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Fig. 4 | Genome Biology

Fig. 4

From: Cell type-specific CLIP reveals that NOVA regulates cytoskeleton interactions in motoneurons

Fig. 4

MN-specific NOVA binding correlates with MN-specific alternative splicing. a Venn diagram showing overlap between cassette exons differentially spliced in MN and known Nova targets [20] among all expressed alternative exons (see “Methods”). P value is calculated by hypergeometric test. b Illustration of cytoskeleton structures in part of a dendrite and a dendritic spine. Actin filaments are represented in red, microtubules in green, and spectrin in navy. Differentially regulated MN NOVA targets are represented in colors corresponding to their interacting cytoskeletal component(s). c, d UCSC genome browser images illustrating correlation between differential NOVA binding and MN-specific alternative splicing in the cases of Mtss1 E12 (c) and Kcnc3 E3a (d). The YCAY track demarcates clusters of Nova-binding motifs. WSC and MN RNA-seq tracks are RNA-seq results from 3-month-old whole spinal cord (this study) and laser dissected motoneurons [36], respectively, with biological replicates pooled. For alternative splicing visualization, these two tracks share the same maximum heights of flanking exons. Exons differentially spliced (FDR ≤ 0.1) in MNs versus WSC are highlighted in red boxes. The WSC and MN CLIP tracks are pooled HITS-CLIP results, normalized for the given regions so that the highest unchanged peaks in WSC and MN share the same height. Read coverage of RNA-seq and CLIP are scaled on the right axes from zero to the indicated reads per million. Significantly different NOVA binding sites between MNs and WSC (FDR ≤ 0.1) are marked by arrowheads. UCSC gene annotation and transcript direction are shown at the bottom of each panel, with alternative exons marked in gray. For Mtss1 E12, an increase of the NOVA peak (arrowhead) immediately upstream in MNs correlates with increased E12b inclusion in MNs. Similarly, a dramatic increase of NOVA binding immediately downstream of Kcnc3 E3a (arrowhead) correlates with activated E3a splicing in MNs

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