ArticleRNA (New York, N.Y.)2015
A multiprotein occupancy map of the mRNP on the 3' end of histone mRNAs.
Article in RNA (New York, N.Y.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 25 citations in OpenAlex.
- SLBP-independent control of maternal histone mRNA.bioRxiv : the preprint server for biology · 2026Article
- Mechanistic insights into recruitment and regulation of the RNA helicase UPF1 in replication-dependent histone mRNA decay.Nature communications · 2026Article
- Ataxin-2-like promotes translation of nonpolyadenylated reovirus mRNA.Nature communications · 2025Article
- Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs.Nucleic acids research · 2024Article
- Coordinated expression of replication-dependent histone genes from multiple loci promotes histone homeostasis inMolecular biology of the cell · 2023Article
- UPF1-Mediated RNA Decay-Danse Macabre in a Cloud.Biomolecules · 2020Review
- Discovering sequence and structure landscapes in RNA interaction motifs.Nucleic acids research · 2019Article
- ALYREF links 3'-end processing to nuclear export of non-polyadenylated mRNAs.The EMBO journal · 2019Article
- Determining degradation intermediates and the pathway of 3' to 5' degradation of histone mRNA using high-throughput sequencing.Methods (San Diego, Calif.) · 2019Review
- Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- BEAM web server: a tool for structural RNA motif discovery.Bioinformatics (Oxford, England) · 2018Article
- Transcription elongation rate affects nascent histone pre-mRNA folding and 3' end processing.Genes & development · 2018Article
- 3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease.Frontiers in molecular biosciences · 2018Review
- Birth and Death of Histone mRNAs.Trends in genetics : TIG · 2017Review
- DO-RIP-seq to quantify RNA binding sites transcriptome-wide.Methods (San Diego, Calif.) · 2017Article
- FEM1 proteins are ancient regulators of SLBP degradation.Cell cycle (Georgetown, Tex.) · 2017Article
- Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq.RNA (New York, N.Y.) · 2017Article
- Cyclin F-Mediated Degradation of SLBP Limits H2A.X Accumulation and Apoptosis upon Genotoxic Stress in G2.Molecular cell · 2016Article
- A subset of replication-dependent histone mRNAs are expressed as polyadenylated RNAs in terminally differentiated tissues.Nucleic acids research · 2016Article
- TUT7 catalyzes the uridylation of the 3' end for rapid degradation of histone mRNA.RNA (New York, N.Y.) · 2016Article
Corrections and comments
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
Abstract
The animal replication-dependent (RD) histone mRNAs are coordinately regulated with chromosome replication. The RD-histone mRNAs are the only known cellular mRNAs that are not polyadenylated. Instead, the mature transcripts end in a conserved stem-loop (SL) structure. This SL structure interacts with the stem-loop binding protein (SLBP), which is involved in all aspects of RD-histone mRNA metabolism. We used several genomic methods, including high-throughput sequencing of cross-linked immunoprecipitate (HITS-CLIP) to analyze the RNA-binding landscape of SLBP. SLBP was not bound to any RNAs other than histone mRNAs. We performed bioinformatic analyses of the HITS-CLIP data that included (i) clustering genes by sequencing read coverage using CVCA, (ii) mapping the bound RNA fragment termini, and (iii) mapping cross-linking induced mutation sites (CIMS) using CLIP-PyL software. These analyses allowed us to identify specific sites of molecular contact between SLBP and its RD-histone mRNA ligands. We performed in vitro crosslinking assays to refine the CIMS mapping and found that uracils one and three in the loop of the histone mRNA SL preferentially crosslink to SLBP, whereas uracil two in the loop preferentially crosslinks to a separate component, likely the 3'hExo. We also performed a secondary analysis of an iCLIP data set to map UPF1 occupancy across the RD-histone mRNAs and found that UPF1 is bound adjacent to the SLBP-binding site. Multiple proteins likely bind the 3' end of RD-histone mRNAs together with SLBP.
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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.