Non-Coding Nucleic Acids

Non-Coding DNA

Non-Coding Nucleic Acids

Only about 1% of DNA is composed of protein-coding genes, and the remaining 99% are non-coding. Scientists once thought that non-coding DNA was "junk", with no known purpose. However, a number of studies have found that at least some of them are indispensable for cell function, especially for controlling gene activity. For example, noncoding DNA contains sequences that act as regulatory elements, determining when and where genes are turned on and off. These regulatory elements provide sites for transcription factor binding and activate or inhibit the process of transcription. Non-coding DNA contains many types of regulatory elements:

  • Promoters are a region of DNA that leads to the initiation of transcription of a particular gene. It provides binding sites for the protein that performs transcription. The promoter is usually located near the transcription start sites of genes, upstream on the DNA (towards the 5' region of the sense strand).
  • Enhancers are regulatory DNA sequences that enhance the transcription of an associated gene when bound by the transcription factor. They are found to be located up to 1 M bp away from the gene, upstream or downstream from the start site.
  • Silencers are DNA sequences that provide binding sites for proteins that inhibit transcription. They can be located in many locations in the DNA, with the target gene upstream being the most common location. In contrast to the effect of enhancers on DNA transcription, silencers suppress the transcription of DNA.
  • Insulators are a type of cis-regulatory element that is found in multicellular eukaryotes. They function at a distance from the promoter element of the target gene, and their length is usually 300 bp to 2000 bp.

Non-Coding RNA (ncRNAs)

ncRNAs are functional RNA molecules that are transcribed from DNA but not translated into proteins. ncRNAs are ubiquitous in eukaryotes: while 90% of eukaryotic genomes are transcribed, only 1-2% are translated into proteins and the majority are transcribed as ncRNAs. ncRNAs play a core role in the epigenetic regulation of gene expression and seem to be closely related to the regulation of other RNA activity, as well as transcriptional and post-translational modifications of proteins influencing their function. There are a wide variety of ncRNAs that have been discovered, which have a broad range of regulatory functions:

  • miRNAs - miRNAs, also called microRNAs, are small single-stranded molecules of approximately 20-24 nt, of which 50% are located in chromosomal regions that are prone to structural changes. These 20-24 nt single-stranded molecules form RNA induced silencing complexes (RISC), which contains miRNA-interacting proteins such as Dicer. The miRNAs pair with complementary sequences on target mRNAs transcripts through the 3'UTR, leading to gene silencing of the target.
  • siRNAs - siRNAs are long double-stranded RNA molecules processed by Dicer into RNA fragments of 19-24 nt that regulate gene silencing when loaded onto RISC. They mediate post-transcription silencing using RNAi, interfering with the expression of a complementary sequence.
  • piRNAs, also known as Piwi-interacting RNA, are a class of RNA molecules that are approximately 26-31 nt in length. They interact with Piwi proteins of the Argonaute family and are involved in chromatin regulation and transposon activity in germline and somatic cells. piRNAs are characterized by uridine at the 5'end and 2'-O-methyl modification at the 3' end. Their main role is to silence transposable elements during germline development.
  • lncRNAs are generally >200 nt in length, and make up most of all non-coding RNA. They are located in the nucleus or cytoplasm, and rarely encode proteins. After transcription, lncRNAs are subject to splicing, polyadenylation and other post-transcriptional modifications. Some lncRNAs are involved in modifying expression on histones. These RNAs control epigenetic gene silencing and can affect tumor development by regulating genes involved in metastasis and angiogenesis in cancer cells.
  • scRNAs, snRNAs, snoRNAs-short for small cytoplasmic RNA, small nuclear RNA and small nucleolar RNA, these molecules guide chemical modifications of ribosomal RNA, transfer RNA and other small nuclear RNAs.
  • Other non-coding RNAs have been described recently, and their roles are not yet clear. These include enhancer RNAs that have about 800 nt (ranging between 0.1-9 kb) and may play a role in activating transcription, and promoter-associated RNAs, which are weakly expressed but associated with highly expressed genes.

Other Non-Coding Nucleic Acids

In addition to the above common non-coding DNA and RNA, there are also some non-coding nucleic acids, such as

Based on small regulatory RNAs, there are several modes of delivery and intracellular synthesis. ncRNAs do not encode proteins but play a very important role in the regulation of gene expression, gene delivery, gene therapy and the development of diagnostic tools, especially the clinical application of oligonucleotides.

For research use only. Not intended for any clinical use.