Effect of g-quadruplex formation on uv-induced damage and nucleotide excision repair

Download

HIBIT22_paper_84.pdf

Date

2022-10

Author

Azgari, Cem
Adebali, Ogün

Metadata

Show full item record

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

Item Usage Stats

216
views

61
downloads

G-quadruplexes (G4s) are non-B DNA structures formed by four or more guanine tetrads stabilized by a charged ion. The formation and cellular functions of G4s are widely studied. G4s are known to localize at telomeres and promoters with a range of functions including maintaining genome integrity at telomeres and suppressing or initiating transcription. Moreover, G4s can cause mutagenesis if they stay persistent during replication [1]. Although thermodynamically stable G4s are linked to double-strand breaks and genome instability, their effect on UV-induced damages and the interplay between nucleotide excision repair and G4 formation are unclear. Aiming to uncover this relationship, we have obtained genome-wide G4 maps in HeLa cells using G4P-ChIP-seq data and motif finder algorithms Quadron [2] and G4-Miner [3]. Then, we applied Damage-seq and XR-seq methods on HeLa cells, which maps UV-induced damages [(6-4)PPs and CPDs] and nucleotide excision repair of these damages, respectively [4]. Profiles of (6-4)PP and CPD damage around G4 regions suggest that the damage formation on the G4s was lower than in the neighboring regions. On the contrary, we observed higher relative repair on G4s compared to the flanking regions. We are currently working on understanding the reasons behind these profiles that will provide insights into co-occurrence of G4s and UV-induced damage and the response of nucleotide excision repair in these sites.

Subject Keywords

G-quadruplex, Nucleotide excision repair, UV damage, (6-4)PPs, CPDs, XR-seq, Damage-seq

URI

https://hibit2022.ims.metu.edu.tr
https://hdl.handle.net/11511/101895

Conference Name

The International Symposium on Health Informatics and Bioinformatics

Collections

Graduate School of Informatics, Conference / Seminar

Suggestions

OpenMETU
Core

Effect of cortex stiffness variation on cleavage in animal cells AKKAS, N; KERMANIAN, M (1993-09-29) Cytokinesis is the division of the cytoplasm and the plasma membrane into two. Nuclear division and cytokinesis take a relatively short time to happen in animal cells in which cytokinesis takes place by means of furrowing. Here we consider the cleavage of the animal cells only. Although the basic division mechanisms appear to be similar in all animal cells, the divisions that take place during early embryonic development, which are termed as cleavages, are not exactly the same as those that occur later. In ...
Effect of crosslinking on organic solvent nanofiltration performance of cellulose membranes Konca, Kübra; Çulfaz Emecen, Pınar Zeynep; Department of Chemical Engineering (2018) Nanofiltration is a membrane process capable of separation of small molecules and multivalent ions due to their size and/or charge. NF is mainly used in aqueous applications. However, there are many processes that can take advantages of NF in molecules separation dissolved in organic solvents. Main challenge in Organic Solvent Nanofiltration is the limited number of membranes which can withstand a wide range solvents and have stable, predictable separation performance. Cellulose is an alternative polymer th...
Role of Cells in Freezing-Induced Cell-Fluid-Matrix Interactions Within Engineered Tissues Seawright, Angela; Özçelikkale, Altuğ; Dutton, Craig; Han, Bumsoo (ASME International, 2013-09-01) During cryopreservation, ice forms in the extracellular space resulting in freezing-induced deformation of the tissue, which can be detrimental to the extracellular matrix (ECM) microstructure. Meanwhile, cells dehydrate through an osmotically driven process as the intracellular water is transported to the extracellular space, increasing the volume of fluid for freezing. Therefore, this study examines the effects of cellular presence on tissue deformation and investigates the significance of intracellular w...
Effect of heat treatment on the stress and structure evolution of plasma deposited boron nitride thin films Anutgan, T. Aliyeva; Anutgan, M.; Wdemir, O.; Atilgan, I.; Katircioglu, B. (Elsevier BV, 2008-03-25) Boron nitride (BN) thin films are deposited at 573 K by plasma enhanced chemical vapor deposition (PECVD) with ammonia (NH3) and hydrogen diluted diborane (15% B2H6 in H-2) source gases. UV-visible and Fourier transform infrared (FTIR) spectroscopies together with surface profilometry are used for the film characterization. These films are hydrogenated (BN:H) whose hydrogen content is pursued following the 1.5 h annealing process at 748 K, 923 K and 1073 K under nitrogen atmosphere. Hydrogen escape with the...
Effect of fluorine substituted benzothiadiazole on electro-optical properties of donor-acceptor-donor type monomers and their polymers Çakal, Deniz; Önal, Ahmet Muhtar (Elsevier BV, 2020-11-01) A series of trimeric monomers bearing thiophene donor units and fluorinated analogues of benzothiadiazole acceptor units was synthesized via donor-acceptor-donor approach and polymerized electrochemically in order to investigate the effect of fluorine atom on electro-optical properties of both monomers and their corresponding polymers. All monomers exhibited solvatochromic and fluorescent properties. The introduction of fluorine atom into the conjugated backbone increased the oxidation potentials. Upon movi...

Citation Formats

C. Azgari and O. Adebali, “Effect of g-quadruplex formation on uv-induced damage and nucleotide excision repair,” Erdemli, Mersin, TÜRKİYE, 2022, p. 3084, Accessed: 00, 2023. [Online]. Available: https://hibit2022.ims.metu.edu.tr.