Primary transcript RNA

In conjunction with studies performed by van Leeuwen et al. (135-138), Layfield et al. (263) proposed a novel mechanism that could account for an inhibition of 26S proteasome activity in cases of nonfamilial AD. Mutant forms of ubiquitin may inhibit proteolysis within neurons, predisposing these cells to inclusion formation. Molecular misreading of the UBB gene results in a dinucleotide deletion in UBB mRNA (135-138,264). In AD, an age-related posttranscriptional defect in primary transcript RNA processing may occur, leading to dinucleotide deletions within open reading frames that result in frameshifts and produce abnormal extension proteins, as demonstrated by van Leeuwen and coworkers (138). 

Further processing, such as capping, the addition of poly (A), and the excision of the intragenic spacers (naturally occurring genetic recombination) is necessary in order to transform the primary transcript RNA into the final mRNA (Chapter 5). 

Some RNA molecules have intrinsic catalytic activity. The activity of these ribozymes often involves the cleavage of a nucleic acid. An example is the role of RNA in catalyzing the processing of the primary transcript of a gene into mature messenger RNA. 

The primary transcripts generated by RNA polymerase II—one of three distinct nuclear DNA-depen-dent RNA polymerases in eukaryotes—are promptly capped by 7-methylguanosine triphosphate caps (Figure 35-10) that persist and eventually appear on the 5 end of mature cytoplasmic mRNA. These caps are necessary for the subsequent processing of the primary transcript to mRNA, for the translation of the mRNA, and for protection of the mRNA against exonucleolytic attack. 

In addition to affecting the efficiency of promoter utilization, eukaryotic cells employ alternative RNA processing to control gene expression. This can result when alternative promoters, intron-exon splice sites, or polyadenylation sites are used. Occasionally, heterogeneity within a cell results, but more commonly the same primary transcript is processed differendy in different tissues. A few examples of each of these types of regulation are presented below. 

RNA polymerase makes a copy of the sense strand of the DNA using the antisense strand as a template (Fig. 5-8). The sequence of the primary transcript is the same as that of the sense strand of the DNA. RNA polymerase needs no primer—only a template. Either of the two DNA strands can serve as the template strand. Which DNA strand is used as the tern-... 

Eukaryotes have a specific signal for termination of transcription however, prokaryotes seem to have lost this mechanism. Once started, RNA polymerase keeps going, making a primary transcript [pre-mRNA or hnRNA (for heterogeneous nuclear)] until far past the end of the final mRNA message. 

RNA polymerase II separates the strands of the DNA over a short region to initiate transcription and read the DNA sequence. The template strand is read in the 3 to 5 direction as the RNA product (the primary transcript) is synthesized in the 5 to 3 direction. Both exons and introns are transcribed. 

A stretch of DNA that is transcribed as a single continuous RNA strand is called a transcription unit. A unit of transcription may contain one or more sequences encoding different polypeptide chains (translational open reading frames, ORF) or cistrons. The transcription unit is sometimes termed the primary transcript, pre-messenger RNA or heterogeneous nuclear RNA (hnRNA). The primary transcript is further processed to produce mRNA in a form that is relatively stable and readily participates in translation. In order to understand the primary need for processing of this RNA, the biochemical definition of a gene must be discussed. 

Figure 20.19 Summary of transcription, RNA splicing entry of mRNA into the cytosol and polypeptide formation. The difference in shading is to indicate the change from DNA to RNA. Splicing is just one of the four processes involved in the processing of the primary RNA transcript (Figure 20.20).

Figure 20.20 Summary of transcription, RNA processing and polypeptide synthesis. Polymerisation of the DNA template by RNA polymerase produces pre-mRNA (the primary transcript) this is transcription. The pre-mRNA is now processed, which involves capping, polyadenylation, editing and splicing (see text). The resultant mRNA transfers from the nucleus to the cytosol, where amino acids are polymerised to produce a polypeptide using the instructions present in the codons of the mRNA.

RNA polymerase II is responsible for transcription of genes to produce the primary transcript that will, eventually, be converted to mRNA. The polymerase, in order to initiate transcription at the start point for transcription of the first exon in the gene, has to bind to specific short sequences of DNA. They act as binding sites for the RNA... 

Messenger RNAs (mRNAs) transfer genetic information from the cell nucleus to the cytoplasm. The primary transcripts are substantially modified while still in the nucleus (mRNA maturation see p.246). Since mRNAs have to be read codon by codon in the ribosome, they must not form a stable tertiary structure. This is ensured in part by the attachment of RNA-binding proteins, which prevent base pairing. Due to the varying amounts of information that they carry, the lengths of mRNAs also vary widely. Their lifespan is usually short, as they are quickly broken down after translation. 

Our genes are split into coding or exon regions and noncoding or intron regions. The introns are removed from the primary transcript when it is made into a mature or completed RNA such as mRNA, tRNA, and rRNA. 

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