Mutations of the Drosophila melanogaster suppressor of sable [su(s)] gene, which encodes a 150-kDa nuclear protein [Su(s)], increase the accumulation of specific transcripts in a manner that is not well understood but that appears to involve pre-mRNA processing. Here, we report biochemical analysis of purified, recombinant Su(s) [rSu(s)] expressed in baculovirus and in Escherichia coli as maltose binding protein (MBP) fusions and immunocytochemical analysis of endogenous Su(s). This work has shown that purified, baculovirus-expressed rSu(s) binds to RNA in vitro with a high affinity and limited specificity. Systematic evolution of ligands by exponential enrichment was used to identify preferred RNA targets of rSu(s), and a large proportion of RNAs isolated contain a full or partial match to the consensus sequence UCAGUAGUCU, which was confirmed to be a high-affinity rSu(s) binding site. An MBP-Su(s) fusion protein containing the N-terminal third of Su(s) binds RNAs containing this sequence with a higher specificity than full-length, baculovirus-expressed rSu(s). The consensus sequence resembles both a cryptic 5 splice site and a sequence that is found near the 5 end of some Drosophila transcripts. Immunolocalization studies showed that endogenous Su(s) is distributed in a reticulated pattern in Drosophila embryo and salivary gland nuclei. In salivary gland cells, Su(s) is found both in the nucleoplasm and in association with a subset of polytene chromosome bands. Considering these and previous results, we propose two models to explain how su(s) mutations affect nuclear pre-mRNA processing.The Drosophila melanogaster suppressor of sable [su(s)] gene is one of a group of recessive suppressors that, when mutated, modify phenotypes associated with transposon insertion mutations at particular genes (reviewed in reference 38). Upon further examination at the molecular level, it has become apparent that these suppressor genes encode proteins that function more generally in regulating specific aspects of transcription and pre-mRNA processing. For example, suppressor of white-apricot [su(w a )] encodes an alternative splicing factor (47), and the protein encoded by suppressor of forked [su(f)] is homologous to a human polyadenylation factor subunit (40). The su(s) gene encodes a 150-kDa nuclear protein [Su(s)] with relatively little homology to other known proteins. Voelker et al. (43) identified a region within su(s) encoding 77 amino acids that is 28.6% identical to a region in the Drosophila U1 70K protein (23). This region of U1 70K is thought to be an Arg-Ser domain, which is found in numerous splicing factors (2, 11). Although the corresponding region of Su(s) contains two Argrich clusters, the characteristic Arg-Ser dipeptides are virtually absent from Su(s). Thus, the observed similarity between Su(s) and U1 70K may or may not be functionally significant. Voelker et al. (43) also identified a region of Su(s) with weak homology to an RNA recognition motif (RRM). More recently, this region of su(s) was reexamined, ...