RNA

RNA, complex compound of high molecular weight that functions in cellular protein synthesis and replaces DNA (deoxyribonucleic acid) as a carrier of genetic codes in some viruses. RNA consists of ribose nucleotides (nitrogenous bases appended to a ribose sugar) attached by phosphodiester bonds, forming strands of varying lengths. The nitrogenous bases in RNA are adenine, guanine, cytosine, and uracil, which replaces thymine in DNA.

The ribose sugar of RNA is a cyclical structure consisting of five carbons and one oxygen. The presence of a chemically reactive hydroxyl (−OH) group attached to the second carbon group in the ribose sugar molecule makes RNA prone to hydrolysis. This chemical lability of RNA, compared with DNA, which does not have a reactive −OH group in the same position on the sugar moiety (deoxyribose), is thought to be one reason why DNA evolved to be the preferred carrier of genetic information in most organisms. The structure of the RNA molecule was described by R.W. Holley in 1965.

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RNA structure

RNA typically is a single-stranded biopolymer. However, the presence of self-complementary sequences in the RNA strand leads to intrachain base-pairing and folding of the ribonucleotide chain into complex structural forms consisting of bulges and helices. The three-dimensional structure of RNA is critical to its stability and function, allowing the ribose sugar and the nitrogenous bases to be modified in numerous different ways by cellular enzymes that attach chemical groups (e.g., methyl groups) to the chain. Such modifications enable the formation of chemical bonds between distant regions in the RNA strand, leading to complex contortions in the RNA chain, which further stabilizes the RNA structure. Molecules with weak structural modifications and stabilization may be readily destroyed. As an example, in an initiator transfer RNA (tRNA) molecule that lacks a methyl group (tRNA_i^Met), modification at position 58 of the tRNA chain renders the molecule unstable and hence nonfunctional; the nonfunctional chain is destroyed by cellular tRNA quality control mechanisms.

RNAs can also form complexes with molecules known as ribonucleoproteins (RNPs). The RNA portion of at least one cellular RNP has been shown to act as a biological catalyst, a function previously ascribed only to proteins.

Types and functions of RNA

Of the many types of RNA, the three most well-known and most commonly studied are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), which are present in all organisms. These and other types of RNAs primarily carry out biochemical reactions, similar to enzymes. Some, however, also have complex regulatory functions in cells. Owing to their involvement in many regulatory processes, to their abundance, and to their diverse functions, RNAs play important roles in both normal cellular processes and diseases.

In protein synthesis, mRNA carries genetic codes from the DNA in the nucleus to ribosomes, the sites of protein translation in the cytoplasm. Ribosomes are composed of rRNA and protein. The ribosome protein subunits are encoded by rRNA and are synthesized in the nucleolus. Once fully assembled, they move to the cytoplasm, where, as key regulators of translation, they “read” the code carried by mRNA. A sequence of three nitrogenous bases in mRNA specifies incorporation of a specific amino acid in the sequence that makes up the protein. Molecules of tRNA (sometimes also called soluble, or activator, RNA), which contain fewer than 100 nucleotides, bring the specified amino acids to the ribosomes, where they are linked to form proteins.

In addition to mRNA, tRNA, and rRNA, RNAs can be broadly divided into coding (cRNA) and noncoding RNA (ncRNA). There are two types of ncRNAs, housekeeping ncRNAs (tRNA and rRNA) and regulatory ncRNAs, which are further classified according to their size. Long ncRNAs (lncRNA) have at least 200 nucleotides, while small ncRNAs have fewer than 200 nucleotides. Small ncRNAs are subdivided into micro RNA (miRNA), small nucleolar RNA (snoRNA), small nuclear RNA (snRNA), small-interfering RNA (siRNA), and PIWI-interacting RNA (piRNA).

The miRNAs are of particular importance. They are about 22 nucleotides long and function in gene regulation in most eukaryotes. They can inhibit (silence) gene expression by binding to target mRNA and inhibiting translation, thereby preventing functional proteins from being produced. Many miRNAs play significant roles in cancer and other diseases. For example, tumour suppressor and oncogenic (cancer-initiating) miRNAs can regulate unique target genes, leading to tumorigenesis and tumour progression.

Also of functional significance are the piRNAs, which are about 26 to 31 nucleotides long and exist in most animals. They regulate the expression of transposons (jumping genes) by keeping the genes from being transcribed in the germ cells (sperm and eggs). Most piRNA are complementary to different transposons and can specifically target those transposons.

Circular RNA (circRNA) is unique from other RNA types because its 5′ and 3′ ends are bonded together, creating a loop. The circRNAs are generated from many protein-encoding genes, and some can serve as templates for protein synthesis, similar to mRNA. They can also bind miRNA, acting as “sponges” that prevent miRNA molecules from binding to their targets. In addition, circRNAs play an important role in regulating the transcription and alternative splicing of the genes from which circRNAs were derived.

RNA in disease

Important connections have been discovered between RNA and human disease. For example, as described previously, some miRNAs are capable of regulating cancer-associated genes in ways that facilitate tumour development. In addition, the dysregulation of miRNA metabolism has been linked to various neurodegenerative diseases, including Alzheimer disease. In the case of other RNA types, tRNAs can bind to specialized proteins known as caspases, which are involved in apoptosis (programmed cell death). By binding to caspase proteins, tRNAs inhibit apoptosis; the ability of cells to escape programmed death signaling is a hallmark of cancer. Noncoding RNAs known as tRNA-derived fragments (tRFs) are also suspected to play a role in cancer. The emergence of techniques such as RNA sequencing has led to the identification of novel classes of tumour-specific RNA transcripts, such as MALAT1 (metastasis associated lung adenocarcinoma transcript 1), increased levels of which have been found in various cancerous tissues and are associated with the proliferation and metastasis (spread) of tumour cells.

A class of RNAs containing repeat sequences is known to sequester RNA-binding proteins (RBPs), resulting in the formation of foci or aggregates in neural tissues. These aggregates play a role in the development of neurological diseases such as amyotrophic lateral sclerosis (ALS) and myotonic dystrophy. The loss of function, dysregulation, and mutation of various RBPs has been implicated in a host of human diseases.

The discovery of additional links between RNA and disease is expected. Increased understanding of RNA and its functions, combined with the continued development of sequencing technologies and efforts to screen RNA and RBPs as therapeutic targets, are likely to facilitate such discoveries.