MEL-28/ELYS is a large AT-hook protein required for nuclear envelope integrity and chromosome segregation in metazoans. As expected by its fundamental function, MEL-28 is ubiquitously expressed in all cells analyzed. However, mutations in the
mel-28 gene are maternal-effect, causing embryonic lethality in the progeny of homozygous mutant mothers that are otherwise wild-type. Therefore, the function of MEL-28 in most cells is predicted to be buffered by other molecules. To identify additional proteins working with MEL-28 we looked for synthetic phenotypes in
mel-28 homozygous animals using RNAi. The challenge in this type of screen, as with any modifier screen of mel mutants, is to collect large numbers of homozygous animals. To accomplish this in high throughput, we generated a strain with the
mel-28(
t1684) mutation balanced by a GFP-marked chromosome and used a fluorescence-activated cell sorter (FACS) to isolate non-fluorescent
mel-28 homozygous L1 larvae from the rest of the population. Using this approach we have collected, in one sitting, as many as 100,000 larvae, over 99% of which are
mel-28 homozygous. We subjected the
mel-28 larvae to RNAi in 96-well plates and recorded results by high-throughput digital imaging. We present here the results from screening essentially all the genes encoded on Chromosome I. Of the 2260 clones tested, we found 14 that are synthetic sterile with
mel-28. Among these genes we found members of expected molecular complexes. For example, most the nucleoporins known to be on Chromosome I were uncovered. In addition, we find other classes of proteins, like histones, as genetic interactors of
mel-28 suggesting new molecular connections between MEL-28 and chromatin organization. Our results also show that FACS-RNAi screening is a powerful way to uncover tissue-specific roles for pleiotropic genes.