Genomic DNA is constantly damaged by the action of exogenous factors and endogenous reactive metabolites. Apurinic/apyrimidinic sites (AP sites), which occur as a result of DNA glycosylase induced or spontaneous hydrolysis of the N-glycosidic bonds, are the most common damages of DNA. The chemical reactivity of AP sites is the cause of DNA breaks, and DNA-protein and DNA-DNA crosslinks. Repair of AP sites is one of the most important mechanisms for maintaining genome stability. Despite the fact that the main participants of the AP site repair are very well studied, the new proteins that could be involved potentially in this process as "back up" players or perform certain specialized functions are being found. This review is dedicated to one of these proteins, tyrosyl-DNA phosphodiesterase 1 (Tdp1), for which we have recently shown that in addition to its main activity of specific cleavage of the tyrosyl-DNA bond formed via a covalent attachment of topoisomerase 1 (Top1) to DNA, Tdp1 is able to initiate the cleavage of the internal AP sites in DNA and their following repair. Tdp1 was discovered in Saccharomyces cerevisiae yeast as an enzyme hydrolyzing the covalent bond between tyrosyl residue of topoisomerase 1 and 3'-phosphate group in DNA. Tdp1 is the major enzyme which carries out the repair of the irreversible complexes of DNA and topoisomerase 1, which appear. in the presence of Top 1 inhibitors, such as camptothecin, therefore Tdp1 is a very important target for the development of inhibitors--anticancer drugs. Besides, Tdp1 hydrolyzes a wide range of 3'-terminal DNA modifications and the 3'-end nucleosides and its derivatives to form a 3'-phosphate. Tdp1 ability to cleave AP sites suggests its involvement in the base excision repair as an alternative enzyme to cleave AP sites instead of AP endonuclease 1--the major enzyme hydrolyzing AP sites in DNA repair process.
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iScience
January 2025
Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
The regulation of gene expression relies on the coordinated action of transcription factors (TFs) at enhancers, including both activator and repressor TFs. We employed deep learning (DL) to dissect HepG2 enhancers into positive (PAR), negative (NAR), and neutral activity regions. Sharpr-MPRA and STARR-seq highlight the dichotomy impact of NARs and PARs on modulating and catalyzing the activity of enhancers, respectively.
View Article and Find Full Text PDFBioinform Adv
January 2025
Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, D-69120 Heidelberg, Germany.
Motivation: Since their introduction about 10 years ago, methylation clocks have provided broad insights into the biological age of different species, tissues, and in the context of several diseases or aging. However, their application to single-cell methylation data remains a major challenge, because of the inherent sparsity of such data, as many CpG sites are not covered. A methylation clock applicable on single-cell level could help to further disentangle the processes that drive the ticking of epigenetic clocks.
View Article and Find Full Text PDFData Brief
February 2025
Marine Research Institute, Klaipėda University, H. Manto 84, 92294 Klaipėda, Lithuania.
Over the last few decades, climate change in Svalbard (European Arctic) has led to the emergence and growth of periglacial coastal lagoons in the place of retreating glaciers. In these emerging water bodies, new ecosystems are formed, consisting of elements presumably entering the lagoon from the melting glacier, the surrounding tundra water bodies and the coastal ocean. The data presented here were collected from an emerging lagoon in the western region of Spitsbergen, Svalbard, situated between the retreating Eidembreen Glacier and Eidembukta Bay in 2022-2023.
View Article and Find Full Text PDFFront Plant Sci
January 2025
Bio-resource Research and Utilization Joint Key Laboratory of Sichuan and Chongqing, Chongqing Institute of Medicinal Plant Cultivation, Nanchuan, Chongqing, China.
Introduction: Mitochondria are essential organelles that provide energy for plants. They are semi-autonomous, maternally inherited, and closely linked to cytoplasmic male sterility (CMS) in plants. , a widely used medicinal plant from the Caprifoliaceae family, is rich in chlorogenic acid (CGA) and its analogues, which are known for their antiviral and anticancer properties.
View Article and Find Full Text PDFEndocrinology
January 2025
Neuroendocrinology Department, ICMR-National Institute for Research in Reproductive and Child Health, J. M. Street, Parel, Mumbai 400012, India.
Estrogen through its receptors, ERα and ERβ, regulate various aspects of spermatogenesis and male fertility. Since the sperm epigenome is an important contributing factor to male fertility, we evaluated the effects of estrogen signaling activation through the ERs on sperm DNA methylome in adult rats. Whole genome-bisulfite sequencing (WGBS) in caudal sperm DNA was performed.
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