Exposure of Escherichia coli to a variety of DNA‐damaging agents results in the induction of the global ‘SOS response’. Expression of many of the genes in the SOS regulon are controlled by the LexA protein. LexA acts as a transcriptional repressor of these unlinked genes by binding to specific sequences (LexA boxes) located within the promoter region of each LexA‐regulated gene. Alignment of 20 LexA binding sites found in the E. coli chromosome reveals a consensus of 5′‐TACTG(TA)5CAGTA‐3′. DNA sequences that exhibit a close match to the consensus are said to have a low heterology index and bind LexA tightly, whereas those that are more diverged have a high heterology index and are not expected to bind LexA. By using this heterology index, together with other search criteria, such as the location of the putative LexA box relative to a gene or to promoter elements, we have performed computational searches of the entire E. coli genome to identify novel LexA‐regulated genes. These searches identified a total of 69 potential LexA‐regulated genes/operons with a heterology index of < 15 and included all previously characterized LexA‐regulated genes. Probes were made to the remaining genes, and these were screened by Northern analysis for damage‐inducible gene expression in a wild‐type lexA+ cell, constitutive expression in a lexA(Def) cell and basal expression in a non‐inducible lexA(Ind−) cell. These experiments have allowed us to identify seven new LexA‐regulated genes, thus bringing the present number of genes in the E. coli LexA regulon to 31. The potential function of each newly identified LexA‐regulated gene is discussed.

The access to DNA within nucleosomes is greatly restricted for most enzymes and trans-acting factors that bind DNA. We report here that human DNA ligase I, which carries out the ®nal step of Okazaki fragment processing and of many DNA repair pathways, can access DNA that is wrapped about the surface of a nucleosome in vitro and carry out its enzymatic function with high ef®ciency. In addition, we ®nd that ligase activity is not affected by the binding of linker histone (H1) but is greatly in¯uenced by the disposition of the core histone tail domains. These results suggest that the window of opportunity for human DNA ligase I may extend well beyond the ®rst stages of chromatin reassembly after DNA replication or repair.

Repeat sequences in various genomes undergo expansion by poorly understood mechanisms. By using an oligonucleotide system containing such repeats, we recapitulated the last steps in Okazaki fragment processing, which have been implicated in sequence expansion. A template containing either triplet or tandem repeats was annealed to a downstream primer containing complementary repeats at its 5-end. Overlapping upstream primers, designed to strand-displace varying numbers of repeats in the downstream primer, were annealed. Human DNA ligase I joined overlapping segments of repeats generating an expansion product from the primer strands. Joining efficiency decreased with repeat length. Flap endonuclease 1 (FEN1) cleaved the displaced downstream strand and together with DNA ligase I produced non-expanded products. However, both expanded and non-expanded products formed irrespective of relative nuclease and ligase concentrations tested or enzyme addition order, suggesting the preexistence and persistence of intermediates leading to both outcomes. FEN1 activity decreased with the length of repeat segment displaced presumably because the flap forms structures that inhibit cleavage. Increased MgCl 2 disfavored ligation of substrate intermediates that result in expansion products. Examination of expansion in vitro enables dissection of substrate and replication enzyme dynamics on repeat sequences.Sites in which mono-to pentanucleotide DNA sequences are repeated are widespread in the chromosomes of organisms from bacteria to humans. These microsatellite repeats range from tens to hundreds of base pairs in length (1). Typically repeat sequences are highly polymorphic, and the number of repeats at specific sites varies extensively. These segments of repeats are inherently unstable and undergo sequence expansions and deletions. Especially interesting are triplet repeat sequences, because only 3 of the 10 possible triplet repeats (CAG, CGG, and GAA) are prone to expansion (2). Propensity for expansion generally increases with the size of the repeat region, and expansion can range from addition of a few repeats to thousands (3). In addition, the rate and size of sequence expansions vary between and within tissues of organisms (4). Mechanisms of sequence expansion have attracted much attention because of the involvement of triplet repeat expansion in the pathogenesis of at least 11 neurological disorders (3).Genetic studies in yeast and E. coli suggest that one mechanism of expansion involves slipped mispairing of template and primer strands within the repeat region during DNA replication or repair (5, 6). Such mispairing results in formation of a loop in one strand of the helix. Looping of the template strand during replication of the leading or lagging strand would lead to deletion, whereas that in the primer strand would result in expansion. Triplet repeats have been shown to be inherently flexible and mispair to form slipped DNA intermediates (7,8). Additionally, the quasi-palindromic nature of triplet repeats results in the f...

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