Genome-wide Profiling of RNA Binding Targets of hnRNP H

To inform the mechanism of hnRNP H dysfunction in methamphetamine-induced dopamine release and behavior, we surveyed mRNA targets of hnRNP H via cross-linking immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in striatal tissue at baseline and at 30 min post-MA (2 mg/kg, i.p.). To integrate identification of hnRNP H targets with the impact of methamphetamine on downstream gene expression and splicing, we analyzed the transcriptome of the parallel samples used in CLIP-seq. Overall design: Identification of mRNA transcripts bound by hnRNP H in the striata of C57BL/6J wild-type in response to acute methamphetamine versus saline. Transcriptomic analyses for differential gene expression an alternative splicing in the striata of C57BL/6J wild-type in response to acute methamphetamine versus saline. Striata from four mice were pooled per replicate (3 replicates per Treatment). Each replicate used for CLIP-seq and RNA-seq was generated by pooling striata from 4 wild type mice across multiple litters. Each pool consisted of samples from 2 females and 2 males. UPDATE [May-02-2025] The mutant Samples were removed because of an inconsistency in the size of the mutation across samples and within pooled samples. Maintenance of a heterozygous colony led to an alteration in the original 16 bp deletion such that there were both shorter and longer deletions segregating in the colony and in the samples originally posted.