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Hubert JN, Iannuccelli N, Cabau C, Jacomet E, Billon Y, Serre RF, Vandecasteele C, Donnadieu C, Demars J. Detection of DNA methylation signatures through the lens of genomic imprinting. Sci Rep 2024; 14:1694. [PMID: 38242932 PMCID: PMC10798973 DOI: 10.1038/s41598-024-52114-3] [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: 10/03/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024] Open
Abstract
Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice.
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Affiliation(s)
- Jean-Noël Hubert
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Eva Jacomet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
- ENVT, 31326, Castanet-Tolosan, France
| | | | - Rémy-Félix Serre
- INRAE, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
- Qualyse, Le Treuil, INRAE, 19000, Tulle, France
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
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Garner JP, Talbot CF, Del Rosso LA, McCowan B, Kanthaswamy S, Haig D, Capitanio JP, Parker KJ. Rhesus macaque social functioning is paternally, but not maternally, inherited by sons: potential implications for autism. Mol Autism 2023; 14:25. [PMID: 37480043 PMCID: PMC10360241 DOI: 10.1186/s13229-023-00556-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/19/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Quantitative autistic traits are common, heritable, and continuously distributed across the general human population. Patterns of autistic traits within families suggest that more complex mechanisms than simple Mendelian inheritance-in particular, parent of origin effects-may be involved. The ideal strategy for ascertaining parent of origin effects is by half-sibling analysis, where half-siblings share one, but not both, parents and each individual belongs to a unique combination of paternal and maternal half-siblings. While this family structure is rare in humans, many of our primate relatives, including rhesus macaques, have promiscuous breeding systems that consistently produce paternal and maternal half-siblings for a given index animal. Rhesus macaques, like humans, also exhibit pronounced variation in social functioning. METHODS Here we assessed differential paternal versus maternal inheritance of social functioning in male rhesus macaque offspring (N = 407) using ethological observations and ratings on a reverse-translated quantitative autistic trait measurement scale. Restricted Maximum Likelihood mixed models with unbounded variance estimates were used to estimate the variance components needed to calculate the genetic contribution of parents as the proportion of phenotypic variance (σ2P) between sons that could uniquely be attributed to their shared genetics (σ2g), expressed as σ2g/σ2P (or the proportion of phenotypic variance attributable to genetic variance), as well as narrow sense heritability (h2). RESULTS Genetic contributions and heritability estimates were strong and highly significant for sons who shared a father but weak and non-significant for sons who shared a mother. Importantly, these findings were detected using the same scores from the same sons in the same analysis, confirmed when paternal and maternal half-siblings were analyzed separately, and observed with two methodologically distinct behavioral measures. Finally, genetic contributions were similar for full-siblings versus half-siblings that shared only a father, further supporting a selective paternal inheritance effect. LIMITATIONS These data are correlational by nature. A larger sample that includes female subjects, enables deeper pedigree assessments, and supports molecular genetic analyses is warranted. CONCLUSIONS Rhesus macaque social functioning may be paternally, but not maternally, inherited by sons. With continued investigation, this approach may yield important insights into sex differences in autism's genetic liability.
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Affiliation(s)
- Joseph P. Garner
- Department of Comparative Medicine, Stanford University, 300 Pasteur Drive, Edwards R348, Stanford, CA 94305-5342 USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, 1201 Welch Road, MSLS, P-104, Stanford, CA 94305-5485 USA
| | - Catherine F. Talbot
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
- Department of Psychology, Florida Institute of Technology, 150 W. University Blvd., Melbourne, FL 32901 USA
| | - Laura A. Del Rosso
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
| | - Brenda McCowan
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, 4205 VM3B, Davis, CA 95616 USA
| | - Sreetharan Kanthaswamy
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
- School of Mathematical and Natural Sciences, Arizona State University West Campus, 4701 W. Thunderbird Rd., Glendale, AZ 85306 USA
| | - David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA 02138 USA
| | - John P. Capitanio
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
- Department of Psychology, University of California, 1 Shields Ave., Davis, CA 95616 USA
| | - Karen J. Parker
- Department of Comparative Medicine, Stanford University, 300 Pasteur Drive, Edwards R348, Stanford, CA 94305-5342 USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, 1201 Welch Road, MSLS, P-104, Stanford, CA 94305-5485 USA
- California National Primate Research Center, 1 Shields Ave., Davis, CA 95616 USA
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Chang S, Min J, Lu X, Zhang Q, Shangguan S, Zhang T, Wang L. Effect of epigenetic activating of Dlk1-Dio3 imprinted cluster on miR-370 expression due to folate deficiency during nerve development. J Nutr Biochem 2023; 116:109297. [PMID: 36907530 DOI: 10.1016/j.jnutbio.2023.109297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/27/2023] [Accepted: 02/21/2023] [Indexed: 03/13/2023]
Abstract
Proper Dlk1-Dio3 imprinting plays a critical role in embryogenesis, and folic acid deficiency may affect the imprinting of this locus through epigenetic regulation. However, whether and how folic acid directly impacts the imprinting status of Dlk1-Dio3 to affect neural development remain unclear. Here, we found decreased IG-DMR (intergenic -differentially methylated regions) methylation in the folate-deficient encephalocele in humans, suggesting that abnormal Dlk1-Dio3 imprinting status is related to neural tube defects (NTDs) caused by folate deficiency. Similar results were obtained with folate-deficient embryonic stem cells. By miRNA chip analysis, folic acid deficiency led to changes in multiple miRNAs, including the upregulation of 15 miRNAs located in the Dlk1-Dio3 locus. Real-time PCR confirmed that seven of these miRNAs were upregulated, especially miR-370. In contrast to normal embryonic development, in which expression of miR-370 is highest at E9.5, the abnormally high and sustained expression of miRNA-370 in folate-deficient E13.5 embryos may contribute to NTDs. In addition, we found that DNMT3A (de novo DNA methyltransferases 3A) is a direct target gene of miR-370 in neural cells, and DNMT3A participates in the role of miR-370 in inhibiting cell migration. Finally, in the folate-deficient mouse model, Dlk1-Dio3 epigenetic activation was found in fetal brain tissue, along with the upregulation of miR-370 and the downregulation of DNMT3A. Collectively, our findings demonstrate a pivotal role of folate in the epigenetic regulation of Dlk1-Dio3 imprinting during neurogenesis, revealing an elegant mechanism for the activation of Dlk1-Dio3 locus miRNAs in folic acid deficiency.
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Affiliation(s)
- Shaoyan Chang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020
| | - Jie Min
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020; Department 2 of Nephrology, Beijing Children's Hospital Affiliated to Capital Medical University, Beijing Key Laboratory for Chronic Renal Disease and Blood Purification, Key Laboratory of Major Diseases in Children, National Center for Children's Health, Beijing, China, 100045
| | - Xiaolin Lu
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020
| | - Qingyu Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020
| | - Shaofang Shangguan
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020
| | - Ting Zhang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020
| | - Li Wang
- Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China, 100020.
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Mendel's laws of heredity on his 200th birthday: What have we learned by considering exceptions? Heredity (Edinb) 2022; 129:1-3. [PMID: 35778507 DOI: 10.1038/s41437-022-00552-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 12/20/2022] Open
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Hubert JN, Demars J. Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches. Front Genet 2022; 13:838534. [PMID: 35368671 PMCID: PMC8965095 DOI: 10.3389/fgene.2022.838534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting represents a noteworthy inheritance mechanism leading to allele-specific regulations dependent of the parental origin. Imprinted loci are especially involved in essential mammalian functions related to growth, development and behavior. In this mini-review, we first offer a summary of current representations associated with genomic imprinting through key results of the three last decades. We then outline new perspectives allowed by the spread of new omics technologies tackling various interacting levels of imprinting regulations, including genomics, transcriptomics and epigenomics. We finally discuss the expected contribution of new omics data to unresolved big questions in the field.
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Duenk P, Bijma P, Wientjes YCJ, Calus MPL. Review: optimizing genomic selection for crossbred performance by model improvement and data collection. J Anim Sci 2021; 99:skab205. [PMID: 34223907 PMCID: PMC8499581 DOI: 10.1093/jas/skab205] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/02/2021] [Indexed: 11/26/2022] Open
Abstract
Breeding programs aiming to improve the performance of crossbreds may benefit from genomic prediction of crossbred (CB) performance for purebred (PB) selection candidates. In this review, we compared genomic prediction strategies that differed in 1) the genomic prediction model used or 2) the data used in the reference population. We found 27 unique studies, two of which used deterministic simulation, 11 used stochastic simulation, and 14 real data. Differences in accuracy and response to selection between strategies depended on i) the value of the purebred crossbred genetic correlation (rpc), ii) the genetic distance between the parental lines, iii) the size of PB and CB reference populations, and iv) the relatedness of these reference populations to the selection candidates. In studies where a PB reference population was used, the use of a dominance model yielded accuracies that were equal to or higher than those of additive models. When rpc was lower than ~0.8, and was caused mainly by G × E, it was beneficial to create a reference population of PB animals that are tested in a CB environment. In general, the benefit of collecting CB information increased with decreasing rpc. For a given rpc, the benefit of collecting CB information increased with increasing size of the reference populations. Collecting CB information was not beneficial when rpc was higher than ~0.9, especially when the reference populations were small. Collecting only phenotypes of CB animals may slightly improve accuracy and response to selection, but requires that the pedigree is known. It is, therefore, advisable to genotype these CB animals as well. Finally, considering the breed-origin of alleles allows for modeling breed-specific effects in the CB, but this did not always lead to higher accuracies. Our review shows that the differences in accuracy and response to selection between strategies depend on several factors. One of the most important factors is rpc, and we, therefore, recommend to obtain accurate estimates of rpc of all breeding goal traits. Furthermore, knowledge about the importance of components of rpc (i.e., dominance, epistasis, and G × E) can help breeders to decide which model to use, and whether to collect data on animals in a CB environment. Future research should focus on the development of a tool that predicts accuracy and response to selection from scenario specific parameters.
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Affiliation(s)
- Pascal Duenk
- Animal Breeding and Genomics, Wageningen University and
Research, P.O. Box 338, 6700 AH Wageningen,
The Netherlands
| | - Piter Bijma
- Animal Breeding and Genomics, Wageningen University and
Research, P.O. Box 338, 6700 AH Wageningen,
The Netherlands
| | - Yvonne C J Wientjes
- Animal Breeding and Genomics, Wageningen University and
Research, P.O. Box 338, 6700 AH Wageningen,
The Netherlands
| | - Mario P L Calus
- Animal Breeding and Genomics, Wageningen University and
Research, P.O. Box 338, 6700 AH Wageningen,
The Netherlands
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