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Molecular mechanisms of recruitment, function and regulation of UPF1 in histone mRNA decay

https://doi.org/10.1101/2025.02.23.639735

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/wrna.1684openalex-snapshot

Assembly of multicomponent machines in RNA metabolism: A common theme in mRNA decay pathways

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NMRPipe: A multidimensional spectral processing system based on UNIX pipes

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Identification of helix capping and β-turn motifs from NMR chemical shifts

inferredcites →https://doi.org/10.1007/s10858-019-00243-7openalex-snapshot

Improving the sensitivity of FT-NMR spectroscopy by apodization weighted sampling

inferredcites →https://doi.org/10.1016/j.cell.2010.11.043openalex-snapshot

Upf1 ATPase-Dependent mRNP Disassembly Is Required for Completion of Nonsense- Mediated mRNA Decay

inferredcites →https://doi.org/10.1016/j.jmb.2004.08.055openalex-snapshot

Crystallographic Structure of the Nuclease Domain of 3′hExo, a DEDDh Family Member, Bound to rAMP

inferredcites →https://doi.org/10.1016/j.jmb.2018.12.011openalex-snapshot

The Biophysical Basis for Phosphorylation-Enhanced DNA-Binding Autoinhibition of the ETS1 Transcription Factor

inferredcites →https://doi.org/10.1016/j.molcel.2005.08.012openalex-snapshot

Exon-Junction Complex Components Specify Distinct Routes of Nonsense-Mediated mRNA Decay with Differential Cofactor Requirements

inferredcites →https://doi.org/10.1016/j.molcel.2011.02.010openalex-snapshot

Molecular Mechanisms for the RNA-Dependent ATPase Activity of Upf1 and Its Regulation by Upf2

inferredcites →https://doi.org/10.1016/j.molcel.2014.02.027openalex-snapshot

Deep Sequencing Shows Multiple Oligouridylations Are Required for 3′ to 5′ Degradation of Histone mRNAs on Polyribosomes

inferredcites →https://doi.org/10.1016/j.sbi.2010.03.011openalex-snapshot

SF1 and SF2 helicases: family matters

inferredcites →https://doi.org/10.1016/j.tig.2017.07.014openalex-snapshot

Birth and Death of Histone mRNAs

inferredcites →https://doi.org/10.1016/j.ymeth.2018.11.001openalex-snapshot

Determining degradation intermediates and the pathway of 3′ to 5′ degradation of histone mRNA using high-throughput sequencing

inferredcites →https://doi.org/10.1016/s0079-6565(98)00025-9openalex-snapshot

Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients

inferredcites →https://doi.org/10.1016/s1097-2765(03)00278-8openalex-snapshot

A 3′ Exonuclease that Specifically Interacts with the 3′ End of Histone mRNA

inferredcites →https://doi.org/10.1017/s1355838201001820openalex-snapshot

The stem-loop binding protein forms a highly stable and specific complex with the 3′ stem-loop of histone mRNAs

inferredcites →https://doi.org/10.1038/emboj.2008.17openalex-snapshot

Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways

inferredcites →https://doi.org/10.1038/nsmb.1561openalex-snapshot

The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner

inferredcites →https://doi.org/10.1038/nsmb.2287openalex-snapshot

The cryo-EM structure of the UPF–EJC complex shows UPF1 poised toward the RNA 3′ end

inferredcites →https://doi.org/10.1038/nsmb.2450openalex-snapshot

Eri1 degrades the stem-loop of oligouridylated histone mRNAs to induce replication-dependent decay

inferredcites →https://doi.org/10.1038/nsmb1330openalex-snapshot

NMD factors UPF2 and UPF3 bridge UPF1 to the exon junction complex and stimulate its RNA helicase activity

inferredcites →https://doi.org/10.1038/nsmb741openalex-snapshot

The structural basis for the interaction between nonsense-mediated mRNA decay factors UPF2 and UPF3

inferredcites →https://doi.org/10.1038/nsmb972openalex-snapshot

Regulated degradation of replication-dependent histone mRNAs requires both ATR and Upf1

inferredcites →https://doi.org/10.1038/s41467-019-11337-zopenalex-snapshot

A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides

inferredcites →https://doi.org/10.1038/s41467-019-13080-xopenalex-snapshot

Insights into the assembly and architecture of a Staufen-mediated mRNA decay (SMD)-competent mRNP

inferredcites →https://doi.org/10.1073/pnas.1406381111openalex-snapshot

Molecular mechanisms for the regulation of histone mRNA stem-loop–binding protein by phosphorylation

inferredcites →https://doi.org/10.1073/pnas.2100178118openalex-snapshot

Replication-dependent histone biosynthesis is coupled to cell-cycle commitment

inferredcites →https://doi.org/10.1074/jbc.m602947200openalex-snapshot

Characterization of 3′hExo, a 3′ Exonuclease Specifically Interacting with the 3′ End of Histone mRNA

inferredcites →https://doi.org/10.1074/jbc.ra120.013824openalex-snapshot

The RNA-binding protein PTBP1 promotes ATPase-dependent dissociation of the RNA helicase UPF1 to protect transcripts from nonsense-mediated mRNA decay

inferredcites →https://doi.org/10.1074/mcp.o114.042259openalex-snapshot

xiNET: Cross-link Network Maps With Residue Resolution

inferredcites →https://doi.org/10.1091/mbc.e04-11-1023openalex-snapshot

Nuclear Import of the Stem–Loop Binding Protein and Localization during the Cell Cycle

inferredcites →https://doi.org/10.1093/bioinformatics/btu830openalex-snapshot

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

inferredcites →https://doi.org/10.1093/nar/gkac1026openalex-snapshot

UPF1 mutants with intact ATPase but deficient helicase activities promote efficient nonsense-mediated mRNA decay

inferredcites →https://doi.org/10.1093/nar/gkg563openalex-snapshot

ExPASy: the proteomics server for in-depth protein knowledge and analysis

inferredcites →https://doi.org/10.1093/nar/gkr791openalex-snapshot

N- and C-terminal Upf1 phosphorylations create binding platforms for SMG-6 and SMG-5:SMG-7 during NMD

inferredcites →https://doi.org/10.1093/nar/gks1320openalex-snapshot

Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains

inferredcites →https://doi.org/10.1093/nar/gkt1197openalex-snapshot

Structural and functional analysis of the three MIF4G domains of nonsense-mediated decay factor UPF2

inferredcites →https://doi.org/10.1093/nar/gkv1527openalex-snapshot

Human nonsense-mediated mRNA decay factor UPF2 interacts directly with eRF3 and the SURF complex

inferredcites →https://doi.org/10.1098/rstb.2018.0170openalex-snapshot

Role of oligouridylation in normal metabolism and regulated degradation of mammalian histone mRNAs

inferredcites →https://doi.org/10.1101/gad.10.23.3028openalex-snapshot

The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing.

inferredcites →https://doi.org/10.1101/gad.1389006openalex-snapshot

Binding of a novel SMG-1–Upf1–eRF1–eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay

inferredcites →https://doi.org/10.1101/gad.1622708openalex-snapshot

Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5′ to 3′ and 3′ to 5′

inferredcites →https://doi.org/10.1101/gad.913001openalex-snapshot

Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay

inferredcites →https://doi.org/10.1126/science.1228705openalex-snapshot

Structure of Histone mRNA Stem-Loop, Human Stem-Loop Binding Protein, and 3′hExo Ternary Complex

inferredcites →https://doi.org/10.1126/science.aaz7758openalex-snapshot

Structure of an active human histone pre-mRNA 3′-end processing machinery

inferredcites →https://doi.org/10.1126/science.abi6983openalex-snapshot

OpenCell: Endogenous tagging for the cartography of human cellular organization

inferredcites →https://doi.org/10.1128/mcb.00382-12openalex-snapshot

The Prolyl Isomerase Pin1 Targets Stem-Loop Binding Protein (SLBP) To Dissociate the SLBP-Histone mRNA Complex Linking Histone mRNA Decay with SLBP Ubiquitination

inferredcites →https://doi.org/10.1128/mcb.11.5.2416openalex-snapshot

Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps.

inferredcites →https://doi.org/10.1128/mcb.19.5.3561openalex-snapshot

Stem-Loop Binding Protein Facilitates 3′-End Formation by Stabilizing U7 snRNP Binding to Histone Pre-mRNA

inferredcites →https://doi.org/10.1128/mcb.20.12.4188-4198.2000openalex-snapshot

Stem-Loop Binding Protein, the Protein That Binds the 3′ End of Histone mRNA, Is Cell Cycle Regulated by Both Translational and Posttranslational Mechanisms

inferredcites →https://doi.org/10.1128/mcb.23.5.1590-1601.2003openalex-snapshot

Phosphorylation of Stem-Loop Binding Protein (SLBP) on Two Threonines Triggers Degradation of SLBP, the Sole Cell Cycle-Regulated Factor Required for Regulation of Histone mRNA Processing, at the End of S Phase

inferredcites →https://doi.org/10.1128/mcb.25.16.6879-6888.2005openalex-snapshot

Translation Termination Is Involved in Histone mRNA Degradation when DNA Replication Is Inhibited

inferredcites →https://doi.org/10.1128/mcb.3.4.539openalex-snapshot

Regulation of Human Histone Gene Expression: Kinetics of Accumulation and Changes in the Rate of Synthesis and in the Half-Lives of Individual Histone mRNAs During the HeLa Cell Cycle

inferredcites →https://doi.org/10.1261/rna.042531.113openalex-snapshot

The C-terminal extension of Lsm4 interacts directly with the 3′ end of the histone mRNP and is required for efficient histone mRNA degradation

inferredcites →https://doi.org/10.1261/rna.058107.116openalex-snapshot

TUT7 catalyzes the uridylation of the 3′ end for rapid degradation of histone mRNA

inferredcites →https://doi.org/10.1261/rna.070136.118openalex-snapshot

UPFront and center in RNA decay: UPF1 in nonsense-mediated mRNA decay and beyond

inferredcites →https://doi.org/10.1261/rna.079188.122openalex-snapshot

Modulation of RNA-binding properties of the RNA helicase UPF1 by its activator UPF2

inferredcites →https://doi.org/10.1261/rna.079233.122openalex-snapshot

Knockouts of TUT7 and 3′hExo show that they cooperate in histone mRNA maintenance and degradation

inferredcites →https://doi.org/10.15252/embj.2021108898openalex-snapshot

An alternative UPF1 isoform drives conditional remodeling of nonsense‐mediated mRNA decay

inferredcites →https://doi.org/10.3390/biom10070999openalex-snapshot

UPF1-Mediated RNA Decay—Danse Macabre in a Cloud

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Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.12677/md.2026.161024openalex-snapshot

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