RNA sequencing
Genomics · Bioinformatics · Molecular Biology
Say it: ar-en-AY SEE-kwen-sing
RNA sequencing (RNA-seq) is a method that uses high-throughput sequencing to identify and count the RNA molecules in a sample.
Also: RNA-seq, RNA-Seq, whole transcriptome shotgun sequencing
Definition
What is RNA sequencing?
RNA sequencing reads the transcriptome. RNA is extracted from cells or tissue, often after enriching for messenger RNA by capturing its poly-A tails or after removing the abundant ribosomal RNA. Because sequencers read DNA, the RNA is copied into complementary DNA (cDNA) by the enzyme reverse transcriptase. The RNA or cDNA is broken into short fragments, fitted with adapters and run on a next-generation sequencer, which produces millions of short reads.
Software matches the reads to a reference genome, or assembles them without one, and counts how many fall in each gene. These counts measure expression, so comparing samples reveals genes that are more or less active in, for example, a tumor versus healthy tissue. Reads that span exon junctions show how RNAs were spliced, and the data can also uncover new transcripts and sequence variants.
RNA-seq has largely replaced microarrays because it needs no known sequence in advance and measures a much wider range of expression levels. Single-cell RNA-seq applies the same idea to individual cells, letting researchers tell apart cell types within a tissue.
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- TranscriptomeThe transcriptome is the full set of RNA molecules made in a cell, tissue or organism at a given time, showing which genes are active.
- Next-generation sequencingNext-generation sequencing (NGS) is a set of high-throughput methods that read the sequences of millions of short DNA fragments in parallel.
- Gene expressionGene expression is the use of a gene's information to make a working product, usually a protein or a functional RNA molecule.
- Reverse transcriptaseReverse transcriptase is an enzyme that builds DNA from an RNA template, letting retroviruses such as HIV turn their RNA genome into DNA.
- RNA splicingRNA splicing is the step in which introns are cut out of a newly made RNA and its exons are joined, producing a mature RNA ready for use.
- BioinformaticsBioinformatics is the science of using computers to gather, store, analyze and share biological data, especially DNA, RNA and protein sequences.
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Written for biofideX in plain words, after checking these references:
- NCI Dictionary of Cancer Terms: RNA sequencing
- NCBI MeSH: RNA-Seq
- Wang, Gerstein and Snyder, RNA-Seq: a revolutionary tool for transcriptomics, Nature Reviews Genetics (2009)
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