36.Many genes in both bacteria and eukaryotes contain numerous sequences that potentially cause pauses in or premature terminations of transcription. Nevertheless, the transcription of these genes within a cell normally produces multiple RNA molecules thousands of nucleotides long without pausing or terminating prematurely. However, when a single round of transcription takes place on such templates in a test tube, RNA synthesis is frequently interrupted by pauses and premature terminations, which reduce the rate at which transcription takes place and frequently shorten the length of the mRNA molecules produced. Most pauses and premature terminations appear when RNA polymerase temporarily backtracks (i.e., backs up) for one or two nucleotides along the DNA. Experimental findings have demonstrated that most transcriptional delays and premature terminations disappear if several RNA polymerases are simultaneously transcribing the DNA molecule. Propose an explanation for faster transcription and longer mRNA when the template DNA is being transcribed by multiple RNA polymerases.

37. Alternative splicing takes place in more than 90% of the human genes that encode proteins. Researchers have found that how a pre-mRNA is spliced is affected by the pre-mRNA’s promoter sequence (D. Auboeuf et al. 2002. Science 298:416–419). In addition, factors that affect the rate of elongation of the RNA polymerase during transcription affect the type of splicing that takes place. These findings suggest that the process of transcription affects splicing. Propose one or more mechanisms that would explain how transcription might affect alternative splicing.

38. Duchenne muscular dystrophy (DMD) is an X-linked recessive genetic disease caused by mutations in the gene that encodes dystrophin, a large protein that plays an important role in the development of normal muscle fibers. The gene that encodes dystrophin is immense, spanning 2.5 million base pairs, and includes 79 exons and 78 introns. Many of the mutations that cause DMD produce premature stop codons, which bring protein synthesis to a halt, resulting in a greatly shortened and nonfunctional form of dystrophin. Some geneticists have proposed treating DMD patients by introducing small RNA molecules that cause the spliceosome to skip the exon containing the stop codon. The introduction of the small RNAs will produce a protein that is somewhat shortened (because an exon is skipped and some amino acids are missing) but may still result in a protein that has some function (A. Goyenvalle et al. 2004. Science 306:1796–1799). The small RNAs used for exon skipping are complementary to bases in the pre-mRNA. If you were designing small RNAs to bring about exon skipping for the treatment of DMD, what sequences should the small RNAs contain?