The polyadenosine RNA-binding protein ZC3H14 interacts with the THO complex and coordinately regulates the processing of neuronal transcripts

Abstract

The polyadenosine RNA-binding protein ZC3H14 is important in RNA processing. Although ZC3H14 is ubiquitously expressed, mutation of the ZC3H14 gene causes a non-syndromic form of intellectual disability. Here, we examine the function of ZC3H14 in the brain by identifying ZC3H14-interacting proteins using unbiased mass spectrometry. Through this analysis, we identified physical interactions between ZC3H14 and multiple RNA processing factors. Notably, proteins that comprise the THO complex were amongst the most enriched proteins. We demonstrate that ZC3H14 physically interacts with THO components and that these proteins are required for proper RNA processing, as loss of ZC3H14 or THO components leads to extended bulk poly(A) tail length. Furthermore, we identified the transcripts Atp5g1 and Psd95 as shared RNA targets of ZC3H14 and the THO complex. Our data suggest that ZC3H14 and the THO complex are important for proper processing of Atp5g1 and Psd95 RNA, as depletion of ZC3H14 or THO components leads to decreased steady-state levels of each mature transcript accompanied by accumulation of Atp5g1 and Psd95 pre-mRNA in the cytoplasm. Taken together, this work provides the first unbiased identification of nuclear ZC3H14-interacting proteins from the brain and links the functions of ZC3H14 and the THO complex in the processing of RNA.

The Polyadenosine RNA Binding Protein ZC3H14 is Required in Mice for Proper Dendritic Spine Density

“…3C). These ZC3H14 isoforms are primarily localized to the nucleus but can be detected in the cytoplasm of neurons (Bienkowski et al, 2017; Guthrie et al, 2011; Hector et al, 2002; Morris & Corbett, 2018). As shown in Figure 3A (Δ 13/ Δ 13 +Iso1 and Δ 13/ Δ 13 +Iso3), exogenous expression of either ZC3H14 Iso1 or ZC3H14 Iso3 appears to rescue dendritic spine density, which is confirmed through a semi-automated quantitative analysis of dendritic spine density [Δ 13/ Δ 13 (+Iso1) p <0.01; Δ 13/ Δ 13 (+Iso3) p <0.02] (Fig.…”

“…Previous work has demonstrated that there is a pool of ZC3H14 present in the cytoplasm of neurons (Bienkowski et al, 2017; Morris & Corbett, 2018). To determine whether ZC3H14 is present in synaptosomes, which contain postsynaptic dendritic spines and presynaptic terminals (Chicurel, Terrian, & Potter, 1993), fractionation was performed as illustrated in Figure 7A.…”

“…Studies of cultured primary Drosophila neurons reveal that Nab2 is present within puncta in neurites, associated with both ribonucleoprotein complexes and polyribosomes (Bienkowski et al, 2017). In addition, cell fractionation assays from whole mouse brain reveal a cytoplasmic pool of ZC3H14, although the majority of the protein is found in the nucleus (Morris & Corbett, 2018). These observations regarding the localization of ZC3H14 are consistent with studies of the budding yeast Nab2 protein, which show that Nab2 is a shuttling RNA binding protein that can exit the nucleus in an poly(A) RNA-dependent manner (Green et al, 2002).…”

Mechanisms of nuclear mRNA export: A structural perspective

“…The Yra1‐Pcf11 interaction is conserved from yeast to humans, and has been suggested to modulate the assembly of the 3′‐end processing machinery . Recent work also shows that human THO interacts with the poly(A) RNA binding protein ZC3H14, and their interaction is required for proper control of bulk poly(A) tail length . Together, this multitude of connections between TREX and pre‐mRNA processing steps suggests that decision‐making during mRNA export is concurrent with pre‐mRNA processing.…”

“…59,60 Recent work also shows that human THO interacts with the poly(A) RNA binding protein ZC3H14, and their interaction is required for proper control of bulk poly(A) tail length. 61 Together, this multitude of connections between TREX and pre-mRNA processing steps suggests that decision-making during mRNA export is concurrent with pre-mRNA processing. These connections may direct, step by step, the ATPase-powered remodeling reactions to ultimately mark mature transcripts with the export receptor, thereby ensuring the fidelity of gene expression specifically at the stage of mRNP nuclear maturation.…”