To identify susceptibility variants for hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), we conducted a genome-wide association study by genotyping 440,794 SNPs in 355 chronic HBV carriers with HCC and 360 chronic HBV carriers without HCC, all of Chinese ancestry. We identified one intronic SNP (rs17401966) in KIF1B on chromosome 1p36.22 that was highly associated with HBV-related HCC and confirmed this association in five additional independent samples, consisting of 1,962 individuals with HCC, 1,430 control subjects and 159 family trios. Across the six studies, the association with rs17401966 was highly statistically significant (joint odds ratio = 0.61, P = 1.7 x 10(-18)). In addition to KIF1B, the association region tagged two other plausible causative genes, UBE4B and PGD. Our findings provide evidence that the 1p36.22 locus confers susceptibility to HBV-related HCC, and suggest that KIF1B-, UBE4B- or PGD-related pathways might be involved in the pathogenesis of this malignancy.

Expression of the tryptophanase operon of Escherichia coli is regulated by catabolite repression and tryptophan-induced transcription antitermination. An induction site activated by l-tryptophan is created in the translating ribosome during synthesis of TnaC, the 24-residue leader peptide. Replacing the tnaC stop codon with a tryptophan codon allows tryptophan-charged tryptophan transfer RNA to substitute for tryptophan as inducer. This suggests that the ribosomal A site occupied by the tryptophanyl moiety of the charged transfer RNA is the site of induction. The location of tryptophan-12 of nascent TnaC in the peptide exit tunnel was crucial for induction. These results show that a nascent peptide sequence can influence translation continuation and termination within a translating ribosome.

Chromatin rearrangement occurs during nucleotide excision repair (NER). Here we show that Snf6 and Snf5, two subunits of the SWI/SNF chromatin-remodeling complex in Saccharomyces cerevisiae, copurify with the NER damage-recognition heterodimer Rad4-Rad23. This interaction between SWI/SNF and Rad4-Rad23 is stimulated by UV irradiation. We demonstrate that NER in the transcriptionally silent, nucleosome-loaded HML locus is reduced in yeast cells lacking functional SWI/SNF. In addition, using a restriction enzyme accessibility assay, we observed UV-induced nucleosome rearrangement at the silent HML locus. Notably, this rearrangement is markedly attenuated when SWI/SNF is inactivated. These results indicate that the SWI/SNF chromatin-remodeling complex is recruited to DNA lesions by damage-recognition proteins to increase DNA accessibility for NER in chromatin.

Expression of the tryptophanase (tna) operon of Escherichia coli is regulated by catabolite repression and tryptophan-induced transcription antitermination. In a previous study, we reproduced the regulatory features of this operon observed in vivo by using an in vitro S-30 system. We also found that, under inducing conditions, the leader peptidyl-tRNA (TnaC-peptidyl-tRNA Pro ) is not cleaved; it accumulates in the S-30 reaction mixture. In this paper, we examine the requirements for TnaC-peptidyl-tRNA Pro accumulation and cleavage, in vitro. We show that this peptidyl-tRNA remains bound to the translating ribosome. Removal of free tryptophan and addition of release factor 1 or 2 leads to hydrolysis of TnaCpeptidyl-tRNA Pro and release of TnaC from the ribosome-mRNA complex. Release factor-mediated cleavage is prevented by the addition of tryptophan. TnaC of the ribosome-bound TnaC-peptidyl-tRNA Pro was transferable to puromycin. This transfer was also blocked by tryptophan. Tests with various tryptophan analogs as substitutes for tryptophan revealed the existence of strict structural requirements for tryptophan action. Our findings demonstrate that the addition of tryptophan to ribosomes bearing nascent TnaC-peptidyl-tRNA Pro inhibits both TnaC peptidyl-tRNA Pro hydrolysis and TnaC peptidyl transfer. The associated translating ribosome therefore remains attached to the leader transcript where it blocks Rho factor binding and subsequent transcription termination. E scherichia coli and many other Gram-negative bacteria use the enzyme tryptophanase to degrade L-tryptophan to indole, pyruvate, and ammonia (1). This ability allows tryptophan to be used as a source of carbon, nitrogen, and energy (2). The tryptophanase (tna) operon of E. coli consists of two major structural genes, tnaA, encoding tryptophanase, and tnaB, encoding a low affinity, high capacity tryptophan permease (3, 4). This operon also contains a 319-bp transcribed leader regulatory region, preceding tnaA. Initiation of transcription of the operon is regulated by catabolite repression. Once initiated, continuation of transcription into the tnaA-tnaB structural genes is regulated by a transcription antitermination mechanism that is activated by the inducer, tryptophan. Induction prevents Rho factor from terminating transcription in the leader region of the operon (5-9). The transcript of the tna operon leader region contains a coding region, tnaC, specifying a 24-residue leader peptide, TnaC (3). There is appreciable evidence demonstrating that translation of tnaC is essential for tryptophan induction, and that induction prevents Rho factor-dependent transcription termination in the leader region of the operon. Thus, (i) replacing the tnaC start codon by a stop codon eliminates induction (10, 11); (ii) replacing the crucial Trp codon at position 12 of tnaC by codons for other amino acids, also eliminates induction (8, 11); (iii) a minimal E. coli tna operon introduced into two bacterial species that lack tryptophanase, Enterobacter aerogenes and Salmo...

Mammalian cells exhibit complex cellular responses to DNA damage, including cell cycle arrest, DNA repair and apoptosis. Defects in any one of these responses can result in carcinogenesis. Absence of the chromatin remodeling complex Swi/Snf is found in many instances of cancer, and we have investigated its role in the UV damage response. The human carcinoma cell line SW13 is deficient in Swi/Snf and is very sensitive to UV radiation. In contrast, SW13 cells with ectopic Brg1 expression regain active Swi/Snf and become significantly more resistant to UV radiation. Sensitivity to UV light correlates well with dramatic UV induced apoptosis in SW13 cells, but not in SW13 cells expressing Brg1. We show that SW13 cells synchronized at the G(1)/S border progress into S phase after UV irradiation, and this checkpoint deficiency is corrected after Brg1 expression is restored. Interestingly, Brg1 expression in SW13 cells restores expression of two DNA damage responsive genes, Gadd45a and p21. Furthermore, Gadd45a induction and p21 degradation were observed in the Brg1-expressing SW13 cells after UV irradiation. Our findings demonstrate that Swi/Snf protects cells against deleterious consequences of UV induced DNA damage. These results also indicate that Swi/Snf may modulate checkpoint activation after UV damage via regulation of the two PCNA-binding proteins Gadd45a and p21.

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Gong (2009) The chromatin remodeling factor BRG1 stimulates nucleotide excision repair by facilitating recruitment of XPC to sites of DNA damage, Cell Cycle, 8:23, 3953-3959,

Expression of the tryptophanase (tna) operon in Escherichia coli is regulated by catabolite repression and tryptophan-induced transcription antitermination. The key feature of this antitermination mechanism has been shown to be the retention of uncleaved TnaC-peptidyltRNA in the translating ribosome. This ribosome remains stalled at the tna stop codon and blocks the access of Rho factor to the tna transcript, thereby preventing transcription termination. In normal S-30 preparations, synthesis of a TnaC peptide containing arginine instead of tryptophan at position 12 (Arg 12 -TnaC) was shown to be insensitive to added tryptophan, i.e. Arg 12 -TnaC-peptidyl-tRNA was cleaved, and there was normal Rho-dependent transcription termination. When the S-30 extract used was depleted of release factor 2, Arg 12 -TnaCtRNA Pro was accumulated in the absence or presence of added tryptophan. Under these conditions the accumulation of Arg 12 -TnaC-tRNA Pro prevented Rho-dependent transcription termination, mimicking normal induction. Using a minimal in vitro transcription system consisting of a tna template, RNA polymerase, and Rho, it was shown that RNA sequences immediately adjacent to the tnaC stop codon, the presumed boxA and rut sites, contributed most significantly to Rho-dependent termination. The tna boxA-like sequence appeared to serve as a segment of the Rho "entry" site, despite its likeness to the boxA element.Escherichia coli and many other Gram-negative bacteria use the enzyme tryptophanase to degrade L-tryptophan to indole, pyruvate, and ammonia (1), allowing these microorganisms to utilize tryptophan as a source of carbon, nitrogen, and energy (2). The tryptophanase (tna) operon of E. coli has two major structural genes, tnaA, encoding tryptophanase, and tnaB, encoding a low affinity tryptophan permease (3, 4). Initiation of transcription of the tna operon is regulated by catabolite repression (5-7). Once initiated, continuation of transcription into the tnaA-tnaB structural gene region depends on tryptophan-induced transcription antitermination. Antitermination is achieved by some feature of induction that prevents Rho factor from terminating transcription in the leader region of the operon (5-7). The tna operon contains a 319-base pair transcribed leader region upstream of the tnaA initiation codon. The transcript of this leader region bears a coding segment, tnaC, specifying a 24-residue leader peptide, TnaC, that contains a single tryptophan residue. Synthesis of TnaC is essential for induction (3,8,9). Replacing the tnaC start codon by a stop codon (9, 10) or replacing Trp codon 12 by a codon for some other amino acid (10) prevents induction.Evidence supporting the essential role of Rho factor in mediating transcription termination in the tna operon leader region was provided by analyses of Rho mutants (8), examination of Rho-inhibiting drugs (11), and deletion of a leader region sequence-rich in C residues (10). Mutations in rho that reduce Rho factor activity as well as addition of bicyclomycin, an inhibi...