cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation.

TitlecTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation.
Publication TypeJournal Article
Year of Publication2017
AuthorsHwang, H-W, Saito, Y, Park, CY, Blachère, NE, Tajima, Y, Fak, JJ, Zucker-Scharff, I, Darnell, RB
JournalNeuron
Volume95
Issue6
Pagination1334-1349.e5
Date Published2017 Sep 13
ISSN1097-4199
KeywordsAnimals, Antigens, Neoplasm, Astrocytes, Brain, Cells, Cultured, Female, Humans, Male, Mice, Microglia, Nerve Tissue Proteins, Neurons, Organ Specificity, Polyadenylation, Polypyrimidine Tract-Binding Protein, Protein Isoforms, Protein-Serine-Threonine Kinases, RNA-Binding Proteins
Abstract

Alternative polyadenylation (APA) is increasingly recognized to regulate gene expression across different cell types, but obtaining APA maps from individual cell types typically requires prior purification, a stressful procedure that can itself alter cellular states. Here, we describe a new platform, cTag-PAPERCLIP, that generates APA profiles from single cell populations in intact tissues; cTag-PAPERCLIP requires no tissue dissociation and preserves transcripts in native states. Applying cTag-PAPERCLIP to profile four major cell types in the mouse brain revealed common APA preferences between excitatory and inhibitory neurons distinct from astrocytes and microglia, regulated in part by neuron-specific RNA-binding proteins NOVA2 and PTBP2. We further identified a role of APA in switching Araf protein isoforms during microglia activation, impacting production of downstream inflammatory cytokines. Our results demonstrate the broad applicability of cTag-PAPERCLIP and a previously undiscovered role of APA in contributing to protein diversity between different cell types and cellular states within the brain.

DOI10.1016/j.neuron.2017.08.024
Alternate JournalNeuron
PubMed ID28910620
PubMed Central IDPMC5637551
Grant ListR01 NS081706 / NS / NINDS NIH HHS / United States
UM1 HG008901 / HG / NHGRI NIH HHS / United States
R01 NS034389 / NS / NINDS NIH HHS / United States
R35 NS097404 / NS / NINDS NIH HHS / United States
R56 NS034389 / NS / NINDS NIH HHS / United States