Additional file 1:Figure S1. of Corepressor diversification by alternative mRNA splicing is species specific
Creators: name: Privalsky, Martin
name: Snyder, Chelsea
name: Goodson, Michael
Publisher: name: Figshare
Year: 2016
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences

description: Electrophoretograms depicting alternative splicing in Danio, Trachemys, Gallus, and Xenopus. Alternative mRNA splicing was analyzed for each species by PCR as described in the Materials and Methods; photographs of representative ethidium bromide-stained electrophoretograms (as employed for our bar-graph quantifications) are shown. (A). Danio liver. (B) Danio whole 84 h. stage hatchling. (C) Trachemys liver. (D) Gallus liver. (E) Xenopus liver. The splice site analyzed is indicated below each lane; colored bars next to the stained DNA bands in each lane identify the splice variants in that lane from largest to smallest at that location (red bars therefore indicate S28+, S40b+, S44+/45+, S47b+, N28+, N37b+, or N45a+; blue bars indicate S28-, S40b-, S44+/45-, S47b-, N28-, N37b-, or 45a-; green bars indicate S44-/45+ or S47-. black bars indicate S44-/45-). “Background” faint DNA bands (not labeled with bars) likely resulted from artifactual cross-hybridization of given PCR primer pairs to irrelevant nucleic acid sites (confirmed by their absence in follow-up PCR analysis using novel primer pairs and/or by DNA sequence analysis). Figure S2. Electrophoretograms depicting alternative splicing in Monodelphis and Mus. The analysis and labeling are as in Additional file 1: Figure S1. (A). Monodelphis liver. (B) Mus liver. (C) Mus brain hypothalamus. Figure S3. Extended survey of alternate splicing in Danio rerio. Primer pairs (detailed in Additional file 1: Table S1) were used to survey potential alternative splicing within the open reading frame of SMRT and NCoR. Brain (A) and liver (B) RNAs were tested. Primers 7 and 8 amplify a partially overlapping region that includes the SMRT 40b+/b‐ alternative splicing already noted in Figs. 2 and 3. Black fill = longest splice variant at that location, diagonal hatching = intermediate length splice variant at that location, open fill = shortest splice variant at that location. Mean and range are shown (n = 2) for each. Figure S4. Alternative splicing in Drosophila melanogaster adults. RNA was extracted, and the alternative splicing at the indicated locations was analyzed using an ordered series of primer pairs that encompass the known coding region (Additional file 1: Table S1 and Fig. S2). No more than two spliced products were detected at any given location. Mean and standard deviation are shown (n = 3) for each. Figure S5. Gene-tree depiction of alternative splicing for SMRT and NCoR. Vertical distance is proportional to the minimal number of events to generate the alternative splicing detected in each lineage at the sites depicted. Each alternative splicing event is labeled as S (SMRT) or N (NCoR) with the number and −/+ symbols indicating the specific exon variant (as in Fig. 1); green text indicates the appearance of that specific splice variant, red text indicates its loss. Vertical boxed black text above each terminal arrow indicates the alternative splice sites utilized in each of the extant species studied here, with the species listed on top in blue; the corepressor configurations predicted in the absence of alternative splicing are indicated in horizontal boxed black text: (N28+,N37b+,N45a + and S28+,S40-,S44+,S45+,S47b+). The presence of an alternative splice variant in a given species was scored as a positive if detected in any of the tissues or whole organism samples used in this study. In all but Danio a given alternative splice variant was present or absent in all the developmental and tissue samples tested for that species (although at differing relative abundances). (PDF 14424 kb)