RBP atlas: an exploration of interactions between mRNA and proteins and their impact on cardiomyocyte biology — University of Technology
  1. Schedule
  2. Symposium III
  3. RBP atlas: an exploration of interactions between mRNA and proteins and their impact on cardiomyocyte biology

RBP atlas: an exploration of interactions between mRNA and proteins and their impact on cardiomyocyte biology (14225)

Yalin Liao 1 , Bernd Fischer 2 , Alfredo Castello 2 , Hao Yang 1 , Sophia Foehr 2 , Stephan Leicht 2 , Rastislav Horos 2 , Eloisa Pagler 1 , Jeroen Krijgsveld 2 , Matthias Hentze 2 , Thomas Preiss 1
  1. Department of Genome Biology, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
  2. European Molecular Biology Laboratory, Heidelberg, Germany

Background: RNA-binding proteins (RBPs) control all aspects of RNA fate, often by organizing multiple functionally related RNAs into “post-transcriptional-operons”. RBP functional defects furthermore underlie a broad spectrum of human pathologies. How such RBP networks operate in cardiomyocytes and respond to (patho-) physiological cues in the heart is poorly understood.

Aim: Characterize cellular repertoire of RBPs in cardiomyocytes, and investigate changes to the RBP-RNA interaction network responding to metabolic challenges.

Method: We chose to investigate this in murine HL-1 cell, a cardiomycoyte cell line that can be propagated in culture while maintaining the ability to contract and other differentiated cardiac morphological and functional properties (Claycomb et al., Proc Natl Acad Sci USA. 95:297984). We use a recently developed “mRNA interactome capture” method (Castello et al., Cell. 149:1393-406).
Result: We have now identified ~1100 proteins as the first cardiomyocyte “mRNA interactome”. Domain features and gene ontology enrichment broadly validate the sensitivity and specificity of the capture. Of direct relevance to cardiac biology, ~180 RBP genes are associated with heart disease (based on genecards.org), most of these have no established RNA links. Notably, ~80 cardiomyocyte RBPs are enzymes of intermediary metabolism, which otherwise perform house-keeping metabolic functions; these are enriched for functions in energy metabolism, mitochondrial localization and dinucleotide co-factor requirement. Furthermore, in a single “RBDmap” validation experiment, 320 proteins were validated by uncovering their RNA binding regions, including a wide range of classical/non-classical RNA-binding domains. A highlight of HL-1 RBDmap is illustrating RNA binding nature for domains such as Rossmann fold, nucleotide binding (e.g. ATP, GTP, NAD+), iron-sulfur cluster binding, and those harboring gene mutations of mitochondrial diseases.

Discussion: Our work links cellular metabolism and gene expression through RNA-binding by metabolic enzymes (Hentze & Preiss., Trends Biochem Sci. 35:423-6). Ongoing work is focused on charactering RNA regulatory functions of mitochondrial enzymes in TCAC/OXPHOS under pathological conditions, such as hypoxia, and defining how their dysregulations may be part of diseases processes.

  1. Claycomb WC, Lanson NA Jr, Stallworth BS, Egeland DB, Delcarpio JB, Bahinski A, Izzo NJ Jr. 1998. HL-1 cells: a cardiac muscle cell line that contracts and retains phenotypic characteristics of the adult cardiomyocyte. Proc Natl Acad Sci USA. 95:2979–84.
  2. Castello A, Fischer B, Eichelbaum K, Horos R, Beckmann BM, Strein C, Davey NE, Humphreys DT, Preiss T, Steinmetz LM, Krijgsveld J, Hentze MW. 2012. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell. 149:1393–406.
  3. Hentze MW, Preiss T. 2010. The REM phase of gene regulation. Trends Biochem Sci. 35:423-6.
#jajRNA14