Current and Future Methodology for Quantitation and Site-Specific Mapping the Location of DNA Adducts

Boysen, Gunnar; Nookaew, Intawat

doi:10.3390/toxics10020045

Cited by 10 publications

(3 citation statements)

References 110 publications

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“…We inferred the RNA modifications of dRNA sequences using our developed epitranscriptional/epigenomical landscape inferring from glitches of ONT signals (ELIGOS) software ( Nookaew et al, 2020 ; Jenjaroenpun et al, 2021 ; Boysen and Nookaew, 2022 ) with two approaches. First, profiling of RNA modifications of the individual growth condition was performed by comparing the error at specific base (ESB) with the RNA background error model (rBEM).…”

Section: Methodsmentioning

confidence: 99%

Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae

Wongsurawat

Jenjaroenpun

Wanchai

et al. 2022

Front. Bioeng. Biotechnol.

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Direct sequencing of single molecules through nanopores allows for accurate quantification and full-length characterization of native RNA or complementary DNA (cDNA) without amplification. Both nanopore-based native RNA and cDNA approaches involve complex transcriptome procedures at a lower cost. However, there are several differences between the two approaches. In this study, we perform matched native RNA sequencing and cDNA sequencing to enable relevant comparisons and evaluation. Using Saccharomyces cerevisiae, a eukaryotic model organism widely used in industrial biotechnology, two different growing conditions are considered for comparison, including the poly-A messenger RNA isolated from yeast cells grown in minimum media under respirofermentative conditions supplemented with glucose (glucose growth conditions) and from cells that had shifted to ethanol as a carbon source (ethanol growth conditions). Library preparation for direct RNA sequencing is shorter than that for direct cDNA sequencing. The sequence characteristics of the two methods were different, such as sequence yields, quality score of reads, read length distribution, and mapped on reference ability of reads. However, differential gene expression analyses derived from the two approaches are comparable. The unique feature of direct RNA sequencing is RNA modification; we found that the RNA modification at the 5′ end of a transcript was underestimated due to the 3′ bias behavior of the direct RNA sequencing. Our comprehensive evaluation from this work could help researchers make informed choices when selecting an appropriate long-read sequencing method for understanding gene functions, pathways, and detailed functional characterization.

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Section: Methodsmentioning

confidence: 99%

Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae

Wongsurawat

Jenjaroenpun

Wanchai

et al. 2022

Front. Bioeng. Biotechnol.

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“…Other methods such as DIIP assay or CPD‐seq, XR‐seq, damage‐seq, cisplatin‐seq, and tXR‐seq are also used for similar purposes [101–106] . While seemingly promising, these methods possess several limitations, such as limited enzyme specificities for DNA adduct identification, short fragments alignment‐related issues during post‐sequencing data analysis, and being confined to some adduct types due to the non‐availability of antibodies against all known DNA adducts [107] . These limitations suggest the need for developing alternative approaches.…”

Section: Linking Adducts Chemistry To Dna Sitesmentioning

confidence: 99%

Unlocking The Mysteries of DNA Adducts with Artificial Intelligence

Arora,

Satija,

Mittal

et al. 2023

ChemBioChem

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Cellular genome is considered a dynamic blueprint of a cell since it encodes genetic information that gets temporally altered due to various endogenous and exogenous insults. Largely, the extent of genomic dynamicity is controlled by the trade‐off between DNA repair processes and the genotoxic potential of the causative agent (genotoxins or potential carcinogens). A subset of genotoxins form DNA adducts by covalently binding to the cellular DNA, triggering structural or functional changes that lead to significant alterations in cellular processes via genetic (e.g., mutations) or non‐genetic (e.g., epigenome) routes. Identification, quantification, and characterization of DNA adducts are indispensable for their comprehensive understanding and could expedite the ongoing efforts in predicting carcinogenicity and their mode of action. In this review, we elaborate on using Artificial Intelligence (AI)‐based modeling in adducts biology and present multiple computational strategies to gain advancements in decoding DNA adducts. The proposed AI‐based strategies encompass predictive modeling for adduct formation via metabolic activation, novel adducts’ identification, prediction of biochemical routes for adduct formation, adducts’ half‐life predictions within biological ecosystems, and, establishing methods to predict the link between adducts chemistry and its location within the genomic DNA. In summary, we discuss some futuristic AI‐based approaches in DNA adduct biology.

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“…We recently demonstrated that Oxford Nanopore Technologies (ONT), which is a third-generation sequencing platform can detect nucleic acid modifications ( Jenjaroenpun et al, 2020 ; Nookaew et al, 2020 ; Boysen and Nookaew, 2022 ). The ONT platform sequences native DNA and RNA, with nucleotide bases having their own electrical signal known as a “squiggle.” The ONT platform can detect modified bases because of the difference in the squiggle between modified and unmodified bases ( Xu and Seki, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Nanopore Sequencing for Detection and Characterization of Phosphorothioate Modifications in Native DNA Sequences

et al. 2022

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Bacterial DNA is subject to various modifications involved in gene regulation and defense against bacteriophage attacks. Phosphorothioate (PT) modifications are protective modifications in which the non-bridging oxygen in the DNA phosphate backbone is replaced with a sulfur atom. Here, we expand third-generation sequencing techniques to allow for the sequence-specific mapping of DNA modifications by demonstrating the application of Oxford Nanopore Technologies (ONT) and the ELIGOS software package for site-specific detection and characterization of PT modifications. The ONT/ELIGOS platform accurately detected PT modifications in a plasmid carrying synthetic PT modifications. Subsequently, studies were extended to the genome-wide mapping of PT modifications in the Salmonella enterica genomes within the wild-type strain and strains lacking the PT regulatory gene dndB (ΔdndB) or the PT synthetic gene dndC (ΔdndC). PT site-specific signatures were observed in the established motifs of GAAC/GTTC. The PT site locations were in close agreement with PT sites previously identified using the Nick-seq technique. Compared to the wild-type strain, the number of PT modifications are 1.8-fold higher in ΔdndB and 25-fold lower in ΔdndC, again consistent with known regulation of the dnd operon. These results demonstrate the suitability of the ONT platform for accurate detection and identification of the unusual PT backbone modifications in native genome sequences.

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Current and Future Methodology for Quantitation and Site-Specific Mapping the Location of DNA Adducts

Cited by 10 publications

References 110 publications

Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae

Native RNA or cDNA Sequencing for Transcriptomic Analysis: A Case Study on Saccharomyces cerevisiae

Unlocking The Mysteries of DNA Adducts with Artificial Intelligence

Nanopore Sequencing for Detection and Characterization of Phosphorothioate Modifications in Native DNA Sequences

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