@article {53,
	title = {Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function.},
	journal = {Neuron},
	volume = {101},
	year = {2019},
	month = {2019 Feb 20},
	pages = {707-720.e5},
	abstract = {<p>RNA-binding proteins (RBPs) regulate genetic diversity, but the degree to which they do so in individual cell types in~vivo is unknown. We developed NOVA2 cTag-crosslinking and immunoprecipitation (CLIP) to generate functional RBP-RNA maps from different neuronal populations in the mouse brain. Combining cell type datasets from Nova2-cTag and Nova2 conditional knockout mice revealed differential NOVA2 regulatory actions on alternative splicing (AS) on the same transcripts expressed in different neurons. This includes functional differences in transcripts expressed in cortical and cerebellar excitatory versus inhibitory neurons, where we find NOVA2 is required for, respectively, development of laminar structure, motor coordination, and synapse formation. We also find that NOVA2-regulated AS is coupled to NOVA2 regulation of intron retention in hundreds of transcripts, which can sequester the trans-acting splicing factor PTBP2. In summary, cTag-CLIP complements single-cell RNA sequencing (RNA-seq) studies by providing a means for understanding RNA regulation of functional cell diversity.</p>},
	issn = {1097-4199},
	doi = {10.1016/j.neuron.2018.12.019},
	author = {Saito, Yuhki and Yuan, Yuan and Zucker-Scharff, Ilana and Fak, John J and Jereb, Sa{\v s}a and Tajima, Yoko and Licatalosi, Donny D and Darnell, Robert B}
}
@article {39,
	title = {Differential 3{\textquoteright} Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types.},
	journal = {Elife},
	volume = {7},
	year = {2018},
	month = {2018 Mar 26},
	abstract = {<p>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{\textquoteright}UTR length. We characterize , a transcript that shifted from expressing a short 3{\textquoteright}UTR isoform to a longer one during granule cell differentiation. We show that  regulates granule cell precursor proliferation and that its long 3{\textquoteright}UTR 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.</p>},
	issn = {2050-084X},
	doi = {10.7554/eLife.34042},
	author = {Jereb, Sa{\v s}a and Hwang, Hun-Way and Van Otterloo, Eric and Govek, Eve-Ellen and Fak, John J and Yuan, Yuan and Hatten, Mary E and Darnell, Robert B}
}
