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S L Ooi

Publications and source records attributed to S L Ooi.

7 recordsLinked to original sources
PubMed2001

A DNA microarray-based genetic screen for nonhomologous end-joining mutants in Saccharomyces cerevisiae.

We describe a microarray-based screen performed by imposing different genetic selections on thousands of yeast mutants in parallel, representing most genes in the yeast genome. The presence or absence of mutants was detected by oligonucleotide arrays that hybridize to 20-nucleotide "barcodes." We used this method to screen for components of the nonhomologous end-joining (NHEJ) pathway. Known components of the pathway were identified, as well as a gene not previously known to be involved in NHEJ, NEJ1. Nej1 protein interacts with the amino terminus of LIF1/XRCC4, a recently recognized "guardian of the genome" against cancer.

CCAAT-Binding Factor↗
PubMed2001

Human L1 retrotransposition: cis preference versus trans complementation.

Long interspersed nuclear elements (LINEs or L1s) comprise approximately 17% of human DNA; however, only about 60 of the approximately 400,000 L1s are mobile. Using a retrotransposition assay in cultured human cells, we demonstrate that L1-encoded proteins predominantly mobilize the RNA that encodes them. At much lower levels, L1-encoded proteins can act in trans to promote retrotransposition of mutant L1s and other cellular mRNAs, creating processed pseudogenes. Mutant L1 RNAs are mobilized at 0.2 to 0.9% of the retrotransposition frequency of wild-type L1s, whereas cellular RNAs are mobilized at much lower frequencies (ca. 0.01 to 0.05% of wild-type levels). Thus, we conclude that L1-encoded proteins demonstrate a profound cis preference for their encoding RNA. This mechanism could enable L1 to remain retrotransposition competent in the presence of the overwhelming number of nonfunctional L1s present in human DNA.

Base Sequence↗
PubMed1998

Intronic snoRNA biosynthesis in Saccharomyces cerevisiae depends on the lariat-debranching enzyme: intron length effects and activity of a precursor snoRNA.

The eukaryotic small nucleolar RNAs (snoRNAs) are involved in processing of pre-rRNA and modification of rRNA nucleotides. Some snoRNAs are derived from mono- or polycistronic transcription units, whereas others are encoded in introns of protein genes. The present study addresses the role of the RNA lariat-debranching enzyme (Dbr1p) in the synthesis and function of intronic snoRNAs in the yeast Saccharomyces cerevisiae. Intronic snoRNA production was determined to depend on Dbr1p. Accumulation of mature intronic snoRNAs is reduced in a dbr1 mutant; instead, intronic snoRNAs are "trapped" within host intron lariats. Interestingly, the extent of intronic snoRNA accumulation in the form of lariats in dbr1 cells varied among different intronic snoRNAs. Intronic snoRNAs encoded within shorter introns, such as U24 and snR38, accumulate more unprocessed lariat precursors than those encoded within longer introns, e.g., U18 and snR39. This correlation was corroborated by experiments conducted with model intron:U24 snoRNA constructs. These results support a splicing-dependent exonucleolytic pathway for the biosynthesis of intronic snoRNAs. Curiously, U24 in a lariat may be functional in directing methylation of ribosomal RNA.

Animals↗
PubMed1995

New primer strategy improves precision of differential display.

To increase the reproducibility and to reduce the false positives in the initial mRNA differential display, modified long composite primers were developed based on both mRNA differential display and RNA arbitrarily primed PCR fingerprinting methods. Ten-base nucleotides were added at the 5' ends of the primers used in the initial mRNA differential display. These included a restriction site to aid cloning. PCR began with one low-stringency cycle (40 degrees C for annealing) followed by 35 high-stringency cycles (60 degrees C for annealing). The modified method significantly improved the reproducibility and sensitivity of the mRNA differential display while still keeping the characteristics of the original method.

Animals↗
PubMed1980

Mutagenicity of nitrosated alpha-amino acid derivatives N-acetyl-N'-nitrosotryptophan and its methyl ester in bacteria.

DL-N-acetyl-N'-nitrosotryptophan (I) and its methyl ester (II), readily formed under mild conditions by the reaction of nitrite with N-acetyltryptophan or its methyl ester, are model compounds for the study of the nitrosation of alpha-amino acid side chains, considered relevant to possible role of nitrosation of peptides and proteins in the aetiology of gastrointestinal cancer. Both compounds were assayed for mutagenicity in a series of Escherichia coli WP2 strains (trp- leads to trp+) and in several strains of Salmonella typhimurium (his- leads to his+), in the presence and absence of a post-mitochondrial supernatant (S9) from livers of rats treated with Aroclor 1254. Compound I was mutagenic to the following E. coli strains: WP2; WP2uvrA; WP2pKM101; WP2-98 and TA 100. Compound II was consistently less mutagenic than compound I to the E. coli strains, inactive in S. typhimurium TA 98 and TA 100, but more active than I in TA 1535. Neither compound was detectably mutagenic to E. coli WP2 lexA. Addition of S9 did not enhance the mutagenicity of either compound, and in some cases reduced the mutagenic to any of the E. coli strains tested, and nitrite alone (at pH 7.1) was very feebly mutagenic at doses where molar equivalents of compounds I were markedly active. The rate of decay of compound I in pH 5.9 was closely paralleled by decay of its mutagenicity. These data and the pattern of cytotoxicity and mutagenicity in several DNA-repair mutants of E. coli suggest that both compounds react with DNA to form excisable DNA-adducts which cause mutation by error-prone repair.

Escherichia coli↗