miRBase is the principal online repository designed to curate and distribute microRNA (miRNA) sequence data and associated functional annotation. It serves as the definitive source for miRNA nomenclature, ensuring consistency across scientific literature. The database acts as an independent arbiter, assigning unique and stable names to newly discovered miRNA genes before their formal publication. This function maintains standardization in a rapidly evolving field of genetic research.
Foundational Context Understanding microRNAs
MicroRNAs are a class of small, non-coding RNA molecules that play a regulatory function within cells. These molecules are relatively short, typically consisting of only 18 to 25 nucleotides. They do not code for proteins but instead act as genetic fine-tuners, influencing the amount of protein produced from other genes.
The primary role of a microRNA is to regulate gene expression after the genetic information has been transcribed into messenger RNA (mRNA). A microRNA molecule integrates into a complex known as the RNA-induced silencing complex (RISC), which then searches for complementary sequences on target mRNA transcripts. Binding of the microRNA-RISC complex to the mRNA generally leads to two outcomes: the repression of protein synthesis or the accelerated degradation of the mRNA molecule.
This post-transcriptional regulation is a fundamental biological process that affects virtually every aspect of cellular activity. MicroRNAs are involved in processes such as cell differentiation, proliferation, programmed cell death, and metabolism. Because of their broad influence, the dysregulation of microRNAs has been implicated in many disease states, including various cancers and cardiovascular disorders.
The Standardized Content of miRBase
The core function of miRBase is to provide a structured collection of microRNA sequences and their related information. Each entry in the database is organized around two primary sequence types: the mature microRNA and its precursor hairpin. The mature microRNA, often designated as ‘miR,’ is the final, functional molecule, while the precursor, designated as ‘mir,’ is the longer, hairpin-shaped RNA molecule from which the mature form is processed.
A central feature of the database is its rigorous, standardized naming convention for microRNA genes. Each name begins with a three- or four-letter prefix that identifies the source species, such as hsa for Homo sapiens or mmu for Mus musculus. This prefix is followed by a sequential number, for example, hsa-miR-21, which provides an unambiguous identifier for the microRNA gene locus in the human genome.
To ensure stable referencing, every sequence and precursor is assigned a unique accession number that does not change between database updates. Precursor hairpins receive an identifier beginning with “MI,” while mature microRNA sequences are given a “MIMAT” identifier. This system allows researchers to track specific sequences even as annotation evolves. The database also organizes entries by species, providing genomic coordinates that map the microRNA genes to their precise location on the chromosome when an assembled genome is available.
Data Integrity and Curation Methodology
miRBase’s authority stems from its comprehensive and rigorous data curation methodology. The database relies on expert manual review and computational validation to verify the quality of new microRNA submissions. Researchers seeking to name a novel microRNA must submit their sequence and supporting data, which is then reviewed before an official name is assigned. This assignment is often a requirement for publication in scientific journals.
The process requires that novel microRNA genes are supported by experimental evidence, such as cloning or evidence of expression and processing. This verification ensures that the submitted sequences represent true microRNAs and not merely random fragments of other RNA types. For organisms with an assembled genome, miRBase maps each entry to its genomic location, often annotating whether the microRNA is located within an intron of a protein-coding gene.
The database maintains a versioning system, releasing new, numbered versions that reflect the continuous discovery of microRNAs. This iterative approach allows researchers to track changes, including sequences that may be updated or removed if subsequent data casts doubt on their authenticity. By integrating and analyzing short RNA deep-sequencing data, miRBase can identify and flag a subset of entries as “high confidence,” providing users with an indication of the strongest supporting evidence.
Practical Application for Research
Researchers utilize miRBase as an entry point for almost any study involving microRNAs, accessing the data through a web interface or bulk download files for large-scale computational analysis. The website provides multiple search options, allowing users to quickly retrieve information by entering a microRNA name, sequence, or stable accession number. Users can also search by genomic coordinate to find all microRNA genes within a specific chromosomal region.
The standardized nomenclature and sequence data provided by miRBase are fundamental for downstream bioinformatics tools. Data from the repository are used for developing target prediction algorithms, which computationally estimate which messenger RNAs are regulated by a given microRNA. Furthermore, the sequence alignments and species groupings are used for phylogenetic analysis to study the evolutionary history of microRNA families. The resource facilitates gene expression studies, allowing scientists to reliably compare their experimental results against an authoritative set of microRNA annotations.