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Wang J, Hua G, Cai G, Ma Y, Yang X, Zhang L, Li R, Liu J, Ma Q, Wu K, Zhao Y, Deng X. Genome-wide DNA methylation and transcriptome analyses reveal the key gene for wool type variation in sheep. J Anim Sci Biotechnol 2023; 14:88. [PMID: 37420295 DOI: 10.1186/s40104-023-00893-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 05/07/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Wool fibers are valuable materials for textile industry. Typical wool fibers are divided into medullated and non-medullated types, with the former generated from primary wool follicles and the latter by either primary or secondary wool follicles. The medullated wool is a common wool type in the ancestors of fine wool sheep before breeding. The fine wool sheep have a non-medullated coat. However, the critical period determining the type of wool follicles is the embryonic stage, which limits the phenotypic observation and variant contrast, making both selection and studies of wool type variation fairly difficult. RESULTS During the breeding of a modern fine (MF) wool sheep population with multiple-ovulation and embryo transfer technique, we serendipitously discovered lambs with ancestral-like coarse (ALC) wool. Whole-genome resequencing confirmed ALC wool lambs as a variant type from the MF wool population. We mapped the significantly associated methylation locus on chromosome 4 by using whole genome bisulfite sequencing signals, and in turn identified the SOSTDC1 gene as exons hypermethylated in ALC wool lambs compare to their half/full sibling MF wool lambs. Transcriptome sequencing found that SOSTDC1 was expressed dozens of times more in ALC wool lamb skin than that of MF and was at the top of all differentially expressed genes. An analogy with the transcriptome of coarse/fine wool breeds revealed that differentially expressed genes and enriched pathways at postnatal lamb stage in ALC/MF were highly similar to those at the embryonic stage in the former. Further experiments validated that the SOSTDC1 gene was specifically highly expressed in the nucleus of the dermal papilla of primary wool follicles. CONCLUSION In this study, we conducted genome-wide differential methylation site association analysis on differential wool type trait, and located the only CpG locus that strongly associated with primary wool follicle development. Combined with transcriptome analysis, SOSTDC1 was identified as the only gene at this locus that was specifically overexpressed in the primary wool follicle stem cells of ALC wool lamb skin. The discovery of this key gene and its epigenetic regulation contributes to understanding the domestication and breeding of fine wool sheep.
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Affiliation(s)
- Jiankui Wang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Guoying Hua
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Ganxian Cai
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yuhao Ma
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xue Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Letian Zhang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Rui Li
- Jinfeng Animal Husbandry Group Co., Ltd., Chifeng, 024000, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qing Ma
- Animal Science Institute of Ningxia Agriculture and Forestry Academy, Yinchuan, 750002, China
| | - Keliang Wu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Yaofeng Zhao
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Xuemei Deng
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & Beijing Key Laboratory for Animal Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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Talukdar FR, Escobar Marcillo DI, Laskar RS, Novoloaca A, Cuenin C, Sbraccia P, Nisticò L, Guglielmi V, Gheit T, Tommasino M, Dogliotti E, Fortini P, Herceg Z. Bariatric surgery-induced weight loss and associated genome-wide DNA-methylation alterations in obese individuals. Clin Epigenetics 2022; 14:176. [PMID: 36528638 PMCID: PMC9759858 DOI: 10.1186/s13148-022-01401-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Obesity is a multifactorial and chronic condition of growing universal concern. It has recently been reported that bariatric surgery is a more successful treatment for severe obesity than other noninvasive interventions, resulting in rapid significant weight loss and associated chronic disease remission. The identification of distinct epigenetic patterns in patients who are obese or have metabolic imbalances has suggested a potential role for epigenetic alterations in causal or mediating pathways in the development of obesity-related pathologies. Specific changes in the epigenome (DNA methylome), associated with metabolic disorders, can be detected in the blood. We investigated whether such epigenetic changes are reversible after weight loss using genome-wide DNA methylome analysis of blood samples from individuals with severe obesity (mean BMI ~ 45) undergoing bariatric surgery. RESULTS Our analysis revealed 41 significant (Bonferroni p < 0.05) and 1169 (false discovery rate p < 0.05) suggestive differentially methylated positions (DMPs) associated with weight loss due to bariatric surgery. Among the 41 significant DMPs, 5 CpGs were replicated in an independent cohort of BMI-discordant monozygotic twins (the heavier twin underwent diet-induced weight loss). The effect sizes of these 5 CpGs were consistent across discovery and replication sets (p < 0.05). We also identified 192 differentially methylated regions (DMRs) among which SMAD6 and PFKFB3 genes were the top hypermethylated and hypomethylated regions, respectively. Pathway enrichment analysis of the DMR-associated genes showed that functional pathways related to immune function and type 1 diabetes were significant. Weight loss due to bariatric surgery also significantly decelerated epigenetic age 12 months after the intervention (mean = - 4.29; p = 0.02). CONCLUSIONS We identified weight loss-associated DNA-methylation alterations targeting immune and inflammatory gene pathways in blood samples from bariatric-surgery patients. The top hits were replicated in samples from an independent cohort of BMI-discordant monozygotic twins following a hypocaloric diet. Energy restriction and bariatric surgery thus share CpGs that may represent early indicators of response to the metabolic effects of weight loss. The analysis of bariatric surgery-associated DMRs suggests that epigenetic regulation of genes involved in endothelial and adipose tissue function is key in the pathophysiology of obesity.
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Affiliation(s)
- Fazlur Rahman Talukdar
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - David Israel Escobar Marcillo
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Ruhina Shirin Laskar
- Nutrition and Metabolism Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | - Paolo Sbraccia
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lorenza Nisticò
- Centre for Behavioral Sciences and Mental Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Valeria Guglielmi
- Obesity Center-Internal Medicine Unit, Department of Systems Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Tarik Gheit
- Early Detection, Prevention, and Infections Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
| | | | - Eugenia Dogliotti
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Paola Fortini
- Section of Mechanisms, Biomarkers and Models, Dept Environment and Health, Istituto Superiore Di Sanità, Viale Regina Elena, No. 299, 00161 Rome, Italy
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research On Cancer (IARC), 150 Cours Albert Thomas, Lyon, France
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Inaba Y, Iwamoto S, Nakayama K. Genome-wide DNA methylation status of Mongolians exhibits signs of cellular stress response related to their nomadic lifestyle. J Physiol Anthropol 2022; 41:30. [PMID: 35986394 PMCID: PMC9388360 DOI: 10.1186/s40101-022-00305-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/10/2022] [Indexed: 11/29/2022] Open
Abstract
Background Epigenetics is crucial for connecting environmental stresses with physiological responses in humans. Mongolia, where nomadic livestock pastoralism has been the primal livelihood, has a higher prevalence of various chronic diseases than the surrounding East Asian regions, which are more suitable for crop farming. The genes related to dietary stress and pathogenesis of related disorders may have varying epigenetic statuses among the human populations with diverse dietary cultures. Hence, to understand such epigenetic differences, we conducted a comparative analysis of genome-wide DNA methylation of Mongolians and crop-farming East Asians. Methods Genome-wide DNA methylation status of peripheral blood cells (PBCs) from 23 Mongolian adults and 24 Thai adults was determined using the Infinium Human Methylation 450K arrays and analyzed in combination with previously published 450K data of 20 Japanese and 8 Chinese adults. CpG sites/regions differentially methylated between Mongolians and crop-farming East Asians were detected using a linear model adjusted for sex, age, ethnicity, and immune cell heterogeneity on RnBeads software. Results Of the quality-controlled 389,454 autosomal CpG sites, 223 CpG sites were significantly differentially methylated among Mongolians and the four crop farming East Asian populations (false discovery rate < 0.05). Analyses focused on gene promoter regions revealed that PM20D1 (peptidase M20 domain containing 1), which is involved in mitochondrial uncoupling and various processes, including cellular protection from reactive oxygen species (ROS) and thermogenesis, was the top differentially methylated gene. Moreover, gene ontology enrichment analysis revealed that biological processes related to ROS metabolism were overrepresented among the top 1% differentially methylated genes. The promoter regions of these genes were generally hypermethylated in Mongolians, suggesting that the metabolic pathway detoxifying ROS might be globally suppressed in Mongolians, resulting in the high susceptibility of this population to various chronic diseases. Conclusions This study showed a significantly diverse DNA methylation status among Mongolians and crop-farming East Asians. Further, we found an association between the differentially methylated genes and various metabolic and neurodegenerative diseases. Knowledge of the epigenetic regulators might help in proper understanding, treatment, and control of such disorders, and physiological adaptation in the future. Supplementary Information The online version contains supplementary material available at 10.1186/s40101-022-00305-0.
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Rossetti C, Cherix A, Guiraud LF, Cardinaux JR. New Insights Into the Pivotal Role of CREB-Regulated Transcription Coactivator 1 in Depression and Comorbid Obesity. Front Mol Neurosci 2022; 15:810641. [PMID: 35242012 PMCID: PMC8886117 DOI: 10.3389/fnmol.2022.810641] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 01/07/2022] [Indexed: 11/13/2022] Open
Abstract
Depression and obesity are major public health concerns, and there is mounting evidence that they share etiopathophysiological mechanisms. The neurobiological pathways involved in both mood and energy balance regulation are complex, multifactorial and still incompletely understood. As a coactivator of the pleiotropic transcription factor cAMP response element-binding protein (CREB), CREB-regulated transcription coactivator 1 (CRTC1) has recently emerged as a novel regulator of neuronal plasticity and brain functions, while CRTC1 dysfunction has been associated with neurodegenerative and psychiatric diseases. This review focuses on recent evidence emphasizing the critical role of CRTC1 in the neurobiology of depression and comorbid obesity. We discuss the role of CRTC1 downregulation in mediating chronic stress-induced depressive-like behaviors, and antidepressant response in the light of the previously characterized Crtc1 knockout mouse model of depression. The putative role of CRTC1 in the alteration of brain energy homeostasis observed in depression is also discussed. Finally, we highlight rodent and human studies supporting the critical involvement of CRTC1 in depression-associated obesity.
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Affiliation(s)
- Clara Rossetti
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Antoine Cherix
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Laboratory for Functional and Metabolic Imaging (LIFMET), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laetitia F. Guiraud
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Jean-René Cardinaux
- Center for Psychiatric Neuroscience, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Prilly, Switzerland
- Service of Child and Adolescent Psychiatry, Department of Psychiatry, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
- *Correspondence: Jean-René Cardinaux,
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