Primary transcript
A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.
Pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA). Once pre-mRNA has been completely processed, it is termed "mature messenger RNA", or simply "messenger RNA". The term hnRNA is often used as a synonym for pre-mRNA, although, in the strict sense, hnRNA may include nuclear RNA transcripts that do not end up as cytoplasmic mRNA.
There are several steps contributing to the production of primary transcripts. All these steps involve a series of interactions to initiate and complete the transcription of DNA in the nucleus of eukaryotes. Certain factors play key roles in the activation and inhibition of transcription, where they regulate primary transcript production. Transcription produces primary transcripts that are further modified by several processes. These processes include the 5' cap, 3'-polyadenylation, and alternative splicing. In particular, alternative splicing directly contributes to the diversity of mRNA found in cells. The modifications of primary transcripts have been further studied in research seeking greater knowledge of the role and significance of these transcripts. Experimental studies based on molecular changes to primary transcripts and the processes before and after transcription have led to greater understanding of diseases involving primary transcripts.
Experiments[edit]
A study by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at Roswell Park Comprehensive Cancer Center (then known as the Roswell Park Memorial Institute) in Buffalo, New York and from the Cell and Molecular Biology Program at University of Wisconsin in Madison, Wisconsin was made to understand cellular processes involving primary transcripts. Researchers wanted to understand whether 5-Fluorouracil (FUra), a drug known for use in cancer treatment, inhibits or shuts down dihydrofolate reductase (DHFR) pre-mRNA processing and/or nuclear mRNA stability in methotrexate-resistant KB cells. Long-term exposure to FUra had no effect on the level of DHFR pre-mRNA containing certain introns, which are sections of pre-mRNA that are usually cut out of the sequence as a part of processing. However, levels of total DHFR mRNA decreased two-fold in cells exposed to 1.0 μM FUra. There was no significant change in the half-life, which refers to the time it takes 50% of the mRNA to decay, of total DHFR mRNA or pre-mRNA observed in cells exposed to FUra. And nuclear/cytoplasmic RNA labeling experiments demonstrated that the rate of nuclear DHFR RNA changing to cytoplasmic DHFR mRNA decreased in cells treated with FUra. These results provide further evidence that FUra may help in the processing of mRNA precursors and/or affect the stability of nuclear DHFR mRNA.[11]
Judith Lengyel and Sheldon Penman from the department of Biology at the Massachusetts Institute of Technology (MIT) in Cambridge, Massachusetts wrote an article about one type of primary transcript involved in the genes of two dipterans, or insects that have two wings: Drosophila and Aedes. The article describes how researchers looked at hnRNA, or basically pre-mRNA, primary transcripts in the two kinds of insects. The size of hnRNA transcripts and the fraction of hnRNA that is converted to mRNA in cell lines, or groups of cells derived from a single cell of whatever one is studying, of Drosophila melanogaster and Aedes albopictus were compared. Both insects are dipterans, but Aedes has a larger genome than Drosophila. This means that Aedes has more DNA, which means more genes. The Aedes line make larger hnRNA than did the Drosophila line even though the two cell lines grew under similar conditions and produced mature or processed mRNA of the same size and sequence complexity. These data suggest that the size of hnRNA increases with increasing genome size, which is obviously shown by Aedes.[12]
Ivo Melcak, Stepanka Melcakova, Vojtech Kopsky, Jaromıra Vecerova and Ivan Raska from the department of Cell Biology at the Institute of Experimental Medicine, at the Academy of Sciences of Czech Republic in Prague studied the influences of nuclear speckles on pre-mRNA. Nuclear speckles (speckles) are a part of the nuclei of cells and are enriched with splicing factors known for involvement in mRNA processing. Nuclear speckles have shown to serve neighboring active genes as storage places of these splicing factors. In this study, researchers showed that, in HeLa cells which derived from cells of a person who had cervical cancer and have proven useful for experiments, the first group of spliceosomes on pre-mRNA come from these speckles. Researchers used microinjections of spliceosome-accepting and mutant adenovirus pre-mRNAs with differential splicing factor binding to make different groups and then followed the sites in which they were heavily present. Spliceosome-accepting pre-mRNAs were rapidly targeted into the speckles, but the targeting was found to be temperature-dependent. The polypyrimidine tract sequences in mRNA promote the construction of spliceosome groups and is required for targeting, but, by itself, was not sufficient. The downstream flanking sequences were particularly important for the targeting of the mutant pre-mRNAs in the speckles. In supportive experiments, the behavior of the speckles was followed after the microinjection of antisense deoxyoligoribonucleotides (complementary sequences of DNA and or RNA to a specific sequence) and, in this case, specific sequences of snRNAs. snRNAs are known for helping in the processing of pre-mRNA as well. Under these conditions, spliceosome groups formed on endogenous pre-mRNAs. Researchers concluded that the spliceosome groups on microinjected pre-mRNA form inside the speckles. Pre-mRNA targeting and buildup in the speckles is a result of the loading of splicing factors to the pre-mRNA, and the spliceosome groups gave rise to the speckled pattern observed.[13]
Related diseases[edit]
Research has also led to greater knowledge about certain diseases related to changes within primary transcripts. One study involved estrogen receptors and differential splicing. The article entitled, "Alternative splicing of the human estrogen receptor alpha primary transcript: mechanisms of exon skipping" by Paola Ferro, Alessandra Forlani, Marco Muselli and Ulrich Pfeffer from the laboratory of Molecular Oncology at National Cancer Research Institute in Genoa, Italy, explains that 1785 nucleotides of the region in the DNA that codes for the estrogen receptor alpha (ER-alpha) are spread over a region that holds more than 300,000 nucleotides in the primary transcript. Splicing of this pre-mRNA frequently leads to variants or different kinds of the mRNA lacking one or more exons or regions necessary for coding proteins. These variants have been associated with breast cancer progression.[14] In the life cycle of retroviruses, proviral DNA is incorporated in transcription of the DNA of the cell being infected. Since retroviruses need to change their pre-mRNA into DNA so that this DNA can be integrated within the DNA of the host it is affecting, the formation of that DNA template is a vital step for retrovirus replication. Cell type, the differentiation or changed state of the cell, and the physiological state of the cell, result in a significant change in the availability and activity of certain factors necessary for transcription. These variables create a wide range of viral gene expression. For example, tissue culture cells actively producing infectious virions of avian or murine leukemia viruses (ASLV or MLV) contain such high levels of viral RNA that 5–10% of the mRNA in a cell can be of viral origin. This shows that the primary transcripts produced by these retroviruses do not always follow the normal path to protein production and convert back into DNA in order to multiply and expand.[15]