While investigating possible relationships between nonsense-mediated mRNA decay and RNAi, we noticed that some smg mutants have altered responses to RNAi. Feeding RNAi targeting either unc-54 or dpy-13 (but not unc-22) is more efficient in some, but not all, smg mutants. “More efficient” describes RNAi responses that are intermediate between the strongly enhanced RNAi of eri-1(mg366) (enhanced RNA interference) and a “normal” RNAi response of our N2 strain. Twelve of 23 smg mutants, including all five tested alleles of smg-1, exhibited more efficient RNAi when compared to N2. RNAi efficiency of the remaining 11 smg mutants, including alleles of smg-2, smg-3, smg-4, smg-5, and smg-6, was indistinguishable from N2.
We subsequently discovered that our stock of N2 (hereafter termed N2-Anderson) is less sensitive to feeding RNAi than that of three other N2 stocks, one obtained from the CGC and two obtained from the Scott Kennedy and John White labs. The “more efficient” RNAi of N2-CGC strains is similar to that described above for certain smg mutants. RNAi efficiency of an N2 obtained from Judith Kimble’s lab is indistinguishable from N2-Anderson. These results suggested that N2-Anderson and possibly N2-Kimble contain a modifier of RNAi efficiency. We therefore crossed eri-1(mg366) repeatedly into an N2-Anderson genetic background. RNAi of the resulting strain [eri-1(mg366)-Anderson] is less efficient than that of the starting eri-1(mg366) mutant. Thus, N2-Anderson has a weak Rde (RNAi defective) phenotype that modifies the Eri phenotype of eri-1(mg366).
We recently learned from Harrison Gabel and Gary Ruvkun (Gabel et al., A) of mut-16(mg461) and its subtle Rde phenotype. They kindly communicated the sequences of primers that distinguish mut-16(mg461) from mut-16(+), and we genotyped the several different N2 stocks in our lab. Both N2-Anderson and N2-Kimble contain mut-16(mg461), but N2-CGC does not. Thus, the apparent increased RNAi efficiency of smg mutants described above may be due to decreased RNAi efficiency of N2-Anderson and related strains (see Gabel et al., A and Gabel et al., B for more detailed information).
The presence of mut-16(mg461) in N2-Anderson provides an obvious avenue for its inheritance in current smg strains. We isolated “r” alleles of smg genes in the late 1980s in both N2 and non-N2 genetic backgrounds (for example, transposon-active strains) whose mut-16 genotype has not yet been tested. All smg alleles, however, were outcrossed with N2-Anderson while being cleaned up, and this may have introduced mut-16(mg461) into some backgrounds but not others.
The Anderson and Kimble lab stocks of N2 were brought from the MRC-Cambridge to Madison in the early 1980s. Gabel et al., A (this issue of WGB) demonstrate that CB3388 [ncl-1(e1865)], which was isolated in Cambridge by Ed Hedgecock around 1980, contains mut-16(mg461). If the numerous instances of mut-16(mg461) found in today’s strains are related by descent, then mut-16(mg461) likely existed in at least some Cambridge strains in the early 1980s.
We are presently uncertain whether all differences we observe concerning the efficiency of RNAi in smg mutants are due to mut-16(mg461), but it seems possible, and we’re currently genotyping mut-16(mg461) in a number of key strains.