Comprehensive analysis of the FMR1 locus transcriptional landscape

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DESCRIPTION (provided by applicant): Fragile X syndrome (FXS) is the most common form of inherited mental retardation (Oostra, 1996). It is caused by a CGG expansion in the 5' UTR of FMR1, which leads to the absence of the fragile X mental retardation protein (FMRP). However, longitudinal clinical observations of fragile X patients have shown that the severity of the cognitive, behavioral and morphological symptoms of FXS is highly variable. Therefore we searched for novel functional transcripts expressed from the FMR1 locus and identified FMR4, a long non-coding RNA with a strong biological (anti-apoptotic) activity. Another group identified a second long non-coding transcript originating from the FMR1 locus, ASFMR1, but it is yet unclear if it has any biological activity. Interestingly, both FMR4 and ASFMR1, similar to FMR1, are silenced in fragile X patients and up-regulated in pre-mutation carriers. Expression analyses have shown that FMR4 and ASFMR1 are expressed in a wide range of human adult and embryonic tissues. In situ hybridization studies demonstrated that FMR4 is localized to the nucleus suggesting that FMR4 exerts a nuclear mode of action. Since FMR4 has pronounced biological activity and is silenced in FXS, FMR4 is a new candidate gene for involvement in FXS and related disorders. It is unresolved if the activity of FMR4, ASFMR1, and yet uncharacterized FMR1-derived non-coding RNAs is linked to expression and silencing of FMR1 in FXS. It has been previously demonstrated that non-coding RNAs can serve as an interface for chromatin- modifying complexes and that short non-coding RNAs, e.g. microRNAs, can induce or repress the transcription of genes by directing epigenetic modifications via interaction with promoter-associated RNAs in mammalian cells. It is therefore of interest to explore whether such regulation exists at the FMR1 promoter and whether such regulation can be manipulated to restore FMR1 expression in fragile X patients.