The primary antibodies used were mouse monoclonal anti-Dscam (Shi et al., 2007), rabbit polyclonal anti-GFP (Invitrogen), mouse monoclonal anti-tubulin (Sigma), mouse monoclonal anti-dFMRP (Developmental Studies Hybridoma Bank), rat monoclonal anti-Elav (Developmental Studies Hybridoma Bank), and mouse monoclonal anti-βGal (Developmental Studies Hybridoma Bank). Larval brains (∼150) were dissected from wandering third instars
in PBS and washed two times with PBS. Crude homogenates were generated by homogenizing brains in lysis buffer (50 mM Tris/HCl [pH 7.5]; 150 mM KCl; 1 mM EDTA; 0.5% TX100) in the presence of RNase Veliparib manufacturer inhibitor and protease inhibitor and centrifuged for 30 min at 20,000 × g, 4°C.
The equal amount of supernatant was incubated for 1 hr at 4°C with Dynabeads Protein-G (Life Technologies) precoupled GSI-IX mouse with same amount of monoclonal anti-dFMRP antibody 5B6 (Developmental Studies Hybridoma Bank) or normal mouse IgG as a negative control. Beads were washed five times with lysis buffer, supplemented with 10 μg glycogen (Invitrogen) and 10 pg of firefly luciferase mRNA (Promega), and then processed for RNA extraction. Total RNA was extracted from brains of third-instar larvae, using a standard Trizol protocol (Invitrogen). First-strand cDNA was synthesized with Invitrogen SuperScript III First-Strand Synthesis SuperMix (Invitrogen). cDNA from 10 ng RNA was used for each real-time PCR reaction (15 μl), using the Absolute QPCR SYBR Green mix (Thermo Scientific) with Applied Biosystems 7300. After the cycle number at the threshold level of log-based fluorescence (Ct) had been collected for each sample, ΔCt for each test gene was calculated by subtracting
the Ct number of the reference gene (elav) from that of the test gene (Cttest-Ctelav) ( Yuan et al., 2006). This normalizes transcript levels of test genes to elav. Our extensive tests showed that hiw mutations do not alter elav or Chmp1 transcript levels. The ΔCt of each test gene was statistically compared between wild-type much and hiw and then converted to fold change. The Mann-Whitney test was used to determine the statistical significance of changes in different transcripts. For RNA-immunoprecipitation, ΔCt for Dscam mRNA was calculated by subtracting the Ct number of the reference mRNA (α-tubulin) from that of Dscam mRNA. We used α-tubulin mRNA as the reference because mammalian α-tubulin mRNA does not bind to FMRP ( Darnell et al., 2011). Three independent RNA immunoprecipitation experiments were done and the values of ΔCt were compared between control antibody and anti-dFMRP antibody by using two-tailed paired Student’s t test.