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Tapia Del Fierro A, den Hamer B, Benetti N, Jansz N, Chen K, Beck T, Vanyai H, Gurzau AD, Daxinger L, Xue S, Ly TTN, Wanigasuriya I, Iminitoff M, Breslin K, Oey H, Krom YD, van der Hoorn D, Bouwman LF, Johanson TM, Ritchie ME, Gouil QA, Reversade B, Prin F, Mohun T, van der Maarel SM, McGlinn E, Murphy JM, Keniry A, de Greef JC, Blewitt ME. SMCHD1 has separable roles in chromatin architecture and gene silencing that could be targeted in disease. Nat Commun 2023; 14:5466. [PMID: 37749075 PMCID: PMC10519958 DOI: 10.1038/s41467-023-40992-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The interplay between 3D chromatin architecture and gene silencing is incompletely understood. Here, we report a novel point mutation in the non-canonical SMC protein SMCHD1 that enhances its silencing capacity at endogenous developmental targets. Moreover, it also results in enhanced silencing at the facioscapulohumeral muscular dystrophy associated macrosatellite-array, D4Z4, resulting in enhanced repression of DUX4 encoded by this repeat. Heightened SMCHD1 silencing perturbs developmental Hox gene activation, causing a homeotic transformation in mice. Paradoxically, the mutant SMCHD1 appears to enhance insulation against other epigenetic regulators, including PRC2 and CTCF, while depleting long range chromatin interactions akin to what is observed in the absence of SMCHD1. These data suggest that SMCHD1's role in long range chromatin interactions is not directly linked to gene silencing or insulating the chromatin, refining the model for how the different levels of SMCHD1-mediated chromatin regulation interact to bring about gene silencing in normal development and disease.
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Affiliation(s)
- Andres Tapia Del Fierro
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bianca den Hamer
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Natalia Benetti
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Natasha Jansz
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelan Chen
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Tamara Beck
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Hannah Vanyai
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Alexandra D Gurzau
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Lucia Daxinger
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Shifeng Xue
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Thanh Thao Nguyen Ly
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
| | - Iromi Wanigasuriya
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Megan Iminitoff
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Kelsey Breslin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Harald Oey
- Queensland Institute of Medical Research, Brisbane, QLD, Australia
| | - Yvonne D Krom
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Dinja van der Hoorn
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Linde F Bouwman
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Timothy M Johanson
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Matthew E Ritchie
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Quentin A Gouil
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Bruno Reversade
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore
- Genome Institute of Singapore, A*STAR, Singapore, Singapore
| | - Fabrice Prin
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | - Timothy Mohun
- Crick Advanced Light Microscopy Facility, The Francis Crick Institute, London, UK
| | | | - Edwina McGlinn
- EMBL Australia, Monash University, Clayton, VIC, Australia
- Australian Regenerative Medicine Institute, Monash University, Clayton, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Andrew Keniry
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Jessica C de Greef
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Marnie E Blewitt
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- The Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.
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2
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Wang X, Li G, Jiang Y, Tang J, Fan Y, Ren J. Genomic insights into the conservation and population genetics of two Chinese native goat breeds. J Anim Sci 2022; 100:skac274. [PMID: 35998083 PMCID: PMC9585554 DOI: 10.1093/jas/skac274] [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: 10/14/2021] [Accepted: 08/20/2022] [Indexed: 11/14/2022] Open
Abstract
Chinese goats are an important group of goats worldwide. However, there are few studies on the conservation priority, genetic relationship, and potential gene flow between Chinese and global goat breeds. Here, we genotyped 239 goats from conservation populations of the Chinese Guangfeng and Ganxi breeds using the GoatSNP50 BeadChip. The conservation priority, population structure, selection signatures and introgression of these goats were analyzed in the context of 36 global goat breeds. First, we showed that Guangfeng and Ganxi goats had the largest effective population sizes across the global breeds 13 generations ago. Nevertheless, Ganxi goats have recently experienced a high degree of inbreeding, resulting in their conservation priority based on total gene and allelic diversities being lower than that of most other Chinese breeds (including Guangfeng goats). Population structure and admixture analyses showed that an average of 18% of Guangfeng genomic components were introgressed from Boer goats approximately 18-yr ago. Next, we reconstructed the subfamily structure of the core populations of Guangfeng and Ganxi goats, and proposed reasonable conservation strategies for inbreeding management. Moreover, a list of candidate genes under selection for fertility, immunity, growth, and meat quality were detected in Guangfeng and Ganxi goats. Finally, we identified some genes related to body development and reproduction, which were introgressed from Boer goats and may be beneficial for improving performance and productivity of Guangfeng goats. In conclusion, this study not only provides new insights into the conservation and utilization of Guangfeng and Ganxi goats but also enriches our understanding of artificial introgression from exotic goats into Chinese local goats.
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Affiliation(s)
- Xiaopeng Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Guixin Li
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yongchuang Jiang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jianhong Tang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
- Laboratory Animal Engineering Research Center of Ganzhou, Gannan Medical University, Ganzhou 341000, China
| | - Yin Fan
- Department of Animal Science, Jiangxi Biotech Vocational College, Nanchang 330200, China
| | - Jun Ren
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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3
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Spoormakers TJP, Veraa S, Graat EAM, van Weeren PR, Brommer H. A comparative study of breed differences in the anatomical configuration of the equine vertebral column. J Anat 2021; 239:829-838. [PMID: 33991425 PMCID: PMC8450477 DOI: 10.1111/joa.13456] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/28/2021] [Accepted: 04/28/2021] [Indexed: 12/18/2022] Open
Abstract
The importance of the equine thoracolumbar vertebral column in orthopaedic disorders is well recognized and diagnostic imaging becomes more feasible, but little is known about variations in the anatomical configuration within breeds. In this descriptive post-mortem study, anatomical variations in three widely differing breeds: Warmblood horses, Shetland ponies and semi-feral Konik horses are described. The caudal cervical (C), thoracic (T), lumbar (L) and sacral (S) regions of the vertebral column of 30 Warmblood horses, 29 Shetland ponies and 18 Konik horses were examined using computed tomography and visualized by volume rendering. Homologous/morphologic variations in the caudal cervical area were frequently seen in Warmblood horses (43%), which was significantly more than in the other breeds (p < 0.001). The as standard described equine formula of 18 T, 6 L and 5 S vertebrae was seen in 78% of Konik horses, but only in 53% Warmblood horses and 38% Shetland ponies, which was significantly different (p < 0.05). Overall, Shetland ponies showed a higher tendency of thoracoization, lumbarization and more variations in the number of vertebrae and pairs of ribs. Ankylosed intertransverse joints (ITJs) between transverse processes of the lumbar vertebrae were most common between the second last and last lumbar vertebra and prevalence was significantly higher in Shetland ponies (61%), than in Warmblood horses (38%) and Konik horses (7%) (p < 0.0001). Cranial to the second last lumbar vertebra there were fewer ITJs ankylosed (14%) in Warmblood horses (p < 0.0095), and this decrease in number of ankylosed ITJs was different compared to the change in ankylosed ITJs in Shetland ponies (p < 0.005). ITJs occurred asymmetrically in 15% (12/77) of the cases. A limitation of the study was that clinical data of the horses were only incompletely available, precluding any conclusions about the potential clinical implications of anatomical variations. Knowledge of variation in osseous anatomy of the equine thoracolumbar vertebral column is important for the interpretation of diagnostic imaging. To assess the functional importance and clinical relevance of this variation, follow-up studies are necessary.
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Affiliation(s)
- Tijn Jan Pieter Spoormakers
- Department of Clinical Sciences, Equine Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Stefanie Veraa
- Department of Clinical Sciences, Division of Diagnostic Imaging, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Elisabeth Anna Maria Graat
- Department of Animal Sciences, Adaptation Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Paul René van Weeren
- Department of Clinical Sciences, Equine Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Harold Brommer
- Department of Clinical Sciences, Equine Division, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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4
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Shao L, Zhang Y, Gong X, Dong Z, Wei W, Sun H, Sun R, Cong L, Cong X, Jin S. Effects of MLL5 and HOXA regulated by NRP1 on radioresistance in A549. Oncol Lett 2021; 21:403. [PMID: 33777226 PMCID: PMC7988706 DOI: 10.3892/ol.2021.12664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 02/02/2021] [Indexed: 12/17/2022] Open
Abstract
Radiotherapy is widely used in the management of lung cancer, and physicians are aware that the effect of radiotherapy is dependent on radiosensitivity. Although a series of blockers and activators targeting molecules related to radioresistance have been developed as radiation sensitizers, compensatory mechanisms or drug resistance limits their clinical efficacy. The identification of a key molecule related to lung cancer cell radioresistance or an effective molecular target is a challenging but important problem in radiation oncology. A previous study found that neuropilin 1 (NRP1) is related to radioresistance in A549 cells and is associated with VEGF, PI3K-Akt, MAPK-ERK, P38, NF-κβ and TGF-β. Inhibition of NRP1 can increase the radiosensitivity of A549 cells. Therefore, NRP1 may be a molecular target for radiotherapy-sensitizing drugs in lung cancer. The present study investigated the key downstream genes of NRP1, verified their regulation and clarified their roles in regulating lung cancer radioresistance. NRP1 positively regulated the downstream homeobox genes (HOXs) HOXA6, HOXA9 and mixed lineage leukaemia 5 (MLL5) in addition to MLL5-regulated HOXA6 and HOXA9, but these genes did not regulate NRP1. MLL5, HOXA6 and HOXA9 levels were decreased in tumour tissues and positively correlated with NRP1. All of these genes were induced by ionizing radiation in vivo and in vitro. NRP1 expression was significantly lower in squamous cell carcinoma compared with that in adenocarcinoma, and lymph node metastasis occurred more often in patients with lung cancer with high MLL5 and NRP1 expression compared with patients with low MLL5 and NRP1 expression. Collectively, these data confirmed that NRP1 is associated with MLL5 and regulates radioresistance through HOXA6 and HOXA9.
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Affiliation(s)
- Lihong Shao
- National Health Commission Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, Jilin 130000, P.R. China.,Department of Radiation Oncology and Therapy, Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Yuyu Zhang
- National Health Commission Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, Jilin 130000, P.R. China.,Department of Radiation Oncology and Therapy, Jilin Provincial Key Laboratory of Radiation Oncology and Therapy, The First Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Xinkou Gong
- Department Radiology, 2nd Hospital Affiliated to Jilin University, Changchun, Jilin 130000, P.R. China
| | - Zhuo Dong
- National Health Commission Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, Jilin 130000, P.R. China
| | - Wei Wei
- National Health Commission Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, Jilin 130000, P.R. China
| | - Hongyan Sun
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Ran Sun
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Lele Cong
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Xianling Cong
- Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130000, P.R. China
| | - Shunzi Jin
- National Health Commission Key Laboratory of Radiobiology, School of Public Health, Jilin University, Changchun, Jilin 130000, P.R. China
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5
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Villamil CI. Phenotypic integration of the cervical vertebrae in the Hominoidea (Primates). Evolution 2018; 72:490-517. [DOI: 10.1111/evo.13433] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/30/2022]
Affiliation(s)
- Catalina I. Villamil
- Department of Anthropology; Dickinson College; P.O. Box 1773 Carlisle Pennsylvania 17013
- Center for the Study of Human Origins, Department of Anthropology; New York University; 25 Waverly Place New York New York 10003
- New York Consortium in Evolutionary Primatology; New York New York 10024
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6
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Naruse C, Shibata S, Tamura M, Kawaguchi T, Abe K, Sugihara K, Kato T, Nishiuchi T, Wakana S, Ikawa M, Asano M. New insights into the role of Jmjd3 and Utx in axial skeletal formation in mice. FASEB J 2017; 31:2252-2266. [PMID: 28188179 DOI: 10.1096/fj.201600642r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Jmjd3 and Utx are demethylases specific for lysine 27 of histone H3. Previous reports indicate that Jmjd3 is essential for differentiation of various cell types, such as macrophages and epidermal cells in mice, whereas Utx is involved in cancer and developmental diseases in humans and mice, as well as Hox regulation in zebrafish and nematodes. Here, we report that Jmjd3, but not Utx, is involved in axial skeletal formation in mice. A Jmjd3 mutant embryo (Jmjd3Δ18/Δ18), but not a catalytically inactive Utx truncation mutant (Utx-/y), showed anterior homeotic transformation. Quantitative RT-PCR and microarray analyses showed reduced Hox expression in both Jmjd3Δ18/Δ18 embryos and tailbuds, whereas levels of Hox activators, such as Wnt signaling factors and retinoic acid synthases, did not decrease, which suggests that Jmjd3 plays a regulatory role in Hox expression during axial patterning. Chromatin immunoprecipitation analyses of embryo tailbud tissue showed trimethylated lysine 27 on histone H3 to be at higher levels at the Hox loci in Jmjd3Δ18/Δ18 mutants compared with wild-type tailbuds. In contrast, trimethylated lysine 4 on histone H3 levels were found to be equivalent in wild-type and Jmjd3Δ18/Δ18 tailbuds. Demethylase-inactive Jmjd3 mutant embryos showed the same phenotype as Jmjd3Δ18/Δ18 mice. These results suggest that the demethylase activity of Jmjd3, but not that of Utx, affects mouse axial patterning in concert with alterations in Hox gene expression.-Naruse, C., Shibata, S., Tamura, M., Kawaguchi, T., Abe, K., Sugihara, K., Kato, T., Nishiuchi, T., Wakana, S., Ikawa, M., Asano, M. New insights into the role of Jmjd3 and Utx in axial skeletal formation in mice.
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Affiliation(s)
- Chie Naruse
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shinwa Shibata
- Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Masaru Tamura
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Takayuki Kawaguchi
- Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Kanae Abe
- Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Kazushi Sugihara
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Tomoaki Kato
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Takumi Nishiuchi
- Division of Functional Genomics, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
| | - Shigeharu Wakana
- Technology and Development Team for Mouse Phenotype Analysis, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Masahito Ikawa
- Animal Resource Center for Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Masahide Asano
- Institute of Laboratory Animals, Graduate School of Medicine, Kyoto University, Kyoto, Japan; .,Division of Transgenic Animal Science, Advanced Science Research Center, Kanazawa University, Kanazawa, Japan
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Kappen C. Folate supplementation in three genetic models: implications for understanding folate-dependent developmental pathways. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2005; 135C:24-30. [PMID: 15800896 PMCID: PMC3938158 DOI: 10.1002/ajmg.c.30050] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Supplementation of a pregnant mother's diet with folate has been shown to protect the developing embryo from birth defects in humans as well as rodent animal models. Folate supplementation not only reverses a potential nutritional deficiency; folate effectively prevents defects even when the mother's nutritional status is normal. These findings indicate that folate is able to interact with the molecular pathways that control normal embryonic development. Supplementation studies in animals provide the experimental starting point for the identification of such folate-responsive pathways. This review summarizes the progress to date in understanding the folate response in genetic models of birth defects in the mouse.
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Affiliation(s)
- Claudia Kappen
- Department of Genetics, Cell Biology and Anatomy, Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha 68198-5455, USA.
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