Chapter 21 RNA Splicing and Processing. 21.1 Introduction. pre-mRNA – The nuclear transcript that is processed by modification and splicing to give an mRNA. RNA splicing – The process of excising introns from RNA and connecting the exons into a continuous mRNA. 21.1 Introduction.
Figure 21.01: RNA is modified in the nucleus by additions to the 5’ and 3’ ends and by splicing to remove the introns.
Figure 21.02: The cap blocks the 5’ end of mRNA and is methylated at several positions.
Figure 21.03: The ends of nuclear introns are defined by the GU-AG rule.
Figure 21.04: Splicing junctions are recognized only in the correct pairwise combinations.
Figure 21.05: Splicing occurs in two stages. First the 5’ exon is cleaved off, and then it is joined to the 3’ exon.
Figure 21.07: The spliceosome is ~12 MDa. Five snRNPs account for almost half of the mass.
Figure 21.10: The commitment (E) complex formation.
Figure 21.11: There are two routes for initial recognition of 5’ and 3’ splice sites by either intron definition or exon definition.
Figure 21.12: The splicing reaction proceeds through discrete stages.
21.10 Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns
Figure 21.15: Three classes of splicing reactions proceed by two transesterifications.
21.11 Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression
Figure 21.18: The EJC (exon junction complex) is deposited near the splice junction as a consequence of the splicing reaction.
Figure 21.20: The EJC complex couples splicing with NMD.
21.12 Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes
Figure 21.21: Different modes of alternative splicing.
Figure 21.23: Sex determination in D. melanogaster involves a pathway in which different splicing events occur in females.
21.13 Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers
Figure 21.24: Exonic and intronic sequences can modulate the splice site selection by functioning as splicing enhancers or silencers.
Figure 21.25: The Nova and Fox families of RNA binding proteins can promote or suppress splice site selection in a context dependent fashion.
Figure 21.26: Splicing usually occurs only in cis between exons carried on the same physical RNA molecule.
Figure 21.29: The sequence AAUAAA is necessary for cleavage to generate a 3’ end for polyadenylation.
Figure 21.30: The 3’ processing complex consists of several activities.
Figure 21.31: Transcription by Pol I and Pol III uses specific terminators to end transcription.
Figure 21.33: Generation of the 3’ end of histone H3 mRNA depends on a conserved hairpin and a sequence that base pairs with U7 snRNA.
Figure 21.34: The intron in yeast tRNAPhe base pairs with the anticodon to change the structure of the anticodon arm.
Figure 21.36: The 3’ and 5’ cleavages in S. cerevisiae pre-tRNA are catalyzed by different subunits of the endonuclease.
21.18 tRNA Splicing Involves Cutting and Rejoining in Separate Reactions
Figure 21.38: Splicing of tRNA requires separate nuclease and ligase activities.
Figure 21.39: The unfolded protein response occurs by activating special splicing of HAC1 mRNA to produce a transcription factor recognizing the UPRE.
Figure 21.40: Mature eukaryotic rRNAs are generated by cleavage and trimming events from a primary transcript.
Figure 21.42: A snoRNA base pairs with a region of rRNA that is to be methylated.