Primary transcripts

In the context of gene expression analysis, gene products include proximal products, such as primary transcripts, intermediate products, such as mRNA, tRNA, and rRNA, and distal products including proteins and peptides. 

Elastin is a heavily crosslinked biopolymer that is formed in a process named elastogenesis. In this section, the role of elastin and the different steps of elastin production will be described, starting with transcription of the genetic code and processing of the primary transcript, followed by translation into the elastin precursor protein and its transport to the extracellular matrix. Finally, the crosslinking and fiber formation, which result in the transition from tropoelastin to elastin, are described. 

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. 

Figure 37-1. This figure illustrates that genes can be transcribed off both strands of DNA. The arrowheads indicate the direction of transcription (polarity). Note that the template strand is always read in the 3 to 5 direction. The opposite strand is called the coding strand because it is identical (except for T for L) changes) to the mRNA transcript (the primary transcript in eukaryotic cells) that encodes the protein product of the gene.

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. 

The mechanisms whereby introns are removed from the primary transcript in the nucleus, exons are ligated to form the mRNA molecule, and the mRNA molecule is transported to the cytoplasm are being elucidated. Four different splicing reaction mechanisms have been described. The one most frequently used in eukaryotic cells is described below. Although the sequences of nu-... 

Figure 37-11. The processing of the primary transcript to mRNA. In this hy-potheticai transcript, the 5 (ieft) end of the intron is cut (i) and a lariat forms between the G at the 5 end of the intron and an A near the 3 end, in the consensus sequence UACUAAC. This sequence is caiied the branch site, and it is the 3 most A that forms the S -2 bond with the G. The 3 (right) end of the intron is then cut (-ll-). This reieases the iariat, which is digested, and exon 1 is joined to exon 2atG residues.

The relationship between hnRNA and the corresponding mature mRNA in eukaryotic cells is now apparent. The hnRNA molecules are the primary transcripts plus their early processed products, which, after the addition of caps and poly(A) tails and removal of the portion corresponding to the introns, are transported to the cytoplasm as mature mRNA molecules. 

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. 

Figure 43-3. The "information pathway." Information flows from the gene to the primary transcript to mRNA to protein. Hormones can affect any of the steps involved and can affect the rates of processing, degradation, or modification of the various products.

The cTs-regulatory elements described above and the factors that bind to these elements determine the spatial and temporal expression of the Ddc primary transcript. Like a number of other genes that are expressed in... 

In Drosophila the two tissue-specific mRNAs are generated by alternative splicing of a single primary transcript (Fig. 9). In vertebrates the two tissue specific AADC transcripts are generated from two alternative promoters (Fig. 11) (Albert et al., 1992 Ichinose et al., 1992 Thai et al., 1993). In neural tissue transcription initiates from exon Nl, whereas in non-neural tissue transcription initiates from exon LI. This produces two distinct primary transcripts that are then spliced from the first exon (LI or Nl) to exon 2 to generate two tissue-specific mRNAs. Translation initiates within exon 2, such that the same AADC protein product is synthesized from both AADC mRNAs. 

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-... 

To make mRNA, the primary transcript must be spliced to bring the protein-coding sequences (exons) together and to remove the intervening sequences (introns). The splice signals consist of a 5 and a 3 set of sequences that are always found at splice junctions. However, this is generally believed to provide too little information to recognize a splice site specifically and correctly. Some sequences in the intron are also important. 

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. 

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