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Alsegehy S, Southey BR, Hernandez AG, Rund LA, Antonson AM, Nowak RA, Johnson RW, Rodriguez-Zas SL. Epigenetic disruptions in the offspring hypothalamus in response to maternal infection. Gene 2024; 910:148329. [PMID: 38431234 DOI: 10.1016/j.gene.2024.148329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/16/2024] [Accepted: 02/27/2024] [Indexed: 03/05/2024]
Abstract
DNA methylation is an epigenetic modification that can alter gene expression, and the incidence can vary across developmental stages, inflammatory conditions, and sexes. The effects of viral maternal viral infection and sex on the DNA methylation patterns were studied in the hypothalamus of a pig model of immune activation during development. DNA methylation at single-base resolution in regions of high CpG density was measured on 24 individual hypothalamus samples using reduced representation bisulfite sequencing. Differential over- and under-methylated sites were identified and annotated to proximal genes and corresponding biological processes. A total of 120 sites were differentially methylated (FDR-adjusted p-value < 0.05) between maternal infection or sex groups. Among the 66 sites differentially methylated between groups exposed to inflammatory signals and control, most sites were over-methylated in the challenged group and included sites in the promoter regions of genes SIRT3 and NRBP1. Among the 54 differentially methylated sites between females and males, most sites were over-methylated in females and included sites in the promoter region of genes TNC and EIF4G1. The analysis of the genes proximal to the differentially methylated sites suggested that biological processes potentially impacted include immune response, neuron migration and ensheathment, peptide signaling, adaptive thermogenesis, and tissue development. These results suggest that translational studies should consider that the prolonged effect of maternal infection during gestation may be enacted through epigenetic regulatory mechanisms that may differ between sexes.
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Affiliation(s)
- Samah Alsegehy
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Lauretta A Rund
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Adrienne M Antonson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Romana A Nowak
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rodney W Johnson
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Sandra L Rodriguez-Zas
- Informatics Program, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61820, USA.
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Posynick BJ, Brown CJ. Escape From X-Chromosome Inactivation: An Evolutionary Perspective. Front Cell Dev Biol 2019; 7:241. [PMID: 31696116 PMCID: PMC6817483 DOI: 10.3389/fcell.2019.00241] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022] Open
Abstract
Sex chromosomes originate as a pair of homologus autosomes that then follow a general pattern of divergence. This is evident in mammalian sex chromosomes, which have undergone stepwise recombination suppression events that left footprints of evolutionary strata on the X chromosome. The loss of genes on the Y chromosome led to Ohno’s hypothesis of dosage equivalence between XY males and XX females, which is achieved through X-chromosome inactivation (XCI). This process transcriptionally silences all but one X chromosome in each female cell, although 15–30% of human X-linked genes still escape inactivation. There are multiple evolutionary pathways that may lead to a gene escaping XCI, including remaining Y chromosome homology, or female advantage to escape. The conservation of some escape genes across multiple species and the ability of the mouse inactive X to recapitulate human escape status both suggest that escape from XCI is controlled by conserved processes. Evolutionary pressures to minimize dosage imbalances have led to the accumulation of genetic elements that favor either silencing or escape; lack of dosage sensitivity might also allow for the escape of flanking genes near another escapee, if a boundary element is not present between them. Delineation of the elements involved in escape is progressing, but mechanistic understanding of how they interact to allow escape from XCI is still lacking. Although increasingly well-studied in humans and mice, non-trivial challenges to studying escape have impeded progress in other species. Mouse models that can dissect the role of the sex chromosomes distinct from sex of the organism reveal an important contribution for escape genes to multiple diseases. In humans, with their elevated number of escape genes, the phenotypic consequences of sex chromosome aneuplodies and sexual dimorphism in disease both highlight the importance of escape genes.
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Affiliation(s)
- Bronwyn J Posynick
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, Molecular Epigenetics Group, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada
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Zhang L, wang X, Chen C, Wang W, Yang K, Shen D, Wang S, gao B, Guo Y, Mao J, song C. Development of retrotransposons insertion polymorphic markers and application in the genetic variation evaluation of Chinese Bama miniature pigs. CANADIAN JOURNAL OF ANIMAL SCIENCE 2019. [DOI: 10.1139/cjas-2018-0138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Retrotransposons are genetic elements that can amplify themselves in a genome and are abundant in many eukaryotic organisms. In this study, we established some new short interspersed nuclear elements (SINE) and endogenous retroviruses (ERV) retrotransposons insertion polymorphism (RTIP) markers based on BLAT alignment tool strategy, and followed by PCR evaluation. We investigated the genetic variations among four subpopulations of Chinese Bama miniature pigs (BM), including BM in national conservation farm (BM-cov), BM inbreeding population (BM-inb) and BM closed Herd (BM-clo) in Guangxi University, and BM in the Experimental pig farm of Yangzhou University (BM-yzu). Genetic distance, polymorphism information content (PIC) and heterozygosity (He) of these markers in four of BM subpopulations were measured. Twelve SINE and twenty-eight ERV polymorphic molecular markers were identified in the four subpopulations. The BM-cov pigs represented the highest He and PIC, which indicated that BM-cov pigs maintain relatively highly genetic diversity. BM-inb pigs represented the lowest He and PIC indicating less variation and a high degree of inbreeding. Microsatellites polymorphism in four BM populations also well supported the results of these RTIP markers. In summary, retrotransposons insertion polymorphic markers could be a useful tool for population genetic variation analysis. Current SINE and ERV variation data may also provide a reference guide for the conservation and utilization of the BM miniature pig resource.
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Chen C, Wang W, Wang X, Shen D, Wang S, Wang Y, Gao B, Wimmers K, Mao J, Li K, Song C. Retrotransposons evolution and impact on lncRNA and protein coding genes in pigs. Mob DNA 2019; 10:19. [PMID: 31080521 PMCID: PMC6501411 DOI: 10.1186/s13100-019-0161-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/11/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Retrotransposons are the major determinants of genome sizes and they have shaped both genes and genomes in mammalian organisms, but their overall activity, diversity, and evolution dynamics, particularly their impact on protein coding and lncRNA genes in pigs remain largely unknown. RESULTS In the present study, we performed de novo detection of retrotransposons in pigs by using multiple pipelines, four distinct families of pig-specific L1 s classified into 51 distinct subfamilies and representing four evolution models and three expansion waves of pig-specific SINEs represented by three distinct families were identified. ERVs were classified into 18 families and found two most "modern" subfamilies in the pig genome. The transposition activity of pig L1 was verified by experiment, the sense and antisense promoter activities of young L1 5'UTRs and ERV LTRs and expression profiles of young retrotransposons in multiple tissues and cell lines were also validated. Furthermore, retrotransposons had an extensive impact on lncRNA and protein coding genes at both the genomic and transcriptomic levels. Most protein coding and lncRNA (> 80%) genes contained retrotransposon insertions, and about half of protein coding genes (44.30%) and one-fourth (24.13%) of lncRNA genes contained the youngest retrotransposon insertions. Nearly half of protein coding genes (43.78%) could generate chimeric transcripts with retrotransposons. Significant distribution bias of retrotransposon composition, location, and orientation in lncRNA and protein coding genes, and their transcripts, were observed. CONCLUSIONS In the current study, we characterized the classification and evolution profile of retrotransposons in pigs, experimentally proved the transposition activity of the young pig L1 subfamily, characterized the sense and antisense expression profiles and promoter activities of young retrotransposons, and investigated their impact on lncRNA and protein coding genes by defining the mobilome landscapes at the genomic and transcriptomic levels. These findings help provide a better understanding of retrotransposon evolution in mammal and their impact on the genome and transcriptome.
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Affiliation(s)
- Cai Chen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Wei Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaoyan Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Dan Shen
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Saisai Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Yali Wang
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Bo Gao
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Klaus Wimmers
- Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Jiude Mao
- Life Science Center, University of Missouri, Columbia, MO 65211 USA
| | - Kui Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chengyi Song
- Institute of Animal Mobilome and Genome, College of Animal Science & Technology, Yangzhou University, Yangzhou, 225009 Jiangsu China
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Arayataweegool A, Srisuttee R, Mahattanasakul P, Tangjaturonsasme N, Kerekhanjanarong V, Kitkumthorn N, Mutirangura A. Head and neck squamous cell carcinoma drives long interspersed element‐1 hypomethylation in the peripheral blood mononuclear cells. Oral Dis 2018; 25:64-72. [DOI: 10.1111/odi.12944] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 07/12/2018] [Accepted: 07/15/2018] [Indexed: 01/05/2023]
Affiliation(s)
- Areeya Arayataweegool
- Program of Medical Science Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Ratakorn Srisuttee
- Faculty of Medicine King Mongkut's Institute of Technology Ladkrabang Bangkok Thailand
| | - Patnarin Mahattanasakul
- Department of Otolaryngology, Head and Neck Surgery Faculty of Medicine Chulalongkorn University Bangkok Thailand
- Department of Otolaryngology, Head and Neck Surgery King Chulalongkorn Memorial Hospital Thai Red Cross Society Bangkok Thailand
| | - Napadon Tangjaturonsasme
- Department of Otolaryngology, Head and Neck Surgery Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Virachai Kerekhanjanarong
- Department of Otolaryngology, Head and Neck Surgery Faculty of Medicine Chulalongkorn University Bangkok Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology Faculty of Dentistry Mahidol University Bangkok Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases Department of Anatomy Faculty of Medicine Chulalongkorn University Bangkok Thailand
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Protasova MS, Gusev FE, Grigorenko AP, Kuznetsova IL, Rogaev EI, Andreeva TV. Quantitative Analysis of L1-Retrotransposons in Alzheimer's Disease and Aging. BIOCHEMISTRY (MOSCOW) 2017; 82:962-971. [PMID: 28941465 DOI: 10.1134/s0006297917080120] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
LINE1 retrotransposons are members of a class of mobile genetic elements capable of retrotransposition in the genome via a process of reverse transcription. LINE1 repeats, integrating into different chromosomal loci, affect the activity of genes and cause different genomic mutations. Somatic variability of the human genome is linked to the activity of some subfamilies of LINE1, in particular, a high level of LINE1 retrotranspositions has been observed in brain tissues. However, the contribution of LINE1 to genomic variability during normal aging and in age-related neurodegenerative diseases is poorly understood. We conducted quantitative real-time PCR analysis of active subfamilies of LINE1 repeats (aL1) using genomic DNA extracted from brain specimens of Alzheimer's disease (AD) patients and individuals without neuropsychiatric pathologies, as well as DNA extracted from blood specimens of individuals of different ages (healthy and AD subjects). Inter-individual quantitative variations of active families of aL1 repeats in the genome were observed. No significant age-dependent differences were identified. Likewise, no difference of aL1 copy number in brain and blood were indicated between AD patients and the aged-matched control group without dementia. These data imply that aging and the AD-associated neurodegenerative process are not the major factors contributing to the retrotransposition processes of active LINE1 repeats.
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Affiliation(s)
- M S Protasova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
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Pruksananonda K, Wasinarom A, Sereepapong W, Sirayapiwat P, Rattanatanyong P, Mutirangura A. Epigenetic modification of long interspersed elements-1 in cumulus cells of mature and immature oocytes from patients with polycystic ovary syndrome. Clin Exp Reprod Med 2016; 43:82-9. [PMID: 27358825 PMCID: PMC4925871 DOI: 10.5653/cerm.2016.43.2.82] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/24/2016] [Accepted: 05/06/2016] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE The long interspersed elements (LINE-1, L1s) are a group of genetic elements found in large numbers in the human genome that can translate into phenotype by controlling genes. Growing evidence supports the role of epigenetic in polycystic ovary syndrome (PCOS). The purpose of this study is to evaluate the DNA methylation levels in LINE-1 in a tissue-specific manner using cumulus cells from patients with PCOS compared with normal controls. METHODS The study included 19 patients with PCOS and 22 control patients who were undergoing controlled ovarian hyperstimulation. After oocyte retrieval, cumulus cells were extracted. LINE-1 DNA methylation levels were analysed by bisulfite treatment, polymerase chain reaction, and restriction enzyme digestion. The Connection Up- and Down-Regulation Expression Analysis of Microarrays software package was used to compare the gene regulatory functions of intragenic LINE-1. RESULTS The results showed higher LINE-1 DNA methylation levels in the cumulus cells of mature oocytes in PCOS patients, 79.14 (±2.66) vs. 75.40 (±4.92); p=0.004, but no difference in the methylation of cumulus cells in immature oocytes between PCOS and control patients, 70.33 (±4.79) vs. 67.79 (±5.17); p=0.155. However, LINE-1 DNA methylation levels were found to be higher in the cumulus cells of mature oocytes than in those of immature oocytes in both PCOS and control patients. CONCLUSION These findings suggest that the epigenetic modification of LINE-1 DNA may play a role in regulating multiple gene expression that affects the pathophysiology and development of mature oocytes in PCOS.
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Affiliation(s)
- Kamthorn Pruksananonda
- Reproductive Medicine Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Artisa Wasinarom
- Reproductive Medicine Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wisan Sereepapong
- Reproductive Medicine Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Porntip Sirayapiwat
- Reproductive Medicine Division, Department of Obstetrics and Gynecology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Prakasit Rattanatanyong
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Disease, Department of Anatomy, King Chulalongkorn Memorial Hospital, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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Jachowicz JW, Torres-Padilla ME. LINEs in mice: features, families, and potential roles in early development. Chromosoma 2015; 125:29-39. [PMID: 25975894 DOI: 10.1007/s00412-015-0520-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 04/27/2015] [Accepted: 05/05/2015] [Indexed: 01/08/2023]
Abstract
Approximately half of the mammalian genome is composed of repetitive elements, including LINE-1 (L1) elements. Because of their potential ability to transpose and integrate into other regions of the genome, their activation represents a threat to genome stability. Molecular pathways have emerged to tightly regulate and repress their transcriptional activity, including DNA methylation, histone modifications, and RNA pathways. It has become evident that Line-L1 elements are evolutionary diverse and dedicated repression pathways have been recently uncovered that discriminate between evolutionary old and young elements, with RNA-directed silencing mechanisms playing a prominent role. During periods of epigenetic reprogramming in development, specific classes of repetitive elements are upregulated, presumably due to the loss of most heterochromatic marks in this process. While we have learnt a lot on the molecular mechanisms that regulate Line-L1 expression over the last years, it is still unclear whether reactivation of Line-L1 after fertilization serves a functional purpose or it is a simple side effect of reprogramming.
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Affiliation(s)
- Joanna W Jachowicz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, 67404, Illkirch, France
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, 67404, Illkirch, France.
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