Rinn & Chang Ann. Rev. Biochem 81:145, 2012 “The New RNA World” “RNA molecules perform a stunningly diverse and elegantly complex set of functions” 2012 ENCODE project: although only ~1.5% human genome is protein-coding, up to 75% is transcribed (much being cell- type specific) Nature 489:101, 2012

RNA content in eukaryotic cells Total cellular RNA ~ 4% mRNA and small regulatory RNAs (eg. snRNA, snoRNA, miRNA, siRNA…) Adapted from Imam Nucl. Acids Res. 38:1559, 2009 Probe: gene X NuclCyto ~ 96% non-coding RNAs (mostly rRNA and tRNA) Northern blot analysis using RNA isolated from cytoplasm vs. nucleus

“Traditional” view of gene expression in eukaryotes Zhang Nature Reviews Genetics 3: 698, 2002 Why is this picture out-of-date?

Montes et al. Gene 501:104, 2012 CTD code and pre-mRNA processing CTD - 52 heptad repeats (of YSPTSPS) in humans, 26 in yeast dynamic changes in its phosphorylation profile “Cracking the CTD code” PIC: pre-initiation complex

Types of splicing 1. Nuclear pre-mRNA (spliceosomal) 2. Nuclear pre-tRNA 3. Group I intron 4. Group II intron 5. Archaeal pre-tRNA, pre-rRNA 2-step transesterification & lariat excised intron endonuclease & ligase machinery - self-splicing - two-step transesterification & lariat intron (autocatalytic, ribozyme) Cis-elements in spliceosomal introns Wahl et al Cell 136: 701, 2009 (autocatalytic, ribozyme) - mobile genetic element - mobile genetic retroelement

Splicing of pre-mRNAs via two transesterification reactions OH Brown Fig ’OH Same biochemical pathway in group II intron ribozymes 1 st step 2 nd step

McManus & Gravely Curr.Opin.Gen.Dev 21:373, 2011 U1 snRNA base pairs with 5’ splice site U2AF-65kD protein binds pyrimidine tract U2 snRNA base pairs with branchpoint site U2AF-35kD protein recognizes AG at 3’ splice site SR proteins (“Ser-Arg” rich splicing activators) bind enhancers (ESE or ISE) & recruit other splicing factors… BBP (or SF1 in mammals) – branchpoint bridging protein hnRNPs (repressors) bind silencers (ESS or ISS) Irimia & Blencowe Curr Opin Cell Biol 24:323, 2012

How to determine that specific nucleotides at splice site are important? Time course of splicing for labelled pre-mRNAs in HeLa cell nuclear extract Gaur Proc Natl Acad Sci 97:115 (2000) Site-directed mutation (at A of 3’splice site) and monitor effect using in vitro splicing assay

Montes et al. Gene 501:104, 2012 Step-wise assembly of spliceosomal machinery 3D structure by cryo-EM Azubel Mol Cell Sept 2004 How many proteins does the spliceosome contain?

Conformational rearrangements during spliceosomal assembly Wahl et al Cell 136: 701, 2009 U1 snRNP - base-pairing between branchpoint region and U2 snRNA is stabilized by Arg-Ser rich domain of U2AF65 and components of U2 snRNP RRM: RNA recognition motif RS: Arg-Ser rich motif

“Gel mobility shift” or “gel retardation” assays One way to monitor specific RNA-protein interactions: Native, non-denaturing gel electrophoresis & autoradiography 1 2 Incubate protein extract 5’3’ *** *** Unlabelled RNA competitor 3 4 with labelled RNA 1 = RNA, no incubation (control) 2 = RNA incubated with protein 3 = 2 + “cold” competitor RNA 4 = 2 + more competitor RNA Cho PNAS 108:8233, 2011

Shen & Green Mol Cell 16:363, 2004 UV-crosslinking studies - if RNA & protein physically very close, can covalently link by UV treatment - RS (Arg-Ser rich domain) & RBD (RNA binding domain) of U2AF65 - TEV linker cleaved with specific protease - RNase to degrade any RNA not protected by protein - pre-mRNA labelled with single radioactive phosphate at 5’ ss or BP or...

How to detect protein-protein interactions? - fusion protein (eg. GST-CTD) attached to resin - determine which proteins bind specifically to column 1. Affinity chromatography Lodish Fig.3-43 Alberts Fig Co-immunoprecipitation

FRET Fluorescence resonance energy transfer (in vivo) 2 different fluorophores (or quencher) Chudakov Trends Biotech 12:605, 2005 RNA-RNA interactions Protein-protein interactions

Will & Luhrmann Cold Spring Harbor Perspectives Biol 3:7, 2011 “only stem-loop 1 of U5 snRNA is shown” - U1 and U4 snRNPs leave spliceosome - U6 snRNA base-pairs with 5’ end of intron & restructuring of base-pairing between U6 and U2 snRNAs Dynamic network of RNA interactions (snRNA-snRNA, snRNA-intron...) in spliceosome Precatalytic spliceosome Catalytically activated spliceosome

Site-directed mutagenesis – loss of function One way of examining specific, short RNA-RNA interactions: followed by suppressor mutations – restoration of function Smith Mol Cell 26:883, 2007 Assay to monitor effect on splicing (eg. in vitro splicing assay…) U6 5’ …UGAUC…3’ | | | | | U2 3 ’…ACUAG…5’ wt Mutant Double mutant

Is the spliceosome a ribozyme (like group II introns)?.... or is splicing catalyzed by protein? Prp8 can be crosslinked to 5’ SS, the branchpoint region, and to 3’ SS “Colored regions encompass residues that exhibit interactions with the factors indicated.” Wahl et al Cell 136: 701, 2009 Candidate protein: Prp8 (in U5 snRNP)

Trans-splicing of pre-mRNAs In C. elegans, ~ 70% mRNAs are trans-spliced and in trypanosomes virtually all mRNAs are trans-spliced (so have the same 22 nt at end of 5’ UTRs for all mRNAs) - separate SL “spliced leader” RNA provides the first (non-coding) exon - biochemical mechanism is fundamentally the same as cis- splicing - excised intron is Y-shaped - found in certain protists (eg. trypanosomes) and “lower” animals (eg. nematodes) Blumenthal WormBook pp1-9.

Landfear PNAS 100:7, 2003 In trypanosomes & nematodes, some genes are organized in operons !

Figure 1. Spliceosome assembly and disease-associated mutations in spliceosome components. The broken lines and rectangles represent introns and exons, respectively. The left panel shows the assembly of the major (U2 type) spliceosome. U1 and U2 small nuclear ribonucleoproteins (snRNPs) are recruited to the consensus 50 splice site (50 SS) and branch point (A), respectively. The U2-auxiliary factor heterodimer (U2AF2/U2AF1) interacts with the polypyrimidine track (Y) and 30 splice site (30 SS), forming complex A. The U4/6 and U5 snRNPs join the assembling spliceosome followed by remodeling of the complex leading to removal of the U1 and U4 snRNP and formation of the catalytic complex (complex C). Two transesterification reactions join the exons and release an intron lariat that is subsequently degraded and the spliceosome components are recycled for subsequent rounds of splicing. The right panel shows the assembly of the minor (U12 type) spliceosome, in which U1, U2, U4, and U6 are replaced by homologous U11, U12, U4atac, and U6atac snRNPs, respectively. The red star indicates the components that are mutated in neoplasias. The black star indicates the components that are mutated in retinitis pigmentosa. The orange star indicates the mutation in U4atac that is associated with microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Abbreviations: ESEs, exonic splicing enhancers; ESSs, exonic splicing silencers Singh & Cooper Trends Mol Med 18:472, d Minor Class of Spliceosomal Introns “AT-AC introns: an “ATtACk on dogma” Mount, Science 271:1690, 1996