Primary transcript
A primary transcript is the single-stranded ribonucleic acid (
Pre-mRNA is synthesized from a
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
Production
The steps contributing to the production of primary transcripts involve a series of molecular interactions that initiate transcription of DNA within a cell's nucleus. Based on the needs of a given cell, certain DNA sequences are transcribed to produce a variety of RNA products to be translated into functional proteins for cellular use. To initiate the transcription process in a cell's nucleus, DNA double helices are unwound and hydrogen bonds connecting compatible nucleic acids of DNA are broken to produce two unconnected single DNA strands.[1] One strand of the DNA template is used for transcription of the single-stranded primary transcript mRNA. This DNA strand is bound by an RNA polymerase at the promoter region of the DNA.[2]
In eukaryotes, three kinds of RNA—
Studies of primary transcripts produced by RNA polymerase II reveal that an average primary transcript is 7,000 nucleotides in length, with some growing as long as 20,000 nucleotides in length.[2] The inclusion of both exon and intron sequences within primary transcripts explains the size difference between larger primary transcripts and smaller, mature mRNA ready for translation into protein.
Regulation
A number of factors contribute to the activation and inhibition of transcription and therefore regulate the production of primary transcripts from a given DNA template.
Activation of RNA polymerase activity to produce primary transcripts is often controlled by sequences of DNA called
Inhibition of RNA polymerase activity can also be regulated by DNA sequences called
R-loops
R-loops 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. Introns reduce R-loop formation and DNA damage in highly expressed yeast genes.[7]
RNA processing
Transcription, a highly regulated phase in gene expression, produces primary transcripts. However, transcription is only the first step which should be followed by many modifications that yield functional forms of RNAs.[8] Otherwise stated, the newly synthesized primary transcripts are modified in several ways to be converted to their mature, functional forms to produce different proteins and RNAs such as mRNA, tRNA, and rRNA.
Processing
The basic primary transcript modification process is similar for tRNA and rRNA in both eukaryotic and prokaryotic cells. On the other hand, primary transcript processing varies in mRNAs of prokaryotic and eukaryotic cells.
5' capping
Shortly after transcription is initiated in eukaryotes, a pre-mRNA's 5' end is modified by the addition of a
Polyadenylation
In eukaryotes, polyadenylation further modifies pre-mRNAs during which a structure called the
Alternative splicing
Eukaryotic pre-mRNAs have their introns spliced out by spliceosomes made up of small nuclear ribonucleoproteins.[9][10]
In complex eukaryotic cells, one primary transcript is able to prepare large amounts of mature mRNAs due to alternative splicing. Alternative splicing is regulated so that each mature mRNA may encode a multiplicity of proteins.
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.[8] 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.[8] 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.[8] Alternative splicing can be affected by various factors, including mutations such as chromosomal translocation.
In prokaryotes, splicing is done by
Experiments
A study by Cindy L. Wills and Bruce J. Dolnick from the Department of Experimental Therapeutics at
Judith Lengyel and Sheldon Penman from the department of Biology at the
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
Related diseases
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]
See also
References
- ^ ISBN 978-0-8153-4184-0.
- ^ a b Alberts B (1994). "RNA Synthesis and RNA Processing". Molecular Biology of the Cell (3rd ed.). New York: Garland Science.
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ignored (help) - ^ Griffiths AJ. "An Introduction to Genetic Analysis". NCBI. New York: W.H. Freeman.
- ^ ISBN 978-1-60535-173-5.
- ^ Brown TA (2002). "Assembly of the Transcription Initiation Complex". Genomes (2nd ed.). Oxford: Wiley-Liss.
- ISBN 978-0-7167-7601-7.
- PMID 28757210.
- ^ a b c d e f g h i j k Cooper GM (2000). "RNA Processing and Turnover". The Cell: A Molecular Approach (2nd ed.). Sunderland (MA): Sinauer Associates; 2000.
- ISBN 0-07-284611-9.
- S2CID 21330280.
- PMID 2592384.
- S2CID 39038640.
- PMID 11179423.
- PMID 12883652.
- ^ Coffin JM, Hughes SH, Varmus HE, editors. Retroviruses. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 1997. Available from: https://www.ncbi.nlm.nih.gov/books/NBK19441/