| What’s a pre mRNA? | The nuclear transcript that is processed by modification and splicing to give an mRNA. |
| What’s RNA splicing? | The process of excising introns from RNA and connecting the exons into a continuous mRNA. |
| How is RNA modified? | RNA is modified in the nucleus by additions to the 5’ and 3’ ends and by splicing to remove the introns. |
| What is heterogeneous nuclear RNA? | RNA that comprises transcripts of nuclear genes made by RNA polymerase II; it has a wide size distribution and low stability. |
| What’s hnRNP? | The ribonucleoprotein form of hnRNA (heterogeneous nuclear RNA), in which the hnRNA is complexed with proteins. |
| Why the pre mRNA only found in the nucleus? | Pre-mRNAs are not exported until processing is complete; thus they are found only in the nucleus. |
| How is the 5’ cap formed? | A 5′ cap is formed by adding a G to the terminal base of the transcript via a 5′–5′ link. |
| When does the capping process take place? | The capping process takes place during transcription and may be important for release from pausing of transcription. |
| Is the 5′ cap of mRNA methylated? | Yes, The 5′ cap of most mRNA is monomethylated, but some small noncoding RNAs are trimethylated. |
| How does the cap structure affect the mRNA function? | The cap structure is recognized by protein factors to influence mRNA stability, splicing, export, and translation. |
| What are splice sites? | Splice sites are the sequences immediately surrounding the exon–intron boundaries. They are named for their positions relative to the intron. |
| What is sequence of the splice site of the 5’ end of the intron? | The 5′ splice site at the 5′ (left) end of the intron includes the consensus sequence GU. |
| What is sequence of the splice site of the 3’end of the intron? | The 3′ splice site at the 3′ (right) end of the intron includes the consensus sequence AG. |
| What is the GU-AG rule? | The GU-AG rule (originally called the GT-AG rule in terms of DNA sequence) describes the requirement for these constant dinucleotides at the first two and last two positions of introns in pre-mRNAs. |
| What is the rule followed by minor introns? | There exist minor introns relative to the major introns that follow the GU-AG rule.
Minor introns follow a general AU-AC rule with a different set of consensus sequences at the exon–intron boundaries. |
| What does splicing depend on? | Splicing depends only on recognition of pairs of splice sites. |
| What’s the function of the additional conserved sequences? | All 5′ splice sites are functionally equivalent, and all 3′ splice sites are functionally equivalent.
Additional conserved sequences at both 5′ and 3′ splice sites define functional splice sites among numerous other potential sites in the pre-mRNA. |
| How are splicing junctions recognized? | Splicing junctions are recognized only in the correct pairwise combinations. |
| What does splicing require? | Splicing requires the 5′ and 3′ splice sites and a branch site just upstream of the 3′ splice site.
The branch sequence is conserved in yeast but less well conserved in multicellular eukaryotes. |
| What’s a lariat? | A lariat is formed when the intron is cleaved at the 5′ splice site, and the 5′ end is joined to a 2′ position at an A at the branch site in the intron. |
| When is the intron released as a lariat? | The intron is released as a lariat when it is cleaved at the 3′ splice site, and the left and right exons are then ligated together. |
| What are the two stages of splicing? | Splicing occurs in two stages. First the 5’ exon is cleaved off, and then it is joined to the 3’ exon. |
| What are small cytoplasmic RNAs (scRNA; scyrps)? | RNAs that are present in the cytoplasm (and sometimes are also found in the nucleus). |
| small nuclear RNA (snRNA; snurps)? | One of many small RNA species confined to the nucleus; several of them are involved in splicing or other RNA processing reactions. |
| small nucleolar RNA (snoRNA) ? | A small nuclear RNA that is localized in the nucleolus. |
| What are the five snRNPs and what do they form? | The five snRNPs involved in splicing are U1, U2, U5, U4, and U6.
Together with some additional proteins, the snRNPs form the spliceosome. |
| What does All the snRNPs contain except U6? | All the snRNPs except U6 contain a conserved sequence that binds the Sm proteins that are recognized by antibodies (anti-SM) generated in autoimmune disease. |
| what is transesterification? | A reaction that breaks and makes chemical bonds in a coordinated transfer so that no energy is required. |
| How does U1 snRNP initiates splicing ? | U1 snRNP initiates splicing by binding to the 5′ splice site by means of an RNA–RNA pairing reaction. |
| What does the commitment complex contain? | The commitment complex (or E complex) contains U1 snRNP bound at the 5′ splice site and the protein U2AF bound to a pyrimidine tract between the branch site and the 3′ splice site. |
| What’s the role of SR proteins? | In cells of multicellular eukaryotes, SR proteins play an essential role in initiating the formation of the commitment complex. |
| How can Pairing splice sites be accomplished? | Pairing splice sites can be accomplished by intron definition or exon definition. |
| What are the two routes for initial recognition of 5’ and 3’ splice sites by? | There are two routes for initial recognition of 5’ and 3’ splice sites by either intron definition or exon definition. |
| What’s the spliceosome assembly pathway? | The commitment complex progresses to pre-spliceosome (the A complex) in the presence of ATP.
Recruitment of U5 and U4/U6 snRNPs converts the A complex to the mature spliceosome (the B1 complex).
The B1 complex is next converted to the B2 complex in which U1 snRNP is released to allow U6 snRNA to interact with the 5′ splice site.
When U4 dissociates from U6 snRNP, U6 snRNA can pair with U2 snRNA to form the catalytic active site.
Both transesterification reactions take place in the activated spliceosome (the C complex).
The splicing reaction is reversible at all steps. |
| How does the alternative splicing pathway work? | An alternative splicing pathway uses another set of snRNPs that comprise the U12 spliceosome.
The target introns are defined by longer consensus sequences at the splice junctions rather than strictly according to the GU-AG or AU-AC rules.
Major and minor spliceosomes share critical protein factors, including SR proteins. |
| How does Group II introns excise themselves from RNA? | Group II introns excise themselves from RNA by an autocatalytic splicing event (autosplicing or self-splicing). |
| How is the splicing of group II introns similar to splicing of nuclear introns? | The splice junctions and mechanism of splicing of group II introns are similar to splicing of nuclear introns.
A group II intron folds into a secondary structure that generates a catalytic site resembling the structure of U6-U2-nuclear intron. |
| How is the Splicing Temporally and Functionally Coupled with Multiple Steps in Gene Expression? | Splicing can occur during or after transcription.
The transcription and splicing machineries are physically and functionally integrated.
Splicing is connected to mRNA export and stability control. |
| What is exon junction complex (EJC)? | A protein complex that assembles at exon–exon junctions during splicing and assists in RNA transport, localization, and degradation. |
| Why is the The EJC (exon junction complex) is deposited near the splice junction? | The EJC (exon junction complex) is deposited near the splice junction as a consequence of the splicing reaction. |
| What’s the effect of splicing in the nucleus? | Splicing in the nucleus can influence mRNA translation in the cytoplasm. |
| What is nonsense-mediated mRNA decay (NMD)? | A pathway that degrades an mRNA that has a nonsense mutation prior to the last exon. |
| What’s the function of alternative splicing? | Specific exons or exonic sequences may be excluded or included in the mRNA products by using alternative splicing sites.
Alternative splicing contributes to structural and functional diversity of gene products. |
| How does sex determination in drosophila works? | Sex determination in Drosophila involves a series of alternative splicing events in genes encoding successive products of a pathway. |
| With what type sites is Alternative splicing often associated with? | Alternative splicing is often associated with weak splice sites. |
| Which exon associated sequences are more evolutionary conserved? | Sequences surrounding alternative exons are often more evolutionarily conserved than sequences flanking constitutive exons. |
| How is splicing regulated? | Specific exonic and intronic sequences can enhance or suppress splice site selection. |
| What mediates the effect of splicing enhancers and silencers ? | The effect of splicing enhancers and silencers is mediated by sequence-specific RNA binding proteins, many of which may be developmentally regulated and/or expressed in a tissue-specific manner. |
| What affects the outcome of alternative splicing? | The rate of transcription can directly affect the outcome of alternative splicing. |
| What’s the function of The Nova and Fox families of RNA binding proteins ? | The Nova and Fox families of RNA binding proteins can promote or suppress splice site selection in a context dependent fashion. |
| How does the splicing reaction normally occur? | Splicing reactions usually occur only in cis between splice sites on the same molecule of RNA. |
| Where does trans splicing occur ? | trans-splicing occurs in trypanosomes and worms where a short sequence (SL RNA) is spliced to the 5′ ends of many precursor mRNAs. |
| SL RNAs have a structure resembling What sites? | SoL RNAs have a structure resembling the Sm-binding site of U snRNAs. |
| What does The sequence AAUAAA signal for? | The sequence AAUAAA is a signal for cleavage to generate a 3′ end of mRNA that is polyadenylated. |
| What does the RNA cleavage reaction require? | The reaction requires a protein complex that contains a specificity factor, an endonuclease, and poly(A) polymerase
The specificity factor and endonuclease cleave RNA downstream of AAUAAA. |
| The specificity factor and poly(A) polymerase Function? | The specificity factor and poly(A) polymerase add ~200 A residues |
| What’s the function of the poly(A) tail? | The poly(A) tail controls mRNA stability and influences translation. |
| What Cytoplasmic polyadenylation other roles? | Cytoplasmic polyadenylation plays a role in Xenopus embryonic development. |
| What terminates pol II transcription? | The mRNA 3′ end formation signals termination of Pol II transcription. |
| Where does RNA polymerase III terminate transcription? | RNA polymerase III terminates transcription in a poly(U)4 sequence embedded in a GC-rich sequence. |
| How does tRNA splicing occur? | tRNA splicing occurs by successive cleavage and ligation reactions. |
| What does the splicing of tRNA require? | Splicing of tRNA requires separate nuclease and ligase activities. |
| Where does RNA polymerase I terminates transcription? | RNA polymerase I terminates transcription at an 18-base terminator sequence. |
| How is The large and small rRNAs released? | The large and small rRNAs are released by cleavage from a common precursor rRNA; the 5S rRNA is separately transcribed. |
| What is The C/D group of snoRNAs function ? | The C/D group of snoRNAs is required for modifying the 2′ position of ribose with a methyl group. |
| What is the function of The H/ACA group of snoRNAs ? | The H/ACA group of snoRNAs is required for converting uridine to pseudouridine. |
| How does the snoRNA generate a substrate for modification? | In each case the snoRNA base pairs with a sequence of rRNA that contains the target base to generate a typical structure that is the substrate for modification. |
