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CGG repeat expansions in the Fragile X mental retardation 1 ( FMR1 ) gene are responsible for a family of associated disorders characterized by either intellectual disability and autism Fragile X Syndrome (FXS), or adult-onset neurodegeneration Fragile X-associated Tremor/Ataxia Syndrome. However, the  FMR1  locus is complex and encodes several long non-coding RNAs, whose expression is altered by repeat expansion mutations. The role of these lncRNAs is thus far unknown; therefore we investigated the functionality of  FMR4 , which we previously identified. “Full”-length expansions of the  FMR1  triplet repeat cause silencing of both  FMR1  and  FMR4 , thus we are interested in potential loss-of-function that may add to phenotypic manifestation of FXS. Since the two transcripts do not exhibit  cis -regulation of one another, we examined the potential for  FMR4  to regulate target genes at distal genomic loci using gene expression microarrays. We identified  FMR4 -responsive genes, including the methyl-CpG-binding domain protein 4 ( MBD4 ). Furthermore, we found that in differentiating human neural precursor cells,  FMR4  expression is developmentally regulated in opposition to expression of both  FMR1  (which is expected to share a bidirectional promoter with  FMR4 ) and  MBD4 . We therefore propose that  FMR4 ’s function is as a gene-regulatory lncRNA and that this transcript may function in normal development. Closer examination of  FMR4  increases our understanding of the role of regulatory lncRNA and the consequences of  FMR1  repeat expansions.

Changes in expression of the long non-coding RNA FMR4 associate with altered gene expression during differentiation of human neural precursor cells