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===R-loops===
[[R-loop]]s are formed during transcription. An R-loop is a three-stranded nucleic acid structure containing a DNA-RNA hybrid region and an associated non-template single-stranded DNA. Actively transcribed regions of [[DNA]] often form R-loops that are vulnerable to [[DNA damage (naturally occurring)|DNA damage]]. Introns reduce R-loop formation and DNA damage in highly expressed yeast genes.<ref name="pmid28757210">{{cite journal | vauthors = Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B | title = Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability | journal =
==RNA processing==
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===Alternative splicing===
Eukaryotic pre-mRNAs have their introns spliced out by [[spliceosome]]s made up of [[snRNP|small nuclear ribonucleoproteins]].<ref>Weaver, Robert F. (2005). ''Molecular Biology'', p.432-448. McGraw-Hill, New York, NY. {{ISBN|0-07-284611-9}}.</ref><ref>{{
In complex eukaryotic cells, one primary transcript is able to prepare large amounts of mature mRNAs due to alternative splicing. Alternate splicing is regulated so that each mature mRNA may encode a multiplicity of proteins. [[File:Alternativ splicing.png|thumb|Alternative splicing of the primary transcript]] The effect of alternative splicing in gene expression can be seen in complex eukaryotes which have a fixed number of genes in their genome yet produce much larger numbers of different gene products.<ref name="Cooper GM"/> Most eukaryotic pre-mRNA transcripts contain multiple introns and exons. The various possible combinations of 5' and 3' splice sites in a pre-mRNA can lead to different excision and combination of exons while the introns are eliminated from the mature mRNA. Thus, various kinds of mature mRNAs are generated.<ref name="Cooper GM"/> Alternative splicing takes place in a large protein complex called the [[spliceosome]]. Alternative splicing is crucial for tissue-specific and developmental regulation in gene expression.<ref name="Cooper GM"/> Alternative splicing can be affected by various factors, including mutations such as [[chromosomal translocation]].
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==Experiments==
A study by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at 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 [[micromolar|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.<ref>{{cite journal |
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 [[dipteran]]s, 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.<ref>{{cite journal |
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 factor]]s 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 [[spliceosome]]s 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 [[snRNA]]s. 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.<ref>{{cite journal |
==Related diseases==
Research has also led to greater knowledge about certain diseases related to changes within primary transcripts. One study involved [[estrogen receptor]]s 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.<ref>{{cite journal |
== See also ==
*[[Transcription (biology)]]
*[[Transcriptome]]
== References ==
{{Reflist}}
== External links ==
*[https://web.archive.org/web/20060813113552/http://www.scienceden.com/mbiology/concepts/rna Scienceden.com RNA Article]
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