2019
DOI: 10.1016/j.cell.2019.09.004
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RETRACTED: Genomic Decoding of Neuronal Depolarization by Stimulus-Specific NPAS4 Heterodimers

Abstract: Cells regulate gene expression in response to salient external stimuli. In neurons, depolarization leads to the expression of inducible transcription factors (ITFs) that direct subsequent gene regulation. Depolarization encodes both a neuron's action potential (AP) output and synaptic inputs, via excitatory postsynaptic potentials (EPSPs). However, it is unclear if distinct types of electrical activity can be transformed by an ITF into distinct modes of genomic regulation. Here, we show that APs and EPSPs in m… Show more

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Cited by 75 publications
(59 citation statements)
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“…Advanced techniques, such as MCP-FP (MS2 bacteriophage coat protein-FP), λN-FP (N protein of bacteriophage λ-FP), RCas9-FP (dead RNA Cas9-FP), and fluorescent RNA aptamer system, have allowed visualization of RNA trafficking in live cells. Co-expression of a MCP-FP or λN-FP protein construct and a reporter construct containing phage protein binding motif sequence upstream of 3′ UTR of interest allowed tracking of mRNA localization in live cells [75,76]. Simultaneous delivery of RCas9-FP and target-specific single guide RNA allowed binding of the Cas9 to the mRNA of interest and visual tracking of endogenous mRNAs in live cells [77].…”
Section: Box 2 Experimental Approaches To Study Localization Of Mrnasmentioning
confidence: 99%
“…Advanced techniques, such as MCP-FP (MS2 bacteriophage coat protein-FP), λN-FP (N protein of bacteriophage λ-FP), RCas9-FP (dead RNA Cas9-FP), and fluorescent RNA aptamer system, have allowed visualization of RNA trafficking in live cells. Co-expression of a MCP-FP or λN-FP protein construct and a reporter construct containing phage protein binding motif sequence upstream of 3′ UTR of interest allowed tracking of mRNA localization in live cells [75,76]. Simultaneous delivery of RCas9-FP and target-specific single guide RNA allowed binding of the Cas9 to the mRNA of interest and visual tracking of endogenous mRNAs in live cells [77].…”
Section: Box 2 Experimental Approaches To Study Localization Of Mrnasmentioning
confidence: 99%
“…In this study, we implemented a proximity-ligation assay to systematically characterize changes in the nuclear proteome triggered by neuronal stimulation. While advances in transcriptomic technologies have enabled the identification of genes that undergo activitydependent changes in expression (Brigidi et al, 2019;Chen et al, 2017;Fernandez-Albert et al, 2019;Tyssowski et al, 2018), the systematic identification of proteins that undergo changes in subcellular localization and/or stability has been more challenging. Our results provide the first, to our knowledge, unbiased characterization of the population of proteins that undergo changes in nuclear abundance following neuronal silencing and/or glutamatergic stimulation, and does so in a manner that is independent of translation or transcription.…”
Section: Discussionmentioning
confidence: 99%
“…. While the activity-dependent transcriptome and translatome of neurons has been characterized using RNA sequencing (Brigidi et al, 2019;Hrvatin et al, 2018;Lacar et al, 2016;Tyssowski et al, 2018) and TRAP-seq (Chen et al, 2017;Fernandez-Albert et al, 2019), little work has been done to characterize the population of proteins that undergo activity-dependent changes in nuclear abundance due to regulated transport or stability. By inhibiting translation to exclude changes due to protein synthesis, the present study focused on identifying pre-existing proteins that undergo activitydependent changes in concentration in the nucleus via regulated nucleocytoplasmic trafficking and/or changes in stability.…”
mentioning
confidence: 99%
“…where a modified TF does not bind as well to its canonical motif. Here, de novo motif finding methods can recover the true binding motif, then MEIRLOP can determine enrichment of this motif, as performed in Bloodgood et al [59].…”
Section: Discussionmentioning
confidence: 99%