a, Chromosome 2 RefSeq genes and CLIP tags from the neocortex of two mouse littermates (Brain A, 46,106 tags in 10,740 clusters; Brain B, 100,874 tags in 15,805 clusters). b, Cluster Density (#tags/cluster length; black) in the Grin1 transcript; c, (i) Grin1 E4 and (ii) E19 tags, one color per biologic replicate, predict Nova-dependent exon skipping and inclusion, respectively (experimental validation20 is shown).

a, CLIP tags around all known Nova-regulated cassette exons; one color per transcript. Tags were mapped onto a composite transcript containing an alternative (dark blue/red box) and flanking constitutive (light blue box) exons. Tags are from transcripts showing Nova-dependent exon inclusion (top panel) or exclusion (bottom panel); experimental validation is shown (insets). b, Normalized complexity map (see methods) of Nova-RNA interactions recapitulate predicted maps18 (insets) for Nova-dependent exon inclusion (red) or exclusion (blue).

a, Distribution of Nova CLIP tag clusters (RefSeq mm8; CDS refers to introns/exons between UTRs). b, Intergenic clusters were plotted relative to the closest annotated start (5′ end) or stop (3′ end) codon. c, Distribution of 2,465 clusters in 3′ UTRs (defined as distance from stop codon to closest transcript termination site). d, CLIP tag clusters relative to the closest poly(A) site (transcript end in UCSC known genes), plotted as clusters per 50 nt in 2,465 3′ UTRs (green bars) or in 43 Nova-dependent 3′ UTRs identified with exon arrays (black bars).

a, Nova CLIP tags near Cugbp2 poly(A) site 2 (pA2); each color represents a biologic replicate. Right panel: RPA measuring cleavage at pA2 in WT (+/+), Nova2 heterozygous (+/−) and KO (−/−) P10 neocortex, with actin as a normalization control and ΔC (see text) shown. b, qRT-PCR validation of Nova-dependent poly(A) regulation, using RNA from three WT or Nova2 KO littermates, presented as long 3′ UTR isoform relative to total transcript abundance, normalized to WT (1.0; dotted line); error bars represent standard deviation. c-d, Composite (c) and normalized complexity (d) maps for Nova-regulated alternative polyadenylation sites (as in Fig. 2). e, Nova binds YCAY elements to directly regulate alternative polyadenylation. Left panel: qRT-PCR analysis of cells transfected with WT or Mutant (3 YACY mutations) poly(A) reporter constructs cotransfected with a control (−) or Nova2 expressing (+) plasmid, or WT vs. Nova2 KO neocortex (* = p < 0.02, ** = p < 0.01); error bars represent standard deviation. Right panel: RPA for cleavage of Slc8a1 poly(A) site 2, otherwise as described in (a).