FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons
- Rockefeller University, United States
Abstract
Neurons rely on translation of synaptic mRNAs in order to generate activity-dependent changes in plasticity. Here we develop a strategy combining compartment-specific CLIP and TRAP in conditionally tagged mice to precisely define the ribosome-bound dendritic transcriptome of CA1 pyramidal neurons. We identify CA1 dendritic transcripts with differentially localized mRNA isoforms generated by alternative polyadenylation and alternative splicing, including many which have altered protein-coding capacity. Among dendritic mRNAs, FMRP targets were found to be overrepresented. Cell-type specific FMRP-CLIP and TRAP in microdissected CA1 neuropil revealed 383 dendritic FMRP targets and suggests that FMRP differentially regulates functionally distinct modules in CA1 dendrites and cell bodies. FMRP regulates ~15-20% of mRNAs encoding synaptic functions and 10% of chromatin modulators, in the dendrite and cell body, respectively. In the absence of FMRP, dendritic FMRP targets had increased ribosome association, consistent with a function for FMRP in synaptic translational repression. Conversely, downregulation of FMRP targets involved in chromatin regulation in cell bodies and suggest a role for FMRP in stabilizing mRNAs containing stalled ribosomes in this compartment. Together, the data support a model in which FMRP regulates the translation and expression of synaptic and nuclear proteins within different compartments of a single neuronal cell type.
Data availability
Sequencing data have been deposited in GEO under accession code GSE174303, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174303, token: qbqdiogwzxuflob
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Cell-type and compartment-specific TRAP-seq, RNAseq, FMRP-CLIP, and PAPERCLIP from mouse microdissected CA1.NCBI Gene Expression Omnibus, GSE174303.
Article and author information
Author details
Funding
Leon Levy Foundation
- Caryn R Hale
Simons Foundation
- Caryn R Hale
- Kirsty Sawicka
- Kevin Mora
- John J Fak
- Jin Joo Kang
- Paula Cutrim
- Robert B Darnell
National Institute of General Medical Sciences (R35NS097404)
- Caryn R Hale
- Kirsty Sawicka
- Kevin Mora
- John J Fak
- Jin Joo Kang
- Paula Cutrim
- Robert B Darnell
Howard Hughes Medical Institute
- Robert B Darnell
National Institutes of Health (NS081706)
- Caryn R Hale
- Kirsty Sawicka
- Kevin Mora
- John J Fak
- Jin Joo Kang
- Paula Cutrim
- Robert B Darnell
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Ethics
Animal experimentation: All mouse procedures were conducted according to the Institutional Animal Care and Use Committee (IACUC) guidelines at the Rockefeller University using protocol numbers 14678, 17013 and 20028.
Copyright
© 2021, Hale et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons
eLife 10:e71892.
https://doi.org/10.7554/eLife.71892
