Neuropsychiatric Implications Of RNA-Binding Proteins HuD And KSRP Revealed By Genome-Wide Identification Of Their Targets

Abstract

Posttranscriptional mechanisms are critical for neuronal development and function, as they allow for faster responses to environmental cues and provide spatially restricted compartments for local control of gene expression in both axons and dendrites. Many RNA-binding proteins (RBPs) post-transcriptionally regulate the stability of mRNAs by binding to AU-rich instability-conferring elements (AREs) in the 3’ untranslated regions (3’UTRs). These sequences are present in about 20% of forebrain transcripts indicating that specific ARE-binding proteins (ARE-BPs) play an important role in controlling the expressing of thousands of brain mRNAs. We previously identified two ARE-BPs expressed in neurons, the ELAV-like protein HuD (ELAVL4) and the KH-domain protein KSRP (KHSRP). These proteins competitively bind to the 3’UTRs of GAP-43 and other growth- and plasticity-associated transcripts, either stabilizing (HuD) or destabilizing (KSRP) their target RNAs. HuD and KSRP also have different expression patterns, cellular localization, and control different aspects of neuronal differentiation, with HuD promoting and KSRP halting process outgrowth. Mutant mouse models demonstrate that both proteins play important roles in controlling behavioral phenotypes while genetic analyses in patient populations revealed that HuD is a risk gene for Parkinson’s disease while KSRP expression was one of the blood biomarkers for schizophrenia. We have used a variety of tools including UV-crosslinking and immunoprecipitation (CLIP)-Chip and RNA-IP and sequencing (RIP-seq) assays to identify the repertoire of neuronal targets regulated by these RBPs and found that KSRP and HuD bind both distinct and shared sets of target mRNAs in developing mouse brains. In agreement with the role of HuD in neural development and synaptic plasticity, a number of its targets are significantly enriched in axon guidance and long-term potentiation pathways. Analyses of the 530 common coding targets revealed that besides GAP-43, target transcripts include Blc11b, Ctnnb1, Eif4g2, Fez1, Fscn1, Gabbr1, Gria2, Grm5, Ncam1, Nrxn1, Reln, Stmn1, Plxn1, Pxln2, Sox11, Tcf4 and other developmentally-regulated transcripts. Localized mRNAs binding selectively to either HuD or KSRP were also identified. Both unique and common target mRNAs are also significantly associated with a number of neurological disorders such as Alzheimer’s, Huntington’s and Parkinson’s disease, as well as mood disorders, schizophrenia and mental retardation. Based upon these findings, we propose a post-transcriptional interactome model for the impact of these proteins in neuropsychiatric disorders.