Differential 3' processing of specific transcripts expands regulatory and protein diversity across neuronal cell types
- The Rockefeller University, United States
- University of Colorado, United States
Abstract
Alternative polyadenylation (APA) regulates mRNA translation, stability, and protein localization. However, it is unclear to what extent APA regulates these processes uniquely in specific cell types. Using a new technique, cTag-PAPERCLIP, we discovered significant differences in APA between the principal types of mouse cerebellar neurons, the Purkinje and granule cells, as well as between proliferating and differentiated granule cells. Transcripts that differed in APA in these comparisons were enriched in key neuronal functions and many differed in coding sequence in addition to 3'UTR length. We characterize Memo1, a transcript that shifted from expressing a short 3'UTR isoform to a longer one during granule cell differentiation. We show that Memo1 regulates granule cell precursor proliferation and that its long 3'TR isoform is targeted by miR-124, contributing to its downregulation during development. Our findings provide insight into roles for APA in specific cell types and establish a platform for further functional studies.
Data availability
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Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell TypesPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE108480).
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MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous systemPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE42880).
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Role of Tet1/3 Genes and Chromatin Remodeling Genes in Cerebellar Circuit FormationPublicly available at the NCBI Gene Expression Omnibus (accession no: GSE74402).
Article and author information
Author details
Funding
National Institutes of Health (NS034389)
- Robert B Darnell
Howard Hughes Medical Institute
- Robert B Darnell
Simons Foundation (SFARI 240432)
- Robert B Darnell
National Institute of Dental and Craniofacial Research (K99DE026823)
- Eric Van Otterloo
National Institutes of Health (NS081706)
- Robert B Darnell
National Institutes of Health (NS097404)
- Robert B Darnell
National Institutes of Health (1UM1HG008901)
- 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: Animals were maintained in an AAALAC-approved animal facility and all procedures were performed in accordance with IACUC guidelines (protocol number 17013).
Copyright
© 2018, Jereb 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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Differential 3' processing of specific transcripts expands regulatory and protein diversity across neuronal cell types
eLife 7:e34042.
https://doi.org/10.7554/eLife.34042
Further reading
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Cerebellar dysfunction leads to postural instability. Recent work in freely moving rodents has transformed investigations of cerebellar contributions to posture. However, the combined complexity of terrestrial locomotion and the rodent cerebellum motivate new approaches to perturb cerebellar function in simpler vertebrates. Here, we adapted a validated chemogenetic tool (TRPV1/capsaicin) to describe the role of Purkinje cells — the output neurons of the cerebellar cortex — as larval zebrafish swam freely in depth. We achieved both bidirectional control (activation and ablation) of Purkinje cells while performing quantitative high-throughput assessment of posture and locomotion. Activation modified postural control in the pitch (nose-up/nose-down) axis. Similarly, ablations disrupted pitch-axis posture and fin-body coordination responsible for climbs. Postural disruption was more widespread in older larvae, offering a window into emergent roles for the developing cerebellum in the control of posture. Finally, we found that activity in Purkinje cells could individually and collectively encode tilt direction, a key feature of postural control neurons. Our findings delineate an expected role for the cerebellum in postural control and vestibular sensation in larval zebrafish, establishing the validity of TRPV1/capsaicin-mediated perturbations in a simple, genetically tractable vertebrate. Moreover, by comparing the contributions of Purkinje cell ablations to posture in time, we uncover signatures of emerging cerebellar control of posture across early development. This work takes a major step towards understanding an ancestral role of the cerebellum in regulating postural maturation.
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