ArticleNucleic acids research2011
Conservation defines functional motifs in the squint/nodal-related 1 RNA dorsal localization element.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 28 citations in OpenAlex.
- Translational control of furina by an RNA regulon is important for left-right patterning, heart morphogenesis and cardiac valve function.Development (Cambridge, England) · 2023Article
- The RNA-binding protein Igf2bp3 is critical for embryonic and germline development in zebrafish.PLoS genetics · 2021Article
- RNA structural dynamics regulate early embryogenesis through controlling transcriptome fate and function.Genome biology · 2020Article
- Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility.eLife · 2019Article
- The translational regulation of maternal mRNAs in time and space.FEBS letters · 2018Review
- Translational co-regulation of a ligand and inhibitor by a conserved RNA element.Nucleic acids research · 2018Article
- Methods to study maternal regulation of germ cell specification in zebrafish.Methods in cell biology · 2016Article
- Keeping a lid on nodal: transcriptional and translational repression of nodal signalling.Open biology · 2016Review
- Article
- RNA-ID, a highly sensitive and robust method to identify cis-regulatory sequences using superfolder GFP and a fluorescence-based assay.RNA (New York, N.Y.) · 2012Article
- Known and novel post-transcriptional regulatory sequences are conserved across plant families.RNA (New York, N.Y.) · 2012Article
- The function of introns.Frontiers in genetics · 2012Article
- Identification of nucleotide patterns enriched in secreted RNAs as putative cis-acting elements targeting them to exosome nano-vesicles.BMC genomics · 2011Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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