2016
DOI: 10.1261/rna.055871.116
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The PUF binding landscape in metazoan germ cells

Abstract: PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. Without FBF, adult germlines lose all stem cells. A major gap in our understanding of PUF proteins, including FBF, is a global view of their binding sites in their native context (i.e., their "binding landscape"). To understand the interactions underlying FBF function, we used iCLIP (individual-nucleotide resolution UV c… Show more

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Cited by 51 publications
(110 citation statements)
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References 96 publications
(143 reference statements)
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“…In the absence of both FBF-1 and FBF-2, all cells in the mitotic zone precociously enter meiosis after the L4 stage of development when maintained at 20°C (Crittenden et al, 2002), but are maintained in a mitotic state if grown at 25°C (Merritt and Seydoux, 2010). FBF-1 and FBF-2 recognize the same motif present in the 3′UTR of their target mRNAs in vitro and form complexes with largely the same mRNAs in vivo Merritt and Seydoux, 2010;Prasad et al, 2016). Despite high similarity between FBF-1 and FBF-2 (89% identity at the amino acid level) and apparent redundancy in their control of the switch from spermatogenesis to oogenesis, single fbf-1 and fbf-2 mutants have distinct phenotypes, suggesting that these genes play unique roles (Lamont et al, 2004).…”
Section: Introductionmentioning
confidence: 99%
“…In the absence of both FBF-1 and FBF-2, all cells in the mitotic zone precociously enter meiosis after the L4 stage of development when maintained at 20°C (Crittenden et al, 2002), but are maintained in a mitotic state if grown at 25°C (Merritt and Seydoux, 2010). FBF-1 and FBF-2 recognize the same motif present in the 3′UTR of their target mRNAs in vitro and form complexes with largely the same mRNAs in vivo Merritt and Seydoux, 2010;Prasad et al, 2016). Despite high similarity between FBF-1 and FBF-2 (89% identity at the amino acid level) and apparent redundancy in their control of the switch from spermatogenesis to oogenesis, single fbf-1 and fbf-2 mutants have distinct phenotypes, suggesting that these genes play unique roles (Lamont et al, 2004).…”
Section: Introductionmentioning
confidence: 99%
“…We observed significant (hypergeometric distribution P < 0.05) overlap of DLC‐1‐associated mRNAs with the targets of FBF‐1 ( P < 10 −59 ), GLD‐2 ( P < 10 −7 ), LIN‐41 ( P < 0.01), and OMA‐1 ( P = 0.02; Table ). The significant overlap with FBF‐1 targets was expected since the targets of FBF‐1 and FBF‐2 are highly similar .…”
Section: Resultsmentioning
confidence: 90%
“…Indeed, within the 10 most significant recovered motifs, we found two motifs similar to those recognized by PUF family RNA-binding proteins that include FBF-2 ( Fig. 3B, C; [24,53]). The top-scoring motif is a lowaffinity OMA-1-binding site (UA[a/u]-rich repeats, Fig.…”
Section: Binding Motifs In the 3 0 Utrs Of Mrnas Isolated With Dlc-1mentioning
confidence: 76%
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“…Despite their different methodologies, RIP and CLIP can produce complementary data when used to study the same RBPs under similar conditions (van der Brug et al 2008;Sanford et al 2009;Kershner and Kimble 2010;Jungkamp et al 2011;Mukherjee et al 2011;Brooks et al 2015;Hansen et al 2015;Ennajdaoui et al 2016;Prasad et al 2016;Uren et al 2016). Therefore, our goal has been to combine aspects of both techniques to produce a single procedure that quantifies RBP-RNA interactions at the whole-transcript level and at the binding site level.…”
Section: Introductionmentioning
confidence: 99%