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Zhu YL, Meng LL, Ma JH, Yuan X, Chen SW, Yi XR, Li XY, Wang Y, Tang YS, Xue M, Zhu MZ, Peng J, Lu XJ, Huang JZ, Song ZC, Wu C, Zheng KZ, Dai QQ, Huang F, Fang HS. Loss of LBP triggers lipid metabolic disorder through H3K27 acetylation-mediated C/EBPβ- SCD activation in non-alcoholic fatty liver disease. Zool Res 2024; 45:79-94. [PMID: 38114435 PMCID: PMC10839665 DOI: 10.24272/j.issn.2095-8137.2023.022] [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: 05/21/2023] [Accepted: 08/24/2023] [Indexed: 12/21/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is associated with mutations in lipopolysaccharide-binding protein ( LBP), but the underlying epigenetic mechanisms remain understudied. Herein, LBP -/- rats with NAFLD were established and used to conduct integrative targeting-active enhancer histone H3 lysine 27 acetylation (H3K27ac) chromatin immunoprecipitation coupled with high-throughput and transcriptomic sequencing analysis to explore the potential epigenetic pathomechanisms of active enhancers of NAFLD exacerbation upon LBP deficiency. Notably, LBP -/- reduced the inflammatory response but markedly aggravated high-fat diet (HFD)-induced NAFLD in rats, with pronounced alterations in the histone acetylome and regulatory transcriptome. In total, 1 128 differential enhancer-target genes significantly enriched in cholesterol and fatty acid metabolism were identified between wild-type (WT) and LBP -/- NAFLD rats. Based on integrative analysis, CCAAT/enhancer-binding protein β (C/EBPβ) was identified as a pivotal transcription factor (TF) and contributor to dysregulated histone acetylome H3K27ac, and the lipid metabolism gene SCD was identified as a downstream effector exacerbating NAFLD. This study not only broadens our understanding of the essential role of LBP in the pathogenesis of NAFLD from an epigenetics perspective but also identifies key TF C/EBPβ and functional gene SCD as potential regulators and therapeutic targets.
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Affiliation(s)
- Ya-Ling Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
- Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Lei-Lei Meng
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jin-Hu Ma
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xin Yuan
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Shu-Wen Chen
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xin-Rui Yi
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xin-Yu Li
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yi Wang
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Yun-Shu Tang
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
- Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Min Xue
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Mei-Zi Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jin Peng
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xue-Jin Lu
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Jian-Zhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Zi-Chen Song
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chong Wu
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
| | - Ke-Zhong Zheng
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Qing-Qing Dai
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Fan Huang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China. E-mail:
| | - Hao-Shu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, Anhui 230032, China
- Laboratory Animal Research Center, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China. E-mail:
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2
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Ma J, You D, Chen S, Fang N, Yi X, Wang Y, Lu X, Li X, Zhu M, Xue M, Tang Y, Wei X, Huang J, Zhu Y. Epigenetic association study uncovered H3K27 acetylation enhancers and dysregulated genes in high-fat-diet-induced nonalcoholic fatty liver disease in rats. Epigenomics 2022; 14:1523-1540. [PMID: 36851897 DOI: 10.2217/epi-2022-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Aim: To evaluate the regulatory landscape underlying the active enhancer marked by H3K27ac in high-fat diet (HFD)-induced nonalcoholic fatty liver disease (NAFLD) in rats. Materials & methods: H3K27ac chromatin immunoprecipitation and high-throughput RNA sequencing to construct regulatory profiles and transcriptome of liver from NAFLD rat model induced by HFD. De novo motif analysis for differential H3K27ac peaks. Functional enrichment, Kyoto Encyclopedia of Genes and Genomes pathway and protein-protein interaction network were examined for differential peak-genes. The mechanism was further verified by western blot, chromatin immunoprecipitation-quantitative PCR and real-time PCR. Results: A total of 1831 differential H3K27ac peaks were identified significantly correlating with transcription factors and target genes (CYP8B1, PLA2G12B, SLC27A5, CYP7A1 and APOC3) involved in lipid and energy homeostasis. Conclusion: Altered acetylation induced by HFD leads to the dysregulation of gene expression, further elucidating the epigenetic mechanism in the etiology of NAFLD.
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Affiliation(s)
- Jinhu Ma
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Dandan You
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Shuwen Chen
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Nana Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xinrui Yi
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Yi Wang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xuejin Lu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xinyu Li
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Meizi Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Min Xue
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Yunshu Tang
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Xiaohui Wei
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
| | - Jianzhen Huang
- College of Animal Science & Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yaling Zhu
- Department of Pathophysiology, Anhui Medical University, Hefei, 230032, China
- Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, 230032, China
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3
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Acosta-Rodríguez V, Rijo-Ferreira F, Izumo M, Xu P, Wight-Carter M, Green CB, Takahashi JS. Circadian alignment of early onset caloric restriction promotes longevity in male C57BL/6J mice. Science 2022; 376:1192-1202. [PMID: 35511946 PMCID: PMC9262309 DOI: 10.1126/science.abk0297] [Citation(s) in RCA: 139] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Caloric restriction (CR) prolongs lifespan, yet the mechanisms by which it does so remain poorly understood. Under CR, mice self-impose chronic cycles of 2-hour-feeding and 22-hour-fasting, raising the question whether calories, fasting, or time of day are causal. We show that 30%-CR is sufficient to extend lifespan 10%; however, a daily fasting interval and circadian-alignment of feeding act together to extend lifespan 35% in male C57BL/6J mice. These effects are independent of body weight. Aging induces widespread increases in gene expression associated with inflammation and decreases in expression of genes encoding components of metabolic pathways in liver from ad lib fed mice. CR at night ameliorates these aging-related changes. Thus, circadian interventions promote longevity and provide a perspective to further explore mechanisms of aging. Timed caloric restriction at night enhances longevity.
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Affiliation(s)
- Victoria Acosta-Rodríguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Filipa Rijo-Ferreira
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mariko Izumo
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Pin Xu
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Mary Wight-Carter
- Animal Resources Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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4
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Toriumi K, Berto S, Koike S, Usui N, Dan T, Suzuki K, Miyashita M, Horiuchi Y, Yoshikawa A, Asakura M, Nagahama K, Lin HC, Sugaya Y, Watanabe T, Kano M, Ogasawara Y, Miyata T, Itokawa M, Konopka G, Arai M. Combined glyoxalase 1 dysfunction and vitamin B6 deficiency in a schizophrenia model system causes mitochondrial dysfunction in the prefrontal cortex. Redox Biol 2021; 45:102057. [PMID: 34198071 PMCID: PMC8253914 DOI: 10.1016/j.redox.2021.102057] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Methylglyoxal (MG) is a reactive and cytotoxic α-dicarbonyl byproduct of glycolysis. Our bodies have several bio-defense systems to detoxify MG, including an enzymatic system by glyoxalase (GLO) 1 and GLO2. We identified a subtype of schizophrenia patients with novel mutations in the GLO1 gene that results in reductions of enzymatic activity. Moreover, we found that vitamin B6 (VB6) levels in peripheral blood of the schizophrenia patients with GLO1 dysfunction are significantly lower than that of healthy controls. However, the effects of GLO1 dysfunction and VB6 deficiency on the pathophysiology of schizophrenia remains poorly understood. Here, we generated a novel mouse model for this subgroup of schizophrenia patients by feeding Glo1 knockout mice VB6-deficent diets (KO/VB6(−)) and evaluated the combined effects of GLO1 dysfunction and VB6 deficiency on brain function. KO/VB6(−) mice accumulated homocysteine in plasma and MG in the prefrontal cortex (PFC), hippocampus, and striatum, and displayed behavioral deficits, such as impairments of social interaction and cognitive memory and a sensorimotor deficit in the prepulse inhibition test. Furthermore, we found aberrant gene expression related to mitochondria function in the PFC of the KO/VB6(−) mice by RNA-sequencing and weighted gene co-expression network analysis (WGCNA). Finally, we demonstrated abnormal mitochondrial respiratory function and subsequently enhanced oxidative stress in the PFC of KO/VB6(−) mice in the PFC. These findings suggest that the combination of GLO1 dysfunction and VB6 deficiency may cause the observed behavioral deficits via mitochondrial dysfunction and oxidative stress in the PFC. A combination of Glo1 KO and VB6 deficiency induces MG accumulation in the brain. Glo1 KO/VB6(−) mice exhibit schizophrenia-like behavioral deficits. Gene expression related to mitochondria is impaired in the PFC of the Glo1 KO/VB6(−). Mitochondria in the PFC of the Glo1 KO/VB6(−) mice show respiratory dysfunction. Oxidative stress is enhanced in the PFC of the Glo1 KO/VB6(−).
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Affiliation(s)
- Kazuya Toriumi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29403, USA
| | - Shin Koike
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA; Center for Medical Research and Education, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Department of Neuroscience and Cell Biology, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan; Global Center for Medical Engineering and Informatics, Osaka University, Osaka, 565-0871, Japan
| | - Takashi Dan
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Kazuhiro Suzuki
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry, Graduate School of Medicine, Shinshu University, Nagano, 390-8621, Japan
| | - Mitsuhiro Miyashita
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Yasue Horiuchi
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Akane Yoshikawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan; Department of Psychiatry and Behavioral Science, Graduate School of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Mai Asakura
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Kenichiro Nagahama
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hsiao-Chun Lin
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Sugaya
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Takaki Watanabe
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
| | - Yuki Ogasawara
- Department of Analytical Biochemistry, Meiji Pharmaceutical University, Tokyo 204-8588, Japan
| | - Toshio Miyata
- Division of Molecular Medicine and Therapy, Tohoku University Graduate School of Medicine, Sendai, 980-8575, Japan
| | - Masanari Itokawa
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390-9111, USA
| | - Makoto Arai
- Schizophrenia Research Project, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, 156-8506, Japan.
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5
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Lu Y, Liu B, Ma J, Yang S, Huang J. Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation. Front Genet 2021; 12:664334. [PMID: 33859677 PMCID: PMC8042274 DOI: 10.3389/fgene.2021.664334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 03/09/2021] [Indexed: 11/15/2022] Open
Abstract
Inadequate sleep prevails in modern society and it impairs the circadian transcriptome. However, to what extent acute sleep deprivation (SD) has impact on the circadian rhythms of peripheral tissues is not clear. Here, we show that in mouse lung, a 10-h acute sleep deprivation can alter the circadian expression of approximately 3,000 genes. We found that circadian rhythm disappears in genes related to metabolism and signaling pathways regulating protein phosphorylation after acute sleep deprivation, while the core circadian regulators do not change much in rhythmicity. Importantly, the strong positive correlation between mean expression and amplitude (E-A correlation) of cycling genes has been validated in both control and sleep deprivation conditions, supporting the energetic cost optimization model of circadian gene expression. Thus, we reveal that acute sleep deprivation leads to a profound change in the circadian gene transcription that influences the biological functions in lung.
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Affiliation(s)
- Yuntao Lu
- Department of Pulmonary and Critical Care Medicine, Huadong Hospital, Fudan University, Shanghai, China
| | - Bing Liu
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Junjie Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuo Yang
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ju Huang
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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6
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Gene-expression correlates of the oscillatory signatures supporting human episodic memory encoding. Nat Neurosci 2021; 24:554-564. [PMID: 33686299 PMCID: PMC8016736 DOI: 10.1038/s41593-021-00803-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/19/2021] [Indexed: 12/13/2022]
Abstract
In humans, brain oscillations support critical features of memory formation. However, understanding the molecular mechanisms underlying this activity remains a major challenge. Here, we measured memory-sensitive oscillations using intracranial electroencephalography recordings from the temporal cortex of patients performing an episodic memory task. When these patients subsequently underwent resection, we employed transcriptomics on the temporal cortex to link gene expression with brain oscillations and identified genes correlated with oscillatory signatures of memory formation across six frequency bands. A co-expression analysis isolated oscillatory signature-specific modules associated with neuropsychiatric disorders and ion channel activity, with highly correlated genes exhibiting strong connectivity within these modules. Using single-nucleus transcriptomics, we further revealed that these modules are enriched for specific classes of both excitatory and inhibitory neurons, and immunohistochemistry confirmed expression of highly correlated genes. This unprecedented dataset of patient-specific brain oscillations coupled to genomics unlocks new insights into the genetic mechanisms that support memory encoding.
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7
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Zhu Y, Zeng Q, Li F, Fang H, Zhou Z, Jiang T, Yin C, Wei Q, Wang Y, Ruan J, Huang J. Dysregulated H3K27 Acetylation Is Implicated in Fatty Liver Hemorrhagic Syndrome in Chickens. Front Genet 2021; 11:574167. [PMID: 33505421 PMCID: PMC7831272 DOI: 10.3389/fgene.2020.574167] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/23/2020] [Indexed: 12/29/2022] Open
Abstract
Epigenetic regulation of gene expression has been reported in the pathogenesis of metabolic disorders such as diabetes and liver steatosis in humans. However, the molecular mechanisms of fatty liver hemorrhagic syndrome (FLHS) in chickens have been rarely studied. H3K27ac chromatin immunoprecipitation coupled with high-throughput sequencing and high-throughput RNA sequencing was performed to compare genome-wide H3K27ac profiles and transcriptomes of liver tissue between healthy and FLHS chickens. In total, 1,321 differential H3K27ac regions and 443 differentially expressed genes were identified (| log2Fold change| ≥ 1 and P-value ≤ 0.05) between the two groups. Binding motifs for transcription factors involved in immune processes and metabolic homeostasis were enriched among those differential H3K27ac regions. Differential H3K27ac peaks were associated with multiple known FLHS risk genes, involved in lipid and energy metabolism (PCK1, APOA1, ANGPTL4, and FABP1) and the immune system (FGF7, PDGFRA, and KIT). Previous studies and our current results suggested that the high-energy, low-protein (HELP) diet might have an impact on histone modification and chromatin structure, leading to the dysregulation of candidate genes and the peroxisome proliferator-activated receptor (PPAR) signaling pathway, which causes excessive accumulation of fat in the liver tissue and induces the development of FLHS. These findings highlight that epigenetic modifications contribute to the regulation of gene expression and play a central regulatory role in FLHS. The PPAR signaling pathway and other genes implicated in FLHS are of great importance for the development of novel and specific therapies for FLHS-susceptible commercial laying hens.
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Affiliation(s)
- Yaling Zhu
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China.,Department of Pathophysiology, Anhui Medical University, Hefei, China.,Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Qingjie Zeng
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Fang Li
- Department of Pathophysiology, Anhui Medical University, Hefei, China
| | - Haoshu Fang
- Department of Pathophysiology, Anhui Medical University, Hefei, China.,Laboratory Animal Research Center, College of Basic Medical Science, Anhui Medical University, Hefei, China
| | - Zhimin Zhou
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Tao Jiang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Chao Yin
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Qing Wei
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yujie Wang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jiming Ruan
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jianzhen Huang
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, China
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8
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Conboy K, Henshall DC, Brennan GP. Epigenetic principles underlying epileptogenesis and epilepsy syndromes. Neurobiol Dis 2020; 148:105179. [PMID: 33181318 DOI: 10.1016/j.nbd.2020.105179] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/06/2020] [Accepted: 11/08/2020] [Indexed: 12/21/2022] Open
Abstract
Epilepsy is a network disorder driven by fundamental changes in the function of the cells which compose these networks. Driving this aberrant cellular function are large scale changes in gene expression and gene expression regulation. Recent studies have revealed rapid and persistent changes in epigenetic control of gene expression as a critical regulator of the epileptic transcriptome. Epigenetic-mediated gene output regulates many aspects of cellular physiology including neuronal structure, neurotransmitter assembly and abundance, protein abundance of ion channels and other critical neuronal processes. Thus, understanding the contribution of epigenetic-mediated gene regulation could illuminate novel regulatory mechanisms which may form the basis of novel therapeutic approaches to treat epilepsy. In this review we discuss the effects of epileptogenic brain insults on epigenetic regulation of gene expression, recent efforts to target epigenetic processes to block epileptogenesis and the prospects of an epigenetic-based therapy for epilepsy, and finally we discuss technological advancements which have facilitated the interrogation of the epigenome.
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Affiliation(s)
- Karen Conboy
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland
| | - David C Henshall
- Department of Physiology and Medical Physics, RCSI University of Medicine and Health Sciences, Dublin, Ireland; FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland.
| | - Gary P Brennan
- FutureNeuro, the SFI Research Centre for Chronic and Rare Neurological Diseases, RCSI University of Medicine and Health Sciences, Dublin, Ireland; School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Dublin, Ireland
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9
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Hesse J, Malhan D, Yalҫin M, Aboumanify O, Basti A, Relógio A. An Optimal Time for Treatment-Predicting Circadian Time by Machine Learning and Mathematical Modelling. Cancers (Basel) 2020; 12:cancers12113103. [PMID: 33114254 PMCID: PMC7690897 DOI: 10.3390/cancers12113103] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/15/2020] [Accepted: 10/20/2020] [Indexed: 02/07/2023] Open
Abstract
Tailoring medical interventions to a particular patient and pathology has been termed personalized medicine. The outcome of cancer treatments is improved when the intervention is timed in accordance with the patient's internal time. Yet, one challenge of personalized medicine is how to consider the biological time of the patient. Prerequisite for this so-called chronotherapy is an accurate characterization of the internal circadian time of the patient. As an alternative to time-consuming measurements in a sleep-laboratory, recent studies in chronobiology predict circadian time by applying machine learning approaches and mathematical modelling to easier accessible observables such as gene expression. Embedding these results into the mathematical dynamics between clock and cancer in mammals, we review the precision of predictions and the potential usage with respect to cancer treatment and discuss whether the patient's internal time and circadian observables, may provide an additional indication for individualized treatment timing. Besides the health improvement, timing treatment may imply financial advantages, by ameliorating side effects of treatments, thus reducing costs. Summarizing the advances of recent years, this review brings together the current clinical standard for measuring biological time, the general assessment of circadian rhythmicity, the usage of rhythmic variables to predict biological time and models of circadian rhythmicity.
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Affiliation(s)
- Janina Hesse
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Deeksha Malhan
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Müge Yalҫin
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Ouda Aboumanify
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Alireza Basti
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany; (J.H.); (D.M.); (M.Y.); (O.A.); (A.B.)
- Molecular Cancer Research Center (MKFZ), Medical Department of Hematology, Oncology and Tumor Immunology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin Humboldt—Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Department of Human Medicine, Institute for Systems Medicine and Bioinformatics, MSH Medical School Hamburg—University of Applied Sciences and Medical University, 20457 Hamburg, Germany
- Correspondence: or
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10
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Li Y, Shan Y, Kilaru GK, Berto S, Wang GZ, Cox KH, Yoo SH, Yang S, Konopka G, Takahashi JS. Epigenetic inheritance of circadian period in clonal cells. eLife 2020; 9:54186. [PMID: 32459177 PMCID: PMC7289596 DOI: 10.7554/elife.54186] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
Circadian oscillations are generated via transcriptional-translational negative feedback loops. However, individual cells from fibroblast cell lines have heterogeneous rhythms, oscillating independently and with different period lengths. Here we showed that heterogeneity in circadian period is heritable and used a multi-omics approach to investigate underlying mechanisms. By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. We also discovered differentially co-expressed gene networks that were functionally associated with period length. We further demonstrated that global differential DNA methylation bidirectionally regulated these same gene networks. Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. Together, our findings identify novel gene candidates involved in periodicity, and reveal DNA methylation as an important regulator of circadian periodicity.
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Affiliation(s)
- Yan Li
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yongli Shan
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Gokhul Krishna Kilaru
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Stefano Berto
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Guang-Zhong Wang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Kimberly H Cox
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Seung-Hee Yoo
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Shuzhang Yang
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Genevieve Konopka
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, United States.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, United States
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11
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Rijo-Ferreira F, Acosta-Rodriguez VA, Abel JH, Kornblum I, Bento I, Kilaru G, Klerman EB, Mota MM, Takahashi JS. The malaria parasite has an intrinsic clock. Science 2020; 368:746-753. [PMID: 32409471 PMCID: PMC7409452 DOI: 10.1126/science.aba2658] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/11/2020] [Accepted: 04/06/2020] [Indexed: 01/08/2023]
Abstract
Malarial rhythmic fevers are the consequence of the synchronous bursting of red blood cells (RBCs) on completion of the malaria parasite asexual cell cycle. Here, we hypothesized that an intrinsic clock in the parasite Plasmodium chabaudi underlies the 24-hour-based rhythms of RBC bursting in mice. We show that parasite rhythms are flexible and lengthen to match the rhythms of hosts with long circadian periods. We also show that malaria rhythms persist even when host food intake is evenly spread across 24 hours, suggesting that host feeding cues are not required for synchrony. Moreover, we find that the parasite population remains synchronous and rhythmic even in an arrhythmic clock mutant host. Thus, we propose that parasite rhythms are generated by the parasite, possibly to anticipate its circadian environment.
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Affiliation(s)
- Filipa Rijo-Ferreira
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Victoria A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - John H Abel
- Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Izabela Kornblum
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ines Bento
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Gokhul Kilaru
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth B Klerman
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, João Lobo Antunes, Faculdade de Medicina Universidade de Lisboa, Lisbon, Portugal
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
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12
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Abstract
Recent discussions of human brain evolution have largely focused on increased neuron numbers and changes in their connectivity and expression. However, it is increasingly appreciated that oligodendrocytes play important roles in cognitive function and disease. Whether both cell types follow similar or distinctive evolutionary trajectories is not known. We examined the transcriptomes of neurons and oligodendrocytes in the frontal cortex of humans, chimpanzees, and rhesus macaques. We identified human-specific trajectories of gene expression in neurons and oligodendrocytes and show that both cell types exhibit human-specific up-regulation. Moreover, oligodendrocytes have undergone more pronounced accelerated gene expression evolution in the human lineage compared to neurons. We highlighted human-specific coexpression networks with specific functions. Our data suggest that oligodendrocyte human-specific networks are enriched for alternative splicing and transcriptional regulation. Oligodendrocyte networks are also enriched for variants associated with schizophrenia and other neuropsychiatric disorders. Such enrichments were not found in neuronal networks. These results offer a glimpse into the molecular mechanisms of oligodendrocytes during evolution and how such mechanisms are associated with neuropsychiatric disorders.
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13
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O'Callaghan EK, Green EW, Franken P, Mongrain V. Omics Approaches in Sleep-Wake Regulation. Handb Exp Pharmacol 2018; 253:59-81. [PMID: 29796779 DOI: 10.1007/164_2018_125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Although sleep seems an obvious and simple behaviour, it is extremely complex involving numerous interactions both at the neuronal and the molecular levels. While we have gained detailed insight into the molecules and neuronal networks responsible for the circadian organization of sleep and wakefulness, the molecular underpinnings of the homeostatic aspect of sleep regulation are still unknown and the focus of a considerable research effort. In the last 20 years, the development of techniques allowing the simultaneous measurement of hundreds to thousands of molecular targets (i.e. 'omics' approaches) has enabled the unbiased study of the molecular pathways regulated by and regulating sleep. In this chapter, we will review how the different omics approaches, including transcriptomics, epigenomics, proteomics, and metabolomics, have advanced sleep research. We present relevant data in the framework of the two-process model in which circadian and homeostatic processes interact to regulate sleep. The integration of the different omics levels, known as 'systems genetics', will eventually lead to a better understanding of how information flows from the genome, to molecules, to networks, and finally to sleep both in health and disease.
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Affiliation(s)
- Emma K O'Callaghan
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada.,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada
| | - Edward W Green
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Paul Franken
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Valérie Mongrain
- Center for Advanced Research in Sleep Medicine and Research Center, Hôpital du Sacré-Coeur de Montréal, Montreal, QC, Canada. .,Department of Neuroscience, Université de Montréal, Montreal, QC, Canada.
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14
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Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes. Sci Rep 2017; 7:17244. [PMID: 29222512 PMCID: PMC5722905 DOI: 10.1038/s41598-017-17143-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/22/2017] [Indexed: 11/18/2022] Open
Abstract
Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here: http://github.com/DohertyLab/ExRANGES. To install the package type: devtools::install_github(“DohertyLab/ExRANGES”).
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15
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Fontenot MR, Berto S, Liu Y, Werthmann G, Douglas C, Usui N, Gleason K, Tamminga CA, Takahashi JS, Konopka G. Novel transcriptional networks regulated by CLOCK in human neurons. Genes Dev 2017; 31:2121-2135. [PMID: 29196536 PMCID: PMC5749161 DOI: 10.1101/gad.305813.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/07/2017] [Indexed: 01/01/2023]
Abstract
Fontenot et al. show that CLOCK regulates the expression of genes involved in neuronal migration. Dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. The molecular mechanisms underlying human brain evolution are not fully understood; however, previous work suggested that expression of the transcription factor CLOCK in the human cortex might be relevant to human cognition and disease. In this study, we investigated this novel transcriptional role for CLOCK in human neurons by performing chromatin immunoprecipitation sequencing for endogenous CLOCK in adult neocortices and RNA sequencing following CLOCK knockdown in differentiated human neurons in vitro. These data suggested that CLOCK regulates the expression of genes involved in neuronal migration, and a functional assay showed that CLOCK knockdown increased neuronal migratory distance. Furthermore, dysregulation of CLOCK disrupts coexpressed networks of genes implicated in neuropsychiatric disorders, and the expression of these networks is driven by hub genes with human-specific patterns of expression. These data support a role for CLOCK-regulated transcriptional cascades involved in human brain evolution and function.
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Affiliation(s)
- Miles R Fontenot
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Stefano Berto
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yuxiang Liu
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Gordon Werthmann
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Connor Douglas
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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16
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Usui N, Araujo DJ, Kulkarni A, Co M, Ellegood J, Harper M, Toriumi K, Lerch JP, Konopka G. Foxp1 regulation of neonatal vocalizations via cortical development. Genes Dev 2017; 31:2039-2055. [PMID: 29138280 PMCID: PMC5733496 DOI: 10.1101/gad.305037.117] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
Usui et al. show that deletion of Foxp1 in the developing forebrain leads to impairments in neonatal vocalizations as well as neocortical cytoarchitectonic alterations via neuronal positioning and migration. Sumoylation of Foxp1 affects neuronal differentiation and migration in the developing neocortex. The molecular mechanisms driving brain development at risk in autism spectrum disorders (ASDs) remain mostly unknown. Previous studies have implicated the transcription factor FOXP1 in both brain development and ASD pathophysiology. However, the specific molecular pathways both upstream of and downstream from FOXP1 are not fully understood. To elucidate the contribution of FOXP1-mediated signaling to brain development and, in particular, neocortical development, we generated forebrain-specific Foxp1 conditional knockout mice. We show that deletion of Foxp1 in the developing forebrain leads to impairments in neonatal vocalizations as well as neocortical cytoarchitectonic alterations via neuronal positioning and migration. Using a genomics approach, we identified the transcriptional networks regulated by Foxp1 in the developing neocortex and found that such networks are enriched for downstream targets involved in neurogenesis and neuronal migration. We also uncovered mechanistic insight into Foxp1 function by demonstrating that sumoylation of Foxp1 during embryonic brain development is necessary for mediating proper interactions between Foxp1 and the NuRD complex. Furthermore, we demonstrated that sumoylation of Foxp1 affects neuronal differentiation and migration in the developing neocortex. Together, these data provide critical mechanistic insights into the function of FOXP1 in the developing neocortex and may reveal molecular pathways at risk in ASD.
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Affiliation(s)
- Noriyoshi Usui
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Division of Development of Mental Functions, Research Center for Child Mental Development, University of Fukui, Fukui 910-1193, Japan.,Division of Developmental Higher Brain Functions, Department of Child Development, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, and University of Fukui, Osaka 565-0871, Japan
| | - Daniel J Araujo
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Ashwinikumar Kulkarni
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Marissa Co
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Jacob Ellegood
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario M5S 1A1, Canada
| | - Matthew Harper
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Kazuya Toriumi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA.,Project for Schizophrenia Research, Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Jason P Lerch
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario M5S 1A1, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Genevieve Konopka
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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17
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Foxp1 in Forebrain Pyramidal Neurons Controls Gene Expression Required for Spatial Learning and Synaptic Plasticity. J Neurosci 2017; 37:10917-10931. [PMID: 28978667 DOI: 10.1523/jneurosci.1005-17.2017] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 09/12/2017] [Accepted: 09/14/2017] [Indexed: 12/28/2022] Open
Abstract
Genetic perturbations of the transcription factor Forkhead Box P1 (FOXP1) are causative for severe forms of autism spectrum disorder that are often comorbid with intellectual disability. Recent work has begun to reveal an important role for FoxP1 in brain development, but the brain-region-specific contributions of Foxp1 to autism and intellectual disability phenotypes have yet to be determined fully. Here, we describe Foxp1 conditional knock-out (Foxp1cKO) male and female mice with loss of Foxp1 in the pyramidal neurons of the neocortex and the CA1/CA2 subfields of the hippocampus. Foxp1cKO mice exhibit behavioral phenotypes that are of potential relevance to autism spectrum disorder, including hyperactivity, increased anxiety, communication impairments, and decreased sociability. In addition, Foxp1cKO mice have gross deficits in learning and memory tasks of relevance to intellectual disability. Using a genome-wide approach, we identified differentially expressed genes in the hippocampus of Foxp1cKO mice associated with synaptic function and development. Furthermore, using magnetic resonance imaging, we uncovered a significant reduction in the volumes of both the entire hippocampus as well as individual hippocampal subfields of Foxp1cKO mice. Finally, we observed reduced maintenance of LTP in area CA1 of the hippocampus in these mutant mice. Together, these data suggest that proper expression of Foxp1 in the pyramidal neurons of the forebrain is important for regulating gene expression pathways that contribute to specific behaviors reminiscent of those seen in autism and intellectual disability. In particular, Foxp1 regulation of gene expression appears to be crucial for normal hippocampal development, CA1 plasticity, and spatial learning.SIGNIFICANCE STATEMENT Loss-of-function mutations in the transcription factor Forkhead Box P1 (FOXP1) lead to autism spectrum disorder and intellectual disability. Understanding the potential brain-region-specific contributions of FOXP1 to disease-relevant phenotypes could be a critical first step in the management of patients with these mutations. Here, we report that Foxp1 conditional knock-out (Foxp1cKO) mice with loss of Foxp1 in the neocortex and hippocampus display autism and intellectual-disability-relevant behaviors. We also show that these phenotypes correlate with changes in both the genomic and physiological profiles of the hippocampus in Foxp1cKO mice. Our work demonstrates that brain-region-specific FOXP1 expression may relate to distinct, clinically relevant phenotypes.
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18
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Sun L, Jiang Z, Acosta-Rodriguez VA, Berger M, Du X, Choi JH, Wang J, Wang KW, Kilaru GK, Mohawk JA, Quan J, Scott L, Hildebrand S, Li X, Tang M, Zhan X, Murray AR, La Vine D, Moresco EMY, Takahashi JS, Beutler B. HCFC2 is needed for IRF1- and IRF2-dependent Tlr3 transcription and for survival during viral infections. J Exp Med 2017; 214:3263-3277. [PMID: 28970238 PMCID: PMC5679162 DOI: 10.1084/jem.20161630] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 07/13/2017] [Accepted: 08/16/2017] [Indexed: 01/08/2023] Open
Abstract
Sun et al. show that host cell factor C2 (HCFC2) is necessary for basal and induced Tlr3 transcription; deficiency of HCFC2 compromises survival during influenza virus and herpes simplex virus 1 infections in mice. Transcriptional regulation of numerous interferon-regulated genes, including Toll-like receptor 3 (Tlr3), which encodes an innate immune sensor of viral double-stranded RNA, depends on the interferon regulatory factor 1 (IRF1) and IRF2 transcription factors. We detected specific abrogation of macrophage responses to polyinosinic-polycytidylic acid (poly(I:C)) resulting from three independent N-ethyl-N-nitrosourea–induced mutations in host cell factor C2 (Hcfc2). Hcfc2 mutations compromised survival during influenza virus and herpes simplex virus 1 infections. HCFC2 promoted the binding of IRF1 and IRF2 to the Tlr3 promoter, without which inflammatory cytokine and type I IFN responses to the double-stranded RNA analogue poly(I:C) are reduced in mouse macrophages. HCFC2 was also necessary for the transcription of a large subset of other IRF2-dependent interferon-regulated genes. Deleterious mutations of Hcfc2 may therefore increase susceptibility to diverse infectious diseases.
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Affiliation(s)
- Lei Sun
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zhengfan Jiang
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Victoria A Acosta-Rodriguez
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Michael Berger
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Xin Du
- Department of Genetics, The Scripps Research Institute, La Jolla, CA
| | - Jin Huk Choi
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jianhui Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Kuan-Wen Wang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Gokhul K Kilaru
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jennifer A Mohawk
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jiexia Quan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Lindsay Scott
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Sara Hildebrand
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaohong Li
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Miao Tang
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Xiaoming Zhan
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Anne R Murray
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Diantha La Vine
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Eva Marie Y Moresco
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
| | - Joseph S Takahashi
- Department of Neuroscience, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX
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19
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Involvement of posttranscriptional regulation of Clock in the emergence of circadian clock oscillation during mouse development. Proc Natl Acad Sci U S A 2017; 114:E7479-E7488. [PMID: 28827343 DOI: 10.1073/pnas.1703170114] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circadian clock oscillation emerges in mouse embryo in the later developmental stages. Although circadian clock development is closely correlated with cellular differentiation, the mechanisms of its emergence during mammalian development are not well understood. Here, we demonstrate an essential role of the posttranscriptional regulation of Clock subsequent to the cellular differentiation for the emergence of circadian clock oscillation in mouse fetal hearts and mouse embryonic stem cells (ESCs). In mouse fetal hearts, no apparent oscillation of cell-autonomous molecular clock was detectable around E10, whereas oscillation was clearly visible in E18 hearts. Temporal RNA-sequencing analysis using mouse fetal hearts reveals many fewer rhythmic genes in E10-12 hearts (63, no core circadian genes) than in E17-19 hearts (483 genes), suggesting the lack of functional circadian transcriptional/translational feedback loops (TTFLs) of core circadian genes in E10 mouse fetal hearts. In both ESCs and E10 embryos, CLOCK protein was absent despite the expression of Clock mRNA, which we showed was due to Dicer/Dgcr8-dependent translational suppression of CLOCK. The CLOCK protein is required for the discernible molecular oscillation in differentiated cells, and the posttranscriptional regulation of Clock plays a role in setting the timing for the emergence of the circadian clock oscillation during mammalian development.
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20
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Nohara K, Chen Z, Yoo SH. A Filtration-based Method of Preparing High-quality Nuclei from Cross-linked Skeletal Muscle for Chromatin Immunoprecipitation. J Vis Exp 2017. [PMID: 28715394 DOI: 10.3791/56013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful method to determine protein binding to chromatin DNA. Fiber-rich skeletal muscle, however, has been a challenge for ChIP due to technical difficulty in isolation of high-quality nuclei with minimal contamination of myofibrils. Previous protocols have attempted to purify nuclei before cross-linking, which incurs the risk of altered DNA-protein interaction during the prolonged nuclei preparation process. In the current protocol, we first cross-linked the skeletal muscle tissue collected from mice, and the tissues were minced and sonicated. Since we found that ultracentrifugation was not able to separate nuclei from myofibrils using cross-linked muscle tissue, we devised a sequential filtration procedure to obtain high-quality nuclei devoid of significant myofibril contamination. We subsequently prepared chromatin by using an ultrasonicator, and ChIP assays with anti-BMAL1 antibody revealed robust circadian binding pattern of BMAL1 to target gene promoters. This filtration protocol constitutes an easily applicable method to isolate high-quality nuclei from cross-linked skeletal muscle tissue, allowing consistent sample processing for circadian and other time-sensitive studies. In combination with next-generation sequencing (NGS), our method can be deployed for various mechanistic and genomic studies focusing on skeletal muscle function.
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Affiliation(s)
- Kazunari Nohara
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston;
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Wang GZ, Hickey SL, Shi L, Huang HC, Nakashe P, Koike N, Tu BP, Takahashi JS, Konopka G. Cycling Transcriptional Networks Optimize Energy Utilization on a Genome Scale. Cell Rep 2015; 13:1868-80. [PMID: 26655902 DOI: 10.1016/j.celrep.2015.10.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 09/08/2015] [Accepted: 10/14/2015] [Indexed: 12/22/2022] Open
Abstract
Genes expressing circadian RNA rhythms are enriched for metabolic pathways, but the adaptive significance of cyclic gene expression remains unclear. We estimated the genome-wide synthetic and degradative cost of transcription and translation in three organisms and found that the cost of cycling genes is strikingly higher compared to non-cycling genes. Cycling genes are expressed at high levels and constitute the most costly proteins to synthesize in the genome. We demonstrate that metabolic cycling is accelerated in yeast grown under higher nutrient flux and the number of cycling genes increases ∼40%, which are achieved by increasing the amplitude and not the mean level of gene expression. These results suggest that rhythmic gene expression optimizes the metabolic cost of global gene expression and that highly expressed genes have been selected to be downregulated in a cyclic manner for energy conservation.
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Affiliation(s)
- Guang-Zhong Wang
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Stephanie L Hickey
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lei Shi
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Hung-Chung Huang
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Prachi Nakashe
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nobuya Koike
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Benjamin P Tu
- Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Genevieve Konopka
- Department of Neuroscience, The University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Md. SSG, Diego-Álvarez D, Buades C, Romera-López A, Pérez-Cabornero L, Valero-Hervás D, Cantalapiedra D, Bioinformatics, Felipe-Ponce V, Hernández-Poveda G, José Roca M, Casañs C, Fernández-Pedrosa V, M. CC, C. ÁA, P. JCT, C. ÓR, Marco G, Gil M, Miñambres R, Ballester A. DIAGNÓSTICO MOLECULAR DE ENFERMEDADES GENÉTICAS: DEL DIAGNÓSTICO GENÉTICO AL DIAGNÓSTICO GENÓMICO CON LA SECUENCIACIÓN MASIVA. REVISTA MÉDICA CLÍNICA LAS CONDES 2015. [DOI: 10.1016/j.rmclc.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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