1
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LeDoux MS. Polymerase I as a Target for Treating Neurodegenerative Disorders. Biomedicines 2024; 12:1092. [PMID: 38791054 PMCID: PMC11118182 DOI: 10.3390/biomedicines12051092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/06/2024] [Accepted: 05/11/2024] [Indexed: 05/26/2024] Open
Abstract
Polymerase I (Pol I) is at the epicenter of ribosomal RNA (rRNA) synthesis. Pol I is a target for the treatment of cancer. Given the many cellular commonalities between cancer and neurodegeneration (i.e., different faces of the same coin), it seems rational to consider targeting Pol I or, more generally, rRNA synthesis for the treatment of disorders associated with the death of terminally differentiated neurons. Principally, ribosomes synthesize proteins, and, accordingly, Pol I can be considered the starting point for protein synthesis. Given that cellular accumulation of abnormal proteins such as α-synuclein and tau is an essential feature of neurodegenerative disorders such as Parkinson disease and fronto-temporal dementia, reduction of protein production is now considered a viable target for treatment of these and closely related neurodegenerative disorders. Abnormalities in polymerase I activity and rRNA production may also be associated with nuclear and nucleolar stress, DNA damage, and childhood-onset neuronal death, as is the case for the UBTF E210K neuroregression syndrome. Moreover, restraining the activity of Pol I may be a viable strategy to slow aging. Before starting down the road of Pol I inhibition for treating non-cancerous disorders of the nervous system, many questions must be answered. First, how much Pol I inhibition can neurons tolerate, and for how long? Should inhibition of Pol I be continuous or pulsed? Will cells compensate for Pol I inhibition by upregulating the number of active rDNAs? At present, we have no effective and safe disease modulatory treatments for Alzheimer disease, α-synucleinopathies, or tauopathies, and novel therapeutic targets and approaches must be explored.
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Affiliation(s)
- Mark S. LeDoux
- Department of Psychology and College of Health Sciences, University of Memphis, Memphis, TN 38152, USA; or
- Veracity Neuroscience LLC, Memphis, TN 38157, USA
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2
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Dodel M, Guiducci G, Dermit M, Krishnamurthy S, Alard EL, Capraro F, Rekad Z, Stojic L, Mardakheh FK. TREX reveals proteins that bind to specific RNA regions in living cells. Nat Methods 2024; 21:423-434. [PMID: 38374261 PMCID: PMC10927567 DOI: 10.1038/s41592-024-02181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
Different regions of RNA molecules can often engage in specific interactions with distinct RNA-binding proteins (RBPs), giving rise to diverse modalities of RNA regulation and function. However, there are currently no methods for unbiased identification of RBPs that interact with specific RNA regions in living cells and under endogenous settings. Here we introduce TREX (targeted RNase H-mediated extraction of crosslinked RBPs)-a highly sensitive approach for identifying proteins that directly bind to specific RNA regions in living cells. We demonstrate that TREX outperforms existing methods in identifying known interactors of U1 snRNA, and reveals endogenous region-specific interactors of NORAD long noncoding RNA. Using TREX, we generated a comprehensive region-by-region interactome for 45S rRNA, uncovering both established and previously unknown interactions that regulate ribosome biogenesis. With its applicability to different cell types, TREX is an RNA-centric tool for unbiased positional mapping of endogenous RNA-protein interactions in living cells.
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Affiliation(s)
- Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Giulia Guiducci
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Sneha Krishnamurthy
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Emilie L Alard
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Federica Capraro
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
- Randall Centre for Cell and Molecular Biophysics, King's College London, London, UK
| | - Zeinab Rekad
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Lovorka Stojic
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, London, UK.
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3
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Griffin PT, Kane AE, Trapp A, Li J, Arnold M, Poganik JR, Conway RJ, McNamara MS, Meer MV, Hoffman N, Amorim JA, Tian X, MacArthur MR, Mitchell SJ, Mueller AL, Carmody C, Vera DL, Kerepesi C, Ying K, Noren Hooten N, Mitchell JR, Evans MK, Gladyshev VN, Sinclair DA. TIME-seq reduces time and cost of DNA methylation measurement for epigenetic clock construction. NATURE AGING 2024; 4:261-274. [PMID: 38200273 DOI: 10.1038/s43587-023-00555-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/05/2023] [Indexed: 01/12/2024]
Abstract
Epigenetic 'clocks' based on DNA methylation have emerged as the most robust and widely used aging biomarkers, but conventional methods for applying them are expensive and laborious. Here we develop tagmentation-based indexing for methylation sequencing (TIME-seq), a highly multiplexed and scalable method for low-cost epigenetic clocks. Using TIME-seq, we applied multi-tissue and tissue-specific epigenetic clocks in over 1,800 mouse DNA samples from eight tissue and cell types. We show that TIME-seq clocks are accurate and robust, enriched for polycomb repressive complex 2-regulated loci, and benchmark favorably against conventional methods despite being up to 100-fold less expensive. Using dietary treatments and gene therapy, we find that TIME-seq clocks reflect diverse interventions in multiple tissues. Finally, we develop an economical human blood clock (R > 0.96, median error = 3.39 years) in 1,056 demographically representative individuals. These methods will enable more efficient epigenetic clock measurement in larger-scale human and animal studies.
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Affiliation(s)
- Patrick T Griffin
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Alice E Kane
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Institute for Systems Biology, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Alexandre Trapp
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jien Li
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Matthew Arnold
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Jesse R Poganik
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ryan J Conway
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Maeve S McNamara
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Margarita V Meer
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- San Diego Institute of Science, Altos Labs, San Diego, CA, USA
| | - Noah Hoffman
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - João A Amorim
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Xiao Tian
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Michael R MacArthur
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
- Lewis-Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sarah J Mitchell
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
- Ludwig Princeton Branch, Princeton University, Princeton, NJ, USA
| | - Amber L Mueller
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
- Cell Metabolism, Cell Press, Cambridge, MA, USA
| | - Colleen Carmody
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Daniel L Vera
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA
| | - Csaba Kerepesi
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
- Institute for Computer Science and Control, Eötvös Loránd Research Network, Budapest, Hungary
| | - Kejun Ying
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Nicole Noren Hooten
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - James R Mitchell
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Michele K Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Division of Genetics, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - David A Sinclair
- Blavatnik Institute, Department of Genetics, Paul F. Glenn Center for Biology of Aging Research at Harvard Medical School, Boston, MA, USA.
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4
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Razzaq A, Bejaoui Y, Alam T, Saad M, El Hajj N. Ribosomal DNA Copy Number Variation is Coupled with DNA Methylation Changes at the 45S rDNA Locus. Epigenetics 2023; 18:2229203. [PMID: 37368968 DOI: 10.1080/15592294.2023.2229203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 06/04/2023] [Accepted: 06/20/2023] [Indexed: 06/29/2023] Open
Abstract
The human ribosomal DNA (rDNA) copy number (CN) has been challenging to analyse, and its sequence has been excluded from reference genomes due to its highly repetitive nature. The 45S rDNA locus encodes essential components of the cell, nevertheless rDNA displays high inter-individual CN variation that could influence human health and disease. CN alterations in rDNA have been hypothesized as a possible factor in autism spectrum disorders (ASD) and were shown to be altered in Schizophrenia patients. We tested whether whole-genome bisulphite sequencing can be used to simultaneously quantify rDNA CN and measure DNA methylation at the 45S rDNA locus. Using this approach, we observed high inter-individual variation in rDNA CN, and limited intra-individual copy differences in several post-mortem tissues. Furthermore, we did not observe any significant alterations in rDNA CN or DNA methylation in Autism Spectrum Disorder (ASD) brains in 16 ASD vs 11 control samples. Similarly, no difference was detected when comparing neurons form 28 Schizophrenia (Scz) patients vs 25 controls or oligodendrocytes from 22 Scz samples vs 20 controls. However, our analysis revealed a strong positive correlation between CN and DNA methylation at the 45S rDNA locus in multiple tissues. This was observed in brain and confirmed in small intestine, adipose tissue, and gastric tissue. This should shed light on a possible dosage compensation mechanism that silences additional rDNA copies to ensure homoeostatic regulation of ribosome biogenesis.
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Affiliation(s)
- Aleem Razzaq
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
| | - Yosra Bejaoui
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Mohamad Saad
- Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences, Qatar Foundation, Hamad Bin Khalifa University, Doha, Qatar
- College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
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5
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Baker EC, San AE, Cilkiz KZ, Littlejohn BP, Cardoso RC, Ghaffari N, Long CR, Riggs PK, Randel RD, Welsh TH, Riley DG. Inter-Individual Variation in DNA Methylation Patterns across Two Tissues and Leukocytes in Mature Brahman Cattle. BIOLOGY 2023; 12:biology12020252. [PMID: 36829529 PMCID: PMC9953534 DOI: 10.3390/biology12020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also for understanding how the environment affects variability, and for incorporation into statistical analyses. The inter-individual variation in DNA methylation patterns in female cattle and the effect that a prenatal stressor has on such variability have yet to be quantified. Thus, the objective of this study was to utilize methylation data from mature Brahman females to quantify the inter-individual variation in DNA methylation. Pregnant Brahman cows were transported for 2 h durations at days 60 ± 5; 80 ± 5; 100 ± 5; 120 ± 5; and 140 ± 5 of gestation. A non-transport group was maintained as a control. Leukocytes, amygdala, and anterior pituitary glands were harvested from eight cows born from the non-transport group (Control) and six from the transport group (PNS) at 5 years of age. The DNA harvested from the anterior pituitary contained the greatest variability in DNA methylation of cytosine-phosphate-guanine (mCpG) sites from both the PNS and Control groups, and the amygdala had the least. Numerous variable mCpG sites were associated with retrotransposable elements and highly repetitive regions of the genome. Some of the genomic features that had high variation in DNA methylation are involved in immune responses, signaling, responses to stimuli, and metabolic processes. The small overlap of highly variable CpG sites and features between tissues and leukocytes supports the role of variable DNA methylation in regulating tissue-specific gene expression. Many of the CpG sites that exhibited high variability in DNA methylation were common between the PNS and Control groups within a tissue, but there was little overlap in genomic features with high variability. The interaction between the prenatal environment and the genome could be responsible for the differences in location of the variable DNA methylation.
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Affiliation(s)
- Emilie C. Baker
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Audrey E. San
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Kubra Z. Cilkiz
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Brittni P. Littlejohn
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Rodolfo C. Cardoso
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Noushin Ghaffari
- Department of Computer Science, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Charles R. Long
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Penny K. Riggs
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Ronald D. Randel
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Thomas H. Welsh
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research, College Station, TX 77845, USA
| | - David G. Riley
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Correspondence:
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6
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Regulation of ribosomal RNA gene copy number, transcription and nucleolus organization in eukaryotes. Nat Rev Mol Cell Biol 2023; 24:414-429. [PMID: 36732602 DOI: 10.1038/s41580-022-00573-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/14/2022] [Indexed: 02/04/2023]
Abstract
One of the first biological machineries to be created seems to have been the ribosome. Since then, organisms have dedicated great efforts to optimize this apparatus. The ribosomal RNA (rRNA) contained within ribosomes is crucial for protein synthesis and maintenance of cellular function in all known organisms. In eukaryotic cells, rRNA is produced from ribosomal DNA clusters of tandem rRNA genes, whose organization in the nucleolus, maintenance and transcription are strictly regulated to satisfy the substantial demand for rRNA required for ribosome biogenesis. Recent studies have elucidated mechanisms underlying the integrity of ribosomal DNA and regulation of its transcription, including epigenetic mechanisms and a unique recombination and copy-number control system to stably maintain high rRNA gene copy number. In this Review, we disucss how the crucial maintenance of rRNA gene copy number through control of gene amplification and of rRNA production by RNA polymerase I are orchestrated. We also discuss how liquid-liquid phase separation controls the architecture and function of the nucleolus and the relationship between rRNA production, cell senescence and disease.
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7
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Tan KT, Slevin MK, Meyerson M, Li H. Identifying and correcting repeat-calling errors in nanopore sequencing of telomeres. Genome Biol 2022; 23:180. [PMID: 36028900 PMCID: PMC9414165 DOI: 10.1186/s13059-022-02751-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/16/2022] [Indexed: 12/27/2022] Open
Abstract
Nanopore long-read sequencing is an emerging approach for studying genomes, including long repetitive elements like telomeres. Here, we report extensive basecalling induced errors at telomere repeats across nanopore datasets, sequencing platforms, basecallers, and basecalling models. We find that telomeres in many organisms are frequently miscalled. We demonstrate that tuning of nanopore basecalling models leads to improved recovery and analysis of telomeric regions, with minimal negative impact on other genomic regions. We highlight the importance of verifying nanopore basecalls in long, repetitive, and poorly defined regions, and showcase how artefacts can be resolved by improvements in nanopore basecalling models.
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Affiliation(s)
- Kar-Tong Tan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Michael K Slevin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
- Center for Cancer Genomics, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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8
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Zhang X, Jia X, Zhong B, Wei L, Li J, Zhang W, Fang H, Li Y, Lu Y, Wang X. Evaluating methylation of human ribosomal DNA at each CpG site reveals its utility for cancer detection using cell-free DNA. Brief Bioinform 2022; 23:6634225. [PMID: 35804466 DOI: 10.1093/bib/bbac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/07/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Ribosomal deoxyribonucleic acid (DNA) (rDNA) repeats are tandemly located on five acrocentric chromosomes with up to hundreds of copies in the human genome. DNA methylation, the most well-studied epigenetic mechanism, has been characterized for most genomic regions across various biological contexts. However, rDNA methylation patterns remain largely unexplored due to the repetitive structure. In this study, we designed a specific mapping strategy to investigate rDNA methylation patterns at each CpG site across various physiological and pathological processes. We found that CpG sites on rDNA could be categorized into two types. One is within or adjacent to transcribed regions; the other is distal to transcribed regions. The former shows highly variable methylation levels across samples, while the latter shows stable high methylation levels in normal tissues but severe hypomethylation in tumors. We further showed that rDNA methylation profiles in plasma cell-free DNA could be used as a biomarker for cancer detection. It shows good performances on public datasets, including colorectal cancer [area under the curve (AUC) = 0.85], lung cancer (AUC = 0.84), hepatocellular carcinoma (AUC = 0.91) and in-house generated hepatocellular carcinoma dataset (AUC = 0.96) even at low genome coverage (<1×). Taken together, these findings broaden our understanding of rDNA regulation and suggest the potential utility of rDNA methylation features as disease biomarkers.
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Affiliation(s)
- Xianglin Zhang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaodong Jia
- Senior Department of Oncology, Fifth Medical Center of PLA General Hospital, Beijing 100039, China
| | - Bixi Zhong
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Jiaqi Li
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Wei Zhang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Huan Fang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yanda Li
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
| | - Yinying Lu
- Comprehensive Liver Cancer Center, Fifth Medical Center of PLA General Hospital, Beijing 100039, China.,Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China.,Guangdong Key Laboratory of Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, 518055, China
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing 100084, China
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9
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Ravaioli F, Zampieri M, Morandi L, Pirazzini C, Pellegrini C, De Fanti S, Gensous N, Pirazzoli GL, Sambati L, Ghezzo A, Ciccarone F, Reale A, Monti D, Salvioli S, Caiafa P, Capri M, Bürkle A, Moreno-Villanueva M, Garagnani P, Franceschi C, Bacalini MG. DNA Methylation Analysis of Ribosomal DNA in Adults With Down Syndrome. Front Genet 2022; 13:792165. [PMID: 35571061 PMCID: PMC9094685 DOI: 10.3389/fgene.2022.792165] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 03/18/2022] [Indexed: 01/08/2023] Open
Abstract
Control of ribosome biogenesis is a critical aspect of the regulation of cell metabolism. As ribosomal genes (rDNA) are organized in repeated clusters on chromosomes 13, 14, 15, 21, and 22, trisomy of chromosome 21 confers an excess of rDNA copies to persons with Down syndrome (DS). Previous studies showed an alteration of ribosome biogenesis in children with DS, but the epigenetic regulation of rDNA genes has not been investigated in adults with DS so far. In this study, we used a targeted deep-sequencing approach to measure DNA methylation (DNAm) of rDNA units in whole blood from 69 adults with DS and 95 euploid controls. We further evaluated the expression of the precursor of ribosomal RNAs (RNA45S) in peripheral blood mononuclear cells (PBMCs) from the same subjects. We found that the rDNA promoter tends to be hypermethylated in DS concerning the control group. The analysis of epihaplotypes (the combination of methylated and unmethylated CpG sites along the same DNA molecule) showed a significantly lower intra-individual diversity in the DS group, which at the same time was characterized by a higher interindividual variability. Finally, we showed that RNA45S expression is lower in adults with DS. Collectively, our results suggest a rearrangement of the epigenetic profile of rDNA in DS, possibly to compensate for the extranumerary rDNA copies. Future studies should assess whether the regulation of ribosome biogenesis can contribute to the pathogenesis of DS and explain the clinical heterogeneity characteristic of the syndrome.
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Affiliation(s)
- Francesco Ravaioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Michele Zampieri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Luca Morandi
- Functional and Molecular Neuroimaging Unit, IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Sara De Fanti
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Interdepartmental Centre Alma Mater Research Institute on Global Challenges and Climate Change, University of Bologna, Bologna, Italy
| | - Noémie Gensous
- Department of Internal Medicine and Clinical Immunology, CHU Bordeaux (Groupe Hospitalier Saint-André), Bordeaux, France
- UMR/CNRS 5164, ImmunoConcEpT, CNRS, University of Bordeaux, Bordeaux, France
| | | | - Luisa Sambati
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, U.O.C. Clinica Neurologica Rete Neurologica Metropolitana (NEUROMET), Bologna, Italy
| | | | - Fabio Ciccarone
- IRCCS San Raffaele Roma, Department of Human Sciences and Promotion of the Quality of Life, San Raffaele Roma Open University, Rome, Italy
| | - Anna Reale
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Daniela Monti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, Florence, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Rome, Italy
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Maria Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
- Applied Biomedical Research Center (CRBA), S. Orsola-Malpighi Polyclinic, Bologna, Italy
- CNR Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”—Unit of Bologna, Bologna, Italy
- Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Huddinge, Sweden
| | - Claudio Franceschi
- Laboratory of Systems Medicine of Healthy Aging, Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Bologna, Italy
- *Correspondence: Maria Giulia Bacalini,
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