Figure 3.
Identification of CFM2's RNA Ligands in Coimmunoprecipitation Assays.
(A) Summary of RIP-chip data. The median log2-transformed enrichment ratios (F635/F532) for four replicate CFM2 RIP-chip assays (two with each of two CFM2 antisera) are plotted according to chromosomal position (black line). The median ratios for two negative control immunoprecipitations (one with antibody to OE16 and one with antibody to OE23) are shown for comparison (gray line). Fragments for which fewer than two replicate spots per array yielded an F532 signal above background were excluded and appear as gaps in the curve.
(B) Validation of CFM2's RNA ligands by slot blot hybridization. RNA purified from the pellets and supernatants of immunoprecipitations with antisera to the indicated proteins was hybridized to the indicated intron-specific probes. Immunoprecipitations with CRS1 and OE23 antisera and probing for the trnG-UCC intron served as negative controls. The two anti-CFM2 immunoprecipitations used antibodies from different immunized rabbits. The same fraction of the pellet and supernatant samples was applied to the membrane. Differences in the maximal enrichment observed for ycf3-int1, ndhA-int, and trnL-int are not unexpected because the fraction of the RNA pool bound to CFM2 could differ in each case.