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Sun D, Zhu Y, Peng W, Zheng S, Weng J, Dong S, Li J, Chen Q, Ge C, Liao L, Dong Y, Liu Y, Meng W, Jiang Y. SETDB1 regulates short interspersed nuclear elements and chromatin loop organization in mouse neural precursor cells. Genome Biol 2024; 25:175. [PMID: 38961490 PMCID: PMC11221086 DOI: 10.1186/s13059-024-03327-2] [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: 03/08/2024] [Accepted: 06/28/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Transposable elements play a critical role in maintaining genome architecture during neurodevelopment. Short Interspersed Nuclear Elements (SINEs), a major subtype of transposable elements, are known to harbor binding sites for the CCCTC-binding factor (CTCF) and pivotal in orchestrating chromatin organization. However, the regulatory mechanisms controlling the activity of SINEs in the developing brain remains elusive. RESULTS In our study, we conduct a comprehensive genome-wide epigenetic analysis in mouse neural precursor cells using ATAC-seq, ChIP-seq, whole genome bisulfite sequencing, in situ Hi-C, and RNA-seq. Our findings reveal that the SET domain bifurcated histone lysine methyltransferase 1 (SETDB1)-mediated H3K9me3, in conjunction with DNA methylation, restricts chromatin accessibility on a selective subset of SINEs in neural precursor cells. Mechanistically, loss of Setdb1 increases CTCF access to these SINE elements and contributes to chromatin loop reorganization. Moreover, de novo loop formation contributes to differential gene expression, including the dysregulation of genes enriched in mitotic pathways. This leads to the disruptions of cell proliferation in the embryonic brain after genetic ablation of Setdb1 both in vitro and in vivo. CONCLUSIONS In summary, our study sheds light on the epigenetic regulation of SINEs in mouse neural precursor cells, suggesting their role in maintaining chromatin organization and cell proliferation during neurodevelopment.
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Affiliation(s)
- Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yueyan Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Wenzhu Peng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shenghui Zheng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Shulong Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jiaqi Li
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Qi Chen
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Chuanhui Ge
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Liyong Liao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yuhao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yun Liu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Weida Meng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.
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Zagirova D, Kononkova A, Vaulin N, Khrameeva E. From compartments to loops: understanding the unique chromatin organization in neuronal cells. Epigenetics Chromatin 2024; 17:18. [PMID: 38783373 PMCID: PMC11112951 DOI: 10.1186/s13072-024-00538-6] [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: 02/01/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.
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Affiliation(s)
- Diana Zagirova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
- Research and Training Center on Bioinformatics, Institute for Information Transmission Problems (Kharkevich Institute) RAS, Bolshoy Karetny per. 19, Build.1, Moscow, 127051, Russia
| | - Anna Kononkova
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
| | - Nikita Vaulin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia
| | - Ekaterina Khrameeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, Build.1, Moscow, 121205, Russia.
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3
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Weng J, Zhu YY, Liao LY, Yang XT, Dong YH, Meng WD, Sun DJ, Liu Y, Peng WZ, Jiang Y. Distinct epigenetic modulation of differentially expressed genes in the adult mouse brain following prenatal exposure to low-dose bisphenol A. Cell Biol Toxicol 2024; 40:37. [PMID: 38777957 PMCID: PMC11111541 DOI: 10.1007/s10565-024-09875-4] [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: 12/01/2023] [Accepted: 05/15/2024] [Indexed: 05/25/2024]
Abstract
Bisphenol A (BPA) is a common component in the manufacture of daily plastic consumer goods. Recent studies have suggested that prenatal exposure to BPA can increase the susceptibility of offspring to mental illness, although the underlying mechanisms remain unclear. In this study, we performed transcriptomic and epigenomic profiling in the adult mouse brain following prenatal exposure to low-dose BPA. We observed a sex-specific transcriptional dysregulation in the cortex, with more significant differentially expressed genes was observed in adult cortex from male offspring. Moreover, the upregulated genes primarily influenced neuronal functions, while the downregulated genes were significantly associated with energy metabolism pathways. More evidence supporting impaired mitochondrial function included a decreased ATP level and a reduced number of mitochondria in the cortical neuron of the BPA group. We further investigated the higher-order chromatin regulatory patterns of DEGs by incorporating published Hi-C data. Interestingly, we found that upregulated genes exhibited more distal interactions with multiple enhancers, while downregulated genes displayed relatively short-range interactions among adjacent genes. Our data further revealed decreased H3K9me3 signal on the distal enhancers of upregulated genes, whereas increased DNA methylation and H3K27me3 signals on the promoters of downregulated genes. In summary, our study provides compelling evidence for the potential health risks associated with prenatal exposure to BPA, and uncovers sex-specific transcriptional changes with a complex interplay of multiple epigenetic mechanisms.
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Affiliation(s)
- Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yue-Yan Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Li-Yong Liao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Xin-Tong Yang
- Shanghai Medical college, Fudan University, Shanghai, 200032, China
| | - Yu-Hao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Wei-da Meng
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Dai-Jing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yun Liu
- The MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wen-Zhu Peng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, 200032, China.
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4
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Zhang Z, Jin P, Guo Z, Tu Z, Yang H, Hu M, Li Q, Liu X, Li W, Hou S. Integrated Analysis of Chromatin and Transcriptomic Profiling Identifies PU.1 as a Core Regulatory Factor in Microglial Activation Induced by Chronic Cerebral Hypoperfusion. Mol Neurobiol 2024; 61:2569-2589. [PMID: 37917300 PMCID: PMC11043206 DOI: 10.1007/s12035-023-03734-9] [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: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
In addition to causing white matter lesions, chronic cerebral hypoperfusion (CCH) can also cause damage to gray matter, but the underlying molecular mechanisms remain largely unknown. In order to obtain a better understanding of the relationship between gene expression and transcriptional regulation alterations, novel upstream regulators could be identified using integration analysis of the transcriptome and epigenetic approaches. Here, a bilateral common carotid artery stenosis (BCAS) model was established for inducing CCH in mice. The spatial cognitive function of mice was evaluated, and changes in cortical microglia morphology were observed. RNA-sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were performed on isolated mouse cortical brain tissue. Then, a systematic joint analysis of BCAS hypoperfusion-induced cortex-specific RNA-seq and ATAC-seq was conducted in order to assess the extent of the correlation between the two, and PU.1 was found to be greatly enriched through motif analysis and transcription factor annotation. Also, the core regulatory factor PU.1 induced by BCAS hypoperfusion was shown to be colocalized with microglia. Based on the above analysis, PU.1 plays a key regulatory role in microglial activation induced by CCH. And the transcriptome and epigenomic data presented in this study can help identify potential targets for future research exploring chronic hypoperfusion-induced brain injury.
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Affiliation(s)
- Zengyu Zhang
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengpeng Jin
- Department of Chronic Disease Management, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Zimin Guo
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhilan Tu
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Hualan Yang
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Mengting Hu
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Qinghua Li
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Xingdang Liu
- Department of Nuclear Medicine, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China
| | - Weiwei Li
- Institute of Pediatrics, Children's Hospital of Fudan University, Fudan University, Shanghai, China.
| | - Shuangxing Hou
- Department of Neurology, Shanghai Pudong Hospital, Fudan University Pudong Medical Center, Shanghai, China.
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5
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Del Blanco B, Niñerola S, Martín-González AM, Paraíso-Luna J, Kim M, Muñoz-Viana R, Racovac C, Sanchez-Mut JV, Ruan Y, Barco Á. Kdm1a safeguards the topological boundaries of PRC2-repressed genes and prevents aging-related euchromatinization in neurons. Nat Commun 2024; 15:1781. [PMID: 38453932 PMCID: PMC10920760 DOI: 10.1038/s41467-024-45773-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/02/2024] [Indexed: 03/09/2024] Open
Abstract
Kdm1a is a histone demethylase linked to intellectual disability with essential roles during gastrulation and the terminal differentiation of specialized cell types, including neurons, that remains highly expressed in the adult brain. To explore Kdm1a's function in adult neurons, we develop inducible and forebrain-restricted Kdm1a knockouts. By applying multi-omic transcriptome, epigenome and chromatin conformation data, combined with super-resolution microscopy, we find that Kdm1a elimination causes the neuronal activation of nonneuronal genes that are silenced by the polycomb repressor complex and interspersed with active genes. Functional assays demonstrate that the N-terminus of Kdm1a contains an intrinsically disordered region that is essential to segregate Kdm1a-repressed genes from the neighboring active chromatin environment. Finally, we show that the segregation of Kdm1a-target genes is weakened in neurons during natural aging, underscoring the role of Kdm1a safeguarding neuronal genome organization and gene silencing throughout life.
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Affiliation(s)
- Beatriz Del Blanco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
| | - Sergio Niñerola
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Ana M Martín-González
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Juan Paraíso-Luna
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Minji Kim
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Rafael Muñoz-Viana
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
- Bioinformatics Unit, Hospital universitario Puerta de Hierro Majadahonda, 28220, Majadahonda, Spain
| | - Carina Racovac
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Jose V Sanchez-Mut
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain
| | - Yijun Ruan
- The Jackson laboratory for Genomic Medicine, Farmington, CT, 06030, USA
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang Province, 310058, P.R. China
| | - Ángel Barco
- Instituto de Neurociencias (Universidad Miguel Hernández - Consejo Superior de Investigaciones Científicas). Av. Santiago Ramón y Cajal s/n. Sant Joan d'Alacant, 03550, Alicante, Spain.
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6
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Plaza-Jennings A, Akbarian S. Genomic Exploration of the Brain in People Infected with HIV-Recent Progress and the Road Ahead. Curr HIV/AIDS Rep 2023; 20:357-367. [PMID: 37947981 PMCID: PMC10719125 DOI: 10.1007/s11904-023-00675-9] [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] [Accepted: 10/02/2023] [Indexed: 11/12/2023]
Abstract
PURPOSE OF REVIEW The adult human brain harbors billions of microglia and other myeloid and lymphoid cells highly susceptible to HIV infection and retroviral insertion into the nuclear DNA. HIV infection of the brain is important because the brain is a potentially large reservoir site that may be a barrier to HIV cure strategies and because infection can lead to the development of HIV-associated neurocognitive disorder. To better understand both the central nervous system (CNS) reservoir and how it can cause neurologic dysfunction, novel genomic, epigenomic, transcriptomic, and proteomic approaches need to be employed. Several characteristics of the reservoir are important to learn, including where the virus integrates, whether integrated proviruses are intact or defective, whether integrated proviruses can be reactivated from a latent state to seed ongoing infection, and how this all impacts brain function. RECENT FINDINGS Here, we discuss similarities and differences of viral integration sites between brain and blood and discuss evidence for and against the hypothesis that in the absence of susceptible T-lymphocytes in the periphery, the virus housing in the infected brain is not able to sustain a systemic infection. Moreover, microglia from HIV + brains across a wide range of disease severity appear to share one type of common alteration, which is defined by downregulated expression, and repressive chromosomal compartmentalization, for microglial genes regulating synaptic connectivity. Therefore, viral infection of the brain, including in immunocompetent cases with near-normal levels of CD4 blood lymphocytes, could be associated with an early disruption in microglia-dependent neuronal support functions, contributing to cognitive and neurological deficits in people living with HIV.
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Affiliation(s)
- Amara Plaza-Jennings
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Nash Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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7
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Tam PLF, Leung D. The Molecular Impacts of Retrotransposons in Development and Diseases. Int J Mol Sci 2023; 24:16418. [PMID: 38003607 PMCID: PMC10671454 DOI: 10.3390/ijms242216418] [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: 10/07/2023] [Revised: 11/11/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Retrotransposons are invasive genetic elements that constitute substantial portions of mammalian genomes. They have the potential to influence nearby gene expression through their cis-regulatory sequences, reverse transcription machinery, and the ability to mold higher-order chromatin structures. Due to their multifaceted functions, it is crucial for host fitness to maintain strict regulation of these parasitic sequences to ensure proper growth and development. This review explores how subsets of retrotransposons have undergone evolutionary exaptation to enhance the complexity of mammalian genomes. It also highlights the significance of regulating these elements, drawing on recent studies conducted in human and murine systems.
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Affiliation(s)
- Phoebe Lut Fei Tam
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
| | - Danny Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China;
- Center for Epigenomics Research, The Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong SAR, China
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8
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Akbarian S, Won H. Chromosomal contacts change with age. Science 2023; 381:1049-1050. [PMID: 37676934 DOI: 10.1126/science.adk0961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The three-dimensional organization of the genome is remodeled throughout life.
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Affiliation(s)
| | - Hyejung Won
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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9
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Osipovich AB, Dudek KD, Trinh LT, Kim LH, Shrestha S, Cartailler JP, Magnuson MA. ZFP92, a KRAB domain zinc finger protein enriched in pancreatic islets, binds to B1/Alu SINE transposable elements and regulates retroelements and genes. PLoS Genet 2023; 19:e1010729. [PMID: 37155670 PMCID: PMC10166502 DOI: 10.1371/journal.pgen.1010729] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023] Open
Abstract
Repressive KRAB domain-containing zinc-finger proteins (KRAB-ZFPs) are abundant in mammalian genomes and contribute both to the silencing of transposable elements (TEs) and to the regulation of developmental stage- and cell type-specific gene expression. Here we describe studies of zinc finger protein 92 (Zfp92), an X-linked KRAB-ZFP that is highly expressed in pancreatic islets of adult mice, by analyzing global Zfp92 knockout (KO) mice. Physiological, transcriptomic and genome-wide chromatin binding studies indicate that the principal function of ZFP92 in mice is to bind to and suppress the activity of B1/Alu type of SINE elements and modulate the activity of surrounding genomic entities. Deletion of Zfp92 leads to changes in expression of select LINE and LTR retroelements and genes located in the vicinity of ZFP92-bound chromatin. The absence of Zfp92 leads to altered expression of specific genes in islets, adipose and muscle that result in modest sex-specific alterations in blood glucose homeostasis, body mass and fat accumulation. In islets, Zfp92 influences blood glucose concentration in postnatal mice via transcriptional effects on Mafb, whereas in adipose and muscle, it regulates Acacb, a rate-limiting enzyme in fatty acid metabolism. In the absence of Zfp92, a novel TE-Capn11 fusion transcript is overexpressed in islets and several other tissues due to de-repression of an IAPez TE adjacent to ZFP92-bound SINE elements in intron 3 of the Capn11 gene. Together, these studies show that ZFP92 functions both to repress specific TEs and to regulate the transcription of specific genes in discrete tissues.
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Affiliation(s)
- Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Karrie D. Dudek
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Linh T. Trinh
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Lily H. Kim
- College of Arts and Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Shristi Shrestha
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Jean-Philippe Cartailler
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mark A. Magnuson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Center for Stem Cell Biology, Vanderbilt University, Nashville, Tennessee, United States of America
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, United States of America
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10
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Li J, Zheng S, Dong Y, Xu H, Zhu Y, Weng J, Sun D, Wang S, Xiao L, Jiang Y. Histone Methyltransferase SETDB1 Regulates the Development of Cortical Htr3a-Positive Interneurons and Mood Behaviors. Biol Psychiatry 2023; 93:279-290. [PMID: 36335068 DOI: 10.1016/j.biopsych.2022.08.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 12/27/2022]
Abstract
BACKGROUND GABAergic (gamma-aminobutyric acidergic) interneurons (INs) are highly heterogeneous, and Htr3a labels a subpopulation of cortical INs originating from the embryonic caudal ganglionic eminence. SETDB1 is one of the histone H3K9 methyltransferases and plays an essential role in the excitatory neurons, but its role in regulating cortical inhibitory INs remains largely unknown. METHODS In this study, we generated transgenic mice with conditional knockout of Setdb1 in neural progenitor cells (Setdb1-NS-cKO) and GABAergic neurons (Setdb1-Gad2-cKO). In addition, we performed RNA sequencing, ATAC-seq (assay for transposase-accessible chromatin with sequencing), chromatin immunoprecipitation sequencing, luciferase assay, chromatin conformation capture, and CRISPR (clustered regularly interspaced short palindromic repeats)/dCas9 to study the epigenetic mechanism underlying SETDB1-mediated transcriptional regulation of Htr3a. We also performed in situ hybridization and whole-cell recording to evaluate the functional properties of cortical Htr3a+ INs and behavioral tests for mood. RESULTS We detected significant upregulation of Htr3a expression in the embryonic ganglionic eminence of Setdb1-NS-cKO and identified the endogenous retroviral sequence RMER21B as a new target of SETDB1. RMER21B showed enhancer activity and formed distal chromatin interaction with the promoter of Htr3a. In addition, we observed an increased number and enhanced excitability of Htr3a+ INs in the knockout cortex. Moreover, Setdb1-Gad2-cKO mice exhibited anxiety- and depressive-like behaviors, which were partially reversed by a 5-HT3 receptor antagonist. CONCLUSIONS These findings suggest that SETDB1 represses Htr3a transcription via RMER21B-mediated distal chromatin interaction in the embryonic ganglionic eminence and regulates the development of cortical Htr3a+ INs and mood behaviors.
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Affiliation(s)
- Jiaqi Li
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Shenghui Zheng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Yuhao Dong
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Hao Xu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Yueyan Zhu
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Jie Weng
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Daijing Sun
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | | | - Lei Xiao
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Yan Jiang
- Institutes of Brain Science, State Key Laboratory of Medical Neurobiology, and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
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Plaza-Jennings A, Valada A, Akbarian S. 3D Genome Plasticity in Normal and Diseased Neurodevelopment. Genes (Basel) 2022; 13:1999. [PMID: 36360237 PMCID: PMC9690570 DOI: 10.3390/genes13111999] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/18/2022] [Accepted: 10/26/2022] [Indexed: 10/17/2023] Open
Abstract
Non-random spatial organization of the chromosomal material inside the nuclei of brain cells emerges as an important regulatory layer of genome organization and function in health and disease. Here, we discuss how integrative approaches assessing chromatin in context of the 3D genome is providing new insights into normal and diseased neurodevelopment. Studies in primate (incl. human) and rodent brain have confirmed that chromosomal organization in neurons and glia undergoes highly dynamic changes during pre- and early postnatal development, with potential for plasticity across a much wider age window. For example, neuronal 3D genomes from juvenile and adult cerebral cortex and hippocampus undergo chromosomal conformation changes at hundreds of loci in the context of learning and environmental enrichment, viral infection, and neuroinflammation. Furthermore, locus-specific structural DNA variations, such as micro-deletions, duplications, repeat expansions, and retroelement insertions carry the potential to disrupt the broader epigenomic and transcriptional landscape far beyond the boundaries of the site-specific variation, highlighting the critical importance of long-range intra- and inter-chromosomal contacts for neuronal and glial function.
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Affiliation(s)
- Amara Plaza-Jennings
- Graduate School of Biomedical Sciences, Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aditi Valada
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Schahram Akbarian
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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