Transcriptome-wide survey of binding partner of slam protein in early Drosophila embryos

Purpose: Slam protein and RNA co-localize in early drosophila embryos. slam RNA specifically co-immunoprecipitates with its own protein from embryonic lysate as shown by RNA-IP and QRT-PCR. The goal of this study is to survey transcriptome wide (RNA-seq) targets of slam protein and validate the data from qRT–PCR analysis. Methods: RNA-ip was performed for staged embryos (1.5 – 3 h after egg laying) Using slam antibody or GFP binder. RNA profiles in immune-predicates were generated by deep sequencing. Results: Slam RNA specifically co-predicates with slam protein as shown by both next generation sequencing and RT-QPCR. No mRNA of other genes was detected in all independent experiments or showed the averaged enrichment in the same range. Compare the RNA profile from two independent experiments: Expt1. Wild type embryos, slam Ab (3x) and Diaphanous Ab (control, 4x)) for RNA pull down. Expt2. Wild type embryos (3x) and GFP-Slam transgenic embryos (2x), GFP-binder for RNA pull down.