Splicing of mRNA precursors consists of two steps that are almost invariably tightly coupled to facilitate efficient generation of spliced mRNA. However, we described previously a splicing substrate that is completely blocked after the first step. We have now investigated the basis for this unusual second-step inhibition and unexpectedly elucidated two independent mechanisms. One involves a stem-loop structure located downstream of the 3′splice site, and the other involves an exonic splicing silencer (ESS) situated 3′ to the structure. Both elements contribute to the secondstep block in vitro and also cause exon skipping in vivo. Importantly, we identified far upstream element-binding protein 1 (FUBP1), a single-stranded DNA-and RNA-binding protein not previously implicated in splicing, as a strong ESS binding protein, and several assays implicate it in ESS function. We demonstrate using depletion/add-back experiments that FUBP1 acts as a second-step repressor in vitro and show by siRNA-mediated knockdown and overexpression assays that it modulates exon inclusion in vivo. Together, our results provide additional insights into splicing control, and identify FUBP1 as a splicing regulator. R emoval of introns from pre-mRNAs by splicing is a precise process required for the expression of nearly all genes in human cells. Splicing takes place via two sequential transesterification reactions in the spliceosome, a large complex consisting of several hundred proteins and five small nuclear RNAs (1, 2). During the first step, an adenosine residue designated the branch point, attacks the 5′ splice site (5′SS) to generate the splicing intermediates (free exon1 and lariat-exon2). In the second step, the first exon attacks the 3′ splice site (3′SS), yielding ligated exons and a lariat intron.Splicing, like numerous other cellular processes, must be under strict regulatory control. Indeed, aberrant splicing is involved in a wide range of human diseases (3, 4). Besides the core splicing signals, additional cis-regulatory elements play important roles in splicing and its control. These elements exist within exons and introns and can function both positively and negatively (5-7). Two major classes of exonic elements have been identified, known as exonic splicing enhancers (ESEs) and exonic splicing silencers (ESSs), and both of these contribute to regulation of alternative splicing (AS). ESEs are usually bound by members of the serine/arginine-rich (SR) protein family to enhance recognition of adjacent splice sites. By contrast, ESSs function to inhibit the use of adjacent splice sites, and are generally dependent on the interaction with members of the heterogeneous nuclear ribonucleoprotein(hnRNP) family, as well as other splicing regulators such as NOVA1/2 and RBFOX1/2 (8, 9).A good deal is now known about the structure and function of ESSs. For example, several large-scale strategies have been developed to identify and characterize ESSs (10-12). The sequences of known and selected ESSs share little similarity with each other, ...