Regulation of mrna translation initiation. Stuart Archer, Nikolay Shirokikh, Traude Beilharz and Thomas Preiss

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1 Regulation of mrna translation initiation revealed by TCP seq Stuart Archer, Nikolay Shirokikh, Traude Beilharz and Thomas Preiss

2 Transcription RNA Degradation [ Translation...Or more specifically, translation initiation Protein Degradation [

3 An inconvenient truth: Protein concentraon RNA concentraon RNA seq is love Love is blind Ergo, RNA seq is blind (to translation regulation).

4 Our knowledge about translation initiation now lags far behind our knowledge of transcription initiation. Transcription RNA Pol II ChIP seq (elongation) ATAC seq (initiation) DNase seq (initiation) Histone code ChIP seq (initiation) Transcription factor ChIP seq (initiation) Translation Ribosomal profiling (elongation)?? Initiation???

5 Mechanism of eukaryotic translation initiation Small ribosomal subunit (SSU) docking 5 cap 5 > 3 scanning Start codon recognition LSU joining

6 Translation complex profiling (TCP seq) Formaldehyde X-link Pre sedimentation Total Input fraction RNase SSU fraction Fractionation (gradient sedimentation) RS fraction

7 Translation complex profiling (TCP seq) RNA signal Low bias library work up RNA biotype rrna rrna SSU rrna LSU rrna single pass mapping to yeast genome

8 Translation complex profiling (TCP seq) Overview:Where do TCP seq reads fall on mrna transcripts? Position of 5 ends of footprints

9 TCP seq uncovering gene specific regulation Example: PAB1 (Poly A binding protein) auto regulates its own mrna The A 11 stretch of the PAB1 5 UTR is inhibitory for its translation Xia X. et al 2011

10 TCP seq uncovering gene specific regulation Example: PAB1 (Poly A binding protein) auto regulates its own mrna SSU PAB1 binding A rich site Pileup? Total Input

11 TCP seq uncovering gene specific regulation Example 2: uorfs in the GCN4 5 UTR block utilization of downstream ORFs SSU uorfs main ORF start Total Input

12 TCP seq: Footprint size depends on location 5 UTR Scanning SSUs exhibit longer footprint sizes FP size (nt) start codon ORF (Translating) Why are scanning SSUs so much longer than initiating SSUs and translating ribosomes? Extra cofactors are thought to be required for conferring directionality to scanning, but nothing is known about how they do this.

13 Why are scanning SSUs longer? Pulled model Invariant trailing edge Variable (extended) leading edge Pushed model Variable (extended) trailing edge Invariant leading edge

14 Why are scanning SSUs longer? Leading edge final position(s) Trailing edge final position Footprint Length (nt) iso-5 iso-5 Footprint 5 end location (nt) relative start codon Pushed model Pulled model The longer scanning complexes do not encroach onto the ORF as far as expected if the core SSU were at the trailing edge (i.e. the Pulled model). Our data demonstrates the Pushed model of scanning.

15 Gene expression regulation at the level of translation revealed by TCP seq (AKA the other translational research) Funding: ARC Discovery Grant Stuart Archer 1,2, Nikolay Shirokikh 2, Traude Beilharz 3 and Thomas Preiss 2 1. Monash Bioinformatics Platform, Monash 2. John Curtin School of Medical Research, ANU 3. School of Biomedical Science, Monash Dynamics of ribosome scanning and recycling revealed by translation complex profiling. Nature Jul 28;535(7613): Technical Support: The Australian Cancer Research Foundation Biomolecular Resource Facility (JCSMR, ANU) David Powell and Steve Androulakis at the Monash Bioinformatics Platform Collaborators: Susan Wagner Leos Valasek Alan Hinnebusch VisualiseTCP seq data gene by gene:

16 Summary: TCP seq 1. Genes regulated by 5 UTR blockages exhibit pile ups of scanning SSUs 2. Scanning directionality is probably ensured by a SSUpushed not a SSU pulled mechanism 1. Initiating and terminating SSU conformations can be characterized

17 Footprint sizes of SSUs occupying the start codon +6 Distance from start codon (nt) Start codon occupying SSUs have three distinct 3 end lengths, which would stem from conformational changes around the mrna entry channel.

18 Entry channel conformation changes during start codon recognition (5 ) (3 ) exit (5 )? exit (5 ) mrna entry (3 ) mrna entry (3 ) Open pre AUG recognition Closed post AUG recognition Llacer J.L et al 2015

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