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Simó-Mirabet P, Naya-Català F, Calduch-Giner JA, Pérez-Sánchez J. The Expansion of Sirtuin Gene Family in Gilthead Sea Bream ( Sparus aurata)-Phylogenetic, Syntenic, and Functional Insights across the Vertebrate/Fish Lineage. Int J Mol Sci 2024; 25:6273. [PMID: 38892461 PMCID: PMC11172991 DOI: 10.3390/ijms25116273] [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: 04/15/2024] [Revised: 05/31/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
The Sirtuin (SIRT1-7) family comprises seven evolutionary-conserved enzymes that couple cellular NAD availability with health, nutrition and welfare status in vertebrates. This study re-annotated the sirt3/5 branch in the gilthead sea bream, revealing three paralogues of sirt3 (sirt3.1a/sirt3.1b/sirt3.2) and two of sirt5 (sirt5a/sirt5b) in this Perciform fish. The phylogeny and synteny analyses unveiled that the Sirt3.1/Sirt3.2 dichotomy was retained in teleosts and aquatic-living Sarcopterygian after early vertebrate 2R whole genome duplication (WGD). Additionally, only certain percomorphaceae and gilthead sea bream showed a conserved tandem-duplicated synteny block involving the mammalian-clustered sirt3.1 gene (psmd13-sirt3.1a/b-drd4-cdhr5-ctsd). Conversely, the expansion of the Sirt5 branch was shaped by the teleost-specific 3R WGD. As extensively reviewed in the literature, human-orthologues (sirt3.1/sirt5a) showed a high, conserved expression in skeletal muscle that increased as development advanced. However, recent sirt3.2 and sirt5b suffered an overall muscle transcriptional silencing across life, as well as an enhanced expression on immune-relevant tissues and gills. These findings fill gaps in the ontogeny and differentiation of Sirt genes in the environmentally adaptable gilthead sea bream, becoming a good starting point to advance towards a full understanding of its neo-functionalization. The mechanisms originating from these new paralogs also open new perspectives in the study of cellular energy sensing processes in vertebrates.
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Affiliation(s)
| | | | | | - Jaume Pérez-Sánchez
- Instituto de Acuicultura Torre de la Sal (IATS, CSIC), 12595 Ribera de Cabanes, Castellón, Spain; (P.S.-M.); (F.N.-C.); (J.A.C.-G.)
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2
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Dossmann L, Emperle M, Dukatz M, de Mendoza A, Bashtrykov P, Jeltsch A. Specific DNMT3C flanking sequence preferences facilitate methylation of young murine retrotransposons. Commun Biol 2024; 7:582. [PMID: 38755427 PMCID: PMC11099192 DOI: 10.1038/s42003-024-06252-z] [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: 01/05/2024] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
The DNA methyltransferase DNMT3C appeared as a duplication of the DNMT3B gene in muroids and is required for silencing of young retrotransposons in the male germline. Using specialized assay systems, we investigate the flanking sequence preferences of DNMT3C and observe characteristic preferences for cytosine at the -2 and -1 flank that are unique among DNMT3 enzymes. We identify two amino acids in the catalytic domain of DNMT3C (C543 and V547) that are responsible for the DNMT3C-specific flanking sequence preferences and evolutionary conserved in muroids. Reanalysis of published data shows that DNMT3C flanking preferences are consistent with genome-wide methylation patterns in mouse ES cells only expressing DNMT3C. Strikingly, we show that CpG sites with the preferred flanking sequences of DNMT3C are enriched in murine retrotransposons that were previously identified as DNMT3C targets. Finally, we demonstrate experimentally that DNMT3C has elevated methylation activity on substrates derived from these biological targets. Our data show that DNMT3C flanking sequence preferences match the sequences of young murine retrotransposons which facilitates their methylation. By this, our data provide mechanistic insights into the molecular co-evolution of repeat elements and (epi)genetic defense systems dedicated to maintain genomic stability in mammals.
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Affiliation(s)
- Leonie Dossmann
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Max Emperle
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Dukatz
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Alex de Mendoza
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, E1 4NS, London, UK
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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3
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Wang J, Qin Y, Kang Y, Li X, Wang Y, Li H, Czajkowsky DM, Shao Z. Temporal profiling with ultra-deep RRBS sequencing reveals the relative rarity of stably maintained methylated CpG sites in human cells. Acta Biochim Biophys Sin (Shanghai) 2022; 54:1935-1938. [PMID: 36789696 PMCID: PMC10157517 DOI: 10.3724/abbs.2022185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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4
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Zhang J, Zhang XQ, Ling XZ, Zhao XH, Zhou KZ, Wang JY, Zhang GX. Prediction of the Effect of Methylation in the Promoter Region of ZP2 Gene on Egg Production in Jinghai Yellow Chickens. Vet Sci 2022; 9:vetsci9100570. [PMID: 36288183 PMCID: PMC9609111 DOI: 10.3390/vetsci9100570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/09/2022] [Accepted: 10/14/2022] [Indexed: 11/19/2022] Open
Abstract
Egg production in chickens is a quantitative trait. The aim of this study was to investigate the effect of promoter methylation of the Zona pellucida 2 (ZP2) gene on egg production. Real-time fluorescence quantification showed that the expression of the ZP2 gene in the ovaries of 300-day-old Jinghai yellow chickens in the high-laying group was significantly higher than that in the low-laying group (p < 0.01). A series of deletion fragments of the ZP2 gene promoter in Jinghai yellow chickens had different promoter activities in DF-1 cells, and the core region of the ZP2 gene promoter was found to be between −1552 and −1348. Four CpG islands in the promoter region of the ZP2 gene were detected by software prediction. The overall degree of methylation of the ZP2-1 amplified fragment was negatively correlated with mRNA expression to some extent (R = −0.197); the overall degree of methylation of the ZP2-2 amplified fragment was also negatively correlated with mRNA expression to some extent (R = −0.264), in which the methylation of methylcytosine (mC)-9, mC-20, and mC-21 sites was significantly negatively correlated with mRNA expression (p < 0.05). In addition, the mC-20 and mC-21 sites are located on the Sp1 transcription factor binding site, and it is speculated that these two sites may be the main sites for regulating transcription. In summary, the methylation sites mC-20 and mC-21 of the ZP2 gene may inhibit the binding of Sp1 and DNA, affect the transcription of the ZP2 gene, and then affect the number of eggs produced by the Jinghai yellow chickens.
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Affiliation(s)
- Jin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Xiang-Qian Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Xuan-Ze Ling
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Xiu-Hua Zhao
- Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150001, China
| | - Kai-Zhi Zhou
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Jin-Yu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
| | - Gen-Xi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225000, China
- Correspondence:
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Epigenetic clock and methylation studies in marsupials: opossums, Tasmanian devils, kangaroos, and wallabies. GeroScience 2022; 44:1825-1845. [PMID: 35449380 PMCID: PMC9213610 DOI: 10.1007/s11357-022-00569-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
The opossum (Monodelphis domestica), with its sequenced genome, ease of laboratory care and experimental manipulation, and unique biology, is the most used laboratory marsupial. Using the mammalian methylation array, we generated DNA methylation data from n = 100 opossum samples from the ear, liver, and tail. We contrasted postnatal development and later aging effects in the opossum methylome with those in mouse (Mus musculus, C57BL/6 J strain) and other marsupial species such as Tasmanian devil, kangaroos, and wallabies. While the opossum methylome is similar to that of mouse during postnatal development, it is distinct from that shared by other mammals when it comes to the age-related gain of methylation at target sites of polycomb repressive complex 2. Our immunohistochemical staining results provide additional support for the hypothesis that PRC2 activity increases with later aging in mouse tissues but remains constant in opossum tissues. We present several epigenetic clocks for opossums that are distinguished by their compatibility with tissue type (pan-tissue and blood clock) and species (opossum and human). Two dual-species human-opossum pan-tissue clocks accurately measure chronological age and relative age, respectively. The human-opossum epigenetic clocks are expected to provide a significant boost to the attractiveness of opossum as a biological model. Additional epigenetic clocks for Tasmanian devil, red kangaroos and other species of the genus Macropus may aid species conservation efforts.
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Rubino E, Boschi S, Giorgio E, Pozzi E, Marcinnò A, Gallo E, Roveta F, Grassini A, Brusco A, Rainero I. Analysis of the DNA methylation pattern of the promoter region of calcitonin gene-related peptide 1 gene in patients with episodic migraine: An exploratory case-control study. NEUROBIOLOGY OF PAIN (CAMBRIDGE, MASS.) 2022; 11:100089. [PMID: 35445161 PMCID: PMC9014443 DOI: 10.1016/j.ynpai.2022.100089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 11/28/2022]
Abstract
Recent studies suggested that epigenetic mechanisms, including DNA methylation, may be involved in migraine pathogenesis. The calcitonin gene-related peptide (CGRP), encoded by calcitonin gene-related peptide 1 (CALCA) gene, plays a key role in the disease. The aim of the study was to evaluate DNA methylation of CALCA gene in patients with episodic migraine. 22 patients with episodic migraine (F/M 15/7, mean age 39.7 ± 13.4 years) and 20 controls (F/M 12/8, mean age 40.5 ± 14.8 years) were recruited. Genomic DNA was extracted from peripheral blood. Cytosine-to-thymine conversion was obtained with sodium bisulfite. The methylation pattern of two CpG islands in the promoter region of CALCA gene was analyzed. No difference of methylation of the 30 CpG sites at the distal region of CALCA promoter was observed between migraineurs and controls. Interestingly, in patients with episodic migraine the methylation level was lower in 2 CpG sites at the proximal promoter region (CpG -1461, p = 0.037, and -1415, p = 0.035, respectively). Furthermore, DNA methylation level at different CpG sites correlates with several clinical characteristics of the disease, as age at onset, presence of nausea/vomiting, depression and anxiety (p < 0.05). In conclusion, we found that DNA methylation profile in two CpG sites at the proximal promoter region of CALCA is lower in migraineurs when compared to controls. Intriguingly, the -1415 hypomethylated unit is located at the CREB binding site, a nuclear transcription factor. In addition, we found a correlation between the level of CALCA methylation and several clinical features of migraine. Further studies with larger sample size are needed to confirm these results.
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Affiliation(s)
- Elisa Rubino
- Department of Neuroscience and Mental Health, AOU Città della Salute e della Scienza di Torino, Italy
| | - Silvia Boschi
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Italy
| | - Elisa Pozzi
- Department of Medical Sciences, University of Torino, Italy
| | - Andrea Marcinnò
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
| | - Erica Gallo
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
| | - Fausto Roveta
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
| | - Alberto Grassini
- Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Italy
| | - Innocenzo Rainero
- Department of Neuroscience and Mental Health, AOU Città della Salute e della Scienza di Torino, Italy.,Department of Neuroscience "Rita Levi Montalcini", University of Torino, Italy
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7
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Xu T, Pereira RM, Martinez GJ. An Updated Model for the Epigenetic Regulation of Effector and Memory CD8 + T Cell Differentiation. THE JOURNAL OF IMMUNOLOGY 2021; 207:1497-1505. [PMID: 34493604 DOI: 10.4049/jimmunol.2100633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/22/2021] [Indexed: 11/19/2022]
Abstract
Naive CD8+ T cells, upon encountering their cognate Ag in vivo, clonally expand and differentiate into distinct cell fates, regulated by transcription factors and epigenetic modulators. Several models have been proposed to explain the differentiation of CTLs, although none fully recapitulate the experimental evidence. In this review article, we will summarize the latest research on the epigenetic regulation of CTL differentiation as well as provide a combined model that contemplates them.
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Affiliation(s)
- Tianhao Xu
- Discipline of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL; and
| | - Renata M Pereira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gustavo J Martinez
- Discipline of Microbiology and Immunology, Center for Cancer Cell Biology, Immunology and Infection, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL; and
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8
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Journo G, Ahuja A, Dias-Polak D, Eran Y, Bergman R, Shamay M. Global CpG DNA Methylation Footprint in Kaposi's Sarcoma. Front Cell Infect Microbiol 2021; 11:666143. [PMID: 34307191 PMCID: PMC8300563 DOI: 10.3389/fcimb.2021.666143] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/11/2021] [Indexed: 01/08/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV), also familiar as human herpesvirus 8 (HHV-8), is one of the well-known human cancer-causing viruses. KSHV was originally discovered by its association with Kaposi's sarcoma (KS), a common AIDS-related neoplasia. Additionally, KSHV is associated with two B-lymphocyte disorders; primary effusion lymphoma (PEL) and Multicentric Castlemans Disease (MCD). DNA methylation is an epigenetic modification that is essential for a properly functioning human genome through its roles in chromatin structure maintenance, chromosome stability and transcription regulation. Genomic studies show that expressed promoters tend to be un-methylated whereas methylated promoters tend to be inactive. We have previously revealed the global methylation footprint in PEL cells and found that many cellular gene promoters become differentially methylated and hence differentially expressed in KSHV chronically infected PEL cell lines. Here we present the cellular CpG DNA methylation footprint in KS, the most common malignancy associated with KSHV. We performed MethylationEPIC BeadChip to compare the global methylation status in normal skin compared to KS biopsies, and revealed dramatic global methylation alterations occurring in KS. Many of these changes were attributed to hyper-methylation of promoters and enhancers that regulate genes associated with abnormal skin morphology, a well-known hallmark of KS development. We observed six-fold increase in hypo-methylated CpGs between early stage of KS (plaque) and the more progressed stage (nodule). These observations suggest that hyper-methylation takes place early in KS while hypo-methylation is a later process that is more significant in nodule. Our findings add another layer to the understanding of the relationship between epigenetic changes caused by KSHV infection and tumorigenesis.
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Affiliation(s)
- Guy Journo
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Anuj Ahuja
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - David Dias-Polak
- Department of Dermatology, Rambam Health Care Campus, Haifa, Israel
| | - Yonatan Eran
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Reuven Bergman
- Department of Dermatology, Rambam Health Care Campus, Haifa, Israel
| | - Meir Shamay
- Daniella Lee Casper Laboratory in Viral Oncology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Charlesworth D, Zhang Y, Bergero R, Graham C, Gardner J, Yong L. Using GC Content to Compare Recombination Patterns on the Sex Chromosomes and Autosomes of the Guppy, Poecilia reticulata, and Its Close Outgroup Species. Mol Biol Evol 2021; 37:3550-3562. [PMID: 32697821 DOI: 10.1093/molbev/msaa187] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Genetic and physical mapping of the guppy (Poecilia reticulata) have shown that recombination patterns differ greatly between males and females. Crossover events occur evenly across the chromosomes in females, but in male meiosis they are restricted to the tip furthest from the centromere of each chromosome, creating very high recombination rates per megabase, as in pseudoautosomal regions of mammalian sex chromosomes. We used GC content to indirectly infer recombination patterns on guppy chromosomes, based on evidence that recombination is associated with GC-biased gene conversion, so that genome regions with high recombination rates should be detectable by high GC content. We used intron sequences and third positions of codons to make comparisons between sequences that are matched, as far as possible, and are all probably under weak selection. Almost all guppy chromosomes, including the sex chromosome (LG12), have very high GC values near their assembly ends, suggesting high recombination rates due to strong crossover localization in male meiosis. Our test does not suggest that the guppy XY pair has stronger crossover localization than the autosomes, or than the homologous chromosome in the close relative, the platyfish (Xiphophorus maculatus). We therefore conclude that the guppy XY pair has not recently undergone an evolutionary change to a different recombination pattern, or reduced its crossover rate, but that the guppy evolved Y-linkage due to acquiring a male-determining factor that also conferred the male crossover pattern. We also identify the centromere ends of guppy chromosomes, which were not determined in the genome assembly.
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Affiliation(s)
- Deborah Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Yexin Zhang
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Roberta Bergero
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chay Graham
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jim Gardner
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Lengxob Yong
- Centre for Ecology and Conservation, University of Exeter, Falmouth, Cornwall, United Kingdom
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10
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Vegfa promoter gene hypermethylation at HIF1α binding site is an early contributor to CKD progression after renal ischemia. Sci Rep 2021; 11:8769. [PMID: 33888767 PMCID: PMC8062449 DOI: 10.1038/s41598-021-88000-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/06/2021] [Indexed: 11/08/2022] Open
Abstract
Chronic hypoxia is a major contributor to Chronic Kidney Disease (CKD) after Acute Kidney Injury (AKI). However, the temporal relation between the acute insult and maladaptive renal response to hypoxia remains unclear. In this study, we analyzed the time-course of renal hemodynamics, oxidative stress, inflammation, and fibrosis, as well as epigenetic modifications, with focus on HIF1α/VEGF signaling, in the AKI to CKD transition. Sham-operated, right nephrectomy (UNx), and UNx plus renal ischemia (IR + UNx) groups of rats were included and studied at 1, 2, 3, or 4 months. The IR + UNx group developed CKD characterized by progressive proteinuria, renal dysfunction, tubular proliferation, and fibrosis. At first month post-ischemia, there was a twofold significant increase in oxidative stress and reduction in global DNA methylation that was maintained throughout the study. Hif1α and Vegfa expression were depressed in the first and second-months post-ischemia, and then Hif1α but not Vegfa expression was recovered. Interestingly, hypermethylation of the Vegfa promoter gene at the HIF1α binding site was found, since early stages of the CKD progression. Our findings suggest that renal hypoperfusion, inefficient hypoxic response, increased oxidative stress, DNA hypomethylation, and, Vegfa promoter gene hypermethylation at HIF1α binding site, are early determinants of AKI-to-CKD transition.
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Rehman SU, Hassan FU, Luo X, Li Z, Liu Q. Whole-Genome Sequencing and Characterization of Buffalo Genetic Resources: Recent Advances and Future Challenges. Animals (Basel) 2021; 11:904. [PMID: 33809937 PMCID: PMC8004149 DOI: 10.3390/ani11030904] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/17/2022] Open
Abstract
The buffalo was domesticated around 3000-6000 years ago and has substantial economic significance as a meat, dairy, and draught animal. The buffalo has remained underutilized in terms of the development of a well-annotated and assembled reference genome de novo. It is mandatory to explore the genetic architecture of a species to understand the biology that helps to manage its genetic variability, which is ultimately used for selective breeding and genomic selection. Morphological and molecular data have revealed that the swamp buffalo population has strong geographical genomic diversity with low gene flow but strong phenotypic consistency, while the river buffalo population has higher phenotypic diversity with a weak phylogeographic structure. The availability of recent high-quality reference genome and genotyping marker panels has invigorated many genome-based studies on evolutionary history, genetic diversity, functional elements, and performance traits. The increasing molecular knowledge syndicate with selective breeding should pave the way for genetic improvement in the climatic resilience, disease resistance, and production performance of water buffalo populations globally.
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Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Faiz-ul Hassan
- Institute of Animal and Dairy Sciences, Faculty of Animal Husbandry, University of Agriculture, Faisalabad 38040, Pakistan;
| | - Xier Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530005, China; (S.u.R.); (X.L.); (Z.L.)
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12
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 2021; 118:e2016274118. [PMID: 33836575 PMCID: PMC7980453 DOI: 10.1073/pnas.2016274118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Université Côte d'Azur, CNRS, INSERM, Institut de Recherche sur le Cancer et le Vieillissement de Nice, F-06100 Nice, France
| | - Thomas Derrien
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Christophe Hitte
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Laura E Kirby
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Bridget Myers
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Elzbieta Sliwerska
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109;
- Department Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
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Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021; 21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
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Affiliation(s)
- Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University
- Center for Evolution and Medicine, Arizona State University
| | - Timothy H. Webster
- Department of Anthropology, University of Utah
- School of Life Sciences, Arizona State University
| | - Ian C. Gilby
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University
- School of Life Sciences, Arizona State University
| | | | - Michael L. Wilson
- Department of Anthropology, University of Minnesota
- Department of Ecology, Evolution and Behavior, University of Minnesota
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
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Farris MH, Texter PA, Mora AA, Wiles MV, Mac Garrigle EF, Klaus SA, Rosfjord K. Detection of CRISPR-mediated genome modifications through altered methylation patterns of CpG islands. BMC Genomics 2020; 21:856. [PMID: 33267773 PMCID: PMC7709351 DOI: 10.1186/s12864-020-07233-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/17/2020] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The development and application of CRISPR technologies for the modification of the genome are rapidly expanding. Advances in the field describe new CRISPR components that are strategically engineered to improve the precision and reliability of CRISPR editing within the genome sequence. Genome modification using induced genome breaks that are targeted and mediated by CRISPR components leverage cellular mechanisms for repair like homology directed repair (HDR) to incorporate genomic edits with increased precision. RESULTS In this report, we describe the gain of methylation at typically hypomethylated CpG island (CGI) locations affected by the CRISPR-mediated incorporation of donor DNA using HDR mechanisms. With characterization of CpG methylation patterns using whole genome bisulfite sequencing, these CGI methylation disruptions trace the insertion of the donor DNA during the genomic edit. These insertions mediated by homology-directed recombination disrupt the generational methylation pattern stability of the edited CGI within the cells and their cellular lineage within the animal strain, persisting across generations. Our approach describes a statistically based workflow for indicating locations of modified CGIs and provides a mechanism for evaluating the directed modification of the methylome of the affected CGI at the CpG-level. CONCLUSIONS With advances in genome modification technology comes the need to detect the level and persistence of methylation change that modifications to the genomic sequence impose upon the collaterally edited methylome. Any modification of the methylome of somatic or germline cells could have implications for gene regulation mechanisms governed by the methylation patterns of CGI regions in the application of therapeutic edits of more sensitively regulated genomic regions. The method described here locates the directed modification of the mouse epigenome that persists over generations. While this observance would require supporting molecular observations such as direct sequence changes or gene expression changes, the observation of epigenetic modification provides an indicator that intentionally directed genomic edits can lead to collateral, unintentional epigenomic changes post modification with generational persistence.
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Affiliation(s)
- M Heath Farris
- The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA.
| | - Pamela A Texter
- The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA
| | - Agustin A Mora
- The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA
| | - Michael V Wiles
- The Jackson Laboratory, Technology Evaluation and Development, Bar Harbor, ME, USA
| | | | - Sybil A Klaus
- The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA
| | - Kristine Rosfjord
- The MITRE Corporation, 7515 Colshire Drive, McLean, Virginia, 22102, USA
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15
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Biohorology and biomarkers of aging: Current state-of-the-art, challenges and opportunities. Ageing Res Rev 2020; 60:101050. [PMID: 32272169 DOI: 10.1016/j.arr.2020.101050] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/06/2020] [Accepted: 03/22/2020] [Indexed: 02/08/2023]
Abstract
The aging process results in multiple traceable footprints, which can be quantified and used to estimate an organism's age. Examples of such aging biomarkers include epigenetic changes, telomere attrition, and alterations in gene expression and metabolite concentrations. More than a dozen aging clocks use molecular features to predict an organism's age, each of them utilizing different data types and training procedures. Here, we offer a detailed comparison of existing mouse and human aging clocks, discuss their technological limitations and the underlying machine learning algorithms. We also discuss promising future directions of research in biohorology - the science of measuring the passage of time in living systems. Overall, we expect deep learning, deep neural networks and generative approaches to be the next power tools in this timely and actively developing field.
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Stimpfel M, Vrtacnik-Bokal E. Minor DNA methylation changes are observed in spermatozoa prepared using different protocols. Andrology 2020; 8:1312-1323. [PMID: 32470185 DOI: 10.1111/andr.12832] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 05/18/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022]
Abstract
BACKGROUND DNA methylation patterns can show transgenerational inheritance and are influenced by lifestyle and environmental factors. It is suggested that these patterns can be changed by assisted reproductive technology. OBJECTIVES To evaluate the impact of two different sperm preparation methods, conventional density gradient centrifugation (DGC) vs. density gradient centrifugation followed by magnetic-activated cell sorting (MACS) of non-apoptotic spermatozoa, on sperm DNA methylation profile. MATERIALS AND METHODS We analyzed semen of patients included in our IVF treatment program. Half of the semen from each included patient was prepared for ICSI using the DGC method and the other half with DGC followed by MACS. The remaining samples were processed for DNA methylation analysis with reduced representation bisulfite sequencing (RRBS). In addition to the DNA methylation profile, we assessed the morphology and DNA fragmentation of spermatozoa. RESULTS RRBS analysis revealed that the average genome-wide methylation level was similar between both groups (DGC vs. MACS group) and ranged from 0.53 to 0.56. Furthermore, RRBS analysis identified 99 differentially methylated regions (DMRs) and 800 differentially methylated positions (DMPs). In the DGC group, 43 DMRs and 392 DMPs were hypermethylated whereas 56 DMRs and 408 DMPs were hypomethylated compared with those in the MACS group. When DMRs and DMPs were annotated to genes, 3 genes associated with imprinting were found: IGF2, PRDM16, and CLF4/BRUNOL4. The percentage of morphologically normal spermatozoa (MACS vs. DGC; 14.0 ± 10.8 vs. 13.2 ± 10.0; P = .335) and of spermatozoa with fragmented DNA of patients with RRBS analysis (22.9 ± 21.1% vs. 34.4 ± 21.2; P = .529) were also similar between groups. DISCUSSION AND CONCLUSION Although the average genome-wide level of sperm DNA methylation was similar in both sample groups, a distinctive number of methylation changes were observed in DMR and DMP levels. A larger number of samples should be analyzed and additional sperm preparation methods should be tested to confirm our findings.
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Affiliation(s)
- Martin Stimpfel
- Department of Human Reproduction, Division of Gynaecology, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Eda Vrtacnik-Bokal
- Department of Human Reproduction, Division of Gynaecology, University Medical Center Ljubljana, Ljubljana, Slovenia
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Khodabandelou G, Routhier E, Mozziconacci J. Genome annotation across species using deep convolutional neural networks. PeerJ Comput Sci 2020; 6:e278. [PMID: 33816929 PMCID: PMC7924482 DOI: 10.7717/peerj-cs.278] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 05/18/2020] [Indexed: 06/12/2023]
Abstract
Application of deep neural network is a rapidly expanding field now reaching many disciplines including genomics. In particular, convolutional neural networks have been exploited for identifying the functional role of short genomic sequences. These approaches rely on gathering large sets of sequences with known functional role, extracting those sequences from whole-genome-annotations. These sets are then split into learning, test and validation sets in order to train the networks. While the obtained networks perform well on validation sets, they often perform poorly when applied on whole genomes in which the ratio of positive over negative examples can be very different than in the training set. We here address this issue by assessing the genome-wide performance of networks trained with sets exhibiting different ratios of positive to negative examples. As a case study, we use sequences encompassing gene starts from the RefGene database as positive examples and random genomic sequences as negative examples. We then demonstrate that models trained using data from one organism can be used to predict gene-start sites in a related species, when using training sets providing good genome-wide performance. This cross-species application of convolutional neural networks provides a new way to annotate any genome from existing high-quality annotations in a related reference species. It also provides a way to determine whether the sequence motifs recognised by chromatin-associated proteins in different species are conserved or not.
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Affiliation(s)
- Ghazaleh Khodabandelou
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université, Paris, France
- Laboratoire Images, Signaux et Systèmes Intelligents (LISSI), Université Val-de-Marne (Paris XII), Paris, France
| | - Etienne Routhier
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université, Paris, France
| | - Julien Mozziconacci
- Laboratoire de Physique Théorique de la Matière Condensée (LPTMC), Sorbonne Université, Paris, France
- CNRS UMR 7196 / INSERM U1154 - Sorbonne Université, Museum national d’Histoire naturelle (MNHN), Paris, France
- Institut Universitaire de France, Paris, France
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18
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Sun S, Wang Y, Zeng W, Du X, Li L, Hong X, Huang X, Zhang H, Zhang M, Fan G, Liu X, Liu S. The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. Sci Rep 2020; 10:8164. [PMID: 32424221 PMCID: PMC7235238 DOI: 10.1038/s41598-020-64398-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Mekong tiger perch (Datnioides undecimradiatus) is an ornamental and vulnerable freshwater fish native to the Mekong basin in Indochina, belonging to the order Lobotiformes. Here, we generated 121X stLFR co-barcode clean reads and 18X Oxford Nanopore MinION reads and obtained a 595 Mb Mekong tiger perch genome, which is the first whole genome sequence in the order Lobotiformes. Based on this genome, the phylogenetic tree analysis suggested that Lobotiformes is more closely related to Sciaenidae than to Tetraodontiformes, resolving a long-time dispute. We depicted the genes involved in pigment development in Mekong tiger perch and results confirmed that the four rate-limiting genes of pigment synthesis had been retained after fish-specific genome duplication. We also estimated the demographic history of Mekong tiger perch, which showed that the effective population size suffered a continuous reduction possibly related to the contraction of immune-related genes. Our study provided a reference genome resource for the Lobotiformes, as well as insights into the phylogenetic position of Lobotiformes and biological conservation.
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Affiliation(s)
- Shuai Sun
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Yue Wang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Wenhong Zeng
- Jiangxi University of Traditional Chinese Medicin, Nanchang, 330004, China
| | - Xiao Du
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Lei Li
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoning Hong
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, 236009, China
| | - Xiaoyun Huang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - He Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Mengqi Zhang
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Guangyi Fan
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
- BGI-Shenzhen, Shenzhen, 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China
| | - Xin Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Shanshan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China.
- BGI-Shenzhen, Shenzhen, 518083, China.
- China National GeneBank, BGI-Shenzhen, Shenzhen, 518120, China.
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19
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Simó-Mirabet P, Perera E, Calduch-Giner JA, Pérez-Sánchez J. Local DNA methylation helps to regulate muscle sirtuin 1 gene expression across seasons and advancing age in gilthead sea bream ( Sparus aurata). Front Zool 2020; 17:15. [PMID: 32467713 PMCID: PMC7227224 DOI: 10.1186/s12983-020-00361-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
Background Sirtuins (SIRTs) are master regulators of metabolism, and their expression patterns in gilthead sea bream (GSB) reveal different tissue metabolic capabilities and changes in energy status. Since little is known about their transcriptional regulation, the aim of this work was to study for the first time in fish the effect of age and season on sirt gene expression, correlating expression patterns with local changes in DNA methylation in liver and white skeletal muscle (WSM). Methods Gene organization of the seven sirts was analyzed by BLAT searches in the IATS-CSIC genomic database (www.nutrigroup-iats.org/seabreamdb/). The presence of CpG islands (CGIs) was mapped by means of MethPrimer software. DNA methylation analyses were performed by bisulfite pyrosequencing. A PCR array was designed for the simultaneous gene expression profiling of sirts and related markers (cs, cpt1a, pgc1α, ucp1, and ucp3) in the liver and WSM of one- and three-year-old fish during winter and summer. Results The occurrence of CGIs was evidenced in the sirt1 and sirt3 promoters. This latter CGI remained hypomethylated regardless of tissue, age and season. Conversely, DNA methylation of sirt1 at certain CpG positions within the promoter varied with age and season in the WSM. Among them, changes at several SP1 binding sites were negatively correlated with the decrease in sirt1 expression in summer and in younger fish. Changes in sirt1 regulation match well with variations in feed intake and energy metabolism, as judged by the concurrent changes in the analyzed markers. This was supported by discriminant analyses, which identified sirt1 as a highly responsive element to age- and season-mediated changes in energy metabolism in WSM. Conclusions The gene organization of SIRTs is highly conserved in vertebrates. GSB sirt family members have CGI- and non-CGI promoters, and the presence of CGIs at the sirt1 promoter agrees with its ubiquitous expression. Gene expression analyses support that sirts, especially sirt1, are reliable markers of age- and season-dependent changes in energy metabolism. Correlation analyses suggest the involvement of DNA methylation in the regulation of sirt1 expression, but the low methylation levels suggest the contribution of other putative mechanisms in the transcriptional regulation of sirt1.
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Affiliation(s)
- Paula Simó-Mirabet
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal, IATS-CSIC, 12595 Ribera de Cabanes s/n, Castellón, Spain
| | - Erick Perera
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal, IATS-CSIC, 12595 Ribera de Cabanes s/n, Castellón, Spain
| | - Josep Alvar Calduch-Giner
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal, IATS-CSIC, 12595 Ribera de Cabanes s/n, Castellón, Spain
| | - Jaume Pérez-Sánchez
- Nutrigenomics and Fish Growth Endocrinology Group, Institute of Aquaculture Torre de la Sal, IATS-CSIC, 12595 Ribera de Cabanes s/n, Castellón, Spain
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20
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Epigenetic Control of a Local Chromatin Landscape. Int J Mol Sci 2020; 21:ijms21030943. [PMID: 32023873 PMCID: PMC7038174 DOI: 10.3390/ijms21030943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/28/2020] [Accepted: 01/29/2020] [Indexed: 12/11/2022] Open
Abstract
Proper regulation of the chromatin landscape is essential for maintaining eukaryotic cell identity and diverse cellular processes. The importance of the epigenome comes, in part, from the ability to influence gene expression through patterns in DNA methylation, histone tail modification, and chromatin architecture. Decades of research have associated this process of chromatin regulation and gene expression with human diseased states. With the goal of understanding how chromatin dysregulation contributes to disease, as well as preventing or reversing this type of dysregulation, a multidisciplinary effort has been launched to control the epigenome. Chemicals that alter the epigenome have been used in labs and in clinics since the 1970s, but more recently there has been a shift in this effort towards manipulating the chromatin landscape in a locus-specific manner. This review will provide an overview of chromatin biology to set the stage for the type of control being discussed, evaluate the recent technological advances made in controlling specific regions of chromatin, and consider the translational applications of these works.
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21
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Zhang L, Dai Z, Yu J, Xiao M. CpG-island-based annotation and analysis of human housekeeping genes. Brief Bioinform 2020; 22:515-525. [PMID: 31982909 DOI: 10.1093/bib/bbz134] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 08/27/2019] [Accepted: 10/03/2019] [Indexed: 11/14/2022] Open
Abstract
By reviewing previous CpG-related studies, we consider that the transcription regulation of about half of the human genes, mostly housekeeping (HK) genes, involves CpG islands (CGIs), their methylation states, CpG spacing and other chromosomal parameters. However, the precise CGI definition and positioning of CGIs within gene structures, as well as specific CGI-associated regulatory mechanisms, all remain to be explained at individual gene and gene-family levels, together with consideration of species and lineage specificity. Although previous studies have already classified CGIs into high-CpG (HCGI), intermediate-CpG (ICGI) and low-CpG (LCGI) densities based on CpG density variation, the correlation between CGI density and gene expression regulation, such as co-regulation of CGIs and TATA box on HK genes, remains to be elucidated. First, this study introduces such a problem-solving protocol for human-genome annotation, which is based on a combination of GTEx, JBLA and Gene Ontology (GO) analysis. Next, we discuss why CGI-associated genes are most likely regulated by HCGI and tend to be HK genes; the HCGI/TATA± and LCGI/TATA± combinations show different GO enrichment, whereas the ICGI/TATA± combination is less characteristic based on GO enrichment analysis. Finally, we demonstrate that Hadoop MapReduce-based MR-JBLA algorithm is more efficient than the original JBLA in k-mer counting and CGI-associated gene analysis.
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Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, 610065, PR China
| | - Zichun Dai
- Medical Big Data Center of Sichuan University, Sichuan University, Chengdu, 610065, PR China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Ming Xiao
- University of Chinese Academy of Sciences, Beijing 100049, PR China
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Abstract
Biological ageing and its mechanistic underpinnings are of immense biomedical and ecological significance. Ageing involves the decline of diverse biological functions and places a limit on a species’ maximum lifespan. Ageing is associated with epigenetic changes involving DNA methylation. Furthermore, an analysis of mammals showed that the density of CpG sites in gene promoters, which are targets for DNA methylation, is correlated with lifespan. Using 252 whole genomes and databases of animal age and promotor sequences, we show a pattern across vertebrates. We also derive a predictive lifespan clock based on CpG density in a selected set of promoters. The lifespan clock accurately predicts maximum lifespan in vertebrates (R2 = 0.76) from the density of CpG sites within only 42 selected promoters. Our lifespan clock provides a wholly new method for accurately estimating lifespan using genome sequences alone and enables estimation of this challenging parameter for both poorly understood and extinct species.
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Genome-wide recombination map construction from single individuals using linked-read sequencing. Nat Commun 2019; 10:4309. [PMID: 31541091 PMCID: PMC6754380 DOI: 10.1038/s41467-019-12210-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/28/2019] [Indexed: 12/19/2022] Open
Abstract
Meiotic recombination rates vary across the genome, often involving localized crossover hotspots and coldspots. Studying the molecular basis and mechanisms underlying this variation has been challenging due to the high cost and effort required to construct individualized genome-wide maps of recombination crossovers. Here we introduce a new method, called ReMIX, to detect crossovers from gamete DNA of a single individual using Illumina sequencing of 10X Genomics linked-read libraries. ReMIX reconstructs haplotypes and identifies the valuable rare molecules spanning crossover breakpoints, allowing quantification of the genomic location and intensity of meiotic recombination. Using a single mouse and stickleback fish, we demonstrate how ReMIX faithfully recovers recombination hotspots and landscapes that have previously been built using hundreds of offspring. ReMIX provides a high-resolution, high-throughput, and low-cost approach to quantify recombination variation across the genome, providing an exciting opportunity to study recombination among multiple individuals in diverse organisms. Variation of recombination rates within genomes has important implications in genetics and evolution. Here, the authors develop a method for building genome-wide recombination maps from single individuals using linked-read sequencing data, and report its application in mouse and stickleback fish.
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Barazandeh A, Mohammadabadi M, Ghaderi-Zefrehei M, Rafeie F, Imumorin IG. Whole genome comparative analysis of CpG islands in camelid and other mammalian genomes. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.07.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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McLain AT, Faulk C. The evolution of CpG density and lifespan in conserved primate and mammalian promoters. Aging (Albany NY) 2019; 10:561-572. [PMID: 29661983 PMCID: PMC5940106 DOI: 10.18632/aging.101413] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022]
Abstract
Gene promoters are evolutionarily conserved across holozoans and enriched in CpG sites, the target for DNA methylation. As animals age, the epigenetic pattern of DNA methylation degrades, with highly methylated CpG sites gradually becoming demethylated while CpG islands increase in methylation. Across vertebrates, aging is a trait that varies among species. We used this variation to determine whether promoter CpG density correlates with species’ maximum lifespan. Human promoter sequences were used to identify conserved regions in 131 mammals and a subset of 28 primate genomes. We identified approximately 1000 gene promoters (5% of the total), that significantly correlated CpG density with lifespan. The correlations were performed via the phylogenetic least squares method to account for trait similarity by common descent using phylogenetic branch lengths. Gene set enrichment analysis revealed no significantly enriched pathways or processes, consistent with the hypothesis that aging is not under positive selection. However, within both mammals and primates, 95% of the promoters showed a positive correlation between increasing CpG density and species lifespan, and two thirds were shared between the primate subset and mammalian datasets. Thus, these genes may require greater buffering capacity against age-related dysregulation of DNA methylation in longer-lived species.
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Affiliation(s)
- Adam T McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN 55108, USA
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26
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Kawakami T, Wallberg A, Olsson A, Wintermantel D, de Miranda JR, Allsopp M, Rundlöf M, Webster MT. Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees. Genetics 2019; 212:1101-1119. [PMID: 31152071 PMCID: PMC6707477 DOI: 10.1534/genetics.119.302008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/30/2019] [Indexed: 12/30/2022] Open
Abstract
Meiotic recombination shuffles genetic variation and promotes correct segregation of chromosomes. Rates of recombination vary on several scales, both within genomes and between individuals, and this variation is affected by both genetic and environmental factors. Social insects have extremely high rates of recombination, although the evolutionary causes of this are not known. Here, we estimate rates of crossovers and gene conversions in 22 colonies of the honeybee, Apis mellifera, and 9 colonies of the bumblebee, Bombus terrestris, using direct sequencing of 299 haploid drone offspring. We confirm that both species have extremely elevated crossover rates, with higher rates measured in the highly eusocial honeybee than the primitively social bumblebee. There are also significant differences in recombination rate between subspecies of honeybee. There is substantial variation in genome-wide recombination rate between individuals of both A. mellifera and B. terrestris and the distribution of these rates overlap between species. A large proportion of interindividual variation in recombination rate is heritable, which indicates the presence of variation in trans-acting factors that influence recombination genome-wide. We infer that levels of crossover interference are significantly lower in honeybees compared to bumblebees, which may be one mechanism that contributes to higher recombination rates in honeybees. We also find a significant increase in recombination rate with distance from the centromere, mirrored by methylation differences. We detect a strong transmission bias due to GC-biased gene conversion associated with noncrossover gene conversions. Our results shed light on the mechanistic causes of extreme rates of recombination in social insects and the genetic architecture of recombination rate variation.
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Affiliation(s)
- Takeshi Kawakami
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, 752 36, Sweden
- Department of Animal and Plant Sciences, University of Sheffield, S10 2TN, United Kingdom
| | - Andreas Wallberg
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Anna Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
| | - Dimitry Wintermantel
- INRA, UE 1255 APIS, Le Magneraud, 17700 Surgères, France
- Centre d'Etudes Biologiques de Chizé, UMR 7372, CNRS and Université de La Rochelle, 79360 Villiers-en-Bois, France
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala 750 07, Sweden
| | - Mike Allsopp
- Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, 7608, South Africa
| | - Maj Rundlöf
- Department of Biology, Lund University, 223 62, Sweden
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala University, 751 05. Sweden
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Skvortsova K, Tarbashevich K, Stehling M, Lister R, Irimia M, Raz E, Bogdanovic O. Retention of paternal DNA methylome in the developing zebrafish germline. Nat Commun 2019; 10:3054. [PMID: 31296860 PMCID: PMC6624265 DOI: 10.1038/s41467-019-10895-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Two waves of DNA methylation reprogramming occur during mammalian embryogenesis; during preimplantation development and during primordial germ cell (PGC) formation. However, it is currently unclear how evolutionarily conserved these processes are. Here we characterise the DNA methylomes of zebrafish PGCs at four developmental stages and identify retention of paternal epigenetic memory, in stark contrast to the findings in mammals. Gene expression profiling of zebrafish PGCs at the same developmental stages revealed that the embryonic germline is defined by a small number of markers that display strong developmental stage-specificity and that are independent of DNA methylation-mediated regulation. We identified promoters that are specifically targeted by DNA methylation in somatic and germline tissues during vertebrate embryogenesis and that are frequently misregulated in human cancers. Together, these detailed methylome and transcriptome maps of the zebrafish germline provide insight into vertebrate DNA methylation reprogramming and enhance our understanding of the relationships between germline fate acquisition and oncogenesis.
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Affiliation(s)
- Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia
| | - Katsiaryna Tarbashevich
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Martin Stehling
- Flow Cytometry Unit, Max-Planck-Institute for Molecular Biomedicine, Roentgenstraße 20, 48149, Münster, Germany
| | - Ryan Lister
- ARC CoE Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
- Molecular Medicine Division, Harry Perkins Institute of Medical Research, Perth, WA, 6009, Australia
| | - Manuel Irimia
- Centre for Genomic Regulation, The Barcelona Institute for Science and Technology, Barcelona, 08003, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, 08002, Spain
- ICREA, Barcelona, 08010, Spain
| | - Erez Raz
- Institute of Cell Biology, Center for Molecular Biology of Inflammation, University of Münster, Münster, 48149, Germany
| | - Ozren Bogdanovic
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW, 2010, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, 2010, Australia.
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28
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Sivaprakasam B, Sadagopan P. Development of an Interactive Web Application "Shiny App for Frequency Analysis on Homo sapiens Genome (SAFA-HsG)". Interdiscip Sci 2019; 11:723-729. [PMID: 31264054 DOI: 10.1007/s12539-019-00340-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/08/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
Abstract
The web application "Shiny App for Frequency Analysis on Homo sapiens Genome (SAFA-HsG)" was developed using R programming-based bioconductor packages and shiny framework. Through the app, preliminary descriptive data analysis on nucleotide frequency, and CpG island, CpG non-island, and CpG island shores and shelves (downstream and upstream) of human reference genome can be carried out, which will help biologists to work on human epigenomics. Table view of these analyses of all chromosomes can be visualized and downloaded by the end users. Similarly, the respective comparative plots can be used for CpG sites comparison. In addition, to introduce the personal genome project, the present study has done a preliminary work on few raw data and are included in the app, which will create interest on personal genome information. The app is hosted on https://SAFA-HsG.shinyapps.io/home/. It is a multi-platform application and can be initiated locally from any computer that has or has not installed R. It is a user-friendly interface, which will allow a biologist, even who has little computer knowledge to access and analyze further.
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Affiliation(s)
- Balamurugan Sivaprakasam
- Department of Computer Science, Vels Institute of Science, Technology and Advanced Studies (VISTAS), Pallavaram, Chennai, 600 117, Tamil Nadu, India.
| | - Prasanna Sadagopan
- Department of Computer Science, Vels Institute of Science, Technology and Advanced Studies (VISTAS), Pallavaram, Chennai, 600 117, Tamil Nadu, India
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29
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Mintoo AA, Zhang H, Chen C, Moniruzzaman M, Deng T, Anam M, Emdadul Huque QM, Guang X, Wang P, Zhong Z, Han P, Khatun A, Awal TM, Gao Q, Liang X. Draft genome of the river water buffalo. Ecol Evol 2019; 9:3378-3388. [PMID: 30962899 PMCID: PMC6434576 DOI: 10.1002/ece3.4965] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/12/2018] [Accepted: 01/02/2019] [Indexed: 11/25/2022] Open
Abstract
Water buffalo (Bubalus bubalis), a large-sized member of the Bovidae family, is considered as an important livestock species throughout Southeast Asia. In order to better understand the molecular basis of buffalo improvement and breeding, we sequenced and assembled the genome (2n=50) of a river buffalo species Bubalus bubalis from Bangladesh. Its genome size is 2.77 Gb, with a contig N50 of 25 kb and the scaffold N50 of 6.9 Mbp. Based on the assembled genome, we annotated 24,613 genes for future functional genomics studies. Phylogenetic tree analysis of cattle and water buffalo lineages showed that they diverged about 5.8-9.8 million years ago. Our findings provide an insight into the water buffalo genome which will contribute in further research on buffalo such as molecular breeding, understanding complex traits, conservation, and biodiversity.
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Affiliation(s)
- Abdul Awal Mintoo
- Lal Teer Seed LimitedDhakaBangladesh
- Lal Teer Livestock LimitedDhakaBangladesh
- MNT Life Sciences CenterGazipurBangladesh
| | - Hailin Zhang
- BGI‐Genomics, BGI‐ShenzhenShenzhenChina
- BGI Education CenterUniversity of Chinese Academy of SciencesBeijingChina
| | | | | | - Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research InstituteChinese Academy of Agricultural SciencesNanningChina
| | - Mahbub Anam
- Lal Teer Seed LimitedDhakaBangladesh
- Lal Teer Livestock LimitedDhakaBangladesh
- MNT Life Sciences CenterGazipurBangladesh
| | | | | | - Ping Wang
- BGI‐Genomics, BGI‐ShenzhenShenzhenChina
| | | | | | | | - Tabith M. Awal
- Lal Teer Seed LimitedDhakaBangladesh
- Lal Teer Livestock LimitedDhakaBangladesh
- MNT Life Sciences CenterGazipurBangladesh
| | - Qiang Gao
- BGI‐Genomics, BGI‐ShenzhenShenzhenChina
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research InstituteChinese Academy of Agricultural SciencesNanningChina
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30
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Talsania K, Mehta M, Raley C, Kriga Y, Gowda S, Grose C, Drew M, Roberts V, Cheng KT, Burkett S, Oeser S, Stephens R, Soppet D, Chen X, Kumar P, German O, Smirnova T, Hautman C, Shetty J, Tran B, Zhao Y, Esposito D. Genome Assembly and Annotation of the Trichoplusia ni Tni-FNL Insect Cell Line Enabled by Long-Read Technologies. Genes (Basel) 2019; 10:genes10020079. [PMID: 30678108 PMCID: PMC6409714 DOI: 10.3390/genes10020079] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 01/09/2019] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
Background: Trichoplusia ni derived cell lines are commonly used to enable recombinant protein expression via baculovirus infection to generate materials approved for clinical use and in clinical trials. In order to develop systems biology and genome engineering tools to improve protein expression in this host, we performed de novo genome assembly of the Trichoplusia ni-derived cell line Tni-FNL. Methods: By integration of PacBio single-molecule sequencing, Bionano optical mapping, and 10X Genomics linked-reads data, we have produced a draft genome assembly of Tni-FNL. Results: Our assembly contains 280 scaffolds, with a N50 scaffold size of 2.3 Mb and a total length of 359 Mb. Annotation of the Tni-FNL genome resulted in 14,101 predicted genes and 93.2% of the predicted proteome contained recognizable protein domains. Ortholog searches within the superorder Holometabola provided further evidence of high accuracy and completeness of the Tni-FNL genome assembly. Conclusions: This first draft Tni-FNL genome assembly was enabled by complementary long-read technologies and represents a high-quality, well-annotated genome that provides novel insight into the complexity of this insect cell line and can serve as a reference for future large-scale genome engineering work in this and other similar recombinant protein production hosts.
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Affiliation(s)
- Keyur Talsania
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Monika Mehta
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Castle Raley
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Yuliya Kriga
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Sujatha Gowda
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Carissa Grose
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Matthew Drew
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Veronica Roberts
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Kwong Tai Cheng
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Sandra Burkett
- Comparative Molecular Cytogenetics Core Facility, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | | | - Robert Stephens
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Daniel Soppet
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Xiongfeng Chen
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Parimal Kumar
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Oksana German
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Tatyana Smirnova
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Christopher Hautman
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Jyoti Shetty
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Bao Tran
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Yongmei Zhao
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
| | - Dominic Esposito
- NCI RAS Initiative, Frederick National Laboratory for Cancer Research Sponsored by the National Cancer Institute, Frederick, MD 21701, USA.
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31
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Zhang L, Xiao M, Zhou J, Yu J. Lineage-associated underrepresented permutations (LAUPs) of mammalian genomic sequences based on a Jellyfish-based LAUPs analysis application (JBLA). Bioinformatics 2018; 34:3624-3630. [DOI: 10.1093/bioinformatics/bty392] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 05/09/2018] [Indexed: 12/25/2022] Open
Affiliation(s)
- Le Zhang
- College of Computer Science, Sichuan University, Chengdu, China
- School of Computer and Information Science, Southwest University, Chongqing, China
| | - Ming Xiao
- School of Computer and Information Science, Southwest University, Chongqing, China
- College of Mobile Telecommunications, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Jingsong Zhou
- College of Computer Science, Sichuan University, Chengdu, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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32
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Dai F, Wang X, Zhang X, Chen Z, Nevo E, Jin G, Wu D, Li C, Zhang G. Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:760-770. [PMID: 28871634 PMCID: PMC5814578 DOI: 10.1111/pbi.12826] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/02/2017] [Accepted: 08/14/2017] [Indexed: 05/03/2023]
Abstract
Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated 'high-confidence' genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.
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Affiliation(s)
- Fei Dai
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiaolei Wang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Xiao‐Qi Zhang
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Zhonghua Chen
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
- School of Science and HealthWestern Sydney UniversityPenrithNSWAustralia
| | - Eviatar Nevo
- Institute of EvolutionUniversity of HaifaHaifaIsrael
| | - Gulei Jin
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Dezhi Wu
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
| | - Chengdao Li
- Western Barley Genetics AllianceWestern Australian State Agricultural Biotechnology CentreSchool of Veterinary and Life SciencesMurdoch UniversityPerthWAAustralia
| | - Guoping Zhang
- Department of AgronomyZhejiang Key Lab of Crop GermplasmZhejiang UniversityHangzhouChina
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33
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Colwell M, Drown M, Showel K, Drown C, Palowski A, Faulk C. Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements. Epigenetics 2018; 13:49-60. [PMID: 29372669 PMCID: PMC5836973 DOI: 10.1080/15592294.2017.1411447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/14/2017] [Accepted: 11/27/2017] [Indexed: 01/14/2023] Open
Abstract
Ultraconserved noncoding elements (UCNEs) constitute less than 1 Mb of vertebrate genomes and are impervious to accumulating mutations. About 4000 UCNEs exist in vertebrate genomes, each at least 200 nucleotides in length, sharing greater than 95% sequence identity between human and chicken. Despite extreme sequence conservation over 400 million years of vertebrate evolution, we show both ordered interspecies and within-species interindividual variation in DNA methylation in these regions. Here, we surveyed UCNEs with high CpG density in 56 species finding half to be intermediately methylated and the remaining near 0% or 100%. Intermediately methylated UCNEs displayed a greater range of methylation between mouse tissues. In a human population, most UCNEs showed greater variation than the LINE1 transposon, a frequently used epigenetic biomarker. Global methylation was found to be inversely correlated to hydroxymethylation across 60 vertebrates. Within UCNEs, DNA methylation is flexible, conserved between related species, and relaxed from the underlying sequence selection pressure, while remaining heritable through speciation.
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Affiliation(s)
- Mathia Colwell
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Melissa Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Kelly Showel
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Chelsea Drown
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Amanda Palowski
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, Saint Paul, MN, USA
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Ocampo Daza D, Larhammar D. Evolution of the receptors for growth hormone, prolactin, erythropoietin and thrombopoietin in relation to the vertebrate tetraploidizations. Gen Comp Endocrinol 2018; 257:143-160. [PMID: 28652136 DOI: 10.1016/j.ygcen.2017.06.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Revised: 06/16/2017] [Accepted: 06/22/2017] [Indexed: 12/19/2022]
Abstract
The receptors for the pituitary hormones growth hormone (GH), prolactin (PRL) and somatolactin (SL), and the hematopoietic hormones erythropoietin (EPO) and thrombopoietin (TPO), comprise a structurally related family in the superfamily of cytokine class-I receptors. GH, PRL and SL receptors have a wide variety of effects in development, osmoregulation, metabolism and stimulation of growth, while EPO and TPO receptors guide the production and differentiation of erythrocytes and thrombocytes, respectively. The evolution of the receptors for GH, PRL and SL has been partially investigated by previous reports suggesting different time points for the hormone and receptor gene duplications. This raises questions about how hormone-receptor partnerships have emerged and evolved. Therefore, we have investigated in detail the expansion of this receptor family, especially in relation to the basal vertebrate (1R, 2R) and teleost (3R) tetraploidizations. Receptor family genes were identified in a broad range of vertebrate genomes and investigated using a combination of sequence-based phylogenetic analyses and comparative genomic analyses of synteny. We found that 1R most likely generated EPOR/TPOR and GHR/PRLR ancestors; following this, 2R resulted in EPOR and TPOR genes. No GHR/PRLR duplicate seems to have survived after 2R. Instead the single GHR/PRLR underwent a local duplication sometime after 2R, generating separate syntenic genes for GHR and PRLR. Subsequently, 3R duplicated the gene pair in teleosts, resulting in two GHR and two PRLR genes, but no EPOR or TPOR duplicates. These analyses help illuminate the evolution of the regulatory mechanisms for somatic growth, metabolism, osmoregulation and hematopoiesis in vertebrates.
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Affiliation(s)
- Daniel Ocampo Daza
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden.
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-75124 Uppsala, Sweden
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35
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Rhyu MG, Oh JH, Hong SJ. Species-specific role of gene-adjacent retroelements in human and mouse gastric carcinogenesis. Int J Cancer 2017; 142:1520-1527. [PMID: 29055047 DOI: 10.1002/ijc.31120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/22/2017] [Accepted: 10/09/2017] [Indexed: 12/15/2022]
Abstract
Helicobacter pylori (HP) infection promotes the recruitment of bone marrow stem cells into chronic gastritis lesions. Some of these marrow stem cells can differentiate into gastric epithelial cells and neoplastic cells. We propose that HP-associated methylation could stabilize trans-differentiation of marrow-derived stem cells and that an unstable methylation status is associated with a risk of gastric cancer. Pathobiologic behavior of experimental mouse gastric cancer is mild compared to invasive and metastatic human gastric cancer. Differences in epigenetic stabilization of adult cell phenotypes between humans and mice could provide a foundation to explore the development of invasive and metastatic gastric cancer. Retroelements are highly repetitive sequences that play an essential role in the generation of species diversity. In this review, we analyzed retroelements adjacent to human and mouse housekeeping genes and proposed a possible epigenetic mechanism for HP-associated carcinogenesis.
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Affiliation(s)
- Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hwan Oh
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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36
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Francescatto M, Lizio M, Philippens I, Pardo LM, Bontrop R, Sakai M, Watanabe S, Itoh M, Hasegawa A, Lassmann T, Severin J, Harshbarger J, Abugessaisa I, Kasukawa T, Carninci P, Hayashizaki Y, Forrest ARR, Kawaji H, Rizzu P, Heutink P. Transcription start site profiling of 15 anatomical regions of the Macaca mulatta central nervous system. Sci Data 2017; 4:170163. [PMID: 29087374 PMCID: PMC5663209 DOI: 10.1038/sdata.2017.163] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 08/29/2017] [Indexed: 01/10/2023] Open
Abstract
Rhesus macaque was the second non-human primate whose genome has been fully
sequenced and is one of the most used model organisms to study human biology and
disease, thanks to the close evolutionary relationship between the two species.
But compared to human, where several previously unknown RNAs have been
uncovered, the macaque transcriptome is less studied. Publicly available RNA
expression resources for macaque are limited, even for brain, which is highly
relevant to study human cognitive abilities. In an effort to complement those
resources, FANTOM5 profiled 15 distinct anatomical regions of the aged macaque
central nervous system using Cap Analysis of Gene Expression, a high-resolution,
annotation-independent technology that allows monitoring of transcription
initiation events with high accuracy. We identified 25,869 CAGE peaks,
representing bona fide promoters. For each peak we provide detailed annotation,
expanding the landscape of ‘known’ macaque genes, and we show
concrete examples on how to use the resulting data. We believe this data
represents a useful resource to understand the central nervous system in
macaque.
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Affiliation(s)
- Margherita Francescatto
- Italian Institute of Technology, Department of Neuroscience and Brain Technologies, Via Morego 30, Genova 16163, Italy
| | - Marina Lizio
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Ingrid Philippens
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | | | - Ronald Bontrop
- Biomedical Primate Research Centre, Postbox 3306, Rijswijk 2280 GH, The Netherlands
| | - Mizuho Sakai
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Shoko Watanabe
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Masayoshi Itoh
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Akira Hasegawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Timo Lassmann
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Telethon Kids Institute, The University of Western Australia, 100 Roberts Road, Subiaco, Western Australia 6008, Australia
| | - Jessica Severin
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Jayson Harshbarger
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Imad Abugessaisa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Takeya Kasukawa
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Piero Carninci
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Alistair R R Forrest
- RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,Harry Perkins Institute of Medical Research, 6 Verdun St, Nedlands, Western Australia 6009, Australia
| | - Hideya Kawaji
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Yokohama Institute, Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.,RIKEN Advanced Center for Computing and Communication, Preventive Medicine and Applied Genomics Unit, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Patrizia Rizzu
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
| | - Peter Heutink
- German Center for Neurodegenerative Diseases, Otfried-Müller Straße 23, Tübingen 72076, Germany
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Sheikh MA, Malik YS, Zhu X. RA-Induced Transcriptional Silencing of Checkpoint Kinase-2 through Promoter Methylation by Dnmt3b Is Required for Neuronal Differentiation of P19 Cells. J Mol Biol 2017; 429:2463-2473. [PMID: 28712951 DOI: 10.1016/j.jmb.2017.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/16/2017] [Accepted: 07/07/2017] [Indexed: 10/19/2022]
Abstract
In a previous study, we identified several novel targets of Dnmt3b using a chromatin library from retinoic acid (RA)-treated P19 cells. The present study describes the regulation of expression and function of checkpoint kinase (Chk2), which was one of the target genes of Dnmt3b. Chromatin immunoprecipitation followed by quantitative PCR analysis showed that recruitment of Dnmt3b on Chk2 promoter is induced following RA treatment of P19 cells. Both bisulfite genomic sequence and COBRA analyses showed that the methylation level of Chk2 promoter is progressively increased during RA-induced neuronal differentiation of P19 cells. Concomitantly, both mRNA and protein expression of Chk2 are reduced as determined by real-time PCR and Western blot analysis, respectively. Suppression of Dnmt3b expression by lentiviral-mediated shRNA resulted in increased expression and reduced methylation of Chk2, which clearly showed that Dnmt3b is responsible for transcriptional silencing of Chk2 gene in RA-treated P19 cells. Neuronal differentiation of P19 cells was inhibited upon enforced Chk2 expression in P19 cells, which showed that the decrease in endogenous expression of Chk2 is essential for normal differentiation. Ectopic Chk2 expression also negatively regulated cell cycle arrest and apoptosis following RA treatment, which could also contribute to impaired neuronal differentiation. Together, this study described the regulation of Chk2 expression through promoter methylation and also presented a novel role of Chk2 during neuronal differentiation, which is independent of its previously known function in DNA damage response.
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Affiliation(s)
- Muhammad Abid Sheikh
- Institute of Cytology and Genetics, Northeast Normal University, Changchun, China; Department of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan
| | - Yousra Saeed Malik
- Institute of Cytology and Genetics, Northeast Normal University, Changchun, China
| | - Xiaojuan Zhu
- Institute of Cytology and Genetics, Northeast Normal University, Changchun, China.
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Neary JL, Perez SM, Peterson K, Lodge DJ, Carless MA. Comparative analysis of MBD-seq and MeDIP-seq and estimation of gene expression changes in a rodent model of schizophrenia. Genomics 2017; 109:204-213. [PMID: 28365388 PMCID: PMC5526217 DOI: 10.1016/j.ygeno.2017.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 03/14/2017] [Accepted: 03/26/2017] [Indexed: 12/11/2022]
Abstract
We conducted a comparative study of multiplexed affinity enrichment sequence methodologies (MBD-seq and MeDIP-seq) in a rodent model of schizophrenia, induced by in utero methylazoxymethanol acetate (MAM) exposure. We also examined related gene expression changes using a pooled sample approach. MBD-seq and MeDIP-seq identified 769 and 1771 differentially methylated regions (DMRs) between F2 offspring of MAM-exposed rats and saline control rats, respectively. The assays showed good concordance, with ~56% of MBD-seq-detected DMRs being identified by or proximal to MeDIP-seq DMRs. There was no significant overlap between DMRs and differentially expressed genes, suggesting that DNA methylation regulatory effects may act upon more distal genes, or are too subtle to detect using our approach. Methylation and gene expression gene ontology enrichment analyses identified biological processes important to schizophrenia pathophysiology, including neuron differentiation, prepulse inhibition, amphetamine response, and glutamatergic synaptic transmission regulation, reinforcing the utility of the MAM rodent model for schizophrenia research.
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Affiliation(s)
- Jennifer L Neary
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Stephanie M Perez
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Kara Peterson
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
| | - Daniel J Lodge
- Department of Pharmacology, Center for Biomedical Neuroscience, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, TX 78229, USA.
| | - Melanie A Carless
- Department of Genetics, Texas Biomedical Research Institute, 7620 NW Loop 410, San Antonio, TX 78227, USA.
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Association of Smoking, Alcohol Use, and Betel Quid Chewing with Epigenetic Aberrations in Cancers. Int J Mol Sci 2017; 18:ijms18061210. [PMID: 28587272 PMCID: PMC5486033 DOI: 10.3390/ijms18061210] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 12/16/2022] Open
Abstract
Numerous environmental factors such as diet, alcohol use, stress, and environmental chemicals are known to elicit epigenetic changes, leading to increased rates of cancers and other diseases. The incidence of head and neck cancer, one of the most common cancers in Taiwanese males, is increasing: oral cancer and nasopharyngeal carcinoma are ranked fourth and tenth respectively, among the top ten cancers in this group, and a major cause of cancer-related deaths in Taiwanese males. Previous studies have identified smoking, alcohol use, and betel quid chewing as the three major causes of head and neck cancers; these three social habits are commonly observed in Taiwanese males, resulting in an increasing morbidity rate of head and neck cancers in this population. In this literature review, we discuss the association between specific components of betel quid, alcohol, and tobacco, and the occurrence of head and neck cancers, lung cancer, gastrointestinal cancers, and urethral cancer. We focus on regulatory mechanisms at the epigenetic level and their oncogenic effects. The review further discusses the application of FDA-approved epigenetic drugs as therapeutic strategies against cancer.
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40
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Hartwig FP, Loret de Mola C, Davies NM, Victora CG, Relton CL. Breastfeeding effects on DNA methylation in the offspring: A systematic literature review. PLoS One 2017; 12:e0173070. [PMID: 28257446 PMCID: PMC5336253 DOI: 10.1371/journal.pone.0173070] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 02/14/2017] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breastfeeding benefits both infants and mothers. Recent research shows long-term health and human capital benefits among individuals who were breastfed. Epigenetic mechanisms have been suggested as potential mediators of the effects of early-life exposures on later health outcomes. We reviewed the literature on the potential effects of breastfeeding on DNA methylation. METHODS Studies reporting original results and evaluating DNA methylation differences according to breastfeeding/breast milk groups (e.g., ever vs. never comparisons, different categories of breastfeeding duration, etc) were eligible. Six databases were searched simultaneously using Ovid, and the resulting studies were evaluated independently by two reviewers. RESULTS Seven eligible studies were identified. Five were conducted in humans. Studies were heterogeneous regarding sample selection, age, target methylation regions, methylation measurement and breastfeeding categorisation. Collectively, the studies suggest that breastfeeding might be negatively associated with promoter methylation of LEP (which encodes an anorexigenic hormone), CDKN2A (involved in tumour suppression) and Slc2a4 genes (which encodes an insulin-related glucose transporter) and positively with promoter methylation of the Nyp (which encodes an orexigenic neuropeptide) gene, as well as influence global methylation patterns and modulate epigenetic effects of some genetic variants. CONCLUSIONS The findings from our systematic review are far from conclusive due to the small number of studies and their inherent limitations. Further studies are required to understand the actual potential role of epigenetics in the associations of breastfeeding with later health outcomes. Suggestions for future investigations, focusing on epigenome-wide association studies, are provided.
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Affiliation(s)
- Fernando Pires Hartwig
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | | | - Neil Martin Davies
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
| | - Cesar Gomes Victora
- Postgraduate Programme in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
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Maldonado LL, Assis J, Araújo FMG, Salim ACM, Macchiaroli N, Cucher M, Camicia F, Fox A, Rosenzvit M, Oliveira G, Kamenetzky L. The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases. BMC Genomics 2017; 18:204. [PMID: 28241794 PMCID: PMC5327563 DOI: 10.1186/s12864-017-3574-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 02/09/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. RESULTS We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus. CONCLUSIONS This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high-quality genome assembly is critical for fully exploring the biology of a pathogenic organism. The E. canadensis (G7) genome presented in this study provides a unique opportunity to address the genetic diversity among the genus Echinococcus and its particular developmental features. At present, there is no unequivocal taxonomic classification of Echinococcus species; however, the genome-wide SNPs analysis performed here revealed the phylogenetic distance among these three Echinococcus species. Additional cestode genomes need to be sequenced to be able to resolve their phylogeny.
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Affiliation(s)
- Lucas L. Maldonado
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juliana Assis
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Flávio M. Gomes Araújo
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Anna C. M. Salim
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Natalia Macchiaroli
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcela Cucher
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Federico Camicia
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Adolfo Fox
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mara Rosenzvit
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Guilherme Oliveira
- Genomics and Computational Biology Group, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
- Instituto Tecnológico Vale, Belém, Brazil
| | - Laura Kamenetzky
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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Abstract
Background The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location. Methods Recent emergence of high resolution 3D map of human genome allowed segregating the genome into the large scale chromatin domains of naturally observable nuclear subcompartments, or Topologically Associated Domains (TADs), designated by spatial chromatin distribution. We utilized the chromatin map to elucidate relations between large scale chromatin state and CpG rich elements landscape. In the course of analysis it was confirmed that genes, Alu and CGI clusters maintain obvious, albeit different in strength, preference for open chromatin. For the first time it was clearly shown that the clusters density of the Alu and CGIs monotonically depend on the chromatin accessibility rate. In particular, the highest density of these elements is found in A1 euchromatin regions characterized by a high density of small length genes replicating in the early S-phase. It implies that these elements mediate (CGIs) or are a side element (Alus) of chromatin accessibility. Results We elucidated that both methylated and non-methylated CGIs display the affinity to chromatin accessibility. As a part of comparative genomics section, we elucidated that the dog’s genome non-canonical structure, outstanding in mammals for its high CGIs abundance compared to gene number, is explained by the presence of dense tandem CGI extended hotspots (500 kb on average) in subtelomeric and pericentromeric regions with highly skewed CG content, and not by CGIs global distribution pattern shift. Conclusions The study underlines the close association of CG-rich elements distribution with the newly introduced large scale chromatin state map, proposing a refined standpoint on interrelation of aforementioned genome elements and the chromatin state. To our expertise, the TAD-associated partition model employed in the study is likely the most substantial one regarding CpG rich clusters distribution among the whole genome chromatin/isochores maps available. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0864-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Vladimir N Babenko
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia.
| | - Irina V Chadaeva
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
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Barnawi J, Jersmann H, Haberberger R, Hodge S, Meech R. Reduced DNA methylation of sphingosine-1 phosphate receptor 5 in alveolar macrophages in COPD: A potential link to failed efferocytosis. Respirology 2016; 22:315-321. [DOI: 10.1111/resp.12949] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 06/24/2016] [Accepted: 07/19/2016] [Indexed: 12/27/2022]
Affiliation(s)
- Jameel Barnawi
- Lung Research; Hanson Institute; Adelaide South Australia Australia
- Department of Medicine; University of Adelaide; Adelaide South Australia Australia
- Department Medical Laboratory Technology; University of Tabuk; Tabuk Saudi Arabia
| | - Hubertus Jersmann
- Lung Research; Hanson Institute; Adelaide South Australia Australia
- Department of Medicine; University of Adelaide; Adelaide South Australia Australia
| | - Rainer Haberberger
- Centre for Neuroscience, Anatomy and Histology; Flinders University; Adelaide South Australia Australia
| | - Sandra Hodge
- Lung Research; Hanson Institute; Adelaide South Australia Australia
- Department of Medicine; University of Adelaide; Adelaide South Australia Australia
| | - Robyn Meech
- Department of Clinical Pharmacology; Flinders University; Adelaide South Australia Australia
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Tobias IC, Brooks CR, Teichroeb JH, Villagómez DA, Hess DA, Séguin CA, Betts DH. Small-Molecule Induction of Canine Embryonic Stem Cells Toward Naïve Pluripotency. Stem Cells Dev 2016; 25:1208-22. [DOI: 10.1089/scd.2016.0103] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Ian C. Tobias
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
| | - Courtney R. Brooks
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
| | - Jonathan H. Teichroeb
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
| | - Daniel A. Villagómez
- Department of Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
- Departamento de Producción Animal, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - David A. Hess
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
- Children's Health Research Institute, the University of Western Ontario, London, Ontario, Canada
- Molecular Medicine Research Group, Krembil Centre for Stem Cell Biology, Robarts Research Institute, the University of Western Ontario, London, Ontario Canada
| | - Cheryle A. Séguin
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
- Children's Health Research Institute, the University of Western Ontario, London, Ontario, Canada
| | - Dean H. Betts
- Department of Physiology and Pharmacology, Schulich School of Medicine & Dentistry, the University of Western Ontario, London, Ontario, Canada
- Children's Health Research Institute, the University of Western Ontario, London, Ontario, Canada
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The CD4(+) T cell methylome contributes to a distinct CD4(+) T cell transcriptional signature in Mycobacterium bovis-infected cattle. Sci Rep 2016; 6:31014. [PMID: 27507428 PMCID: PMC4978967 DOI: 10.1038/srep31014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 07/11/2016] [Indexed: 12/14/2022] Open
Abstract
We hypothesised that epigenetic regulation of CD4+ T lymphocytes contributes to a shift toward a dysfunctional T cell phenotype which may impact on their ability to clear mycobacterial infection. Combined RNA-seq transcriptomic profiling and Reduced Representation Bisulfite Sequencing identified 193 significantly differentially expressed genes and 760 differentially methylated regions (DMRs), between CD4+ T cells from M. bovis infected and healthy cattle. 196 DMRs were located within 10 kb of annotated genes, including GATA3 and RORC, both of which encode transcription factors that promote TH2 and TH17 T helper cell subsets respectively. Gene-specific DNA methylation and gene expression levels for the TNFRSF4 and Interferon-γ genes were significantly negatively correlated suggesting a regulatory relationship. Pathway analysis of DMRs identified enrichment of genes involved in the anti-proliferative TGF-β signaling pathway and TGFB1 expression was significantly increased in peripheral blood leukocytes from TB-infected cattle. This first analysis of the bovine CD4+ T cell methylome suggests that DNA methylation directly contributes to a distinct gene expression signature in CD4+ T cells from cattle infected with M. bovis. Specific methylation changes proximal to key inflammatory gene loci may be critical to the emergence of a non-protective CD4+ T cell response during mycobacterial infection in cattle.
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He X, Tillo D, Vierstra J, Syed KS, Deng C, Ray GJ, Stamatoyannopoulos J, FitzGerald PC, Vinson C. Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution. Genome Biol Evol 2015; 7:3155-69. [PMID: 26507798 PMCID: PMC4994754 DOI: 10.1093/gbe/evv205] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In mammals, the cytosine in CG dinucleotides is typically methylated producing
5-methylcytosine (5mC), a chemically less stable form of cytosine that can spontaneously
deaminate to thymidine resulting in a T•G mismatched base pair. Unlike other eukaryotes
that efficiently repair this mismatched base pair back to C•G, in mammals, 5mCG
deamination is mutagenic, sometimes producing TG dinucleotides, explaining the depletion
of CG dinucleotides in mammalian genomes. It was suggested that new TG dinucleotides
generate genetic diversity that may be critical for evolutionary change. We tested this
conjecture by examining the DNA sequence properties of regulatory sequences identified by
DNase I hypersensitive sites (DHSs) in human and mouse genomes. We hypothesized that the
new TG dinucleotides generate transcription factor binding sites (TFBS) that become
tissue-specific DHSs (TS-DHSs). We find that 8-mers containing the CG dinucleotide are
enriched in DHSs in both species. However, 8-mers containing a TG and no CG dinucleotide
are preferentially enriched in TS-DHSs when compared with 8-mers with neither a TG nor a
CG dinucleotide. The most enriched 8-mer with a TG and no CG dinucleotide in
tissue-specific regulatory regions in both genomes is the AP-1 motif
(TGAC/GTCAN), and we find evidence that
TG dinucleotides in the AP-1 motif arose from CG dinucleotides. Additional TS-DHS-enriched
TFBS containing the TG/CA dinucleotide are the E-Box motif
(GCAGCTGC), the NF-1 motif (GGCA—TGCC), and the
GR (glucocorticoid receptor) motif (G-ACA—TGT-C). Our results support the
suggestion that cytosine methylation is mutagenic in tetrapods producing TG dinucleotides
that create TFBS that drive evolution.
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Affiliation(s)
- Ximiao He
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Desiree Tillo
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jeff Vierstra
- Department of Genome Sciences, University of Washington
| | - Khund-Sayeed Syed
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Callie Deng
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - G Jordan Ray
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Peter C FitzGerald
- Genome Analysis Unit, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Charles Vinson
- Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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Relton CL, Hartwig FP, Davey Smith G. From stem cells to the law courts: DNA methylation, the forensic epigenome and the possibility of a biosocial archive. Int J Epidemiol 2015; 44:1083-93. [PMID: 26424516 PMCID: PMC5279868 DOI: 10.1093/ije/dyv198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The growth in epigenetics continues to attract considerable cross-disciplinary interest, apparently representing an opportunity to move beyond genomics towards the goal of understanding phenotypic variability from molecular through organismal to the societal level. The epigenome may also harbour useful information about life-time exposures (measured or unmeasured) irrespective of their influence on health or disease, creating the potential for a person-specific biosocial archive . Furthermore such data may prove of use in providing identifying information, providing the possibility of a future forensic epigenome . The mechanisms involved in ensuring that environmentally induced epigenetic changes perpetuate across the life course remain unclear. Here we propose a potential role of adult stem cells in maintaining epigenetic states provides a useful basis for formulating such epidemiologically-relevant concepts.
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Affiliation(s)
- Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
| | | | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social & Community Medicine, University of Bristol, Bristol, UK
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Bina M, Wyss P. Impact of the MLL1 morphemes on codon utilization and preservation in CpG Islands. Biopolymers 2015; 103:480-90. [PMID: 25991579 DOI: 10.1002/bip.22681] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 05/04/2015] [Accepted: 05/13/2015] [Indexed: 11/07/2022]
Affiliation(s)
- Minou Bina
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
| | - Phillip Wyss
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907
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Genetic differences and aberrant methylation in the apelin system predict the risk of high-altitude pulmonary edema. Proc Natl Acad Sci U S A 2015; 112:6134-9. [PMID: 25918383 DOI: 10.1073/pnas.1422759112] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hypoxia-inducible factor stimulates the expression of apelin, a potent vasodilator, in response to reduced blood arterial oxygen saturation. However, aberrations in the apelin system impair pulmonary vascular function, potentially resulting in the development of high-altitude (HA)-related disorders. This study aimed to elucidate the genetic and epigenetic regulation of apelin, apelin receptor (APLNR), and endothelial nitric oxide synthase (NOS3) in HA adaptation and HA pulmonary edema (HAPE). A genome-wide association study and sequencing identified variants of apelin, APLNR, and NOS3 that were validated in a larger sample size of HAPE-patients (HAPE-p), HAPE-free controls (HAPE-f), and healthy highland natives (HLs). Apelin-13 and nitrite levels and apelin and NOS3 expression were down-regulated in HAPE-p (P < 0.001). Among the several studied polymorphisms, apelin rs3761581, rs2235312, and rs3115757; APLNR rs11544374 and rs2282623; and NOS3 4b/4a, rs1799983, and rs7830 were associated with HAPE (P < 0.03). The risk allele rs3761581G was associated with a 58.6% reduction in gene expression (P = 0.017), and the risk alleles rs3761581G and rs2235312T were associated with low levels of apelin-13 and nitrite (P < 0.05). The latter two levels decreased further when both of these risk alleles were present in the patients (P < 0.05). Methylation of the apelin CpG island was significantly higher in HAPE-p at 11.92% than in HAPE-f and HLs at ≤ 7.1% (P < 0.05). Moreover, the methylation effect was 9% stronger in the 5' UTR and was associated with decreased apelin expression and apelin-13 levels. The rs3761581 and rs2235312 polymorphisms and methylation of the CpG island influence the expression of apelin in HAPE.
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Alvarado S, Tajerian M, Suderman M, Machnes Z, Pierfelice S, Millecamps M, Stone LS, Szyf M. An epigenetic hypothesis for the genomic memory of pain. Front Cell Neurosci 2015; 9:88. [PMID: 25852480 PMCID: PMC4371710 DOI: 10.3389/fncel.2015.00088] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 02/26/2015] [Indexed: 11/13/2022] Open
Abstract
Chronic pain is accompanied with long-term sensory, affective and cognitive disturbances. What are the mechanisms that mediate the long-term consequences of painful experiences and embed them in the genome? We hypothesize that alterations in DNA methylation, an enzymatic covalent modification of cytosine bases in DNA, serve as a "genomic" memory of pain in the adult cortex. DNA methylation is an epigenetic mechanism for long-term regulation of gene expression. Neuronal plasticity at the neuroanatomical, functional, morphological, physiological and molecular levels has been demonstrated throughout the neuroaxis in response to persistent pain, including in the adult prefrontal cortex (PFC). We have previously reported widespread changes in gene expression and DNA methylation in the PFC many months following peripheral nerve injury. In support of this hypothesis, we show here that up-regulation of a gene involved with synaptic function, Synaptotagmin II (syt2), in the PFC in a chronic pain model is associated with long-term changes in DNA methylation. The challenges of understanding the contributions of epigenetic mechanisms such as DNA methylation within the PFC to pain chronicity and their therapeutic implications are discussed.
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Affiliation(s)
- Sebastian Alvarado
- Department of Biology, Stanford University Palo Alto, CA, USA ; Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Maral Tajerian
- Department of Anesthesiology, Stanford University Palo Alto, CA, USA ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada ; Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada
| | - Matthew Suderman
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Ziv Machnes
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Stephanie Pierfelice
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada
| | - Magali Millecamps
- Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada ; Faculty of Dentistry, McGill University Montréal, QC, Canada
| | - Laura S Stone
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada ; Alan Edwards Centre for Research on Pain, McGill University Montréal, QC, Canada ; Faculty of Dentistry, McGill University Montréal, QC, Canada ; Department of Anesthesiology, Anesthesia Research Unit, Faculty of Medicine, McGill University Montréal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University Montréal, QC, Canada ; Sackler Program for Epigenetics and Developmental Psychobiology, McGill University Montréal, QC, Canada ; Integrated Program in Neuroscience, McGill University Montréal, QC, Canada
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