Small RNA are <200 nt (nucleotide) in length, and are usually non-coding RNA molecules. RNA silencing is often a function of these molecules, with the most common and well-studied example being RNA interference (RNAi), in which endogenously expressed microRNA (miRNA) or exogenously derived small interfering RNA (siRNA) induces the degradation of complementary messenger RNA. Other classes of small RNA have been identified, including piwi-interacting RNA (piRNA) and its subspecies repeat associated small interfering RNA (rasiRNA). Small RNA "is unable to induce RNAi alone, and to accomplish the task it must form the core of the RNA–protein complex termed the RNA-induced silencing complex (RISC), specifically with Argonaute protein". Also, mRNA is used in transcription.
Small RNA can be selected by MicroRNA sequencing, a technique that selects small RNA molecules, then sequences those of 21–25 bp size. The first analysis of small RNAs using miRNA-seq methods examined approximately 1.4 million small RNAs from the model plant Arabidopsis thaliana using Lynx Therapeutics' Massively Parallel Signature Sequencing (MPSS) sequencing platform. This study demonstrated the potential of novel, high-throughput sequencing technologies for the study of small RNAs, and it showed that genomes generate large numbers of small RNAs with plants as particularly rich sources of small RNAs. Later studies used other sequencing technologies, such as a study in C. elegans which identified 18 novel miRNA genes as well as a new class of nematode small RNAs termed 21U-RNAs. Another study comparing small RNA profiles of human cervical tumours and normal tissue, utilized the Illumina (company) Genome Analyzer to identify 64 novel human miRNA genes as well as 67 differentially expressed miRNAs. Applied Biosystems SOLiD sequencing platform has also been used to examine the prognostic value of miRNAs in detecting human breast cancer. Small RNA is useful for certain kinds of study because its molecules "do not need to be fragmented prior to library preparation".
Kinds of small RNA include:
- microRNA (miRNA)
- Piwi-interacting RNA (piRNA)
- small interfering RNA (siRNA)
- small nucleolar RNA (snoRNAs)
- tRNA-derived small RNA (tsRNA)
- small rDNA-derived RNA (srRNA)
- small nuclear RNA, also commonly referred to as U-RNA
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