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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Sequences are fundamental mathematical objects consisting of ordered lists of numbers that follow a specific rule or pattern. Sequences are critical in various mathematical concepts, including calculus, series, and number theory. They can model real-world phenomena such as population growth, financial investments, and physical processes like the diminishing height of a bouncing ball.Each number in a sequence is referred to as a term. Typically, the terms are denoted as a1, a2, a3,…, where...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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An arithmetic sequence is a structured arrangement of numbers where each term is derived by adding a constant value, known as the common difference, to the previous term. This consistent pattern allows for the efficient computation of any term within the sequence as well as the cumulative sum of multiple terms. The formula for finding the nth term of an arithmetic sequence is:Here, aₙ represents the nth term of the sequence, a is the first term, d is the common difference, and n is the...
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miRBase: from microRNA sequences to function.

Ana Kozomara1, Maria Birgaoanu1, Sam Griffiths-Jones1

  • 1School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PT, UK.

Nucleic Acids Research
|November 14, 2018
PubMed
Summary
This summary is machine-generated.

The miRBase database (v22) now includes enhanced quality annotations and functional information for microRNA sequences across 271 organisms. This release improves microRNA research by validating gene annotations and summarizing cellular functions.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • miRBase is a comprehensive microRNA (miRNA) sequence database.
  • The latest release, v22, contains sequences from 271 organisms, including hairpin precursors and mature miRNAs.
  • Accurate miRNA annotations and functional information are crucial for biological research.

Purpose of the Study:

  • To describe improvements in the miRBase database and website.
  • To provide enhanced information on the quality of miRNA gene annotations.
  • To increase the availability of data on the cellular functions of miRNA products.

Main Methods:

  • Collected and mapped 5.5 billion small RNA deep sequencing reads to miRNA sequences.
  • Utilized read mapping patterns to assess the validity of miRNA annotations.
  • Implemented text-mining approaches on open-access articles to extract miRNA functional information.
  • Disseminated Gene Ontology (GO) terms annotated against miRBase sequences.

Main Results:

  • Read mapping provided strong support for 20-65% of miRNA annotations in animal genomes.
  • Evidence was found for the removal of over 200 sequences from the database.
  • Functional information was extracted from over 500,000 sentences across 18,542 papers, linked to 12,519 miRNA entries.
  • Text-mining generated sentence summaries and word clouds for miRNA functional information.

Conclusions:

  • miRBase v22 offers improved data quality and accessibility for miRNA research.
  • Enhanced annotations and functional information facilitate a deeper understanding of miRNA roles.
  • The database and its associated tools are publicly available to the scientific community.