On the basis of mutational analyses in yeast, the highly conserved ACAGAGA sequence of U6 small nuclear RNA (snRNA) and the adjacent U6-U2 helix I have been proposed to be part of the active center of the spliceosome. We report here a detailed analysis of the human U6 snRNA sequence requirements during the first and second step of splicing, using a mammalian in vitro splicing-complementation system and a mutational approach. Positions A53G"4C-" (helix Ib) were identified as important specifically for the first step, but not for spliceosome assembly. A45 of the ACAGAGA sequence and U52 of helix Ia function during the second step; in addition, the bulge separating helices Ia and lb appears critical for the second step. In contrast, no splicing-essential sequences could be identified in the central domain upstream of the ACAGAGA sequence. In sum, our data demonstrate for the mammalian splicing system that discrete positions within the ACAGAGA sequence and helix I of U6 snRNA function during the first and second step of splicing, suggesting that these two sequence elements are closely associated with the catalytic center of the spliceosome. Comparison with previous results in yeast indicates a fundamental conservation of the U6 snRNA function in the pre-mRNA splicing mechanism.Nuclear pre-mRNA splicing involves two sequential transesterification reactions, resulting in mature mRNA and the intron lariat (for review, see refs. 1-3). Before the two steps of splicing, the pre-mRNA has to be assembled into a highly complex ribonucleoprotein structure, the spliceosome (for review, see ref. 4). Spliceosome assembly occurs through an ordered, multistep pathway requiring many splicing factors, among them four small nuclear ribonucleoproteins (U1, U2, U4/U6, and U5 snRNPs). Nuclear pre-mRNA splicing and autocatalytic self-splicing processes are mechanistically similar, which has led to the hypothesis that they are evolutionarly related (5, 6). Specifically, the small nuclear RNA (snRNA) components of the spliceosome may have functionally replaced conserved intron structures of groups I and II self-splicing RNAs (for review, see ref. 7).A strong candidate for a catalytically active component of the spliceosome is U6 RNA, which is the most conserved snRNA (8). An unusual feature of U6 is that it undergoes several conformational transitions during the spliceosome cycle, including a singular form of U6 (9), a U4-U6 basepaired structure (9, 10), and a spliceosomal U6-U2 conformation (11). The latter conformation contains helix I, where the stem I region of U6 and a sequence near the 5' end of U2 RNA interact (11); in this context the U6 stem II region can refold into an intramolecular stem-loop (12); an additional U6-U2 interaction (helix II) forms between sequences near the 3' end of U6 and the 5' end of U2 (13,14). The current model of the active spliceosome implies that the U6-U2 structure is closely associated with the catalytic center, based on the following evidence: (i) Mutational analyses in yeast have shown that U...