Functional characterisation of the non-coding RNA Pantr1 in FOXG1-dependent forebrain development and Rett-syndrome

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Rett-syndrome is an autism-spectrum disorder that is characterized by impaired neurodevelopment with e.g. progressive loss of cognitive capabilities, spastic paralysis, ataxia and epilepsy. 90% of Rett-syndrome cases are ascribed to mutations of MECP2, while the rest is due to mutations in other genes such as FOXG1. FOXG1 haploinsufficiency results in atypical Rett syndrome with similar phenotypes. Recent data suggest that both FOXG1 and MECP2 influence expression of long non-coding RNAs (ncRNA) as well as microRNAs and that these ncRNAs are implicated in disease development and progression. Specifically, our preliminary data showed that miR200 family and the long ncRNA (lncRNA) Pantr1 have decreased transcriptional levels in the hippocampus of Foxg1 heterozygote adult mice. To carry on our initial findings on the role of ncRNAs in atypical Rett-syndrome, we aim to analyse molecular functions of Pantr1 within this project. Bridging the fields of bioinformatics, molecular biology, and biochemistry our approaches to elucidate the function of Pantr1 in neural cells include target prediction and validation, as well as prediction and validation of transcriptional and post-transcriptional regulatory mechanisms. Specifically, we will explore the function of the Pantr1-PURb lncRNA-protein complex that we identified in our preliminary work. Within the proposed project we will (1) determine alterations of the transcriptome after changing expression levels of Pantr1 and PURb using RNA-seq, (2) use chromatin immunoprecipitation by RNA pull down (ChIRP) to analyse whether PURb promotes or hampers Pantr1 from binding to DNA, (3) employ Pantr1 ChIRP followed by mass spectrometry in conditions with and without PURb expression to elucidate whether PURb-binding interferes with association of Pantr1 to other RNA binding proteins, and (4) use iCLIP and ChIP to examine whether binding to Pantr1 interferes with binding of PURb to RNA or DNA. Further, we intend to rescue Pantr1 and miR200 family expression in vivo to analyse if this can revert phenotypical alterations in the adult mouse hippocampus. In addition, we will extend our results to FOXG1-syndrome patient-specific iPSC-derived neurons by studying Pantr1 and miR200 family expression and molecular function. Together, these data on the role of ncRNAs in atypical Rett syndrome will significantly further our understanding of the molecular basis of this neurodevelopmental disorder and may open avenues for novel therapeutic strategies.