Genome-Wide DNA Alterations in X-Irradiated Human Gingiva Fibroblasts

Nath, Neetika; Hagenau, Lisa; Weiß, Stefan; Tzvetkova, Ana; Jensen, Lars Riff; Kaderali, Lars; Port, Matthias; Scherthan, Harry; Kuß, Andreas W.

doi:10.3390/ijms21165778

Cited by 4 publications

(3 citation statements)

References 53 publications

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“…Studies aimed at understanding the molecular effects of the physical mutagens at whole-genome level is increasingly being pursued with the advent of rapid technological developments in the field of genomics such as the next-generation sequencing (NGS). NGS has been used to unravel the molecular effects of spontaneous mutations (Weng et al 2019) as well as those induced by various physical mutagens like gamma-rays (Hase et al 2020), X-rays (Nath et al 2020), ion-beams (Hase et al 2018;Kazama et al 2017), proton beams (Lee et al 2021), and neutrons (Belfield et al 2012). This coupled with superior bioinformatic algorithms provide a holistic approach in novel understanding of the mutagenic effects of various physical mutagens in different genomic backgrounds.…”

Section: Introductionmentioning

confidence: 99%

Title of manuscript: Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

Dhanasekar

Souframanien

2023

Preprint

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Gamma-rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in development of more than 60% of global cowpea mutant varieties. Nevertheless, the characteristics of genome wide mutations induced by gamma-rays has not been studied in cowpea (Vigna unguiculata (L.) Walp.). In the present investigation, mutations elicited by gamma rays in three cowpea mutant lines in M6 generation were characterized through whole-genome sequencing. Gamma rays induced a relatively higher frequency (91.1%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 2.82. A>G transitions including its complementary T>C transitions predominated the transition mutations, while all the four types of transversion mutations were detected with almost equal frequencies (5.6% to 7.4%). Indels constituted about 9% of the total induced variation wherein small insertions (5.3%) were relatively more prominent than small deletions (3.7%). Among the indels, single base indels and in particular those involving A/T bases showed preponderance, albeit indels of up to five bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.3%) and indels (12.7%) potentially altered the encoded amino-acids/peptides. The inherent mutation rate induced by gamma-rays in cowpea was observed to be in the order of 1.76 x 10-6 per base pair. Therefore, gamma-rays with greater tendency to induce SBSs and to a lesser extent indels could be efficiently and effectively exploited in cowpea mutation breeding.

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Section: Introductionmentioning

confidence: 99%

Title of manuscript: Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

Dhanasekar

Souframanien

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Studies aimed at understanding the molecular effects of the physical mutagens at whole-genome level is increasingly being pursued with the advent of rapid technological developments in the eld of genomics such as the nextgeneration sequencing (NGS). NGS has been used to unravel the molecular effects of spontaneous mutations (Weng et al 2019) as well as those induced by various physical mutagens like gamma-rays (Hase et al 2020), X-rays (Nath et al 2020), ion-beams (Hase et al 2018;Kazama et al 2017), proton beams (Lee et al 2021), andneutrons (Bel eld et al 2012). This coupled with superior bioinformatic algorithms provide a holistic approach in novel understanding of the mutagenic effects of various physical mutagens in different genomic backgrounds.…”

Section: Introductionmentioning

confidence: 99%

Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing

Dhanasekar

Souframanien

2022

Preprint

View full text Add to dashboard Cite

Gamma-rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in development of more than 60% of global cowpea mutant varieties. Nevertheless, the characteristics of genome wide mutations induced by gamma-rays has not been studied in cowpea (Vigna unguiculata (L.) Walp.). In the present investigation, mutations elicited by gamma-rays in three cowpea mutant lines in M6 generation were characterized through whole-genome sequencing. Gamma-rays induced a relatively higher frequency (91.1%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 2.82. A > G transitions including its complementary T > C transitions predominated the transition mutations, while all the four types of transversion mutations were detected with almost equal frequencies (5.6–7.4%). Indels constituted about 9% of the total induced variation wherein small insertions (5.3%) were relatively more prominent than small deletions (3.7%). Among the indels, single base indels and in particular those involving A/T bases showed preponderance, albeit indels of up to five bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.3%) and indels (12.7%) potentially altered the encoded amino-acids/peptides. The inherent mutation rate induced by gamma-rays in cowpea was observed to be in the order of 1.76 x 10− 6 per base pair. Therefore, gamma-rays with greater tendency to induce SBSs and to a lesser extent indels could be efficiently and effectively exploited in cowpea mutation breeding.

show abstract

“…More specifically, some works [6-8] analyzed the early stages of the interaction between ionizing radiation and DNA, with particular attention to the role played by radiation track-structure in modulating the induction of DNA cluster damage, which is thought to lead to important endpoints including chromosome aberrations and cell death [9-11]. Another work [12] studied the impact of such damage on nuclear architecture, which is known to play a relevant role in DNA damage induction and repair [13]; other studies [14,15] investigated the consequences of hypoxia on the evolution of the initial damage, and one work analyzed genome-wide DNA alterations in X-irradiated human fibroblasts [16].…”

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confidence: 99%