RNA Synthesis and Splicing

The conversion of DNA nucleotide sequences into RNA sequences is an early step in the expression of genetic information (see Chapter 5). This chapter describes the DNA-dependent RNA polymerases that catalyze this reaction, and the ways in which the product RNA transcript must sometimes be cleaved and modified in various ways before it becomes functional. 

The chapter begins -with an overview of the three stages of RNA synthesis initiation, elongation, and termination. The subunit structure of RNA polymerase from 

The authors next turn to the more complex process of transcription in eukaryotes. The impossibility of coupling transcription and translation in eukaryotes as it occurs in prokaryotes (because of eukaryotic subcellular separation in the nucleus and cytoplasm) is pointed out. The three eukaryotic RNA polymerases that carry out transcription are described and related to the kinds of RNA they synthesize. The role of the eukaryotic TATA box and the TATA-box-binding protein in basal transcription are explained, as are other eukaryotic promoters and enhancers and some of the proteins 

When you have mastered this chapter, you should be able to complete the following objectives. 

Name the three stages of RNA synthesis, and list the functions of RNA polymerase in these processes. 

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Kockx MM, Muhring J, Knaapen MW, de Meyer GR. RNA synthesis and splicing interferes with DNA in situ end labeling techniques used to detect apoptosis. Am J Pathol 1998 152 885-888. 

Chapters 27. 28, and 29 cover DNA replication, recombination, and repair RNA synthesis and splicing and protein synthesis. Evolutionary connections between prokaryotic systems and eukaryotic systems reveal how the basic biochemical processes have been adapted to function in more-complex biological systems. The recently elucidated structure of the ribosome gives students a glimpse into a possible early RNA world, in which nucleic acids, rather than proteins, played almost all the major roles in catalyzing important pathways. 

All eukaryotic cells have four major classes of RNA ri-bosomal RNA (rRNA), messenger RNA (mRNA), transfer RNA (tRNA), and small nuclear RNA (snRNA). The first three are involved in protein synthesis, and snRNA is involved in mRNA splicing. As shown in Table 37-1, these various classes of RNA are different in their diversity, stability, and abundance in cells. 

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.

The notion that RNA existed prior to enzymes and that RNA molecules can be catalytically active is by now well accepted. Indeed, RNA molecules have been observed to catalyze phophodiester bond breaking and synthesis (as occurs during replication and splicing) but also reactions more distant to its stmcture, such as amide bond formation (Wiegand, 1997). RNA thus provided the means to assemble peptides which may have led to the protein world of today (Zhang and Cech, 1998). Reactions catalyzed by RNA molecules have thus far not been employed in biocatalysis and it is unlikely that... 

Nearly all of the RNA of the cell is synthesized (transcribed) in the nucleus, according to the instructions encoded in the DNA. Some of the RNA then moves out of the nucleus into the cytoplasm where it functions in protein synthesis and in some other ways. Many eukaryotic genes consist of several sequences that may be separated in the DNA of a chromosome by intervening sequences of hundreds or thousands of base pairs. The long RNA transcripts made from these split genes must be cut and spliced in the nucleus to form the correct messenger RNA molecules which are then sent out to the ribosomes in the cytoplasm. 

The amount of each mRNA is regulated with respect to the time after infection. RNAs 1 and 2 are both formed shortly after the primary transcript is made, although more of mRNA-2 is made. Later in the viral life cycle, mRNA-1 is not made and mRNA-2 is abundant. If cycloheximide, an inhibitor of protein synthesis, is added to the infected cells before the shift in splicing pattern takes place, the shift does not occur. This inhibition implies that a newly synthesized protein is a positive effector of the shift. Cycloheximide has a similar effect on other mRNA species derived from other primary transcripts at late times. 

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