Figure 4

Alternative splicing in the early embryo. (a) The frequency of 4 different alternative splicing events: Exon skipping (ES), alternative acceptor site (AA), alternative donor site (AD) and intron retention (IR). ES is the most frequent AS event. In most ES events multiple exons are skipped. (b) Schematic representation of an annotated version (top) and a new (bottom) isoform for dnmt1. Black lines between the isoforms represent the conserved area. Functional domains (white bars) were defined by Pfam: DMAP1 binding domain (DMAP1-BD, PF06464), Cytosine specific methyltransferase replication foci domain (Cyt MeTrfase1 RFD, PF12047), CXXC zinc finger domain (“CX”: Znf CXXC, PF02008), Bromo-adjacent homology domain (BAH, PF01426), C-5 cytosine-specific DNA methylase domain (C5_ MeTfrase, PF00145). In the new isoform 19 exons are skipped, and all functional domains except a DMAP1 binding domain are lost. The novel isoform also have a longer 5’UTR relative to the annotated version. (c) Novel pou5f1 isoforms. The annotated version of pou5f1 has two Pfam domains; Homeobox domain (HB, PF00046) and POU (PF00157). We identify 3 novel alternative acceptor sites (arrows 1–3) all within the CDS of pou5f1. The first leads to a 3 nt deletion and removal of one glutamic acid, upstream of the POU; the second a 19 nt insertion causing a frame shift and a truncated Pou5f1 protein with both functional domains lost; the third event gives a 4 nt deletion which truncates the HB. We also detect a longer 3’ UTR post-ZGA (arrow 4).