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33 results on '"Cao, Huifen"'

11. Genome‐wide profiles of DNA damage represent highly accurate predictors of mammalian age.

Author

Cao, Huifen, Deng, Bolin, Song, Tianrong, Lian, Jiabian, Xia, Lu, Chu, Xiaojing, Zhang, Yufei, Yang, Fujian, Wang, Chunlian, Cai, Ye, Diao, Yong, and Kapranov, Philipp

Subjects
*DNA damage, *SINGLE-strand DNA breaks, *BIOMARKERS
Abstract

The identification of novel age‐related biomarkers represents an area of intense research interest. Despite multiple studies associating DNA damage with aging, there is a glaring paucity of DNA damage‐based biomarkers of age, mainly due to the lack of precise methods for genome‐wide surveys of different types of DNA damage. Recently, we developed two techniques for genome‐wide mapping of the most prevalent types of DNA damage, single‐strand breaks and abasic sites, with nucleotide‐level resolution. Herein, we explored the potential of genomic patterns of DNA damage identified by these methods as a source of novel age‐related biomarkers using mice as a model system. Strikingly, we found that models based on genomic patterns of either DNA lesion could accurately predict age with higher precision than the commonly used transcriptome analysis. Interestingly, the informative patterns were limited to relatively few genes and the DNA damage levels were positively or negatively correlated with age. These findings show that previously unexplored high‐resolution genomic patterns of DNA damage contain useful information that can contribute significantly to both practical applications and basic science. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Hotspots of single-strand DNA 'breakome' are enriched at transcriptional start sites of genes

Author

Cao, Huifen, Zhang, Yufei, Cai, Ye, Tang, Lu, Gao, Fan, Xu, Dongyang, and Kapranov, Philipp

Subjects
Biochemistry, Genetics and Molecular Biology (miscellaneous), Molecular Biology, Biochemistry
Abstract

Single-strand breaks (SSBs) represent one of the most common types of DNA damage, yet not much is known about the genome landscapes of this type of DNA lesions in mammalian cells. Here, we found that SSBs are more likely to occur in certain positions of the human genome—SSB hotspots—in different cells of the same cell type and in different cell types. We hypothesize that the hotspots are likely to represent biologically relevant breaks. Furthermore, we found that the hotspots had a prominent tendency to be enriched in the immediate vicinity of transcriptional start sites (TSSs). We show that these hotspots are not likely to represent technical artifacts or be caused by common mechanisms previously found to cause DNA cleavage at promoters, such as apoptotic DNA fragmentation or topoisomerase type II (TOP2) activity. Therefore, such TSS-associated hotspots could potentially be generated using a novel mechanism that could involve preferential cleavage at cytosines, and their existence is consistent with recent studies suggesting a complex relationship between DNA damage and regulation of gene expression.

Published
2022

24. A novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells

Author

Gao, Fan, primary, Cai, Ye, additional, Tang, Lu, additional, Wu, Chun-Lin, additional, Cao, Huifen, additional, Xu, Dongyang, additional, Salazar-García, Lorena, additional, Han, Xueer, additional, Wang, Fang, additional, Ricciardi, Natalie, additional, Wahlestedt, Thor, additional, Cai, DingDing, additional, Wang, Huifang, additional, Chin, Mario P. S., additional, Timmons, James A., additional, Wahlestedt, Claes, additional, and Kapranov, Philipp, additional

Published
2020
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28. The Genome of Medicinal Plant Macleaya cordata Provides New Insights into Benzylisoquinoline Alkaloids Metabolism

Author

Liu, Xiubin, primary, Liu, Yisong, additional, Huang, Peng, additional, Ma, Yongshuo, additional, Qing, Zhixing, additional, Tang, Qi, additional, Cao, Huifen, additional, Cheng, Pi, additional, Zheng, Yajie, additional, Yuan, Zejun, additional, Zhou, Yuan, additional, Liu, Jinfeng, additional, Tang, Zhaoshan, additional, Zhuo, Yixiu, additional, Zhang, Yancong, additional, Yu, Linlan, additional, Huang, Jialu, additional, Yang, Peng, additional, Peng, Qiong, additional, Zhang, Jinbo, additional, Jiang, Wenkai, additional, Zhang, Zhonghua, additional, Lin, Kui, additional, Ro, Dae-Kyun, additional, Chen, Xiaoya, additional, Xiong, Xingyao, additional, Shang, Yi, additional, Huang, Sanwen, additional, and Zeng, Jianguo, additional

Published
2017
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30. Genome-Wide Identification of Arabidopsis LBD29 Target Genes Reveals the Molecular Events behind Auxin-Induced Cell Reprogramming during Callus Formation.

Author

Xu, Chongyi, Cao, Huifen, Xu, Enjun, Zhang, Shiqi, and Hu, Yuxin

Subjects
*ARABIDOPSIS thaliana genetics, *GENE expression in plants, *AUXIN, *CALLUS (Botany), *RNA sequencing
Abstract

Auxin-induced callus formation represents an important cell reprogramming process during in vitro regeneration of plants, in which the pericycle or pericycle-like cells within plant organs are reprogrammed into the pluripotent cell mass termed callus that is generally required for subsequent regeneration of root or shoot. However, the molecular events behind cell reprogramming during auxin-induced callus formation are largely elusive. We previously identified that auxin-induced LATERAL ORGAN BOUNDARIES DOMAIN (LBD) transcription factors act as the master regulators to trigger auxin-induced callus formation. Here, by ChIP-seq (chromatin immunoprecipitation-based sequencing) and RNA sequencing approaches, we identified the potential LBD29 target genes at the genome-wide level and outlined the molecular events of LBD-triggered cell reprogramming during callus formation. We showed that LBD29 preferentially bound to the G-box (CACGTG) and TGGGC[C/T] motifs and potentially targeted >350 genes, among which the genes related to methylation, reactive oxygen species (ROS) metabolism, cell wall hydrolysis and lipid metabolism were rapidly activated, while most of the light-responsive genes were suppressed by LBD29. Further examination of a few representative genes validated that they were targeted by LBD29 and participated in the regulation of cell reprogramming during callus formation. Our data not only outline a framework of the early molecular events behind auxin-induced cell reprogramming of callus formation, but also provide a valuable resource for identification of genes that regulate cell fate switch during in vitro regeneration of plants. [ABSTRACT FROM AUTHOR]

Published
2018
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32. Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

Author

Lin, Kui, primary, Limpens, Erik, additional, Zhang, Zhonghua, additional, Ivanov, Sergey, additional, Saunders, Diane G. O., additional, Mu, Desheng, additional, Pang, Erli, additional, Cao, Huifen, additional, Cha, Hwangho, additional, Lin, Tao, additional, Zhou, Qian, additional, Shang, Yi, additional, Li, Ying, additional, Sharma, Trupti, additional, van Velzen, Robin, additional, de Ruijter, Norbert, additional, Aanen, Duur K., additional, Win, Joe, additional, Kamoun, Sophien, additional, Bisseling, Ton, additional, Geurts, René, additional, and Huang, Sanwen, additional

Published
2014
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