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Zhang L, Leonard N, Passaro R, Luan MS, Van Tuyen P, Han LTN, Cam NH, Vogelnest L, Lynch M, Fine AE, Nga NTT, Van Long N, Rawson BM, Behie A, Van Nguyen T, Le MD, Nadler T, Walter L, Marques-Bonet T, Hofreiter M, Li M, Liu Z, Roos C. Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur. Nat Commun 2024; 15:8531. [PMID: 39358348 PMCID: PMC11447269 DOI: 10.1038/s41467-024-52811-7] [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: 04/26/2023] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive potential of the Cat Ba langur (Trachypithecus poliocephalus), a primate species endemic to Vietnam's famous Ha Long Bay and with less than 100 living individuals one of the most threatened primates in the world. Using high-coverage whole genome data of four wild individuals, we revealed the Cat Ba langur as sister species to its conspecifics of the northern limestone langur clade and found no evidence for extensive secondary gene flow after their initial separation. Compared to other primates and mammals, the Cat Ba langur showed low levels of genetic diversity, long runs of homozygosity, high levels of inbreeding and an excess of deleterious mutations in homozygous state. On the other hand, genetic diversity has been maintained in protein-coding genes and on the gene-rich human chromosome 19 ortholog, suggesting that the Cat Ba langur retained most of its adaptive potential. The Cat Ba langur also exhibits several unique non-synonymous variants that are related to calcium and sodium metabolism, which may have improved adaptation to high calcium intake and saltwater consumption.
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Affiliation(s)
- Liye Zhang
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- International Max Planck Research School for Genome Science (IMPRS-GS), University of Göttingen, Göttingen, Germany.
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Neahga Leonard
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Rick Passaro
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Mai Sy Luan
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Pham Van Tuyen
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Le Thi Ngoc Han
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Nguyen Huy Cam
- Cat Ba Langur Conservation Project (CBLCP), Cat Ba National Park, Cat Ba Island, Cat Hai District, Hai Phong Province, Vietnam
| | - Larry Vogelnest
- Taronga Conservation Society Australia, Mosman, NSW, Australia
| | - Michael Lynch
- Melbourne Zoo, Zoos Victoria, Parkville, VIC, Australia
| | - Amanda E Fine
- Wildlife Conservation Society (WCS), Health Program, New York, NY, USA
| | | | - Nguyen Van Long
- Wildlife Conservation Society (WCS), Vietnam Country Program, Hanoi, Vietnam
| | - Benjamin M Rawson
- World Wildlife Fund for Nature (WWF) International, Gland, Switzerland
| | - Alison Behie
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT, Australia
| | - Truong Van Nguyen
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
| | - Minh D Le
- Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam
- Faculty of Environmental Sciences, University of Science, Vietnam National University, Hanoi, Vietnam
| | - Tilo Nadler
- Three Monkeys Wildlife Conservancy, Nho Quan District, Ninh Binh Province, Ninh Binh, Vietnam
| | - Lutz Walter
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, Cerdanyola del Vallès, Spain
| | - Michael Hofreiter
- Evolutionary Adaptive Genomics, Institute of Biochemistry and Biology, Department of Science, University of Potsdam, Potsdam, Germany.
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing, China.
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
- Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.
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Li W, Almirantis Y, Provata A. Range-limited Heaps' law for functional DNA words in the human genome. J Theor Biol 2024; 592:111878. [PMID: 38901778 DOI: 10.1016/j.jtbi.2024.111878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Heaps' or Herdan-Heaps' law is a linguistic law describing the relationship between the vocabulary/dictionary size (type) and word counts (token) to be a power-law function. Its existence in genomes with certain definition of DNA words is unclear partly because the dictionary size in genome could be much smaller than that in a human language. We define a DNA word as a coding region in a genome that codes for a protein domain. Using human chromosomes and chromosome arms as individual samples, we establish the existence of Heaps' law in the human genome within limited range. Our definition of words in a genomic or proteomic context is different from other definitions such as over-represented k-mers which are much shorter in length. Although an approximate power-law distribution of protein domain sizes due to gene duplication and the related Zipf's law is well known, their translation to the Heaps' law in DNA words is not automatic. Several other animal genomes are shown herein also to exhibit range-limited Heaps' law with our definition of DNA words, though with various exponents. When tokens were randomly sampled and sample sizes reach to the maximum level, a deviation from the Heaps' law was observed, but a quadratic regression in log-log type-token plot fits the data perfectly. Investigation of type-token plot and its regression coefficients could provide an alternative narrative of reusage and redundancy of protein domains as well as creation of new protein domains from a linguistic perspective.
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Affiliation(s)
- Wentian Li
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA(1); The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Yannis Almirantis
- Theoretical Biology and Computational Genomics Laboratory, Institute of Bioscience and Applications, National Center for Scientific Research "Demokritos", 15341 Athens, Greece
| | - Astero Provata
- Statistical Mechanics and Dynamical Systems Laboratory, Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos", 15341 Athens, Greece
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3
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Lainscsek X, Taher L. ENT3C: an entropy-based similarity measure for Hi-C and micro-C derived contact matrices. NAR Genom Bioinform 2024; 6:lqae076. [PMID: 38962256 PMCID: PMC11217677 DOI: 10.1093/nargab/lqae076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 06/05/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024] Open
Abstract
Hi-C and micro-C sequencing have shed light on the profound importance of 3D genome organization in cellular function by probing 3D contact frequencies across the linear genome. The resulting contact matrices are extremely sparse and susceptible to technical- and sequence-based biases, making their comparison challenging. The development of reliable, robust and efficient methods for quantifying similarity between contact matrices is crucial for investigating variations in the 3D genome organization in different cell types or under different conditions, as well as evaluating experimental reproducibility. We present a novel method, ENT3C, which measures the change in pattern complexity in the vicinity of contact matrix diagonals to quantify their similarity. ENT3C provides a robust, user-friendly Hi-C or micro-C contact matrix similarity metric and a characteristic entropy signal that can be used to gain detailed biological insights into 3D genome organization.
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Affiliation(s)
- Xenia Lainscsek
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
| | - Leila Taher
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
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4
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Wong D, Tageldein M, Luo P, Ensminger E, Bruce J, Oldfield L, Gong H, Fischer NW, Laverty B, Subasri V, Davidson S, Khan R, Villani A, Shlien A, Kim RH, Malkin D, Pugh TJ. Cell-free DNA from germline TP53 mutation carriers reflect cancer-like fragmentation patterns. Nat Commun 2024; 15:7386. [PMID: 39191772 DOI: 10.1038/s41467-024-51529-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 08/07/2024] [Indexed: 08/29/2024] Open
Abstract
Germline pathogenic TP53 variants predispose individuals to a high lifetime risk of developing multiple cancers and are the hallmark feature of Li-Fraumeni syndrome (LFS). Our group has previously shown that LFS patients harbor shorter plasma cell-free DNA fragmentation; independent of cancer status. To understand the functional underpinning of cfDNA fragmentation in LFS, we conducted a fragmentomic analysis of 199 cfDNA samples from 82 TP53 mutation carriers and 30 healthy TP53-wildtype controls. We find that LFS individuals exhibit an increased prevalence of A/T nucleotides at fragment ends, dysregulated nucleosome positioning at p53 binding sites, and loci-specific changes in chromatin accessibility at development-associated transcription factor binding sites and at cancer-associated open chromatin regions. Machine learning classification resulted in robust differentiation between TP53 mutant versus wildtype cfDNA samples (AUC-ROC = 0.710-1.000) and intra-patient longitudinal analysis of ctDNA fragmentation signal enabled early cancer detection. These results suggest that cfDNA fragmentation may be a useful diagnostic tool in LFS patients and provides an important baseline for cancer early detection.
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Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Maha Tageldein
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Erik Ensminger
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey Bruce
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Leslie Oldfield
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Haifan Gong
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | | | - Brianne Laverty
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Vallijah Subasri
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Scott Davidson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Reem Khan
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Anita Villani
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Division of Hematology/Oncology, The Hospital for Sick Children, Toroton, Ontario, Canada
| | - Adam Shlien
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada
| | - Raymond H Kim
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Department of Pediatrics, University of Toronto, Torotno, Ontario, Canada.
- Toronto General Hospital Research Institute, Toronto, Ontario, Canada.
| | - Trevor J Pugh
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada.
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5
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Celis K, Moreno MDMM, Rajabli F, Whitehead P, Hamilton-Nelson K, Dykxhoorn DM, Nuytemans K, Wang L, Flanagan M, Weintraub S, Geula C, Gearing M, Dalgard CL, Jin F, Bennett DA, Schuck T, Pericak-Vance MA, Griswold AJ, Young JI, Vance JM. Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk. Alzheimers Dement 2023; 19:3902-3915. [PMID: 37037656 PMCID: PMC10529851 DOI: 10.1002/alz.13075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/03/2023] [Accepted: 03/08/2023] [Indexed: 04/12/2023]
Abstract
INTRODUCTION European local ancestry (ELA) surrounding apolipoprotein E (APOE) ε4 confers higher risk for Alzheimer's disease (AD) compared to African local ancestry (ALA). We demonstrated significantly higher APOE ε4 expression in ELA versus ALA in AD brains from APOE ε4/ε4 carriers. Chromatin accessibility differences could contribute to these expression changes. METHODS We performed single nuclei assays for transposase accessible chromatin sequencing from the frontal cortex of six ALA and six ELA AD brains, homozygous for local ancestry and APOE ε4. RESULTS Our results showed an increased chromatin accessibility at the APOE ε4 promoter area in ELA versus ALA astrocytes. This increased accessibility in ELA astrocytes extended genome wide. Genes with increased accessibility in ELA in astrocytes were enriched for synapsis, cholesterol processing, and astrocyte reactivity. DISCUSSION Our results suggest that increased chromatin accessibility of APOE ε4 in ELA astrocytes contributes to the observed elevated APOE ε4 expression, corresponding to the increased AD risk in ELA versus ALA APOE ε4/ε4 carriers.
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Affiliation(s)
- Katrina Celis
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Maria DM. Muniz Moreno
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Farid Rajabli
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Kara Hamilton-Nelson
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
| | - Derek M. Dykxhoorn
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Karen Nuytemans
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Liyong Wang
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Margaret Flanagan
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Sandra Weintraub
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Changiz Geula
- Northwestern ADC Neuropathology Core, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Marla Gearing
- Goizueta Alzheimer’s Disease Research Center, Emory University, Atlanta, GA, USA, 15213
| | - Clifton L. Dalgard
- The American Genome Center, Uniformed Services University, Bethesda, MD, USA, 20814
- Collaborative Health Initiative Research Program, Henry Jackson Foundation, Bethesda, MD, USA, 20817
- Department of Anatomy Physiology & Genetics, Uniformed Services University, Bethesda, MD, USA, 20814
| | - Fulai Jin
- Cleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, Ohio, USA, 44106
| | - David A. Bennett
- Department of Neurological Sciences, Rush University, Chicago, IL, USA, 60612
| | - Theresa Schuck
- The Department of Pathology and Laboratory Medicine, Institute on Aging and Center for Neurodegenerative Disease Research, The Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA,19104
| | - Margaret A. Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Anthony J. Griswold
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Juan I. Young
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
| | - Jeffery M. Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL, USA, 33136
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, USA, 33136
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Gong S, Gaccioli F, Aye ILMH, Avellino G, Cook E, Lawson ARJ, Harvey LMR, Smith GCS, Charnock-Jones DS. The human placenta exhibits a unique transcriptomic void. Cell Rep 2023; 42:112800. [PMID: 37453066 DOI: 10.1016/j.celrep.2023.112800] [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: 09/22/2022] [Revised: 02/08/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023] Open
Abstract
The human placenta exhibits a unique genomic architecture with an unexpectedly high mutation burden and many uniquely expressed genes. The aim of this study is to identify transcripts that are uniquely absent or depleted in the placenta. Here, we show that 40 of 46 of the other organs have no selectively depleted transcripts and that, of the remaining six, the liver has the largest number, with 26. In contrast, the term placenta has 762 depleted transcripts. Gene Ontology analysis of this depleted set highlighted multiple pathways reflecting known unique elements of placental physiology. For example, transcripts associated with neuronal function are in the depleted set-as expected given the lack of placental innervation. However, this demonstrated overrepresentation of genes involved in mitochondrial function (p = 5.8 × 10-10), including PGC-1α, the master regulator of mitochondrial biogenesis, and genes involved in polyamine metabolism (p = 2.1 × 10-4).
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Affiliation(s)
- Sungsam Gong
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Francesca Gaccioli
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Irving L M H Aye
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Giulia Avellino
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Emma Cook
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | | | | | - Gordon C S Smith
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - D Stephen Charnock-Jones
- Department of Obstetrics and Gynaecology, NIHR Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK; Centre for Trophoblast Research (CTR), Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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7
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Bernhardt L, Dittrich M, Prell A, Potabattula R, Drummer C, Behr R, Hahn T, Schorsch M, Müller T, Haaf T. Age-related methylation changes in the human sperm epigenome. Aging (Albany NY) 2023; 15:1257-1278. [PMID: 36849136 PMCID: PMC10042684 DOI: 10.18632/aging.204546] [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: 11/02/2022] [Accepted: 02/16/2023] [Indexed: 03/01/2023]
Abstract
Advanced paternal age is associated with increased risks for reproductive and offspring medical problems. Accumulating evidence suggests age-related changes in the sperm epigenome as one underlying mechanism. Using reduced representation bisulfite sequencing on 73 sperm samples of males attending a fertility center, we identified 1,162 (74%) regions which were significantly (FDR-adjusted) hypomethylated and 403 regions (26%) being hypermethylated with age. There were no significant correlations with paternal BMI, semen quality, or ART outcome. The majority (1,152 of 1,565; 74%) of age-related differentially methylated regions (ageDMRs) were located within genic regions, including 1,002 genes with symbols. Hypomethylated ageDMRs were closer to transcription start sites than hypermethylated DMRs, half of which reside in gene-distal regions. In this and conceptually related genome-wide studies, so far 2,355 genes have been reported with significant sperm ageDMRs, however most (90%) of them in only one study. The 241 genes which have been replicated at least once showed significant functional enrichments in 41 biological processes associated with development and the nervous system and in 10 cellular components associated with synapses and neurons. This supports the hypothesis that paternal age effects on the sperm methylome affect offspring behaviour and neurodevelopment. It is interesting to note that sperm ageDMRs were not randomly distributed throughout the human genome; chromosome 19 showed a highly significant twofold enrichment with sperm ageDMRs. Although the high gene density and CpG content have been conserved, the orthologous marmoset chromosome 22 did not appear to exhibit an increased regulatory potential by age-related DNA methylation changes.
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Affiliation(s)
- Laura Bernhardt
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Charis Drummer
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen and German Center for Cardiovascular Research, Partner Site Göttingen, Göttingen, Germany
| | - Rüdiger Behr
- Platform Degenerative Diseases, German Primate Center, Leibniz Institute for Primate Research, Göttingen and German Center for Cardiovascular Research, Partner Site Göttingen, Göttingen, Germany
| | | | | | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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8
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Paulin LF, Raveendran M, Harris RA, Rogers J, von Haeseler A, Sedlazeck FJ. SVhound: detection of regions that harbor yet undetected structural variation. BMC Bioinformatics 2023; 24:23. [PMID: 36670361 PMCID: PMC9854228 DOI: 10.1186/s12859-022-05046-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/08/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Recent population studies are ever growing in number of samples to investigate the diversity of a population or species. These studies reveal new polymorphism that lead to important insights into the mechanisms of evolution, but are also important for the interpretation of these variations. Nevertheless, while the full catalog of variations across entire species remains unknown, we can predict which regions harbor additional not yet detected variations and investigate their properties, thereby enhancing the analysis for potentially missed variants. RESULTS To achieve this we developed SVhound ( https://github.com/lfpaulin/SVhound ), which based on a population level SVs dataset can predict regions that harbor unseen SV alleles. We tested SVhound using subsets of the 1000 genomes project data and showed that its correlation (average correlation of 2800 tests r = 0.7136) is high to the full data set. Next, we utilized SVhound to investigate potentially missed or understudied regions across 1KGP and CCDG. Lastly we also apply SVhound on a small and novel SV call set for rhesus macaque (Macaca mulatta) and discuss the impact and choice of parameters for SVhound. CONCLUSIONS SVhound is a unique method to identify potential regions that harbor hidden diversity in model and non model organisms and can also be potentially used to ensure high quality of SV call sets.
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Affiliation(s)
- Luis F Paulin
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Labs, University of Vienna, Medical University of Vienna, Vienna, Austria
- Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
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Nikolaienko O, Lønning PE, Knappskog S. epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data. Gigascience 2022; 12:giad087. [PMID: 37919976 PMCID: PMC10622323 DOI: 10.1093/gigascience/giad087] [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: 06/01/2023] [Revised: 08/03/2023] [Accepted: 09/26/2023] [Indexed: 11/04/2023] Open
Abstract
Low-level mosaic epimutations within the BRCA1 gene promoter occur in 5-8% of healthy individuals and are associated with a significantly elevated risk of breast and ovarian cancer. Similar events may also affect other tumor suppressor genes, potentially being a significant contributor to cancer burden. While this opens a new area for translational research, detection of low-level mosaic epigenetic events requires highly sensitive and robust methodology for methylation analysis. We here present epialleleR, a computational framework for sensitive detection, quantification, and visualization of mosaic epimutations in methylation sequencing data. Analyzing simulated and real data sets, we provide in-depth assessments of epialleleR performance and show that linkage to epihaplotype data is necessary to detect low-level methylation events. The epialleleR is freely available at https://github.com/BBCG/epialleleR and https://bioconductor.org/packages/epialleleR/ as an open-source R/Bioconductor package.
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Affiliation(s)
- Oleksii Nikolaienko
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Per Eystein Lønning
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Oncology, Haukeland University Hospital, Bergen 5021, Norway
| | - Stian Knappskog
- K. G. Jebsen Center for Genome-Directed Cancer Therapy, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
- Department of Oncology, Haukeland University Hospital, Bergen 5021, Norway
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Hyblova M, Gnip A, Kucharik M, Budis J, Sekelska M, Minarik G. Maternal Copy Number Imbalances in Non-Invasive Prenatal Testing: Do They Matter? Diagnostics (Basel) 2022; 12:diagnostics12123056. [PMID: 36553064 PMCID: PMC9777446 DOI: 10.3390/diagnostics12123056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) has become a routine practice in screening for common aneuploidies of chromosomes 21, 18, and 13 and gonosomes X and Y in fetuses worldwide since 2015 and has even expanded to include smaller subchromosomal events. In fact, the fetal fraction represents only a small proportion of cell-free DNA on a predominant background of maternal DNA. Unlike fetal findings that have to be confirmed using invasive testing, it has been well documented that NIPT provides information on maternal mosaicism, occult malignancies, and hidden health conditions due to copy number variations (CNVs) with diagnostic resolution. Although large duplications or deletions associated with certain medical conditions or syndromes are usually well recognized and easy to interpret, very little is known about small, relatively common copy number variations on the order of a few hundred kilobases and their potential impact on human health. We analyzed data from 6422 NIPT patient samples with a CNV detection resolution of 200 kb for the maternal genome and identified 942 distinct CNVs; 328 occurred repeatedly. We defined them as multiple occurring variants (MOVs). We scrutinized the most common ones, compared them with frequencies in the gnomAD SVs v2.1, dbVar, and DGV population databases, and analyzed them with an emphasis on genomic content and potential association with specific phenotypes.
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Affiliation(s)
- Michaela Hyblova
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Correspondence:
| | - Andrej Gnip
- Medirex a.s., Galvaniho 17/C, 820 16 Bratislava, Slovakia
| | | | - Jaroslav Budis
- Geneton s.r.o., Ilkovicova 8, 841 04 Bratislava, Slovakia
| | - Martina Sekelska
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
| | - Gabriel Minarik
- Medirex Group Academy n.o., Novozamocka 67, 949 05 Nitra, Slovakia
- Trisomy Test s.r.o., Novozamocka 67, 949 05 Nitra, Slovakia
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11
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Krishnan B, Yasuhara T, Rumde P, Stanzione M, Lu C, Lee H, Lawrence MS, Zou L, Nieman LT, Sanidas I, Dyson NJ. Active RB causes visible changes in nuclear organization. J Cell Biol 2022; 221:e202102144. [PMID: 35019938 PMCID: PMC8759594 DOI: 10.1083/jcb.202102144] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 10/21/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022] Open
Abstract
RB restricts G1/S progression by inhibiting E2F. Here, we show that sustained expression of active RB, and prolonged G1 arrest, causes visible changes in chromosome architecture that are not directly associated with E2F inhibition. Using FISH probes against two euchromatin RB-associated regions, two heterochromatin domains that lack RB-bound loci, and two whole-chromosome probes, we found that constitutively active RB (ΔCDK-RB) promoted a more diffuse, dispersed, and scattered chromatin organization. These changes were RB dependent, were driven by specific isoforms of monophosphorylated RB, and required known RB-associated activities. ΔCDK-RB altered physical interactions between RB-bound genomic loci, but the RB-induced changes in chromosome architecture were unaffected by dominant-negative DP1. The RB-induced changes appeared to be widespread and influenced chromosome localization within nuclei. Gene expression profiles revealed that the dispersion phenotype was associated with an increased autophagy response. We infer that, after cell cycle arrest, RB acts through noncanonical mechanisms to significantly change nuclear organization, and this reorganization correlates with transitions in cellular state.
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Affiliation(s)
- Badri Krishnan
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Takaaki Yasuhara
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Purva Rumde
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Marcello Stanzione
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Chenyue Lu
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Hanjun Lee
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Michael S. Lawrence
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Linda T. Nieman
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Ioannis Sanidas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
| | - Nicholas J. Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, MA
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12
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Dias JD, Sarica N, Cournac A, Koszul R, Neuveut C. Crosstalk between Hepatitis B Virus and the 3D Genome Structure. Viruses 2022; 14:445. [PMID: 35216038 PMCID: PMC8877387 DOI: 10.3390/v14020445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 02/04/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Viruses that transcribe their DNA within the nucleus have to adapt to the existing cellular mechanisms that govern transcriptional regulation. Recent technological breakthroughs have highlighted the highly hierarchical organization of the cellular genome and its role in the regulation of gene expression. This review provides an updated overview on the current knowledge on how the hepatitis B virus interacts with the cellular 3D genome and its consequences on viral and cellular gene expression. We also briefly discuss the strategies developed by other DNA viruses to co-opt and sometimes subvert cellular genome spatial organization.
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Affiliation(s)
- João Diogo Dias
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Nazim Sarica
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
| | - Axel Cournac
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Romain Koszul
- Unité Régulation Spatiale des Génomes, CNRS, UMR 3525, Institut Pasteur, Université de Paris, 75015 Paris, France; (A.C.); (R.K.)
| | - Christine Neuveut
- Laboratoire de Virologie Moléculaire, Institut de Génétique Humaine, CNRS, Université de Montpellier, 34000 Montpellier, France; (J.D.D.); (N.S.)
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