Global target mRNA specification and regulation by the RNA-binding protein ZFP36

Abstract

BackgroundZFP36, also known as tristetraprolin or TTP, and ELAVL1, also known as HuR, are two disease-relevant RNA-binding proteins (RBPs) that both interact with AU-rich sequences but have antagonistic roles. While ELAVL1 binding has been profiled in several studies, the precise in vivo binding specificity of ZFP36 has not been investigated on a global scale. We determined ZFP36 binding preferences using cross-linking and immunoprecipitation in human embryonic kidney cells, and examined the combinatorial regulation of AU-rich elements by ZFP36 and ELAVL1.ResultsTargets bound and negatively regulated by ZFP36 include transcripts encoding proteins necessary for immune function and cancer, and transcripts encoding other RBPs. Using partial correlation analysis, we were able to quantify the association between ZFP36 binding sites and differential target RNA abundance upon ZFP36 overexpression independent of effects from confounding features. Genes with increased mRNA half-lives in ZFP36 knockout versus wild-type mouse cells were significantly enriched for our human ZFP36 targets. We identified thousands of overlapping ZFP36 and ELAVL1 binding sites, in 1,313 genes, and found that ZFP36 degrades transcripts through specific AU-rich sequences, representing a subset of the U-rich sequences ELAVL1 interacts with to stabilize transcripts.ConclusionsZFP36-RNA target specificities in vivo are quantitatively similar to previously reported in vitro binding affinities. ZFP36 and ELAVL1 bind an overlapping spectrum of RNA sequences, yet with differential relative preferences that dictate combinatorial regulatory potential. Our findings and methodology delineate an approach to unravel in vivo combinatorial regulation by RNA-binding proteins.

LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation

“…mRNA stability can also be augmented by ARE interacting factors. The best-characterized example is the HuR protein, which competes with destabilizing factor for the binding to AREs and leads to the stabilization of the mRNA presumably by displacement of these factors (Lebedeva et al 2011;Mukherjee et al 2014). Likewise, binding of LARP4B to AU-rich sequences in the context of AREs might displace destabilizing factors similarly to the mechanism described for HuR.…”

A census of human RNA-binding proteins

“…Strikingly, the mRNA regulatory protein tristetraprolin (TTP; also known as ZFP36) was the most specifically upregulated RBP in the hippocampus by more than 200-fold. ZFP36 is known to destabilize mRNAs that encode cytokines and other inflammatory immune genes by recruiting the CCR4-NOT1 complex to AU-rich elements in the 3′ untranslated regions (3ʹUTRs) of targets, leading to deadenylation and subsequent degradation of mRNAs [178][179][180] . Recently, it was found that cytokines and other immune-regulatory proteins are expressed in the developing and adult nervous system, in which they are required for normal brain development and synaptic plasticity 181,182 .…”

Cooperativity in RNA–protein interactions: the complex is more than the sum of its partners

“…AU-rich elements (AREs) can be bound by several proteins such as Tristetraprolin (TTP) and the Hu protein family. There are thousands of overlapping TTP and HuR sites on the eukaryotic transcriptome, and depending which protein has the major effect, the mRNA is degraded (TTP) or stabilised (HuR) [20]. Of note, two members of the family, HuD [21] and HuR [22], play an important role in brain development and plasticity.…”