1. Identify and characterize interesting phenomena! 2. Characterization should stimulate some questions/models! 3. Combine biochemistry and genetics
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1 1. Identify and characterize interesting phenomena! 2. Characterization should stimulate some questions/models! 3. Combine biochemistry and genetics to gain mechanistic insight! 4. Return to step 2, as often as necessary!
2 Interesting phenomenon #1! Sharp and Roberts labs 1977! 1. Hybridized Adenovirus mrna (~ 3,000 nt) back to Adenovirus genomic DNA restriction enzyme fragments (15 kb).! 2. Analyzed structure of heteroduplexes in EM!
3 Sharp and Roberts labs 1977! mrna is non-contiguous with the DNA that encodes it! How can one mrna molecule that spans several widely separated parts of the template DNA be generated?!
4 DNA Observation:! Nuclear RNA pool consists of very high molecular weight species as well as lower molecular weight.! Darnell asked if there is a relationship between the high and low molecular weight RNAs!
5 Experiment:! Treat cells with UV for varying periods of time. Thymidine dimers will form, blocking transcription. To assess the effects on the two pools of RNA, pulse cells with 3 H- Uridine and measure counts in each pool! DNA Example UV dose that hits 1X/1000 bp! X! X! X! X! X! X! X! X! X! X! If long RNAs are precursors then both long and short pools should exhibit comparable UV sensitivity! If long and short RNAs are independently transcribed, then they should exhibit different UV sensitivity!
6 Experiment:! Treat cells with UV for varying periods of time. Thymidine dimers will form, blocking transcription. To assess the effects on the two pools of RNA, pulse cells with 3 H- Uridine and measure counts in each pool! DNA Example UV dose that hits 1X/1000 bp! X! X! X! X! X! X! X! X! X! X! If long RNAs are precursors then both long and short pools should exhibit comparable UV sensitivity! If long and short RNAs are independently transcribed, then they should exhibit different UV sensitivity!
7 In eukaryotes sequences are excised from the primary transcript!
8 Question/Model! How can one mrna molecule that spans several widely separated parts of the template DNA be generated?! Model 1: A change in DNA topology! RNA! DNA! Model 2: Processing of a long precursor RNA! How would you distinguish between these models?!
9 Interesting phenomenon #2! The same primary transcript can yield many different mrnas! > 50% of human genes undergo alternative splicing!
10 !! DSCAM is a fly gene encoding 38,016 splice isoforms Receptor diversity -> complex neural circuits in development.!
11 Human Dystrophin gene! 260 kb intron! 2.4 Mb! 79 exons, which make up < 1% of the total mrna sequence! (14 kb) estimated to require 16 hours to transcribe!
12 Questions! How are the exons identified?! How are the intervening sequences removed?!
13 How are the intervening sequences removed? (biochemistry)! incubate hot beta-globin! intron containing RNA with! HeLa cell nuclear! extracts, separate! products on denaturing! gel! unspliced! spliced!
14 How are the intervening sequences removed? (biochemistry)!
15 How are the intervening sequences removed? (genetics)! Mutational analysis of spliced reporters in transient transfection assays in mammalian cells or standard mutagenesis in yeast!
16 RNA! - single stranded, though base pairs to form complex secondary and tertiary structures! - contains ribose (hydroxyl group attached to the pentose ring in the 2 position)! - 2 hydroxyl, when not base paired or masked by protein, can chemically attack the adjacent phosphodiester bond and cleave the back bone!
17 group 1 self-splicing introns! Interesting phenomenon #3! RNAs can splice themselves!
18 Two classes of self-splicing introns!
19 Self-splicing introns have specific secondary structures!
20 Splicing proceeds through two isoenergetic transesterification reactions.!
21 RNA The excision of introns and the ligation of exons is catalyzed by! the spliceosome! Spliceosome
22 The spliceosome is made up of 5 small nuclear ribonucleoprotein subunits + > 100 proteins. These snrnps are called: U1, U2, U4, U5, U6, and assemble in a stepwise pathway onto each intron. There are also many additional non-snrnp proteins in the spliceosome.!
23 snrnps.! named U1, U2, U4, U5 and U6! Each snrnp is a small particle composed of a small nuclear RNA molecule bound by a specific set of proteins!
24 Structures of the Spliceosomal snrnas U1, U2, U4, U5 RNA Pol II transcripts TriMethyl G Cap Bound by Sm Proteins U6 RNA Pol III transcript Unusual Cap Not bound by Sm proteins Each snrna has a specific sequence and secondary structure and is bound by additional specific proteins
25 The earliest snrnp to bind to the pre-mrna is U1, which uses its snrna to base-pair to the 5 splice site.!
26 The U2 snrnp binds to the branchpoint via RNA/RNA base-pairs to create a bulged A residue. This forms the pre-spliceosomal A complex, which requires ATP hydrolysis to assemble.!
27 The protein U2AF (U2 Auxiliary Factor) binds to the Polypyrimidine tract and the AG of the 3 splice site and helps U2 snrnp to bind to the branchpoint.! U2AF65! 35!
28 Remember that the splice sites do not always perfectly match the consensus sequences. Thus, the base-pairing interactions between the snrnas and the pre-mrna are not always the same.! U2AF Pre-spliceosome!
29 Pre-mRNA The interactions of U1 with the 5 splice site and U2 with the branchpoint were proven by creating mutant splice sites that bound the snrna so poorly that splicing was inhibited. Compensating mutations in the snrna that restored complementarity (base-pairing) with the splice site restored splicing.!
30 The full spliceosome is formed from the pre-spliceosome by the addition of the U4/U5/U6 Tri-snRNP. This step also requires ATP hydrolysis.!
31 In the U4/U6 Di-snRNP and the U4/U5/U6 Tri-snRNP, the U4 and U6 snrnas are base-paired to each other. This interaction is later disrupted in the formation of the active spliceosome.! U6 snrna Cap 5 U4 snrna
32 After the formation of the full spliceosome, the U1 and the U4 snrnps are detached and the remaining U2, U5 and U6 snrnas are rearranged. This conformational change creates the catalytic spliceosome and requires ATP.!
33 U6 snrna U2 snrna U5 snrna In the catalytically active spliceosome, the U2, U5 and U6 snrnas make very specific contacts with the splice sites.! intron
34 The two transesterification reactions of splicing take place in the mature spliceosome.!
35 After the second transesterification reaction, the spliceosome comes apart. The snrnps are recycled, and the spliced exons and the lariat intron are released.!
36 The lariat intron is debranched by Debranching Enzyme returning it to a typical linear state. This linear intron is quickly degraded by ribonucleases.!
37 Splicing is dynamic, with sequential regulated alterations! in RNA:RNA and RNA:protein interactions!
38 DEAD-box helicases found at every step!
39 Biochemistry 101! Biological Regulatory Mechanisms! February 9, 2015! mrna processing and its regulation, part 1! 1. In Eukaryotes, mrna is non-contiguous with the DNA that encodes it.! 2. To generate the mature mrna intervening sequences (introns) are removed and the expressed (exons) sequences are spliced together.! 3. Elaborate splicing patterns have evolved, with alternate exon usage and even splicing between transcripts.! 4. RNA by virtue of its 2 OH can attack itself.! 5. Secondary structures can direct this suicidal activity to produce selfsplicing RNAs.! 6. An RNA protein-machine, termed the spliceosome, catalyzes splicing by identifying splice sites and providing the correct secondary structures to promote catalysis.! 7. While the the trans-esterification reactions do not require energy, there are several ATP-dependent steps in splicing, allowing regulation.!
40 Splicing Reviews:!! Splicing of Messenger RNA Precursors! Annual Review of Biochemistry! Vol. 55: (Volume publication date July 1986)! R A Padgett, P J Grabowski, M M Konarska, S Seiler, and P A Sharp! Self-Splicing of Group I Introns! Annual Review of Biochemistry! Vol. 59: (Volume publication date July 1990)! T R Cech! Dynamic RNA-RNA Interactions in the Spliceosome! Annual Review of Genetics! Vol. 28: 1-26 (Volume publication date December 1994)! H D Madhani and C Guthrie! Group I and Group II Ribozymes as RNPs: Clues to the Past and Guides to the Future! Philip S. Perlman!
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