RESUMO
PURPOSE: Retrotransposons play important roles during early development when they are transiently de-repressed during epigenetic reprogramming. Long interspersed element-1 (L1), the only autonomous retrotransposon in humans, comprises 17% of the human genome. We applied the Single Cell Transposon Insertion Profiling by Sequencing (scTIPseq) to characterize and map L1 insertions in human embryos. METHODS: Sixteen cryopreserved, genetically tested, human blastocysts, were accessed from consenting couples undergoing IVF at NYU Langone Fertility Center. Additionally, four trios (father, mother, and embryos) were also evaluated. scTIPseq was applied to map L1 insertions in all samples, using L1 locations reported in the 1000 Genomes as controls. RESULTS: Twenty-nine unknown and unique insertions were observed in the sixteen embryos. Most were intergenic; no insertions were located in exons or immediately upstream of genes. The location or number of unknown insertions did not differ between euploid and aneuploid embryos, suggesting they are not merely markers of aneuploidy. Rather, scTIPseq provides novel information about sub-chromosomal structural variation in human embryos. Trio analyses showed a parental origin of all L1 insertions in embryos. CONCLUSION: Several studies have measured L1 expression at different stages of development in mice, but this study for the first time reports unknown insertions in human embryos that were inherited from one parent, confirming no de novo L1 insertions occurred in parental germline or during embryogenesis. Since one-third of euploid embryo transfers fail, future studies would be useful for understanding whether these sub-chromosomal genetic variants or de novo L1 insertions affect embryo developmental potential.
Assuntos
Blastocisto , Elementos Nucleotídeos Longos e Dispersos , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Blastocisto/metabolismo , Feminino , Embrião de Mamíferos/metabolismo , Desenvolvimento Embrionário/genética , Mutagênese Insercional/genética , Aneuploidia , Genoma Humano/genética , Fertilização in vitro , Masculino , Variação Genética/genética , Camundongos , Mapeamento Cromossômico/métodosRESUMO
Avian genomes are characterized as being more compact than other amniotes, with less diversity and density of transposable elements (TEs). In addition, birds usually show bimodal karyotypes, exhibiting a great variation in diploid numbers. Some species present unusually large sex chromosomes, possibly due to the accumulation of repetitive sequences. Avian retrotransposon-like element (AviRTE) is a long interspersed nuclear element (LINE) recently discovered in the genomes of birds and nematodes, and it is still poorly characterized in terms of chromosomal mapping and phylogenetic relationships. In this study, we mapped AviRTE isolated from the Trogon surrucura genome into the T. surrucura (TSU) karyotype. Furthermore, we analyzed the phylogenetic relationships of this LINE in birds and other vertebrates. Our results showed that the distribution pattern of AviRTE is not restricted to heterochromatic regions, with accumulation on the W chromosome of TSU, yet another species with an atypical sex chromosome and TE hybridization. The phylogenetic analysis of AviRTE sequences in birds agreed with the proposed phylogeny of species in most clades, and allowed the detection of this sequence in other species, expanding the distribution of the element.
Assuntos
Aves , Mapeamento Cromossômico , Cariótipo , Filogenia , Retroelementos , Cromossomos Sexuais , Animais , Aves/genética , Aves/classificação , Cromossomos Sexuais/genética , Masculino , Feminino , Elementos Nucleotídeos Longos e DispersosRESUMO
Currently, the marketing of electronic cigarettes as a safe alternative to smoking has increased, which is associated with greater use of these devices, especially among young people and smokers interested in quitting tobacco cigarettes. Given the growing use of this type of product, there is a need to determine the consequences of electronic cigarettes on human health, especially since many of the compounds contained in the aerosol and liquid of these devices have a high potential to be carcinogenic and genotoxic. Additionally, many of these compounds' aerosol concentrations exceed the safe limits. We have evaluated the levels of genotoxicity and changes in DNA methylation patterns associated with vaping. We analyzed a total of 90 peripheral blood samples from a population of vapers (n = 32), smokers (n = 18), and controls (n = 32), in which the frequencies of genotoxicity were determined by the cytokinesis-blocking micronuclei (CBMN) assay and the patterns of methylation of the repetitive elements of LINE-1 through the Quantitative Methylation Specific PCR (qMSP) assay. Here we show an increase in genotoxicity levels associated with vaping habits. Additionally, the group of vapers showed changes at the epigenetic level specifically associated with the loss of methylation of the LINE-1 elements. These changes in LINE-1 methylation patterns were reflected in its representative RNA expression detected in vapers.
Assuntos
Sistemas Eletrônicos de Liberação de Nicotina , Humanos , Adolescente , Metilação de DNA , Elementos Nucleotídeos Longos e Dispersos , Fumar , AerossóisRESUMO
BACKGROUND: Long interspersed element 1 (LINE-1 or L1) retrotransposons are mobile elements that constitute 17-20% of the human genome. Strong correlations between abnormal L1 expression and several human diseases have been reported. This has motivated increasing interest in accurate quantification of the number of L1 copies present in any given biologic specimen. A main obstacle toward this aim is that L1s are relatively long DNA segments with regions of high variability, or largely present in the human genome as truncated fragments. These particularities render traditional alignment strategies, such as seed-and-extend inefficient, as the number of segments that are similar to L1s explodes exponentially. This study uses the pattern matching methodology for more accurate identification of L1s. We validate experimentally the superiority of pattern matching for L1 detection over alternative methods and discuss some of its potential applications. RESULTS: Pattern matching detected full-length L1 copies with high precision, reasonable computational time, and no prior input information. It also detected truncated and significantly altered copies of L1 with relatively high precision. The method was effectively used to annotate L1s in a target genome and to calculate copy number variation with respect to a reference genome. Crucial to the success of implementation was the selection of a small set of k-mer probes from a set of sequences presenting a stable pattern of distribution in the genome. As in seed-and-extend methods, the pattern matching algorithm sowed these k-mer probes, but instead of using heuristic extensions around the seeds, the analysis was based on distribution patterns within the genome. The desired level of precision could be adjusted, with some loss of recall. CONCLUSION: Pattern matching is more efficient than seed-and-extend methods for the detection of L1 segments whose characterization depends on a finite set of sequences with common areas of low variability. We propose that pattern matching may help establish correlations between L1 copy number and disease states associated with L1 mobilization and evolution.
Assuntos
Variações do Número de Cópias de DNA , Genoma Humano , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , RetroelementosRESUMO
This study aimed to understand the impact of LINE-1 and SINE-B1 retroelements on the architecture and karyotypic diversification of five rodent species of the genus Proechimys from different regions of the Amazon. Karyotype comparisons were performed using fluorescent interspecific in situ hybridization. The L1 and B1 retroelements showed a non-random arrangement and a conserved pattern when the genomes of the five species of Proechimys were compared, including the two cytotypes of Proechimys guyannensis The signal homeology among the chromosomes and the degree of similarity among the formed clusters indicate rearrangements such as fusion/fission, and demonstrates that these retroelements can behave as derived characters shared in Proechimys The differentiated distribution and organization of these retroelements in the karyotypes and in the chromosomal fiber, respectively, may represent a strong indication of their role as generating sources of karyotypic diversity in the genus Proechimys and provide insights into the evolutionary relationships between taxa.
Assuntos
Retroelementos , Roedores , Animais , Cromossomos , Elementos Nucleotídeos Longos e Dispersos/genética , Retroelementos/genética , Roedores/genéticaRESUMO
Down syndrome (DS) is the most common chromosomal disorder, resulting from the failure of normal chromosome 21 segregation. Studies have suggested that impairments within the one-carbon metabolic pathway can be of relevance for the global genome instability observed in mothers of individuals with DS. Based on the association between global DNA hypomethylation, genome instability, and impairments within the one-carbon metabolic pathway, the present study aimed to identify possible predictors, within the one-carbon metabolism, of global DNA methylation, measured by methylation patterns of LINE-1 and Alu repetitive sequences, in mothers of individuals with DS and mothers of individuals without the syndrome. In addition, we investigated one-carbon genetic polymorphisms and metabolites as maternal predisposing factors for the occurrence of trisomy 21 in children. Eighty-three samples of mothers of children with DS with karyotypically confirmed free trisomy 21 (case group) and 84 of mothers who had at least one child without DS or any other aneuploidy were included in the study. Pyrosequencing assays were performed to access global methylation. The results showed that group affiliation (case or control), betaine-homocysteine methyltransferase (BHMT) G742A and transcobalamin 2 (TCN2) C776G polymorphisms, and folate concentration were identified as predictors of global Alu DNA methylation values. In addition, thymidylate synthase (TYMS) 28-bp repeats 2R/3R or 3R/3R genotypes are independent maternal predisposing factors for having a child with DS. This study adds evidence that supports the association of impairments in the one-carbon metabolism, global DNA methylation, and the possibility of having a child with DS.
Assuntos
Carbono/metabolismo , Metilação de DNA/genética , Síndrome de Down/genética , Síndrome de Down/metabolismo , Estudo de Associação Genômica Ampla , Instabilidade Genômica/genética , Relações Mãe-Filho , Mães , Adolescente , Adulto , Idoso , Elementos Alu/genética , Betaína-Homocisteína S-Metiltransferase/genética , Betaína-Homocisteína S-Metiltransferase/metabolismo , Feminino , Ácido Fólico/metabolismo , Predisposição Genética para Doença/genética , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Masculino , Pessoa de Meia-Idade , Polimorfismo Genético , Transdução de Sinais/genética , Transdução de Sinais/fisiologia , Timidilato Sintase/genética , Transcobalaminas/genética , Transcobalaminas/metabolismo , Adulto JovemRESUMO
Aim: We investigated GRIN1, GRIN2A, GRIN2B and LINE-1 DNA methylation in first-episode schizophrenia patients, their nonaffected siblings and age- and sex-matched controls testing for associations between DNA methylation and exposition to childhood trauma. Materials & methods: The Childhood Trauma Questionnaire evaluated the history of childhood trauma. Genomic DNA was bisulfite converted and pyrosequencing was employed to quantify DNA methylation. Results:GRIN2A, GRIN2B and LINE-1 DNA methylation was not associated with childhood trauma in patients, siblings and controls. Siblings with childhood trauma had hypermethylation at CpG1 of GRIN1 compared with siblings without trauma. Conclusion: Childhood trauma may influence GRIN1 methylation in subjects with liability to psychosis, but not in frank schizophrenia or controls.
Lay abstract Schizophrenia results from a combination of genetic and environmental influences. We investigated how some changes in genes can be silenced by a process named DNA methylation and may be linked to schizophrenia. For this reason, we hypothesized that childhood trauma, an environmental risk factor, would be associated with DNA methylation in schizophrenia patients compared with their unaffected siblings and controls. Our research has shown that altered blood DNA methylation of one candidate gene for psychiatric disorders may be associated with childhood trauma in the unaffected siblings of schizophrenia patients, but not in frank schizophrenia or controls. We believe that this gene plays an important role in helping identify vulnerable as well as resilient individuals to schizophrenia disorder.
Assuntos
Experiências Adversas da Infância , Suscetibilidade a Doenças , Receptores de N-Metil-D-Aspartato/genética , Esquizofrenia/epidemiologia , Esquizofrenia/etiologia , Adolescente , Adulto , Biomarcadores , Estudos de Casos e Controles , Ilhas de CpG , Metilação de DNA , Feminino , Regulação da Expressão Gênica , Humanos , Elementos Nucleotídeos Longos e Dispersos , Masculino , Pessoa de Meia-Idade , Receptores de N-Metil-D-Aspartato/metabolismo , Medição de Risco , Fatores de Risco , Esquizofrenia/diagnóstico , Irmãos , Adulto JovemRESUMO
Alterations of global DNA methylation have been evaluated in several studies worldwide; however, Long Interspersed Nuclear Elements-1 (LINE-1) methylation in genetically conserved populations such as indigenous communities have not, to our knowledge, been reported. The aim of this study was to evaluate the relationship between LINE-1 methylation patterns and factors such as pesticide exposure and socio-cultural characteristics in the Indigenous Huichol Population of Nayarit, Mexico. A cross-sectional study was conducted in 140 Huichol indigenous individuals. A structured questionnaire was used to determine general and anthropometric characteristics, diet, harmful habits, and pesticide exposure. DNA methylation was determined by pyrosequencing of bisulfite-treated DNA. A lower level of LINE-1 methylation was found in the indigenous population when compared to a Mestizo population previously studied by our group. This difference might be due to the influence of the genetic admixture and differing dietary and lifestyle habits. The males in the indigenous population exhibited increased LINE-1 methylation in comparison to the females. Sex and alcohol consumption showed positive associations with LINE-1 methylation, while weight, current work in the field, current pesticide usage, and folate intake exhibited negative associations with LINE-1 methylation. The results suggest that ethnicity, as well as other internal and environmental factors, might influence LINE-1 methylation.
Assuntos
Metilação de DNA , Grupos Populacionais , Estudos Transversais , Feminino , Humanos , Elementos Nucleotídeos Longos e Dispersos/genética , Masculino , MéxicoRESUMO
PURPOSE: In contrast to hormone receptor driven breast cancer, patients presenting with triple-negative breast cancer (TNBC) often have limited drug treatment options. Efavirenz, a non-nucleoside reverse transcriptase (RT) inhibitor targets abnormally overexpressed long interspersed nuclear element 1 (LINE-1) RT and has been shown to be a promising anticancer agent for treating prostate and pancreatic cancers. However, its effectiveness in treating patients with TNBC has not been comprehensively examined. METHODS: In this study, the effect of Efavirenz on several TNBC cell lines was investigated by examining several cellular characteristics including viability, cell division and death, changes in cell morphology as well as the expression of LINE-1. RESULTS: The results show that in a range of TNBC cell lines, Efavirenz causes cell death, retards cell proliferation and changes cell morphology to an epithelial-like phenotype. In addition, it is the first time that a whole-genome RNA sequence analysis has identified the fatty acid metabolism pathway as a key regulator in this Efavirenz-induced anticancer process. CONCLUSION: In summary, we propose Efavirenz is a potential anti-TNBC drug and that its mode of action can be linked to the fatty acid metabolism pathway.
Assuntos
Alcinos/uso terapêutico , Antineoplásicos/uso terapêutico , Benzoxazinas/uso terapêutico , Ciclopropanos/uso terapêutico , Elementos Nucleotídeos Longos e Dispersos , Inibidores da Transcriptase Reversa/uso terapêutico , Neoplasias de Mama Triplo Negativas/tratamento farmacológico , Morte Celular , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Forma Celular/efeitos dos fármacos , Regulação para Baixo , Ácidos Graxos/metabolismo , Feminino , Humanos , Fenótipo , Transcriptoma , Neoplasias de Mama Triplo Negativas/genética , Neoplasias de Mama Triplo Negativas/patologiaRESUMO
Aim: To evaluate the risk of nonsyndromic orofacial clefts (NSOFCs) associated with LINE-1 methylation, as a marker of global DNA methylation, and the effect of MTHFR functional variants on this variable. Patients & methods: LINE-1 methylation was evaluated by bisulfite modification coupled to DNA pyrosequencing in 95 NSOFC cases and 95 controls. In these subjects, MTHFR genotypes for variants c.C677T (rs1801133) and c.A1298C (rs1801131) were obtained. Results: Middle levels (second tertile) of LINE-1 methylation increase the risk of NSOFCs. In addition, LINE-1 methylation depends on c.A1298C genotypes in controls but not in cases. Conclusion: A nonlinear association between global DNA methylation and NSOFCs was detected in this Chilean population, which appears to be influenced by MTHFR functional variants.