Chimeric RNA

Chimeric RNA, sometimes referred to as a fusion transcript, is composed of exons from two or more different genes that have the potential to encode novel proteins. These mRNAs are different from those produced by conventional splicing as they are produced by two or more gene loci. Chimeric RNA, sometimes referred to as a fusion transcript, is composed of exons from two or more different genes that have the potential to encode novel proteins. These mRNAs are different from those produced by conventional splicing as they are produced by two or more gene loci. In 1956, Francis Crick proposed what is now known as the 'central dogma' of biology: DNA encodes the genetic information required for an organism to carry out its life cycle. In effect, DNA serves as the 'hard drive' which stores genetic data. DNA is replicated and serves as its own template for replication.DNA forms a double helix structure and is a composed of a sugar-phosphate backbone and nitrogenous bases; this can be thought of as a ladder structure where the sides of the ladder are constructed of deoxyribose sugar and phosphate while the rungs of the ladder are composed of paired nitrogenous bases. There are four bases in a DNA molecule:adenine (A), cytosine (C), thymine (T), and guanine (G).Nucleotides are a structural component of DNA and RNA, being made of a molecule of sugar and a molecule of phosphoric acid. The double helix structure of DNA is composed of two antiparallel strands which are oriented in opposite directions. DNA is composed of base pairs in which adenine pairs with thymine and guanine pairs with cytosine.While DNA serves as template for production of ribonucleic acid (RNA), RNA is usually responsible for making protein. The process of making RNA from DNA is called transcription. RNA uses a similar set of bases except that thymine is replaced with uracil.A group of enzymes called RNA polymerases (isolated by biochemists Jerard Hurwitz and Samuel B. Weiss) function in the presence of DNA. These enzymes produce RNA using segments of chromosomal DNA as a template. Unlike replication, where a complete copy of DNA is made, transcription copies only the gene that is to be expressed as a protein. Initially, it was thought that RNA served as a structural template for protein synthesis, essentially ordering amino acids by a series of cavities shaped specifically so that only specific amino acids would fit. Crick was not satisfied with this hypothesis given that the four bases of RNA are hydrophilic and that many amino acids prefer interactions with hydrophobic groups. Additionally, some amino acids are very structurally similar and Crick felt that accurate discrimination would not be possible given the similarities. Crick then proposed that prior to incorporation into proteins, amino acids are first attached to adapter molecules which have unique surface features that can bind to specific bases on the RNA templates. These adapter molecules are called transfer RNA (tRNA). Through a series of experiments involving E. coli and the T4 phage in 1960, it was shown that messenger RNA (mRNA) carriers information from DNA to the ribosomal sites of protein synthesis. The tRNA-amino acid precursors are brought into position by ribosomes where they can read the information provided mRNA templates to synthesize protein. Creating a protein consists of two main steps: transcription of DNA into RNA and translation of RNA into protein. After DNA is transcribed into RNA, the molecule is known as pre-messenger RNA (mRNA) and it consists of exons and introns that can be split apart and rearranged in many different ways. Historically, exons are considered the coding sequence and introns are considered the “junk” DNA. Although this has been shown to be false, it is true that exons are often merged. Depending on the needs of the cell, regulatory mechanisms choose which exons, and sometimes introns, to join together. This process of removing pieces of a pre- mRNA transcript and combining them with other pieces is called splicing. The human genome encodes approximately 25,000 genes but there are significantly more proteins produced. This is accomplished through RNA splicing. The exons of these 25,000 genes can be spliced in many different ways to create countless combinations of RNA transcripts and ultimately countless proteins. Normally, exons from the same pre-mRNA transcript are spliced together. However, occasionally gene products or pre-mRNA transcripts are spliced together so that exons from different transcripts are mixed together in a fusion product known as chimeric RNA. Chimeric RNA often incorporates exons from highly expressed genes, but the chimeric transcript itself is usually expressed at low levels. This chimeric RNA can then be translated into a fusion protein. Fusion proteins are very tissue-specific and they are frequently associated with cancers such as colorectal, prostate, and mesotheliomas. They significantly exploit signal peptides and transmembrane proteins which can alter the localization of proteins, possibly contributing to the disease phenotype. One of the first studies to investigate the generation of chimeric RNA examined the fusion of the first three exons of a gene known as JAZF1 to the last 15 exons of a gene known as JJAZ1. This exact transcript, and the resulting protein, was found specifically in endometrial tissue. While often found in endometrial cancers, these transcripts are expressed in normal tissue as well. Originally thought to be the result of chromosomal fusions, one group investigated whether this was accurate. Using Southern blotting and fluorescence in situ hybridization (FISH) on the genome, the researchers found no evidence of DNA rearrangement. They decided to investigate further by combining human endometrial cells with rhesus fibroblasts and found chimeric products containing sequences from both species. These data suggested that chimeric RNA is generated by splicing parts of genes together rather than chromosomal re-arrangements. They also performed mass spectrometry on the translated protein to verify that the chimeric RNA is translated into protein. Recently, advances in next-generation sequencing have decreased the cost of sequencing significantly, allowing more RNAseq projects to be conducted. These RNAseq projects are able to detect novel RNA transcripts instead of the traditional microarray in which only known transcripts can be detected. Deep sequencing enables detection of transcripts even at very low levels. This has allowed researchers to detect many more chimeric RNAs and fusion proteins and has facilitated understanding their role in health and disease.