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Article ; Online: Human RNA-binding protein HNRNPD interacts with and regulates the repair of deoxyribouridine in DNA.

Wang, Ziyu / Qu, Minghui / Chang, Sijia / Dai, Xiaoxia / You, Changjun

International journal of biological macromolecules

2024 Volume 262, Issue Pt 1, Page(s) 129951

Abstract: Deoxyribouridine (dU) is an abnormal nucleoside in DNA and plays vital roles in multiple biological and physiological processes. Here, we conducted a mass spectrometry-based screen for dU-binding proteins and found that the heterogeneous nuclear ... ...

Abstract	Deoxyribouridine (dU) is an abnormal nucleoside in DNA and plays vital roles in multiple biological and physiological processes. Here, we conducted a mass spectrometry-based screen for dU-binding proteins and found that the heterogeneous nuclear ribonucleoprotein D (HNRNPD) could preferentially bind to dU-containing DNA. We also discovered that HNRNPD engages in the 5-Fluorouracil (5FU)-induced DNA damage response and can modulate the repair of dU in DNA in vitro and in human cells. Moreover, using a shuttle vector- and next-generation sequencing-based method, we unveiled the crucial role of HNRNPD in promoting the replicative bypass of dU in human cells. Taken together, these findings suggested that HNRNPD is a novel dU-bearing DNA-binding protein capable of regulating the removal of dU in DNA, and provided new insights into the molecular mechanisms of dU-associated diseases.
MeSH term(s)	Humans ; DNA/genetics ; Heterogeneous-Nuclear Ribonucleoprotein D/genetics ; Heterogeneous-Nuclear Ribonucleoprotein D/metabolism ; DNA Repair ; DNA Damage
Chemical Substances	DNA (9007-49-2) ; Heterogeneous-Nuclear Ribonucleoprotein D
Language	English
Publishing date	2024-02-05
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	282732-3
ISSN	1879-0003 ; 0141-8130
ISSN (online)	1879-0003
ISSN	0141-8130
DOI	10.1016/j.ijbiomac.2024.129951
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Article ; Online: Human Mitochondrial Protein HSPD1 Binds to and Regulates the Repair of Deoxyinosine in DNA.

Zheng, Xiaofang / Chang, Sijia / Liu, Yini / Dai, Xiaoxia / You, Changjun

Journal of proteome research

2023 Volume 22, Issue 4, Page(s) 1339–1346

Abstract: The generation of deoxyinosine (dI) in DNA is one of the most important sources of genetic mutations, which may lead to cancer and other human diseases. A further understanding of the biological consequences of dI necessitates the identification and ... ...

Abstract	The generation of deoxyinosine (dI) in DNA is one of the most important sources of genetic mutations, which may lead to cancer and other human diseases. A further understanding of the biological consequences of dI necessitates the identification and functional characterizations of dI-binding proteins. Herein, we employed a mass spectrometry-based proteomics approach to detect the cellular proteins that may sense the presence of dI in DNA. Our results demonstrated that human mitochondrial heat shock protein 60 (HSPD1) can interact with dI-bearing DNA. We further demonstrated the involvement of HSPD1 in the sodium nitrite-induced DNA damage response and in the modulation of dI levels
MeSH term(s)	Humans ; Mitochondrial Proteins/genetics ; Mitochondrial Proteins/metabolism ; Chaperonin 60/genetics ; Chaperonin 60/metabolism ; DNA ; DNA Repair
Chemical Substances	Mitochondrial Proteins ; Chaperonin 60 ; deoxyinosine (HN0RQ6SBWQ) ; DNA (9007-49-2) ; HSPD1 protein, human
Language	English
Publishing date	2023-02-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/acs.jproteome.2c00854
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Article ; Online: Comprehensive expression profiles of mRNAs, lncRNAs and miRNAs in Kashin-Beck disease identified by RNA-sequencing.

Dai, Yu / Jian, Can / Wang, Xiaofeng / Dai, Xiaoxia

Molecular omics

2022 Volume 18, Issue 2, Page(s) 154–166

Abstract: Kashin-Beck disease (KBD) is a chronic, endemic and deforming osteochondropathy, whose basic pathological alterations include apoptosis and necrosis of chondrocytes in articular cartilage and growth plates and imbalanced extracellular matrix metabolism. ... ...

Abstract	Kashin-Beck disease (KBD) is a chronic, endemic and deforming osteochondropathy, whose basic pathological alterations include apoptosis and necrosis of chondrocytes in articular cartilage and growth plates and imbalanced extracellular matrix metabolism. Numerous studies have reported that long noncoding RNAs (lncRNAs) and microRNA (miRNAs) are aberrantly expressed in KBD. Our study was comprised of 5 KBD patients and 5 healthy individuals and we compared the expression profiles of mRNAs, lncRNAs and miRNAs through RNA-sequencing (RNA-seq). Bioinformatic analysis of GO and KEGG was employed to conduct functional annotation and pathway enriched analysis. In total, 3194 mRNAs, 4103 lncRNAs and 1550 miRNAs were detected to be differentially expressed by RNA-seq (
MeSH term(s)	Gene Regulatory Networks ; Humans ; Kashin-Beck Disease/genetics ; Kashin-Beck Disease/metabolism ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA, Long Noncoding/genetics ; RNA, Long Noncoding/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Reproducibility of Results
Chemical Substances	MicroRNAs ; RNA, Long Noncoding ; RNA, Messenger
Language	English
Publishing date	2022-02-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2515-4184
ISSN (online)	2515-4184
DOI	10.1039/d1mo00370d
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Article ; Online: Next-Generation Sequencing-Based Analysis of the Roles of DNA Polymerases ν and θ in the Replicative Bypass of 8-Oxo-7,8-dihydroguanine in Human Cells.

Liu, Yini / Zhu, Xiaowen / Wang, Ziyu / Dai, Xiaoxia / You, Changjun

ACS chemical biology

2022 Volume 17, Issue 8, Page(s) 2315–2319

Abstract: DNA polymerase (Pol) ν and Pol θ are two specialized A-family DNA polymerases that function in the translesion synthesis of certain DNA lesions. However, the biological functions of human Pols ν and θ in cellular replicative bypass of 8-oxo-7,8- ... ...

Abstract	DNA polymerase (Pol) ν and Pol θ are two specialized A-family DNA polymerases that function in the translesion synthesis of certain DNA lesions. However, the biological functions of human Pols ν and θ in cellular replicative bypass of 8-oxo-7,8-dihydroguanine (8-oxoG), an important carcinogenesis-related biomarker of oxidative DNA damage, remain unclear. Herein, we showed that depletion of Pols ν and θ in human cells could cause an elevated hypersensitivity to oxidative stress induced by hydrogen peroxide. Using next-generation sequencing-based lesion bypass and mutagenesis assay, we further demonstrated that Pols ν and θ had important roles in promoting translesion synthesis of 8-oxoG in human cells. We also found that the depletion of Pol ν, but not Pol θ, caused a substantial reduction in G → T mutation frequency for 8-oxoG. These findings provided novel insights into the involvement of A-family DNA polymerases in oxidative DNA damage response.
MeSH term(s)	DNA Damage ; DNA Repair ; DNA Replication ; DNA-Directed DNA Polymerase/genetics ; DNA-Directed DNA Polymerase/metabolism ; Guanine/analogs & derivatives ; High-Throughput Nucleotide Sequencing ; Humans ; DNA Polymerase theta
Chemical Substances	8-hydroxyguanine (5614-64-2) ; Guanine (5Z93L87A1R) ; DNA-Directed DNA Polymerase (EC 2.7.7.7) ; POLN protein, human (EC 2.7.7.7)
Language	English
Publishing date	2022-07-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.2c00415
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Article ; Online: Development of an Endonuclease V-Assisted Analytical Method for Sequencing Analysis of Deoxyinosine in DNA.

Zheng, Xiaofang / Chen, Di / Zhao, Yingqi / Dai, Xiaoxia / You, Changjun

Analytical chemistry

2022 Volume 94, Issue 33, Page(s) 11627–11632

Abstract: Deoxyinosine (dI) is a highly mutagenic lesion that preferentially pairs with deoxycytidine during replication, which may induce A to G transition and ultimately contribute to carcinogenesis. Therefore, finding the site of dI modification in DNA is of ... ...

Abstract	Deoxyinosine (dI) is a highly mutagenic lesion that preferentially pairs with deoxycytidine during replication, which may induce A to G transition and ultimately contribute to carcinogenesis. Therefore, finding the site of dI modification in DNA is of great value for both basic research and clinical applications. Herein, we developed a novel method to sequence the dI modification site in DNA, which utilizes endonuclease V (EndoV)-dependent deamination repair to specifically label the modification site with biotin-14-dATP that allows the affinity enrichment of dI-bearing DNA for sequencing. We have achieved efficient determination of the location of the modified nucleotide in dI-bearing plasmid DNA with the assistance of EndoV-dependent deamination repair. We have also successfully applied this approach to locate the dI modification sites in the mitochondrial DNA of human cells. Our method should be generally applicable for genome-wide sequencing analysis of dI modifications in living organisms.
MeSH term(s)	DNA/genetics ; DNA Repair ; Deoxyribonuclease (Pyrimidine Dimer)/genetics ; Deoxyribonuclease (Pyrimidine Dimer)/metabolism ; Humans ; Inosine/analogs & derivatives
Chemical Substances	Inosine (5A614L51CT) ; DNA (9007-49-2) ; Deoxyribonuclease (Pyrimidine Dimer) (EC 3.1.25.1) ; deoxyinosine (HN0RQ6SBWQ)
Language	English
Publishing date	2022-08-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c02126
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Zs.A 4033: Show issues

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Article ; Online: Next-Generation Sequencing-Based Analysis of the Effects of

Yang, Ying / Wang, Ziyu / Wang, Juan / Dai, Xiaoxia / You, Changjun

Analytical chemistry

2022 Volume 94, Issue 32, Page(s) 11248–11254

Abstract: DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The ... ...

Abstract	DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric
MeSH term(s)	Animals ; DNA/genetics ; DNA/metabolism ; DNA Adducts ; DNA Repair ; Deoxyadenosines ; High-Throughput Nucleotide Sequencing ; Humans ; Mammals/metabolism ; Transcription, Genetic
Chemical Substances	DNA Adducts ; Deoxyadenosines ; N(6)-methyldeoxyadenosine ; DNA (9007-49-2)
Language	English
Publishing date	2022-08-03
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c01764
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Article: Evaluating Strategies to Reduce Ruminal Protozoa and Their Impacts on Nutrient Utilization and Animal Performance in Ruminants - A Meta-Analysis.

Dai, Xiaoxia / Faciola, Antonio P

Frontiers in microbiology

2019 Volume 10, Page(s) 2648

Abstract: Several studies have evaluated the effects of complete or partial ruminal protozoa (RP) inhibition; however, to this date, no practical suppressant has been identified and used in large scale. This meta-analysis quantitatively evaluates the effectiveness ...

Abstract	Several studies have evaluated the effects of complete or partial ruminal protozoa (RP) inhibition; however, to this date, no practical suppressant has been identified and used in large scale. This meta-analysis quantitatively evaluates the effectiveness of multiple strategies on inhibiting RP numbers and their influence on ruminal fermentation and animal performance. This study compared 66 peer-reviewed articles (16 manuscripts for complete and 50 manuscripts for partial RP inhibition that used supplemental phytochemicals and lipids, published from 2000 to 2018, to inhibit RP
Language	English
Publishing date	2019-11-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2019.02648
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Article: Development of an Endonuclease V-Assisted Analytical Method for Sequencing Analysis of Deoxyinosine in DNA

Zheng, Xiaofang / Chen, Di / Zhao, Yingqi / Dai, Xiaoxia / You, Changjun

Analytical chemistry. 2022 Aug. 09, v. 94, no. 33

2022

Abstract	Deoxyinosine (dI) is a highly mutagenic lesion that preferentially pairs with deoxycytidine during replication, which may induce A to G transition and ultimately contribute to carcinogenesis. Therefore, finding the site of dI modification in DNA is of great value for both basic research and clinical applications. Herein, we developed a novel method to sequence the dI modification site in DNA, which utilizes endonuclease V (EndoV)-dependent deamination repair to specifically label the modification site with biotin-14-dATP that allows the affinity enrichment of dI-bearing DNA for sequencing. We have achieved efficient determination of the location of the modified nucleotide in dI-bearing plasmid DNA with the assistance of EndoV-dependent deamination repair. We have also successfully applied this approach to locate the dI modification sites in the mitochondrial DNA of human cells. Our method should be generally applicable for genome-wide sequencing analysis of dI modifications in living organisms.
Keywords	analytical chemistry ; analytical methods ; carcinogenesis ; deamination ; deoxycytidine ; humans ; mitochondrial DNA ; mutagens ; plasmids
Language	English
Dates of publication	2022-0809
Size	p. 11627-11632.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c02126
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Article: Next-Generation Sequencing-Based Analysis of the Effects of N¹- and N⁶-Methyldeoxyadenosine Adducts on DNA Transcription

Yang, Ying / Wang, Ziyu / Wang, Juan / Dai, Xiaoxia / You, Changjun

Analytical chemistry. 2022 Aug. 04, v. 94, no. 32

2022

Abstract: DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric N¹- and N⁶-methyldeoxyadenosine (1mdA and 6mdA, respectively) represent an important class of methylated DNA adducts. In this study, ...

Abstract	DNA methylation can occur naturally or be induced by various environmental and chemotherapeutic agents. The regioisomeric N¹- and N⁶-methyldeoxyadenosine (1mdA and 6mdA, respectively) represent an important class of methylated DNA adducts. In this study, we developed a shuttle vector- and next-generation sequencing-based assay to quantitatively assess the effects of 1mdA and 6mdA on the accuracy and efficiency of DNA transcription. Our results revealed that 1mdA can induce multiple types of mutant transcripts and strongly inhibit DNA transcription, whereas 6mdA is a nonmutagenic DNA adduct that can exhibit a subtle but significant inhibitory effect on DNA transcription in vitro and in human cells. Moreover, our results demonstrated that the transcription-coupled nucleotide excision repair pathway is dispensable for the removal of 1mdA and 6mdA from the template DNA strand in human cells. These findings provided new important insights into the functional interplay between DNA methylation modifications and transcription in mammalian cells.
Keywords	DNA adducts ; DNA methylation ; DNA repair ; analytical chemistry ; drug therapy ; humans ; mutants
Language	English
Dates of publication	2022-0804
Size	p. 11248-11254.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.2c01764
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Article: Insights into the associations of copper and zinc with nitrogen metabolism during manure composting with shrimp shell powder

Zhao, Wenya / Gu, Jie / Wang, Xiaojuan / Song, Zilin / Hu, Ting / Dai, Xiaoxia / Wang, Jia

Bioresource technology. 2022 Apr., v. 349

2022

Abstract: The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) ...

Abstract	The application of shrimp shell powder (SSP) in manure composting can promote the maturation of compost and reduce the associated environmental risk. This study investigated the response of adding SSP at different levels (CK: 0, L: 5%, M: 10%, and H: 15%) on heavy metal resistance genes (MRGs), nitrogen functional genes, enzymes, and microorganisms. SSP inhibited nitrification and denitrification via decreasing the abundances of functional genes and key enzymes related to Cu, Zn, and MRGs. The nitrate reductase and nitrous-oxide reductase in the denitrification pathway were lower under H. Phylogenetic trees indicated that Burkholderiales sp. had strong relationships with OTU396 and OTU333, with important roles in the nitrogen cycle and plant growth. Redundancy analysis and structural equation modeling showed the complex response between heavy metal and nitrogen that bio-Cu and bio-Zn had positive significantly relationships with nirK-type and amoA-type bacteria, and amoA-type bacteria might be hotspot of cueO.
Keywords	Burkholderiales ; composts ; copper ; denitrification ; equations ; heavy metals ; metal tolerance ; nitrate reductase ; nitrification ; nitrogen ; nitrogen cycle ; nitrogen metabolism ; nitrous-oxide reductase ; phylogeny ; plant growth ; risk ; shrimp shells ; technology ; zinc
Language	English
Dates of publication	2022-04
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	1065195-0
ISSN	1873-2976 ; 0960-8524
ISSN (online)	1873-2976
ISSN	0960-8524
DOI	10.1016/j.biortech.2021.126431
Database	NAL-Catalogue (AGRICOLA)

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