title: Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element.
abstract: RNA localization is emerging as a general principle of sub-cellular protein localization and cellular organization. However, the sequence and structural requirements in many RNA localization elements remain poorly understood. Whereas transcription factor-binding sites in DNA can be recognized as short degenerate motifs, and consensus binding sites readily inferred, protein-binding sites in RNA often contain structural features, and can be difficult to infer. We previously showed that zebrafish squint/nodal-related 1 (sqt/ndr1) RNA localizes to the future dorsal side of the embryo. Interestingly, mammalian nodal RNA can also localize to dorsal when injected into zebrafish embryos, suggesting that the sequence motif(s) may be conserved, even though the fish and mammal UTRs cannot be aligned. To define potential sequence and structural features, we obtained ndr1 3'-UTR sequences from approximately 50 fishes that are closely, or distantly, related to zebrafish, for high-resolution phylogenetic footprinting. We identify conserved sequence and structural motifs within the zebrafish/carp family and catfish. We find that two novel motifs, a single-stranded AGCAC motif and a small stem-loop, are required for efficient sqt RNA localization. These findings show that comparative sequencing in the zebrafish/carp family is an efficient approach for identifying weak consensus binding sites for RNA regulatory proteins.
authors.affiliation: Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604.
authors.forename: Patrick C
authors.initials: PC
authors.lastname: Gilligan
authors.forename: Pooja
authors.initials: P
authors.lastname: Kumari
authors.forename: Shimin
authors.initials: S
authors.lastname: Lim
authors.forename: Albert
authors.initials: A
authors.lastname: Cheong
authors.forename: Alex
authors.initials: A
authors.lastname: Chang
authors.forename: Karuna
authors.initials: K
authors.lastname: Sampath
mesh_terms: D020413:3' Untranslated Regions; D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004625:Embryo, Nonmammalian / Q000737:chemistry; D019143:Evolution, Molecular; D029941:Fish Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D055456:Nodal Signaling Ligands / Q000235:genetics*; D012333:RNA, Messenger / Q000032:analysis; D016601:RNA-Binding Proteins / Q000378:metabolism; D029961:Zebrafish Proteins / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions; D029941:Fish Proteins; D055456:Nodal Signaling Ligands; D012333:RNA, Messenger; D016601:RNA-Binding Proteins; D029961:Zebrafish Proteins; C485171:ndr1 protein, zebrafish