Similar Datasets
Project description:Strand-specific kethoxal-assisted single-stranded DNA (ssDNA) sequencing (spKAS-seq) for mapping R-loop formation in HEK293T cells with/without the N2-heptynyl-dG treatment .
2024-05-01 | GSE248210 | GEO
Project description:DNA alkylation at the N2 position of guanine (N2-dG) is a prevalent type of DNA minor-groove lesions arising from various exogenous environmental contaminants and endogenous cellular processes. These N2-alkyl-dG lesions can induce G → T mutations during transcription if left unrepaired. However, the repair pathways of N2-alkyl-dG lesions remain incompletely elucidated. In this study, we identified a series of potential N2-alkyl-dG-binding proteins utilizing an affinity pulldown coupled with quantitative proteomic approach. We investigated their roles in DNA damage response and repair of these lesions. High-mobility group protein B3 (HMGB3) and activated RNA polymerase II transcriptional coactivator P15 (SUB1) exhibited preferential binding toward N2-nBudG-containing duplex DNA in quantitative proteomics analysis and in vitro binding assay using recombinant proteins. The presence of HMGB3 and SUB1 protected cells against alkylating agents (e.g., BPDE). Both HMGB3 and SUB1 modulated the repair of N2-nBudG and trans-N2-BPDE-dG in genomic DNA, while HMGB3 wasn’t involved in the repair of cis-N2-BPDE-dG. Together, our findings provided new knowledge about the cellular sensing and repair of minor-groove N2-alkyl-dG lesions.
2024-08-02 | PXD051678 | Pride
Project description:Michael addition of trans-4-hydroxynonenal (HNE) to deoxyguanosine yields diastereomeric 1,N(2)-dG adducts in DNA. When placed opposite dC in the 5'-CpG-3' sequence, the (6S,8R,11S) diastereomer forms a N(2)-dG:N(2)-dG interstrand cross-link [Wang, H.; Kozekov, I. D.; Harris, T. M.; Rizzo, C. J. J. Am. Chem. Soc.2003, 125, 5687-5700]. We refined its structure in 5'-d(G(1)C(2)T(3)A(4)G(5)C(6)X(7)A(8)G(9)T(10)C(11)C(12))-3'·5'-d(G(13)G(14)A(15)C(16)T(17)C(18)Y(19)C(20)T(21)A(22)G(23)C(24))-3' [X(7) is the dG adjacent to the C6 carbon of the cross-link or the α-carbon of the (6S,8R,11S) 1,N(2)-dG adduct, and Y(19) is the dG adjacent to the C8 carbon of the cross-link or the γ-carbon of the HNE-derived (6S,8R,11S) 1,N(2)-dG adduct; the cross-link is in the 5'-CpG-3' sequence]. Introduction of (13)C at the C8 carbon of the cross-link revealed one (13)C8→H8 correlation, indicating that the cross-link existed predominantly as a carbinolamine linkage. The H8 proton exhibited NOEs to Y(19) H1', C(20) H1', and C(20) H4', orienting it toward the complementary strand, consistent with the (6S,8R,11S) configuration. An NOE was also observed between the HNE H11 proton and Y(19) H1', orienting the former toward the complementary strand. Imine and pyrimidopurinone linkages were excluded by observation of the Y(19)N(2)H and X(7) N1H protons, respectively. A strong H8→H11 NOE and no (3)J((13)C→H) coupling for the (13)C8-O-C11-H11 eliminated the tetrahydrofuran species derived from the (6S,8R,11S) 1,N(2)-dG adduct. The (6S,8R,11S) carbinolamine linkage and the HNE side chain were located in the minor groove. The X(7)N(2) and Y(19)N(2) atoms were in the gauche conformation with respect to the linkage, maintaining Watson-Crick hydrogen bonds at the cross-linked base pairs. A solvated molecular dynamics simulation indicated that the anti conformation of the hydroxyl group with respect to C6 of the tether minimized steric interaction and predicted hydrogen bonds involving O8H with C(20)O(2) of the 5'-neighbor base pair G(5)·C(20) and O11H with C(18)O(2) of X(7)·C(18). These may, in part, explain the stability of this cross-link and the stereochemical preference for the (6S,8R,11S) configuration.
| S-EPMC3187658 | biostudies-literature
Project description:transcription profiles of two groups each containing 5 strains of Disseminated gonorrhoeae (DG) and Undisseminated (superficial) gonorrhoeae (UG) were compared. An additional set of comparisons was done between 4 strains from group one Disseminated gonorrhoeae (DG) and another 4 strains from the same group.
2012-06-15 | E-MEXP-3254 | biostudies-arrayexpress
Project description:WT and β-arr1-/- DG astrocytes with pooled cDNA library were sequenced.
2017-02-09 | GSE66471 | GEO
Project description:Bifidobacterium pseudocatenulatum strain:N2 | isolate:N2 Genome sequencing
| PRJNA718013 | ENA
Project description:Streptococcus agalactiae strain:N2 | isolate:N2 Genome sequencing and assembly
| PRJNA759724 | ENA
Project description:Enterococcus faecalis ARO1/DG Genome sequencing
| PRJNA395129 | ENA
Project description:Marinovum algicola DG 898 genome sequencing project
| PRJNA63153 | ENA
Project description:Benzo[a]pyrene (BaP) is a known human carcinogen (IARC Group 1) found in food, coal tar, as well as cigarettes and other smoke. Its diol-epoxide metabolites (Benzo[a]pyrene diol-epoxide [BPDE]) react with DNA forming DNA adducts, predominantly N2-BPDE-deoxyguanosine (N2-BPDE-dG). While the capacity of BPDEs to alkylate DNA and induce mutations is well known, little is known about how the genomic features influence the accumulation of DNA damage at a genome-wide level. To bridge this gap, we developed a single-nucleotide resolution damage sequencing method to map N2-BPDE-dG in a BPDE exposed human lung cell line, and combined this analysis with mass spectrometry to quantify the total absolute levels of the adduct in the genome. Comparing damage abundance with DNase hypersensitive sites, transcription levels, and other genome annotation data showed that although the overall adduct levels increased with increasing concentration of BPDE, the genomic distribution patterns of N2-BPDE-dG were stable and correlated with the genomic features related to chromatin state and transcriptional activities. In addition, we extracted the preferred local DNA sequence contexts for N2-BPDE-dG, i.e., its DNA damage signature, and found that it was highly similar to the mutational signatures identified from smoking-related lung cancers. These results suggest that genomic features and sequence contexts are important in shaping the landscape of DNA damage arising from chemical exposures and provide an effective strategy for linking single-nucleotide resolution damage sequencing data with cancer mutations.
2023-02-01 | GSE224001 | GEO