RNA interference protein splicing, phosphorylation, acetylation, N-linked glycosylation, amidation sulfation… and more! hydroxylation methylation O-linked glycosylation epigenetic modification A-to-I editing replication stoichiometric buffering Goal: Expanding our understanding of gene regulation to the proteome. How does genetic variation affect transcript and protein abundance?
8/20/2014 date 50 40 30 20 10 Body weight (gm) 7/11/2014 7/31/2014 8/20/2014 date female DO mice male DO mice DO mice are genetically and phenotypically diverse Alan Attie & Mark Keller Female DO mice Male DO mice
ground truth Align to CAST Pseudotranscriptome 5’-ATCGGCGTCTTACATTAGCTCAAGGGTGCC-3’ 5’-ATCGGCGTCTTGCTCAAGGGTGCC-3’ Align to B6 Transcriptome 5’-ATCGGCGTCTTACATTAGCTCAAGGGTGCC-3’ To what degree do these diﬀerences aﬀect alignment of RNA-Seq reads and gene abundance es7mates? Simulated reads Real data
Mediation Analysis RNA Protein QTL trans cis RNA Protein Target Causal Intermediates RNA Protein trans QTL cis Target Target Protein ~ pQTLdistant Target Protein ~ pQTLdistant + MediatorProtein x 8000 proteins Target Protein ~ pQTLdistant + MediatorRNA x 21000 Transcripts X
not affect protein abundance. – For local genetic variation that does affect protein abundance, 80% act proximally on transcription (standard model). • 99+% of distant pQTL act on the target protein’s abundance independent of the target’s transcript abundance. • Mediation analysis identifies 700 RNA/protein causal intermediates of distant pQTL and infers >5000 protein interactions. • Stoichiometric buffering is a common post-translational mechanism governing protein abundance of binding partners and complex members. • We can apply our new understanding of the genome- proteome map in DO mice to tune output of liver pathways.