title: Analysis of FMRP mRNA target datasets reveals highly associated mRNAs mediated by G-quadruplex structures formed via clustered WGGA sequences.
abstract: Fragile X syndrome, a common cause of intellectual disability and a well-known cause of autism spectrum disorder, is the result of loss or dysfunction of fragile X mental retardation protein (FMRP), a highly selective RNA-binding protein and translation regulator. A major research priority has been the identification of the mRNA targets of FMRP, particularly as recent studies suggest an excess of FMRP targets among genes implicated in idiopathic autism and schizophrenia. Several large-scale studies have attempted to identify mRNAs bound by FMRP through several methods, each generating a list of putative target genes, leading to distinct hypotheses by which FMRP recognizes its targets; namely, by RNA structure or sequence. However, no in depth analyses have been performed to identify the level of consensus among the studies. Here, we analyze four large FMRP target datasets to generate high-confidence consensus lists, and examine all datasets for sequence elements within the target RNAs to validate reported FMRP binding motifs (GACR, ACUK and WGGA). We found GACR to be highly enriched in FMRP datasets, while ACUK was not. The WGGA pattern was modestly enriched in several, but not all datasets. The previous association between FMRP and G-quadruplexes prompted the analysis of the distribution of WGGA in the target genes. Consistent with the requirements for G-quadruplex formation, we observed highly clustered WGGA motifs in FMRP targets compared with other genes, implicating both RNA structure and sequence in the recognition motif of FMRP. In addition, we generate a list of the top 40 FMRP targets associated with FXS-related phenotypes.
authors.affiliation: Department of Human Genetics.
authors.forename: Joshua A
authors.initials: JA
authors.lastname: Suhl
authors.affiliation: Department of Human Genetics.
authors.forename: Pankaj
authors.initials: P
authors.lastname: Chopra
authors.affiliation: Department of Human Genetics, Department of Cell Biology.
authors.forename: Bart R
authors.initials: BR
authors.lastname: Anderson
authors.affiliation: Department of Cell Biology, Department of Neurology and.
authors.forename: Gary J
authors.initials: GJ
authors.lastname: Bassell
authors.affiliation: Department of Human Genetics, Departments of Biochemistry and Pediatrics, Emory University School of Medicine, Atlanta, GA, USA swarren@emory.edu.
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Warren
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001665:Binding Sites; D051860:Fragile X Messenger Ribonucleoprotein 1 / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D005600:Fragile X Syndrome / Q000235:genetics; D054856:G-Quadruplexes; D006801:Humans; D012333:RNA, Messenger / Q000737:chemistry* / Q000378:metabolism
chemical_list: D051860:Fragile X Messenger Ribonucleoprotein 1; D012333:RNA, Messenger; C497683:FMR1 protein, human