miRBase: Explained – Bioinformatics Review (2023)

FAQs

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.

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.

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.

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 ...

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.

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.

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.

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.

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.

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.

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].

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.

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.

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.

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.

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.

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.

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 ...

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

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].

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.

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.

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.

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.

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).

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.

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.

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.

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.

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).

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.

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.

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.

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.