RNA localization is a key determinant of neurite-enriched proteome - Riboseq
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PROVIDER: PRJEB14945 | ENA |
REPOSITORIES: ENA
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Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells.
2017-07-23 | E-MTAB-4979 | biostudies-arrayexpress
Project description:RNA localization is a key determinant of neurite-enriched proteome - RNAseq
| PRJEB14946 | ENA
Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells. Our results reveal mRNA localization as a key determinant of protein localization to neurites that accounts for around a half of the neurite-localized proteome. Moreover, we identify non-coding RNAs and RNA-binding proteins targeted to neurites.
2018-06-06 | PXD004640 | Pride
Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells. Our results reveal mRNA localization as a key determinant of protein localization to neurites that accounts for around a half of the neurite-localized proteome. Moreover, we identify non-coding RNAs and RNA-binding proteins targeted to neurites.
2018-06-06 | PXD004751 | Pride
Project description:RNA localization and local translation are important biological processes that underlie establishment of body axis, cell migration and synaptic plasticity. However, it is unclear to which extent mRNA localization contributes toward local proteome and how much of protein localization is achieved via protein transport or local translation of uniformly distributed mRNAs. To address this question, we performed genome-wide analysis of the local proteome, transcriptome, and translation rates in neurites and cell bodies of neurons differentiated from mouse embryonic stem cells.
2017-07-23 | E-MTAB-4978 | biostudies-arrayexpress
Project description:Protein subcellular localization is fundamental to the establishment of the body axis, cell migration, synaptic plasticity, and a vast range of other biological processes. Protein localization occurs through three mechanisms: protein transport, mRNA localization, and local translation. However, the relative contribution of each process to neuronal polarity remains unknown. Using neurons differentiated from mouse embryonic stem cells, we analyze protein and RNA expression and translation rates in isolated cell bodies and neurites genome-wide. We quantify 7323 proteins and the entire transcriptome, and identify hundreds of neurite-localized proteins and locally translated mRNAs. Our results demonstrate that mRNA localization is the primary mechanism for protein localization in neurites that may account for half of the neurite-localized proteome. Moreover, we identify multiple neurite-targeted non-coding RNAs and RNA-binding proteins with potential regulatory roles. These results provide further insight into the mechanisms underlying the establishment of neuronal polarity.Subcellular localization of RNAs and proteins is important for polarized cells such as neurons. Here the authors differentiate mouse embryonic stem cells into neurons, and analyze the local transcriptome, proteome, and translated transcriptome in their cell bodies and neurites, providing a unique resource for future studies on neuronal polarity.
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Project description:Neurons exploit mRNA localization and local translation to spatio-temporally regulate gene expression during development. Local translation and retrograde transport of transcription factors regulate nuclear gene expression in response to signaling events at distal neuronal ends. Whether epigenetic factors could also be involved in such regulation is not known. We report that the mRNA encoding the high mobility group N5 (HMGN5) chromatin binding protein localizes to growth cones of both neuronal-like cells and of hippocampal neurons. We show that Hmgn5 3’UTR drives growth cone localization and translation of a reporter gene, and that HMGN5 can be retrogradely transported into the nucleus along neurites. Loss of HMGN5 function induces transcriptional changes and impairs neurite outgrowth while HMGN5 overexpression induces neurite outgrowth and global chromatin decompaction. Interestingly, control of both neurite outgrowth and chromatin structure is dependent on proper growth cone localization of Hmgn5 mRNA. Our results provide the first evidence that mRNA localization and local translation might serve as a mechanism to couple the dynamic neuronal outgrowth process with chromatin regulation in the nucleus.
2015-03-26 | GSE57185 | GEO
Project description:Neurons exploit local mRNA translation and retrograde transport of transcription factors to regulate gene expression in response to signaling events at distal neuronal ends. Whether epigenetic factors could also be involved in such regulation is not known. We report that the mRNA encoding the HMGN5 chromatin binding protein localizes to growth cones of both neuronal-like cells and of hippocampal neurons, where it has the potential to be translated, and that HMGN5 can be retrogradely transported into the nucleus along neurites. Loss of HMGN5 function induces transcriptional changes and impairs neurite outgrowth while HMGN5 overexpression induces neurite outgrowth and chromatin decompaction. Interestingly, control of both neurite outgrowth and chromatin structure is dependent on growth cone localization of Hmgn5 mRNA. Our results provide the first evidence that mRNA localization and local translation might serve as a mechanism to couple the dynamic neuronal outgrowth process with chromatin regulation in the nucleus.
2015-04-17 | PXD001070 | Pride
Project description:blanc09_ripseq_rfl8-riboseq analysis of the rfl8 mutant-Which mitochondrial transcripts are bound by RFL8 protein? -Does the RFL8 loss impact on mitochondrial translation?
2021-04-27 | GSE166446 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE9738: Analysis of gene expression during neurite outgrowth and regeneration (430A and 420A 2.0 array); GSE9739: Analysis of gene expression during neurite outgrowth and regeneration (MG-U74A); GSE9740: Analysis of gene expression during neurite outgrowth and regeneration MG-U74B Experiment Overall Design: Refer to individual Series
2008-04-10 | E-GEOD-9744 | biostudies-arrayexpress