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PROVIDER: PRJNA109717 | ENA |
REPOSITORIES: ENA
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Project description:Background Mismatched oligonucleotides are widely used on microarrays to differentiate specific from nonspecific hybridization. While many experiments rely on such oligos, the hybridization behavior of various degrees of mismatch (MM) structure has not been extensively studied. Here, we present the results of two large-scale microarray experiments on S.cerevisiae and H.sapiens genomic DNA, to explore MM oligonucleotide behavior with real sample mixtures under tiling-array conditions. Results We examined all possible nucleotide substitutions at the central position of 36-nucleotide probes, and found that nonspecific binding by MM oligos depends upon the individual nucleotide substitutions they incorporate: C->A, C->G and T->A (yielding purine-purine mispairs) are most disruptive, whereas A->X were least disruptive. We also quantify a marked GC skew effect: substitutions raising probe GC content exhibit higher intensity (and vice versa). This skew is small in highly-expressed regions (±0.5% of total intensity range) and large (±2% or more) elsewhere. Multiple mismatches per oligo are largely additive in effect: each MM added in a distributed fashion causes an additional 21% intensity drop relative to PM, three-fold more disruptive than adding adjacent mispairs (7% drop per MM). This SuperSeries is composed of the following subset Series: GSE13172: Mismatch oligonucleotides in human GSE13174: Mismatch oligonucleotides in yeast Refer to individual Series
2010-05-05 | E-GEOD-13175 | biostudies-arrayexpress
Project description:Tiled regions surrounding 5 human genes as 36mers, HBG2, TIMP3, SYN3, FLNA, FBX07. The first three of these genes, we tiled with various mismatch oligos in addition to 'perfect match' oligos. Keywords: Mismatch hybridization experiment Tiled perfect match and various designs of mismatch oligonucleotide for several human genes. Goal was to observe the influence of various MM types on hybridization behavior in human, and compare it to yeast (see related slide).
2010-05-05 | E-GEOD-13172 | biostudies-arrayexpress
Project description:Tiled 10kb region centered around ACT1 gene (YFL039C, CHROMOSOME 6 @ coords 48760-59195), double-stranded, 36mers at 1bp spacing, with mismatches and deletions; also tiled 6 genes of interest (YBL092W, YGR155W, YOL040C, YOR312C, YMR242C, YLR229C), coding strand only, 36mers at 1bp spacing, with some mismatches and deletions Keywords: Mismatch hybridization experiment Tiled perfect match and various designs of mismatch oligonucleotide for several yeast genes. Goal was to observe the influence of various MM types on hybridization behavior in yeast and compare it to human (see related slide).
2010-05-05 | E-GEOD-13174 | biostudies-arrayexpress
Project description:Mutation accumulation in mismatch repair deficient yeast
| PRJNA209500 | ENA
Project description:This study aimed to model formamide-based melting for the optimization of the sensitivity and specifcity of oligonucleotide probes in dignostic high-density microarrays. Formamide melting profiles of DNA oligonucleotides were obtained with a high-density microarray targeting 16S rRNA genes of Escherichia coli and Rhodobacter sphaeroides. One or two mismatched versions of perfect match probes were included on the array to systematically analyze the effect of formamide on mismatch stability and mismatch discrimination. A thermodynamics-based mathematical model of formamide denaturation was developed to predict the formamide melting profiles with sufficient accuracy to help with oligonucleotide design in microbial ecology applications.
2012-06-30 | GSE33021 | GEO
Project description:The experiments are done with three libraries by introducing base-pair perturbations on Widom 601: (1) poly(dA:dT) tract library (2) mismatch library (3) insertion library. And additional two more libraries based on native yeast genomic sequences: (4) Park97 mismatch library (5) Park97 insertion library. And we measured the nucleosome positioining in the base-pair resolution for before and after sliding by Chd1 chromatin remodeler.
2022-05-12 | GSE198440 | GEO
Project description:The distribution of somatic mutations across the genome is not uniform. Recently, an unexpected pattern of hyper-mutation was reported at binding sites of transcriptional regulatory factors (TFs). In some human cells, a decrease in DNA repair activity was also observed at TF binding sites, leading to the hypothesis that TFs may increase mutagenesis by interfering with the recognition of DNA lesions by repair enzymes, and thus inhibiting repair. However, direct proof of this surprising TF-induced mutagenesis mechanism is lacking. Here, we show that TF binding to DNA mismatch lesions leads to increased mutation rates at TF binding sites by reducing the efficiency of lesion recognition by MutSα, the main enzyme that initiates mismatch repair in eukaryotic cells. We developed a yeast mutagenesis assay to directly observe the accumulation of mutations in a TF binding site. Upon TF overexpression, the binding site exhibited an increased mutation rate, specifically for mutations resulting from mismatches where the TF strongly reduced MutSα binding in vitro. This trend was amplified in cells with an increased rate of misincorporation errors, and it was not observed in mismatch repair-deficient cells. Analyses of human cancer somatic mutation data revealed a pattern similar to that observed in yeast, with mutations resulting from TF-bound mismatches being specifically enriched in mismatch repair-proficient tumors. Taken together, our results demonstrate that in addition to their well-known roles in gene regulation, TFs also play a role in DNA mutagenesis, by directly interfering with the repair of replication errors. Since a majority of cancer mutations originate from unrepaired replication errors, most commonly mismatches, our results suggest that TF interference with mismatch repair will shape the mutation landscape of regulatory DNA in cancer genomes.
2025-03-31 | GSE235855 | GEO
Project description:The distribution of somatic mutations across the genome is not uniform. Recently, an unexpected pattern of hyper-mutation was reported at binding sites of transcriptional regulatory factors (TFs). In some human cells, a decrease in DNA repair activity was also observed at TF binding sites, leading to the hypothesis that TFs may increase mutagenesis by interfering with the recognition of DNA lesions by repair enzymes, and thus inhibiting repair. However, direct proof of this surprising TF-induced mutagenesis mechanism is lacking. Here, we show that TF binding to DNA mismatch lesions leads to increased mutation rates at TF binding sites by reducing the efficiency of lesion recognition by MutSα, the main enzyme that initiates mismatch repair in eukaryotic cells. We developed a yeast mutagenesis assay to directly observe the accumulation of mutations in a TF binding site. Upon TF overexpression, the binding site exhibited an increased mutation rate, specifically for mutations resulting from mismatches where the TF strongly reduced MutSα binding in vitro. This trend was amplified in cells with an increased rate of misincorporation errors, and it was not observed in mismatch repair-deficient cells. Analyses of human cancer somatic mutation data revealed a pattern similar to that observed in yeast, with mutations resulting from TF-bound mismatches being specifically enriched in mismatch repair-proficient tumors. Taken together, our results demonstrate that in addition to their well-known roles in gene regulation, TFs also play a role in DNA mutagenesis, by directly interfering with the repair of replication errors. Since a majority of cancer mutations originate from unrepaired replication errors, most commonly mismatches, our results suggest that TF interference with mismatch repair will shape the mutation landscape of regulatory DNA in cancer genomes.
2025-03-31 | GSE235854 | GEO