamic programming that searches for alignments with the maximum local complementarity. A score of +5 is assigned for each G:C and A:T pair, +2 is assigned for swinging G:U pairs and -3 for mismatched pairs, opening and elongation parameters are also assigned for -8, 0 and - define 2.0 and [11,12] respectively. Calculates the optimal alignment score at positions i, j, forming an alignment score matrix. The space elongation parameter was used only when the extension to i,j of a given span of space ending at positions i–1,j or j–1,i (but not of spans ending in i-k, j or j ends, i-k for k > 1) resulted in a higher score than adding a nucleotide-nucleotide match at positions i,j. The complementarity scores for the first eleven residues of the 5' end of the miRNA are multiplied by a scale factor of 2.0 to equal the experimentally observed 5'-3' asymmetry attributed, p. Base pairs B. G:C and A:T contributed +10 to the match result in these positions. This scale factor value is adjustable. There are few rules for target prediction: the threshold of the candidate target location is S > 90 and ΔGRAMS<-17 kcal/mol, where S is the sum of a single pair of matching residues along the alignment trace and ΔG is the duplex free energy of a fully dissociated state [11,12].

The algorithm finds the optimal local matches above this threshold between a specific miRNA and a set of 3' UTRs in each genome and then verifies that the sequence of this miRNA and the position of the target site are conserved in the orthologous genes, i.e. . h in humans, mouse or mouse or fugu and zebrafish [12]. Alignment between target sites is transitive in nature (UTR to miRNA to UTR) through a miRNA homologue. The positions of the pairs of destination sites must be within ±10 residues of the aligned UTRs. If this criterion is met, conserved target sites with 90% or greater (human vs. mouse or rat) and 70% or greater (fugu vs. zebrafish) sequence identity are selected as candidate miRNA targets and they are stored in the database (MYSQL) [11]. . John et al., 2005 predicted 10,572 conserved target sites in mice or rats in 4,463 human transcripts, of which 2,307 transcripts from 2,273 genes contained more than one target site. Similarly, using zebrafish as a reference species, they predicted 7057 conserved target sites (conserved in fugu) in 4820 zebrafish transcripts [12].

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The conserved target sites for each miRNA are ranked based on the alignment score, with free energy acting as a secondary ranking criterion. If a single site on an mRNA is targeted (or within 25 nt) of multiple miRNAs, the lowest-energy, highest-scoring miRNA for that site is reported [11].

Recently, MiRBase introduced high-confidence miRNA based on deep pattern sequencing data [10]. To be classified as a high-confidence miRNA, a locus must meet the following criteria [10]:

  • At least 10 reads must be assigned to the two possible mature miRNAs obtained from the hairpin precursor.
  • At least half of the mapping reads for each hairpin parent arm must be from the same 5' end.
  • at least or more than half of the bases (60%) in mature sequences should match the predicted hairpin structure.
  • the predicted hairpin structure should have a folding free energy < 0.2 kcal/mol/nt.
  • the most abundant reads in each arm of the hairpin precursor should pair with the mature miRNA duplex of 0-4 nucleotides at their 3' ends.

That was all about miRBase, if you want to read more about miRNA prediction using deep sequencing data,Click here. We will discuss more miRNA databases in detail in upcoming articles.

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  1. Bartel, D. P. (2004). MicroRNAs: genomics, biogenesis, mechanism and function.she was whole,116(2), 281-297.
  2. Liu, B., Li, J., and Cairns, M.J. (2012). Identification of miRNAs, targets and functions.Bioinformatics Information Sessions,15(1), 1-19.
  3. He, L. and Hannon, G.J. (2004). MicroRNAs: small RNAs with an important role in gene regulation.Nature Reviews Genetics,5(7), 522.
  4. Griffiths-Jones, S. (2006). miRBase: el microARN-Sequenzdatenbank. EnmicroRNA protocols(pp. 129-138). human press.
  5. Griffiths-Jones, S., Grocock, R.J., Van Dongen, S., Bateman, A., and Enright, A.J. (2006). miRBase: microRNA sequences, targets and gene nomenclature.Nucleic Acid Research,34(Supplement_1), D140-D144.
  6. Griffiths-Jones, S. (2010). miRBase: microRNA sequences and annotation.Current protocols in bioinformatics,29(1), 12-9.
  7. Griffiths-Jones, S., Saini, H.K., van Dongen, S., and Enright, A.J. (2007). miRBase: tools for microRNA genomics.Nucleic Acid Research,36(Supplement_1), D154-D158.
  8. Griffiths-Jones, S. (2004). Das microRNA-Registration.Nucleic Acid Research,32(Suplemento_1), D109-D111.
  9. Rehmsmeier, M., Steffen, P., Höchsmann, M. & Giegerich, R. (2004). Fast and effective prediction of microRNA/target duplexes.ARN,10(10), 1507-1517.
  10. Kozomara, A. & Griffiths-Jones, S. (2013). miRBase – Annotate highly reliable microRNAs using deep sequencing data.Nucleic Acid Research,42(D1), D68-D73.
  11. Enright, A. J., John, B., Gaul, U., Tuschl, T., Sander, C. y Marks, D. S. (2003). Alvos de microARN en Drosophila.genome biology,5(1), R1.
  12. John B., Enright A.J., Aravin A., Tuschl T., Sander C., et al. (2005) Correction: Human microRNA targets. doi: info:doi/10.1371/journal.pbio.0030264


How do you analyze microRNA? ›

miRNA expression levels can be studied by several methods: microarray analysis, real-time PCR, Northern blots, in situ hybridization, and solution hybridization. Of these techniques, quantitative reverse transcription PCR (qRT-PCR) is the most sensitive and accurate method.

Do microRNA have to be 100% complementary to their targets explain? ›

If the miRNA is perfectly or nearly complementary to its target, it can specifically cleave the target mRNA. Endogenously expressed miRNAs are usually imperfectly complementary to their target gene(s) and modulates the effect on gene expression via translational repression12.

How many miRNAs are in miRBase? ›

Abstract. miRBase catalogs, names and distributes microRNA gene sequences. The latest release of miRBase (v22) contains microRNA sequences from 271 organisms: 38 589 hairpin precursors and 48 860 mature microRNAs.

How do you find the target genes of miRNA? ›

Stepwise strategy for miRNA target prediction.
  1. Assessment of complementarity between miRNA and 3′-UTR target sequences. ...
  2. Evaluation of the free energy (ΔG) of the interaction. ...
  3. Estimate of the evolutionary conservation of the miRNA target across the species. ...
  4. Assessment of target site accessibility.
Dec 24, 2020

What is bioinformatic analysis of MicroRNA sequencing data? ›

Typically, the bioinformatic analysis of miRNA sequencing data consists of five parts: (1) Data preprocessing, including reads quality filtering and 3′-adapter trimming; (2) Reads mapping and annotation; (3) Sequence feature analysis, including novel miRNA prediction and the analysis of sequence variation of mature ...

How does miRNA detect its target? ›

The commonly accepted mechanism of miRNA targeting in animals involves an interaction between the 5′-end of the miRNA called the 'seed region' and the 3′ untranslated region (3′-UTR) of the mRNA.

What percentage of total RNA is miRNA? ›

miRNA Biogenesis

Although microRNA represents only ~0.01% of total RNA by weight, the average copy number of an individual miRNA species has been estimated at 500/cell, which may be higher than the average expression of mRNA species.

What determines which genes will be regulated by miRNA? ›

Factors that may contribute to the robustness of miRNA-mediated gene regulation include the functionalized compartmentalization and shuttling of miRISC within the cells. The availability and abundancy of miRNAs and their target mRNAs are also contributing factors in determining which genes are regulated.

How many genes are targeted by miRNA? ›

MiRNA-Gene Interaction Data

miRTarbase includes 502,652 high quality experimentally validated miRNA-gene interactions between 2,599 miRNAs and 15,064 genes for the human species.

How do you quantify miRNA in a cell? ›

Several methods have been applied to quantify c-miRNAs, including quantitative real-time PCR, digital PCR, microarray, and high-throughput small RNA-sequencing. These methods need RNA isolation, in some instances small RNA enrichment, and/or reverse transcription before proceeding to miRNA quantification.

How do you separate miRNA from total RNA? ›

In order to isolate circulating miRNAs, the plasma was re-centrifuged at 1000 ×g, 4°C for 10 min. Plasma was collected carefully and aliquoted in 1.5 mL RNase-free tubes and freezed at −80°C immediately for future use. Body fluid samples were centrifuged at 1,000 ×g for 10 min to pellet cellular debris.

What is 5p in miRNA? ›

Instead of the miR/miR* name scheme, a miR-5p/miR-3p nomenclature has been adopted. By the new system, the 5' arm of the miRNA is always designated miR-5p and the 3' arm is miR-3p. However, as this is a recent change, literature will often refer to the original miR/miR* names.

Can miRNA target more than one mRNA? ›

Owing to short base-pairs within miRNA-3′UTR duplex, one miRNA can bind to several even hundreds target mRNAs or a single mRNA can be targeted by many different miRNAs [17], [18].

Why miRNA is a biomarker? ›

These molecules meet most of the required criteria for being an ideal biomarker, such as accessibility, high specificity, and sensitivity. Despite present limitations, miRNAs as biomarkers for various conditions remain an impressive research field.

What is target score in miRDB? ›

All the predicted targets have target prediction scores between 50 - 100. These scores are assigned by the new computational target prediction algorithm. The higher the score, the more confidence we have in this prediction. That is why the search result is ordered by prediction score.

How do you analyze data in RNA sequencing? ›

RNA-seq data analysis typically involves several steps: trimming, alignment, counting and normalization of the sequenced reads, and, very often, differential expression (DE) analysis across conditions.

Why do we use bioinformatics to analyze molecular data? ›

Bioinformatics enables us to handle the huge amounts of data involved and make sense of them. Bioinformatics involves processing, storing and analysing biological data. This might include: Creating databases to store experimental data.

How long does it take to analyze RNA-seq data? ›

Each run takes 16-36hrs depending on the type of sequencing being done. Putting all these steps together and allowing for some amount of troubleshooting and scheduling around other runs, we typically take 1-2wks to get from start to finish.

What activates miRNA? ›

Likewise miRNAs involved in RNAi, activating miRNAs also require of (1) Drosha and Dicer RNase III enzymes, responsible for miRNA biogenesis, and (2) members of the Argonaute (Ago) family proteins, known to be associated with miRNAs during the formation of the effector RNA-Induced Silencing Complex (RISC) [7.

How does miRNA increase gene expression? ›

microRNA controls gene expression mainly by binding with messenger RNA (mRNA) in the cell cytoplasm. Instead of being translated quickly into a protein, the marked mRNA will be either destroyed and its components recycled, or it will be preserved and translated later.

Does miRNA always degrade mRNA? ›

It was primarily acknowledged that miRNAs result in gene expression repression at both the level of mRNA stability by conducting mRNA degradation and the level of translation (at initiation and after initiation) by inhibiting protein translation or degrading the polypeptides through binding complementarily to 3′UTR of ...

Why is miRNA better than Sirna? ›

The major difference between siRNAs and miRNAs is that the former are highly specific with only one mRNA target, whereas the latter have multiple targets. The therapeutic approaches of siRNAs and miRNAs are therefore very different.

Is miRNA coding or noncoding? ›

MicroRNAs are short RNA transcripts of 18–24 nucleotides and they regulate gene expression at the translational level [14]. They are among the most extensively studied and best characterised non-coding RNAs.

Does miRNA affect viral gene expression? ›

Several viruses, including especially herpesviruses, also encode miRNAs and over 200 viral miRNAs have now been identified. Current evidence indicates that viruses use these miRNAs to manipulate both cellular and viral gene expression.

What is the difference between miRNA and mRNA? ›

miRNAs are small single-stranded RNA genes possessing the reverse complement of another protein-coding gene's mRNA transcript. These miRNAs can inhibit the expression of that target protein-coding gene.

What inhibits miRNA? ›

The standard method for inhibiting microRNA (miRNA) function is by steric blocking—using an oligonucleotide that is perfectly complementary to the mature miRNA target. miRNA inhibitors form a duplex with the miRNA guide strand that prevents the miRNA from binding to its intended target.

Can one miRNA regulate many genes? ›

Abstract. MicroRNAs (miRNAs) act as transcriptional regulators and play pivotal roles in carcinogenesis. According to miRNA target databases, one miRNA may regulate many genes as its targets, while one gene may be targeted by many miRNAs.

Does miRNA bind to DNA? ›

Here we provide multiple lines of direct physical evidence that microRNAs can bind to double stranded DNA to form triplex structures and show that mammalian and non-mammalian genomes are enriched with microRNA triplex binding sites.

Does miRNA prevent transcription? ›

miRNAs can inhibit gene expression at transcriptional level. (A) In this case, miRNA-targeted non-coding promoter associated RNA would represent a docking platform for a protein inhibitory complex consisting of elements of RISC, PcG proteins and chromatin modulators.

Can you do qPCR for miRNA? ›

There are a number of commercially available assays for the expression analysis of miRNAs, based on qPCR (Table 2).

How many reads for miRNA seq? ›

The sequence read length in most miRNA-seq datasets that we analyzed was 50 bp, much longer than the typical length of a miRNA (20–23 bp). All adapter sequences need to be trimmed prior to alignment.

How is miRNA sequenced? ›

Novel miRNA sequences are identified based on the characteristic expression pattern that they display due to DICER processing: higher expression of the mature miRNA over the star strand and loop sequences.

Can trizol extract miRNA? ›

In conclusion, the Trizol-based method is efficient as well as economical to use for quantification of circulating miRNAs.

Does Dicer cleave miRNA? ›

The pre-miRNA structure requirement for human Dicer activity is incompletely understood. By large-scale in vitro dicing assays and mutagenesis studies, we showed that human Dicer cleaves most, although not all, of the 161 tested human pre-miRNAs efficiently.

How does miRNA prevent gene expression? ›

miRNAs (microRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. They generally bind to the 3'-UTR (untranslated region) of their target mRNAs and repress protein production by destabilizing the mRNA and translational silencing.

What does 3p and 5p mean on miRNA? ›

5p means the microRNA is from the 5 prime arm of the hairpin and 3p means 3 prime end. Sometimes the 3p arm is also labeled with with an asterisk.

What is Dicer in miRNA? ›

MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression by binding to the cellular transcript leading to translational repression or degradation of the target mRNA. Dicer and Drosha are the miRNA processing enzymes that are required for the maturation of miRNAs.

What is U6 in miRNA? ›

U6 is one of the most widely used internal reference genes for miRNA. U6 has been used as an internal reference gene in renal tissue17, cell lines18 and peripheral blood mononuclear cells10 in kidney disease patients.

Can miRNA cross blood brain barrier? ›

It is known that in pathological states miRNAs can pass from the brain tissue into the blood stream through the BBB, making them potential biomarkers for CNS diseases [59].

What degrades miRNA? ›

Degradation Machinery

XRN2 and XRN1 degrade miRNAs in C. elegans; PNPT1 preferentially degrades a small subset of miRNAs in response to interferon; and RRP41 and XRN1 are also likely to degrade miRNAs in 293T cells.

Which RNA regulates miRNA? ›

The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC). MicroRNA assembles into RISC, activating the complex to target messenger RNA (mRNA) specified by the microRNA.

How do you analyze miRNA? ›

miRNA expression levels can be studied by several methods: microarray analysis, real-time PCR, Northern blots, in situ hybridization, and solution hybridization. Of these techniques, quantitative reverse transcription PCR (qRT-PCR) is the most sensitive and accurate method.

What is the most common miRNA? ›

Abstract. miRNA-21 is among the most abundant and highly conserved microRNAs (miRNAs) recognized. It is expressed in essentially all cells where it performs vital regulatory roles in health and disease.

What are the advantages of miRNA? ›

Evolutionarily conserved, miRNAs modulate vital processes, including cell cycle, metabolism, differentiation and development, tissue patterning, and aging. The human genome contains about 1,000 miRNAs, and each has been suggested to regulate hundreds of transcripts, totaling about a third of all genes.

How do you cite Targetscan? ›

To reference information from this database, please cite one of the following papers: McGeary SE, Lin KS, Shi CY, Pham T, Bisaria N, Kelley GM, Bartel DP. The biochemical basis of microRNA targeting efficacy. Science Dec 5, (2019).

How do you do a microarray analysis? ›

To perform a microarray analysis, mRNA molecules are typically collected from both an experimental sample and a reference sample. For example, the reference sample could be collected from a healthy individual, and the experimental sample could be collected from an individual with a disease like cancer.

How do you isolate microRNA? ›

In order to isolate circulating miRNAs, the plasma was re-centrifuged at 1000 ×g, 4°C for 10 min. Plasma was collected carefully and aliquoted in 1.5 mL RNase-free tubes and freezed at −80°C immediately for future use. Body fluid samples were centrifuged at 1,000 ×g for 10 min to pellet cellular debris.

What do the results from a microarray tell you? ›

The test's results may lead to: finding the genetic cause for your child's medical condition. changes in your child's health care. learning the risk for your child to pass down a genetic change to their children.

How do you interpret gene expression data? ›

A common approach to interpreting gene expression data is gene set enrichment analysis based on the functional annotation of the differentially expressed genes (Figure 13). This is useful for finding out if the differentially expressed genes are associated with a certain biological process or molecular function.

What does microarray analysis tell us? ›

Microarray is a high resolution test to assess very small gains and losses (copy number variants) of genomic information and areas of homozygosity (which might suggest an autosomal recessive condition).

How many reads is enough for RNA-seq? ›

How many reads do I need for my experiment? The number of reads required depends upon the genome size, the number of known genes, and transcripts. Generally, we recommend 5-10 million reads per sample for small genomes (e.g. bacteria) and 20-30 million reads per sample for large genomes (e.g. human, mouse).

What is RNA sequencing for dummies? ›

RNA sequencing (RNA-Seq) is a powerful technique to study the transcriptome of an organism at a given moment. As its name suggests, RNA-Seq is sequencing the RNA molecules from the sample.

Can microarray be wrong? ›

Doctor Anil Malhotra discusses that because whole genome microarray studies examine so much genetic data, the daners of false-positive results are very real. Yes. One of the limitations when you examine so many different numbers of markers at any individual time point is the potential for false-positive results.

What is a question that could be answered by a DNA microarray? ›

DNA microarray analysis is a technique that scientists use to determine whether genes are on or off. Scientists know a gene is on in a cell if its mRNA is present.

How do microRNAs turn off genes? ›

microRNA controls gene expression mainly by binding with messenger RNA (mRNA) in the cell cytoplasm. Instead of being translated quickly into a protein, the marked mRNA will be either destroyed and its components recycled, or it will be preserved and translated later.


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