Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes
Summary: Investigation of translation in rare cell types or subcellular contexts is challenging due to large input requirements for standard approaches. Here, we present “nanoRibo-seq” an optimized approach using 102- to 103-fold less input material than bulk approaches. nanoRibo-seq exhibits rigoro...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-09-01
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| Series: | Cell Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124723010069 |
| _version_ | 1797736867894919168 |
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| author | John E. Froberg Omer Durak Jeffrey D. Macklis |
| author_facet | John E. Froberg Omer Durak Jeffrey D. Macklis |
| author_sort | John E. Froberg |
| collection | DOAJ |
| description | Summary: Investigation of translation in rare cell types or subcellular contexts is challenging due to large input requirements for standard approaches. Here, we present “nanoRibo-seq” an optimized approach using 102- to 103-fold less input material than bulk approaches. nanoRibo-seq exhibits rigorous quality control features consistent with quantification of ribosome protected fragments with as few as 1,000 cells. We compare translatomes of two closely related cortical neuron subtypes, callosal projection neurons (CPN) and subcerebral projection neurons (SCPN), during their early postnatal development. We find that, while translational efficiency is highly correlated between CPN and SCPN, several dozen mRNAs are differentially translated. We further examine upstream open reading frame (uORF) translation and identify that mRNAs involved in synapse organization and axon development are highly enriched for uORF translation in both subtypes. nanoRibo-seq enables investigation of translational regulation of rare cell types in vivo and offers a flexible approach for globally quantifying translation from limited input material. |
| first_indexed | 2024-03-12T13:19:17Z |
| format | Article |
| id | doaj.art-42a16162a3e542219ca4125af0ae847e |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-03-12T13:19:17Z |
| publishDate | 2023-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-42a16162a3e542219ca4125af0ae847e2023-08-26T04:43:13ZengElsevierCell Reports2211-12472023-09-01429112995Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genesJohn E. Froberg0Omer Durak1Jeffrey D. Macklis2Department of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA 02138, USADepartment of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA 02138, USADepartment of Stem Cell and Regenerative Biology, and Center for Brain Science, Harvard University, Cambridge, MA 02138, USA; Corresponding authorSummary: Investigation of translation in rare cell types or subcellular contexts is challenging due to large input requirements for standard approaches. Here, we present “nanoRibo-seq” an optimized approach using 102- to 103-fold less input material than bulk approaches. nanoRibo-seq exhibits rigorous quality control features consistent with quantification of ribosome protected fragments with as few as 1,000 cells. We compare translatomes of two closely related cortical neuron subtypes, callosal projection neurons (CPN) and subcerebral projection neurons (SCPN), during their early postnatal development. We find that, while translational efficiency is highly correlated between CPN and SCPN, several dozen mRNAs are differentially translated. We further examine upstream open reading frame (uORF) translation and identify that mRNAs involved in synapse organization and axon development are highly enriched for uORF translation in both subtypes. nanoRibo-seq enables investigation of translational regulation of rare cell types in vivo and offers a flexible approach for globally quantifying translation from limited input material.http://www.sciencedirect.com/science/article/pii/S2211124723010069CP: Neuroscience |
| spellingShingle | John E. Froberg Omer Durak Jeffrey D. Macklis Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes Cell Reports CP: Neuroscience |
| title | Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
| title_full | Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
| title_fullStr | Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
| title_full_unstemmed | Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
| title_short | Development of nanoRibo-seq enables study of regulated translation by cortical neuron subtypes, showing uORF translation in synaptic-axonal genes |
| title_sort | development of nanoribo seq enables study of regulated translation by cortical neuron subtypes showing uorf translation in synaptic axonal genes |
| topic | CP: Neuroscience |
| url | http://www.sciencedirect.com/science/article/pii/S2211124723010069 |
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