Identification of known and novel promoters and transcripts expressed in the cerebellum. (A) Integrative approach for the identification of promoter and corresponding transcript inventory used in mouse cerebella after birth. We performed mRNA-seq and ChIP-seq experiments with antibodies against Pol II, H3K4me3, and H3K27me3. The flowchart indicates the multiple steps we followed to determine the promoterome and transcriptome of each postnatal stage during cerebellum development. (B) An example of a novel promoter and corresponding transcript identified through the integrative approach. Smarcd3 is also expressed from a novel upstream promoter that was identified by promoter prediction on both the Pol II and H3K4me3 enrichment profiles (blue arrows), and the expression of the corresponding transcript was determined from mRNA-seq profiles (red arrows). It is worth noting that the novel promoter and transcript is known in humans and is also supported by novel gene models of mouse.
