The DOI matches its Crossref record; 62 of the 62 references it cites were found in a registry or an index.
Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets
Open accessAbstract
PUF family proteins are among the best-characterized regulatory RNA-binding proteins in nonmammalian species, but relatively little is known about mRNA targets or functions of mammalian PUF proteins. In this study, we used ribonomic analysis to identify and analyze mRNAs associated with ribonucleoproteins containing an endogenous human PUF protein, Pum1. Pum1-associated mRNAs were highly enriched for genes encoding proteins that function in transcriptional regulation and cell cycle/proliferation, results consistent with the posttranscriptional RNA regulon model and the proposed ancestral functions of PUF proteins in stem cell biology. Analysis of 3' untranslated region sequences of Pum1-associated mRNAs revealed a core Pum1 consensus sequence, UGUAHAUA. Pum1 knockdown demonstrated that Pum1 enhances decay of associated mRNAs, and relocalization of Pum1 to stress granules suggested that Pum1 functions in repression of translation. This study is the first in vivo genome-wide mRNA target identification of a mammalian PUF protein and provides direct evidence that human PUF proteins regulate stability of associated mRNAs. Comparison of Pum1-associated mRNAs to mRNA targets of PUF proteins from Saccharomyces cerevisiae and Drosophila melanogaster demonstrates how a well-conserved RNA-binding domain and cognate binding sequence have been evolutionarily rewired to regulate the collective expression of different sets of functionally related genes.
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“motifs for the alternative splicing factorsRBFOX1, RBFOX2 and RBFOX3 (ref. 4) are conserved in introns downstream of alternative exons, whereas sites for the stability/translation factors PUM1 and PUM2 are most highly conserved in 3′ UTRs24,25”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [25]
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BackgroundDiverse Roles of PUF Proteins in Germline Stem and Progenitor Cell Development in C. elegans
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“FBF-1 requires the presence of a single “extra” nucleotide in the middle of an eight-nucleotide site, whereas PUF-8 requires its absence (Opperman et al., 2005).”
BackgroundInfluentialExpanding the binding specificity for RNA recognition by a PUF domain
Zhou, W. Y., Melamed, D., Bányai, G., Meyer, C., Tuschl, T., Wickens, M., Cao, J., & Fields, S. (2021) · Nature Communications · doi:10.1038/s41467-021-25433-6 · Cited by 22
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“The related UGUAHAUA (H = A/C/U) motif is recognized by human Pum1 [44], Drosophila Pumilio [45], yeast Puf3 [46] and most importantly by P. falciparum Puf2 [7].”
BackgroundPUF-8 and TCER-1 are essential for normal levels of multiple mRNAs in theC. elegansgermline
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“Results from large-scale experiments suggest that these proteins influence the expression of a large number of mRNAs (Galgano et al., 2008; Gerber et al., 2004; Kershner and Kimble, 2010; Mainpal et al., 2011; Morris et al., 2008).”
Post-transcriptional control of executioner caspases by RNA-binding proteinsPreprint
Šubašić, D., Stoeger, T., Eisenring, S., Matia‐González, A. M., Imig, J., Zheng, X., Xiong, L., Gisler, P., Eberhard, R., Holtackers, R., et al. (2016) · Genes & Development · doi:10.1101/gad.285726.116 · Cited by 15
“Interestingly, several of these RBPs, including PUM1, PUM2, FMR1, and FXR2, have been experimentally shown to bind to the caspase-3 3 ′ UTR (Galgano et al. 2008; Morris et al. 2008; Mukherjee et al. 2009; Hafner et al. 2010; Ascano et al. 2012).”
Stem Cell Ribonomics: RNA-Binding Proteins and Gene Networks in Stem Cell Differentiation
Shigunov, P., & Dallagiovanna, B. (2015) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2015.00074 · Cited by 14
“…cycle-related proteins were found to be associated with PUF proteins in different organisms, suggesting that PUF proteins could be directly involved in the control of progression through the cell cycle (Galgano et al., 2008; Morris et al., 2008; Hafner et al., 2010b; Kershner and Kimble, 2010).”
BackgroundInfluentialRewiring of Posttranscriptional RNA Regulons: Puf4p in Fungi as an Example
Jiang, H., Guo, X., Xu, L., & Gu, Z. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss085 · Cited by 13
“In humans, two PUF proteins interact with the microRNA system to regulate genes in transcription, the cell cycle, and cell proliferation (Galgano et al. 2008; Morris et al. 2008).”
BackgroundRNA-Binding Protein Immunopurification-Microarray (RIP-Chip) Analysis to Profile Localized RNAs
Galgano, A., & Gerber, A. P. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-005-8_23 · Cited by 12
Pumilio turns on microRNA function
Triboulet, R., & Gregory, R. I. (2010) · Nature Cell Biology · doi:10.1038/ncb1010-928 · Cited by 12
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PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing
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“PREs are well-studied binding sites for Pumilio proteins across many species (Filipovska et al., 2011; Morris et al., 2008; Van Etten et al., 2012; Wang et al., 2002).”
BackgroundSystematic analysis of the target recognition and repression by the Pumilio proteins
Farberov, S., & Ulitsky, I. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae929 · Cited by 5
“The binding sites of PUM proteins on human mRNAs have been mapped by several cross-linking and immunoprecipitation (CLIP)-based studies ( 1 , 9 , 10 ).”
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“The biological functions of PUM1 and its homologous proteins have been extensively analyzed in various organisms (Morris et al., 2008; Wang et al., 2018; Wickens et al., 2002).”
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Regulation of mRNA decay by Pumilio in Drosophila melanogaster
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“It is thought to repress translation and localize to stress granules (Morris et al., 2008; Namkoong et al., 2018) which may indeed play a role in the stress response described here.”
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“Another possibility is that PABPC1 may compete with other RBPs for similar binding motifs.”
InfluentialPUF family RNA-binding proteins Puf1 and Puf2 promote transcript degradation in Toxoplasma gondii
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DND1-NANOS3 shapes the PGC transcriptome via a heptanucleotide sequence in mRNA 3′ UTRs
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Metadata
- Authors
- Morris, A. R., Mukherjee, N., & Keene, J. D.
- Affiliations
- Duke Medical Center (US)
- Corresponding author
- Keene, Jack D.
- ORCID
- Mukherjee, Neelanjan
- Venue
- Molecular and Cellular Biology
- Publisher
- Informa UK Limited
- Published
- 2008-06-01
- Volume
- 28
- Issue
- 12
- Pages
- 4093-4103
- ISSN
- 0270-7306 (ISSN-L)
- 1098-5549
- PMC
- PMC2423135
- OpenAlex
- W2109821031
- Cited by
- 155
- References
- 62
- Citations by year
- 2026: 6 · 2025: 1 · 2024: 4 · 2023: 2 · 2022: 3 · 2021: 5 · 2020: 10 · 2019: 13 · 2018: 11 · 2017: 7 · 2016: 11 · 2015: 5 · 2014: 12 · 2013: 12 · 2012: 9
- FWCI
- 6.04
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Molecular and Cellular Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- PUM1, PUF proteins, mRNA stability, post-transcriptional regulation, 3' untranslated region, cis-regulatory sequences, stress granules, protein synthesis inhibition, ribonucleoprotein, Saccharomyces cerevisiae, Drosophila melanogaster, transcriptional regulation
- MeSH terms
- Animals, Drosophila melanogaster, HeLa Cells, Humans, Models, Biological, Ribosomes, RNA, Messenger, Saccharomyces cerevisiae, Species Specificity, Protein Biosynthesis, RNA-Binding Proteins, Conserved Sequence, Oxidative Stress, Evolution, Molecular, Oligonucleotide Array Sequence Analysis
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