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FMRP Links Optimal Codons to mRNA stability in Neurons

https://doi.org/10.1101/801449
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What this work says

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

inferredcites →https://doi.org/10.1002/0471142727.mb1312s23openalex-snapshot
Preparation of Yeast RNA
inferredcites →https://doi.org/10.1016/0092-8674(91)90125-iopenalex-snapshot
Absence of expression of the FMR-1 gene in fragile X syndrome
inferredcites →https://doi.org/10.1016/j.cell.2008.07.031openalex-snapshot
The Fragile X Syndrome Protein Represses Activity-Dependent Translation through CYFIP1, a New 4E-BP
inferredcites →https://doi.org/10.1016/j.cell.2008.10.017openalex-snapshot
The Autistic Neuron: Troubled Translation?
inferredcites →https://doi.org/10.1016/j.cell.2011.06.013openalex-snapshot
FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism
inferredcites →https://doi.org/10.1016/j.cell.2015.02.029openalex-snapshot
Codon Optimality Is a Major Determinant of mRNA Stability
inferredcites →https://doi.org/10.1016/j.cell.2016.08.053openalex-snapshot
The DEAD-Box Protein Dhh1p Couples mRNA Decay and Translation by Monitoring Codon Optimality
inferredcites →https://doi.org/10.1016/j.cell.2017.07.033openalex-snapshot
Excess Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by Brd4 Inhibition
inferredcites →https://doi.org/10.1016/j.celrep.2015.03.060openalex-snapshot
Increased Expression of the PI3K Enhancer PIKE Mediates Deficits in Synaptic Plasticity and Behavior in Fragile X Syndrome
inferredcites →https://doi.org/10.1016/j.celrep.2018.07.039openalex-snapshot
Attenuated Codon Optimality Contributes to Neural-Specific mRNA Decay in Drosophila
inferredcites →https://doi.org/10.1016/j.celrep.2018.09.041openalex-snapshot
RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins
inferredcites →https://doi.org/10.1016/j.celrep.2019.02.086openalex-snapshot
Widespread Alterations in Translation Elongation in the Brain of Juvenile Fmr1 Knockout Mice
inferredcites →https://doi.org/10.1016/j.celrep.2019.06.072openalex-snapshot
FMRP Modulates Neural Differentiation through m6A-Dependent mRNA Nuclear Export
inferredcites →https://doi.org/10.1016/j.celrep.2020.02.076openalex-snapshot
FMRP Control of Ribosome Translocation Promotes Chromatin Modifications and Alternative Splicing of Neuronal Genes Linked to Autism
inferredcites →https://doi.org/10.1016/j.mcn.2009.07.003openalex-snapshot
A multi PDZ-domain protein Pdzd2 contributes to functional expression of sensory neuron-specific sodium channel NaV1.8
inferredcites →https://doi.org/10.1016/j.molcel.2014.03.023openalex-snapshot
Fragile X Mental Retardation Protein Regulates Translation by Binding Directly to the Ribosome
inferredcites →https://doi.org/10.1016/j.molcel.2016.02.027openalex-snapshot
Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish
inferredcites →https://doi.org/10.1016/j.molcel.2020.01.006openalex-snapshot
Autism-Misregulated eIF4G Microexons Control Synaptic Translation and Higher Order Cognitive Functions
inferredcites →https://doi.org/10.1016/j.neuron.2007.12.001openalex-snapshot
Correction of Fragile X Syndrome in Mice
inferredcites →https://doi.org/10.1016/j.neuron.2012.07.022openalex-snapshot
Genetic Removal of p70 S6 Kinase 1 Corrects Molecular, Synaptic, and Behavioral Phenotypes in Fragile X Syndrome Mice
inferredcites →https://doi.org/10.1016/j.neuron.2017.07.013openalex-snapshot
Cell-Type-Specific Translation Profiling Reveals a Novel Strategy for Treating Fragile X Syndrome
inferredcites →https://doi.org/10.1016/s1534-5807(01)00025-9openalex-snapshot
Germ Cell Differentiation and Synaptonemal Complex Formation Are Disrupted in CPEB Knockout Mice
inferredcites →https://doi.org/10.1038/nature11737openalex-snapshot
FMRP targets distinct mRNA sequence elements to regulate protein expression
inferredcites →https://doi.org/10.1038/nature12730openalex-snapshot
N6-methyladenosine-dependent regulation of messenger RNA stability
inferredcites →https://doi.org/10.1038/ncomms11194openalex-snapshot
Genome-wide assessment of differential translations with ribosome profiling data
inferredcites →https://doi.org/10.1038/nm.3353openalex-snapshot
Genetic and acute CPEB1 depletion ameliorate fragile X pathophysiology
inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot
Fast gapped-read alignment with Bowtie 2
inferredcites →https://doi.org/10.1038/nmeth.4435openalex-snapshot
Thiol-linked alkylation of RNA to assess expression dynamics
inferredcites →https://doi.org/10.1038/nprot.2006.47openalex-snapshot
RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts
inferredcites →https://doi.org/10.1038/nprot.2012.086openalex-snapshot
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments
inferredcites →https://doi.org/10.1038/nsmb.2466openalex-snapshot
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding
inferredcites →https://doi.org/10.1038/nsmb.3325openalex-snapshot
Integrative classification of human coding and noncoding genes through RNA metabolism profiles
inferredcites →https://doi.org/10.1038/s41593-018-0287-xopenalex-snapshot
Widespread RNA editing dysregulation in brains from autistic individuals
inferredcites →https://doi.org/10.1073/pnas.1522631113openalex-snapshot
Fragile X Mental Retardation Protein (FMRP) controls diacylglycerol kinase activity in neurons
inferredcites →https://doi.org/10.1073/pnas.1809588115openalex-snapshot
Regulatory discrimination of mRNAs by FMRP controls mouse adult neural stem cell differentiation
inferredcites →https://doi.org/10.1073/pnas.1908052116openalex-snapshot
mRNA structure regulates protein expression through changes in functional half-life
inferredcites →https://doi.org/10.1074/jbc.ac119.010078openalex-snapshot
The RNA-binding protein FMRP facilitates the nuclear export of N6-methyladenosine–containing mRNAs
inferredcites →https://doi.org/10.1074/jbc.m111.222893openalex-snapshot
WNK2 Kinase Is a Novel Regulator of Essential Neuronal Cation-Chloride Cotransporters
inferredcites →https://doi.org/10.1093/bioinformatics/btp101openalex-snapshot
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
inferredcites →https://doi.org/10.1093/bioinformatics/bts034openalex-snapshot
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
inferredcites →https://doi.org/10.1093/bioinformatics/btv288openalex-snapshot
INSPEcT: a computational tool to infer mRNA synthesis, processing and degradation dynamics from RNA- and 4sU-seq time course experiments
inferredcites →https://doi.org/10.1093/hmg/ddy292openalex-snapshot
Fragile X mental retardation protein modulates the stability of its m6A-marked messenger RNA targets
inferredcites →https://doi.org/10.1093/nar/gku1235openalex-snapshot
An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1093/nar/gky267openalex-snapshot
HITS-CLIP in various brain areas reveals new targets and new modalities of RNA binding by fragile X mental retardation protein
inferredcites →https://doi.org/10.1093/nar/gkz223openalex-snapshot
Generally applicable transcriptome-wide analysis of translation using anota2seq
inferredcites →https://doi.org/10.1101/762500openalex-snapshot
FMRP binding to a ranked subset of long genes is revealed by coupled CLIP and TRAP in specific neuronal cell types
inferredcites →https://doi.org/10.1101/gr.193342.115openalex-snapshot
Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans
inferredcites →https://doi.org/10.1111/jnc.13353openalex-snapshot
Sipa1l3/SPAR3 is targeted to postsynaptic specializations and interacts with the Fezzin ProSAPiP1/Lzts3
inferredcites →https://doi.org/10.1126/science.aay6912openalex-snapshot
The Ccr4-Not complex monitors the translating ribosome for codon optimality
inferredcites →https://doi.org/10.1128/mcb.00175-18openalex-snapshot
Poly(C)-Binding Protein Pcbp2 Enables Differentiation of Definitive Erythropoiesis by Directing Functional Splicing of the Runx1 Transcript
inferredcites →https://doi.org/10.1146/annurev-pathol-011811-132457openalex-snapshot
Molecular Mechanisms of Fragile X Syndrome: A Twenty-Year Perspective
inferredcites →https://doi.org/10.1155/2016/8301737openalex-snapshot
Emerging Roles of BAI Adhesion-GPCRs in Synapse Development and Plasticity
inferredcites →https://doi.org/10.1186/1471-2105-12-323openalex-snapshot
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
inferredcites →https://doi.org/10.1186/1748-7188-6-26openalex-snapshot
ViennaRNA Package 2.0
inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
inferredcites →https://doi.org/10.1261/rna.058180.116openalex-snapshot
Codon optimality controls differential mRNA translation during amino acid starvation
inferredcites →https://doi.org/10.1371/journal.pgen.1005702openalex-snapshot
Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish
inferredcites →https://doi.org/10.1371/journal.pgen.1010221openalex-snapshot
Single cell transcriptomics reveals dysregulated cellular and molecular networks in a fragile X syndrome model
inferredcites →https://doi.org/10.1371/journal.pone.0228730openalex-snapshot
Codon and amino acid content are associated with mRNA stability in mammalian cells
inferredcites →https://doi.org/10.1523/jneurosci.17-05-01539.1997openalex-snapshot
Fragile X Mental Retardation Protein: Nucleocytoplasmic Shuttling and Association with Somatodendritic Ribosomes
inferredcites →https://doi.org/10.1523/jneurosci.2306-04.2004openalex-snapshot
Fragile X Mental Retardation Protein Is Associated with Translating Polyribosomes in Neuronal Cells
inferredcites →https://doi.org/10.15252/embj.201489947openalex-snapshot
Smg6/Est1 licenses embryonic stem cell differentiation via nonsense‐mediated mRNA decay
inferredcites →https://doi.org/10.15252/embj.201694699openalex-snapshot
Codon identity regulates mRNA stability and translation efficiency during the maternal‐to‐zygotic transition
inferredcites →https://doi.org/10.15252/embr.201948220openalex-snapshot
Codon bias confers stability to human mRNAs
inferredcites →https://doi.org/10.18129/b9.bioc.biostringsopenalex-snapshot
Biostrings
inferredcites →https://doi.org/10.3389/fnmol.2018.00282openalex-snapshot
Targeted Reactivation of FMR1 Transcription in Fragile X Syndrome Embryonic Stem Cells
inferredcites →https://doi.org/10.7554/elife.26129openalex-snapshot
FXR1 regulates transcription and is required for growth of human cancer cells with TP53/FXR2 homozygous deletion
inferredcites →https://doi.org/10.7554/elife.45396openalex-snapshot
Translation affects mRNA stability in a codon-dependent manner in human cells
inferredcites →https://doi.org/10.7554/elife.46919openalex-snapshot
FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory
inferredcites →https://doi.org/10.7554/elife.49708openalex-snapshot
GC content shapes mRNA storage and decay in human cells

What points at this work

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

inferred← citeshttps://doi.org/10.1101/2020.10.16.341222openalex-snapshot
Translation-dependent and independent mRNA decay occur through mutually exclusive pathways that are defined by ribosome density during T Cell activation
inferred← citeshttps://doi.org/10.1186/s13229-020-00384-9openalex-snapshot
Ribosome profiling in mouse hippocampus: plasticity-induced regulation and bidirectional control by TSC2 and FMRP
inferred← citeshttps://doi.org/10.1371/journal.pgen.1010221openalex-snapshot
Single cell transcriptomics reveals dysregulated cellular and molecular networks in a fragile X syndrome model
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