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Yang J, Sun M, Ran Z, Yang T, Kundnani DL, Storici F, Xu P. rNMPID: a database for riboNucleoside MonoPhosphates in DNA. BIOINFORMATICS ADVANCES 2024; 4:vbae063. [PMID: 38736683 PMCID: PMC11088741 DOI: 10.1093/bioadv/vbae063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/27/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Motivation Ribonucleoside monophosphates (rNMPs) are the most abundant non-standard nucleotides embedded in genomic DNA. If the presence of rNMP in DNA cannot be controlled, it can lead to genome instability. The actual regulatory functions of rNMPs in DNA remain mainly unknown. Considering the association between rNMP embedment and various diseases and cancer, the phenomenon of rNMP embedment in DNA has become a prominent area of research in recent years. Results We introduce the rNMPID database, which is the first database revealing rNMP-embedment characteristics, strand bias, and preferred incorporation patterns in the genomic DNA of samples from bacterial to human cells of different genetic backgrounds. The rNMPID database uses datasets generated by different rNMP-mapping techniques. It provides the researchers with a solid foundation to explore the features of rNMP embedded in the genomic DNA of multiple sources, and their association with cellular functions, and, in future, disease. It also significantly benefits researchers in the fields of genetics and genomics who aim to integrate their studies with the rNMP-embedment data. Availability and implementation rNMPID is freely accessible on the web at https://www.rnmpid.org.
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Affiliation(s)
- Jingcheng Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, and Shanghai Cancer Center, Fudan University, Shanghai 200438, China
- Greater Bay Area Institute of Precision Medicine, Guangzhou, Guangdong 511462, China
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Zihan Ran
- Department of Research, Shanghai University of Medicine & Health Sciences Affiliated Zhoupu Hospital, Shanghai 201318, China
- Inspection and Quarantine Department, The College of Medical Technology, Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
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Xu P, Yang T, Kundnani DL, Sun M, Marsili S, Gombolay A, Jeon Y, Newnam G, Balachander S, Bazzani V, Baccarani U, Park V, Tao S, Lori A, Schinazi R, Kim B, Pursell Z, Tell G, Vascotto C, Storici F. Light-strand bias and enriched zones of embedded ribonucleotides are associated with DNA replication and transcription in the human-mitochondrial genome. Nucleic Acids Res 2024; 52:1207-1225. [PMID: 38117983 PMCID: PMC10853789 DOI: 10.1093/nar/gkad1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 11/30/2023] [Accepted: 12/05/2023] [Indexed: 12/22/2023] Open
Abstract
Abundant ribonucleoside-triphosphate (rNTP) incorporation into DNA by DNA polymerases in the form of ribonucleoside monophosphates (rNMPs) is a widespread phenomenon in nature, resulting in DNA-structural change and genome instability. The rNMP distribution, characteristics, hotspots and association with DNA metabolic processes in human mitochondrial DNA (hmtDNA) remain mostly unknown. Here, we utilize the ribose-seq technique to capture embedded rNMPs in hmtDNA of six different cell types. In most cell types, the rNMPs are preferentially embedded on the light strand of hmtDNA with a strong bias towards rCMPs; while in the liver-tissue cells, the rNMPs are predominately found on the heavy strand. We uncover common rNMP hotspots and conserved rNMP-enriched zones across the entire hmtDNA, including in the control region, which links the rNMP presence to the frequent hmtDNA replication-failure events. We show a strong correlation between coding-sequence size and rNMP-embedment frequency per nucleotide on the non-template, light strand in all cell types, supporting the presence of transient RNA-DNA hybrids preceding light-strand replication. Moreover, we detect rNMP-embedment patterns that are only partly conserved across the different cell types and are distinct from those found in yeast mtDNA. The study opens new research directions to understand the biology of hmtDNA and genomic rNMPs.
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Affiliation(s)
- Penghao Xu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Deepali L Kundnani
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Mo Sun
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Stefania Marsili
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Youngkyu Jeon
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Sathya Balachander
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
| | - Veronica Bazzani
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Umberto Baccarani
- Department of Medicine, University of Udine, Udine 33100, Italy
- General Surgery Clinic and Liver Transplant Center, University-Hospital of Udine, Udine 33100, Italy
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta 30329, GA, USA
- Department of Population Science, American Cancer Society, Kennesaw 30144, GA, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Baek Kim
- Center for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta 30322, GA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane Cancer Center, Tulane University of Medicine, New Orleans, LA 70118, USA
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, Udine 33100, Italy
| | - Carlo Vascotto
- Department of Medicine, University of Udine, Udine 33100, Italy
- IMol Polish Academy of Sciences, Warsaw 02-247, Poland
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta 30332, GA, USA
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