ArticleRNA (New York, N.Y.)2016
The PUF binding landscape in metazoan germ cells.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
43 citing papers in PubMed, 57 citations in OpenAlex.
- Crystal structures of Caenorhabditis elegans PUF-3 depict plasticity of RNA recognition that enables germline gene regulation.Nucleic acids research · 2026Article
- Three lncRNAs promote PUM protein condensation and germline differentiation.Nature communications · 2025Article
- Article
- Notch controls APC/CScience advances · 2025Article
- A higher order PUF complex is central to regulation of C. elegans germline stem cells.Nature communications · 2025Article
- A higher order PUF complex is central to regulation ofbioRxiv : the preprint server for biology · 2024Article
- COP9 signalosome component CSN-5 stabilizes PUF proteins FBF-1 and FBF-2 in Caenorhabditis elegans germline stem and progenitor cells.Genetics · 2024Article
- PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans.Developmental cell · 2024Article
- Intra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding.Nature communications · 2023Article
- Two cold shock domain containing proteins trigger the development of infectious Trypanosoma brucei.PLoS pathogens · 2023Article
- Iron-dependent post transcriptional control of mitochondrial aconitase expression.Metallomics : integrated biometal science · 2023Article
- PUMILIO-mediated translational control of somatic cell cycle program promotes folliculogenesis and contributes to ovarian cancer progression.Cellular and molecular life sciences : CMLS · 2022Article
- Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal.Nucleic acids research · 2022Article
- Redundant mechanisms regulating the proliferation vs. differentiation balance in theFrontiers in cell and developmental biology · 2022Review
- Structural recognition of the mRNA 3' UTR by PUF-8 restricts the lifespan of C. elegans.Nucleic acids research · 2021Article
- Differential translational control of 5' IRE-containing mRNA in response to dietary iron deficiency and acute iron overload.Metallomics : integrated biometal science · 2020Article
- Antagonistic control ofeLife · 2020Article
- Article
- A PUF Hub Drives Self-Renewal inGenetics · 2020Article
- Dose-Dependent Effects of GLD-2 and GLD-1 on Germline Differentiation and Dedifferentiation in the Absence of PUF-8.Frontiers in cell and developmental biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 1 country.
Funding
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 crosslinking and immunoprecipitation) to determine binding landscapes of C. elegans FBF-1 and FBF-2 in the germline tissue of intact animals. Multiple iCLIP peak-calling methods were compared to maximize identification of both established FBF binding sites and positive control target mRNAs in our iCLIP data. We discovered that FBF-1 and FBF-2 bind to RNAs through canonical as well as alternate motifs. We also analyzed crosslinking-induced mutations to map binding sites precisely and to identify key nucleotides that may be critical for FBF-RNA interactions. FBF-1 and FBF-2 can bind sites in the 5'UTR, coding region, or 3'UTR, but have a strong bias for the 3' end of transcripts. FBF-1 and FBF-2 have strongly overlapping target profiles, including mRNAs and noncoding RNAs. From a statistically robust list of 1404 common FBF targets, 847 were previously unknown, 154 were related to cell cycle regulation, three were lincRNAs, and 335 were shared with the human PUF protein PUM2.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.