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Gutierrez Fugón OJ, Sharifi O, Heath N, Soto DC, Gomez JA, Yasui DH, Mendiola AJP, O'Geen H, Beitnere U, Tomkova M, Haghani V, Dillon G, Segal DJ, LaSalle JM. Integration of CTCF loops, methylome, and transcriptome in differentiating LUHMES as a model for imprinting dynamics of the 15q11-q13 locus in human neurons. Hum Mol Genet 2024; 33:1711-1725. [PMID: 39045627 DOI: 10.1093/hmg/ddae111] [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: 03/20/2024] [Revised: 06/30/2024] [Accepted: 07/17/2024] [Indexed: 07/25/2024] Open
Abstract
Human cell line models, including the neuronal precursor line LUHMES, are important for investigating developmental transcriptional dynamics within imprinted regions, particularly the 15q11-q13 Angelman (AS) and Prader-Willi (PWS) syndrome locus. AS results from loss of maternal UBE3A in neurons, where the paternal allele is silenced by a convergent antisense transcript UBE3A-ATS, a lncRNA that terminates at PWAR1 in non-neurons. qRT-PCR analysis confirmed the exclusive and progressive increase in UBE3A-ATS in differentiating LUHMES neurons, validating their use for studying UBE3A silencing. Genome-wide transcriptome analyses revealed changes to 11 834 genes during neuronal differentiation, including the upregulation of most genes within the 15q11-q13 locus. To identify dynamic changes in chromatin loops linked to transcriptional activity, we performed a HiChIP validated by 4C, which identified two neuron-specific CTCF loops between MAGEL2-SNRPN and PWAR1-UBE3A. To determine if allele-specific differentially methylated regions (DMR) may be associated with CTCF loop anchors, whole genome long-read nanopore sequencing was performed. We identified a paternally hypomethylated DMR near the SNRPN upstream loop anchor exclusive to neurons and a paternally hypermethylated DMR near the PWAR1 CTCF anchor exclusive to undifferentiated cells, consistent with increases in neuronal transcription. Additionally, DMRs near CTCF loop anchors were observed in both cell types, indicative of allele-specific differences in chromatin loops regulating imprinted transcription. These results provide an integrated view of the 15q11-q13 epigenetic landscape during LUHMES neuronal differentiation, underscoring the complex interplay of transcription, chromatin looping, and DNA methylation. They also provide insights for future therapeutic approaches for AS and PWS.
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Affiliation(s)
- Orangel J Gutierrez Fugón
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Osman Sharifi
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Nicholas Heath
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Daniela C Soto
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, 757 Westwood Plaza #4, Los Angeles, CA 90095, United States
| | - J Antonio Gomez
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
- Department of Natural Science, Seaver College, Pepperdine University, 24255 Pacific Coast Hwy, Malibu, CA 90263, United States
| | - Dag H Yasui
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Aron Judd P Mendiola
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Henriette O'Geen
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Ulrika Beitnere
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Straße 10, 13125 Berlin, Germany
| | - Marketa Tomkova
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
- Ludwig Cancer Research Center, University of Oxford, Old Road Campus Research Build, Roosevelt Dr, Headington, Oxford OX3 7DQ, United Kingdom
| | - Viktoria Haghani
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
| | - Greg Dillon
- Genetics and Neurodevelopmental Disorders Unit, Biogen, 225 Binney Street Cambridge, MA 02142 United States
| | - David J Segal
- Genome Center, Department of Biochemistry and Molecular Medicine, University of California Davis, 451 Health Sciences Dr., Davis, CA 95616, United States
| | - Janine M LaSalle
- Department of Medical Microbiology and Immunology, School of Medicine, University of California Davis, 1275 Med Science Dr, Davis, CA 95616, United States
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Wang SE, Cheng Y, Lim J, Jang MA, Forrest EN, Kim Y, Donahue M, Qiao SN, Xiong Y, Jin J, Wang S, Jiang YH. Mechanism of EHMT2-mediated genomic imprinting associated with Prader-Willi syndrome. RESEARCH SQUARE 2024:rs.3.rs-4530649. [PMID: 39011107 PMCID: PMC11247926 DOI: 10.21203/rs.3.rs-4530649/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Prader-Willi Syndrome (PWS) is caused by loss of expression of paternally expressed genes in the human 15q11.2-q13 imprinting domain. A set of imprinted genes that are active on the paternal but silenced on the maternal chromosome are intricately regulated by a bipartite imprinting center (PWS-IC) located in the PWS imprinting domain. In past work, we discovered that euchromatic histone lysine N-methyltransferase-2 (EHMT2/G9a) inhibitors were capable of un-silencing PWS-associated genes by restoring their expression from the maternal chromosome. Here, in mice lacking the Ehmt2 gene, we document un-silencing of the imprinted Snrpn/Snhg14 gene on the maternal chromosome in the late embryonic and postnatal brain. Using PWS and Angelman syndrome patient derived cells with either paternal or maternal deletion of 15q11-q13, we have found that chromatin of maternal PWS-IC is closed and has compact 3D folding confirmation. We further show that a new and distinct noncoding RNA preferentially transcribed from upstream of the PWS-IC interacts with EHMT2 and forms a heterochromatin complex to silence gene expression of SNRPN in CIS on maternal chromosome. Taken together, these findings demonstrate that allele-specific recruitment of EHMT2 is required to maintain the maternal imprints. Our findings provide novel mechanistic insights and support a new model for imprinting maintenance of the PWS imprinted domain.
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Affiliation(s)
- Sung Eun Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Yubao Cheng
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Jaechul Lim
- Immunobiology, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, South Korea
| | - Mi-Ae Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06351, South Korea
| | - Emily N. Forrest
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Yuna Kim
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place Memphis, TN 38105, USA
| | - Meaghan Donahue
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Sheng-Nan Qiao
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Siyuan Wang
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
- Cell Biology, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
| | - Yong-hui Jiang
- Department of Genetics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
- Neuroscience, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
- Pediatrics, Yale University School of Medicine, 333 Cedar St, New Haven, CT 06520, USA
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3
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Moindrot B, Imaizumi Y, Feil R. Differential 3D genome architecture and imprinted gene expression: cause or consequence? Biochem Soc Trans 2024; 52:973-986. [PMID: 38775198 PMCID: PMC11346452 DOI: 10.1042/bst20230143] [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: 02/12/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Imprinted genes provide an attractive paradigm to unravel links between transcription and genome architecture. The parental allele-specific expression of these essential genes - which are clustered in chromosomal domains - is mediated by parental methylation imprints at key regulatory DNA sequences. Recent chromatin conformation capture (3C)-based studies show differential organization of topologically associating domains between the parental chromosomes at imprinted domains, in embryonic stem and differentiated cells. At several imprinted domains, differentially methylated regions show allelic binding of the insulator protein CTCF, and linked focal retention of cohesin, at the non-methylated allele only. This generates differential patterns of chromatin looping between the parental chromosomes, already in the early embryo, and thereby facilitates the allelic gene expression. Recent research evokes also the opposite scenario, in which allelic transcription contributes to the differential genome organization, similarly as reported for imprinted X chromosome inactivation. This may occur through epigenetic effects on CTCF binding, through structural effects of RNA Polymerase II, or through imprinted long non-coding RNAs that have chromatin repressive functions. The emerging picture is that epigenetically-controlled differential genome architecture precedes and facilitates imprinted gene expression during development, and that at some domains, conversely, the mono-allelic gene expression also influences genome architecture.
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Affiliation(s)
- Benoit Moindrot
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Yui Imaizumi
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
| | - Robert Feil
- Institute of Molecular Genetics of Montpellier (IGMM), University of Montpellier, CNRS, Montpellier, France
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4
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Ordoñez R, Zhang W, Ellis G, Zhu Y, Ashe HJ, Ribeiro-Dos-Santos AM, Brosh R, Huang E, Hogan MS, Boeke JD, Maurano MT. Genomic context sensitizes regulatory elements to genetic disruption. Mol Cell 2024; 84:1842-1854.e7. [PMID: 38759624 PMCID: PMC11104518 DOI: 10.1016/j.molcel.2024.04.013] [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: 10/10/2023] [Revised: 03/11/2024] [Accepted: 04/18/2024] [Indexed: 05/19/2024]
Abstract
Genomic context critically modulates regulatory function but is difficult to manipulate systematically. The murine insulin-like growth factor 2 (Igf2)/H19 locus is a paradigmatic model of enhancer selectivity, whereby CTCF occupancy at an imprinting control region directs downstream enhancers to activate either H19 or Igf2. We used synthetic regulatory genomics to repeatedly replace the native locus with 157-kb payloads, and we systematically dissected its architecture. Enhancer deletion and ectopic delivery revealed previously uncharacterized long-range regulatory dependencies at the native locus. Exchanging the H19 enhancer cluster with the Sox2 locus control region (LCR) showed that the H19 enhancers relied on their native surroundings while the Sox2 LCR functioned autonomously. Analysis of regulatory DNA actuation across cell types revealed that these enhancer clusters typify broader classes of context sensitivity genome wide. These results show that unexpected dependencies influence even well-studied loci, and our approach permits large-scale manipulation of complete loci to investigate the relationship between regulatory architecture and function.
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Affiliation(s)
- Raquel Ordoñez
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Weimin Zhang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Gwen Ellis
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Yinan Zhu
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Hannah J Ashe
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | | | - Ran Brosh
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Emily Huang
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Megan S Hogan
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Biochemistry Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
| | - Matthew T Maurano
- Institute for Systems Genetics, NYU School of Medicine, New York, NY 10016, USA; Department of Pathology, NYU School of Medicine, New York, NY 10016, USA.
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5
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Rengifo Rojas C, Cercy J, Perillous S, Gonthier-Guéret C, Montibus B, Maupetit-Méhouas S, Espinadel A, Dupré M, Hong CC, Hata K, Nakabayashi K, Plagge A, Bouschet T, Arnaud P, Vaillant I, Court F. Biallelic non-productive enhancer-promoter interactions precede imprinted expression of Kcnk9 during mouse neural commitment. HGG ADVANCES 2024; 5:100271. [PMID: 38297831 PMCID: PMC10869267 DOI: 10.1016/j.xhgg.2024.100271] [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: 10/17/2023] [Revised: 12/18/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024] Open
Abstract
It is only partially understood how constitutive allelic methylation at imprinting control regions (ICRs) interacts with other regulation levels to drive timely parental allele-specific expression along large imprinted domains. The Peg13-Kcnk9 domain is an imprinted domain with important brain functions. To gain insights into its regulation during neural commitment, we performed an integrative analysis of its allele-specific epigenetic, transcriptomic, and cis-spatial organization using a mouse stem cell-based corticogenesis model that recapitulates the control of imprinted gene expression during neurodevelopment. We found that, despite an allelic higher-order chromatin structure associated with the paternally CTCF-bound Peg13 ICR, enhancer-Kcnk9 promoter contacts occurred on both alleles, although they were productive only on the maternal allele. This observation challenges the canonical model in which CTCF binding isolates the enhancer and its target gene on either side and suggests a more nuanced role for allelic CTCF binding at some ICRs.
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Affiliation(s)
- Cecilia Rengifo Rojas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jil Cercy
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Sophie Perillous
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Céline Gonthier-Guéret
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bertille Montibus
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Stéphanie Maupetit-Méhouas
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Astrid Espinadel
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Marylou Dupré
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Charles C Hong
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan; Department of Human Molecular Genetics, Gunma University Graduate School of Medicine 3-39-22 Showa, Maebashi, Gunma 371-8511, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, 2-10-1 Okura, Setagaya, Tokyo 157-8535, Japan
| | - Antonius Plagge
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Tristan Bouschet
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Philippe Arnaud
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Isabelle Vaillant
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
| | - Franck Court
- Genetics, Reproduction and Development Institute (iGReD), CNRS, INSERM, Université Clermont Auvergne, Clermont-Ferrand, France.
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6
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Bell CG. Epigenomic insights into common human disease pathology. Cell Mol Life Sci 2024; 81:178. [PMID: 38602535 PMCID: PMC11008083 DOI: 10.1007/s00018-024-05206-2] [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: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/13/2024] [Indexed: 04/12/2024]
Abstract
The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts & The London Faculty of Medicine, Queen Mary University of London, Charterhouse Square, London, EC1M 6BQ, UK.
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Hua D, Gu M, Zhang X, Du Y, Xie H, Qi L, Du X, Bai Z, Zhu X, Tian D. DiffDomain enables identification of structurally reorganized topologically associating domains. Nat Commun 2024; 15:502. [PMID: 38218905 PMCID: PMC10787792 DOI: 10.1038/s41467-024-44782-6] [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: 12/16/2022] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Topologically associating domains (TADs) are critical structural units in three-dimensional genome organization of mammalian genome. Dynamic reorganizations of TADs between health and disease states are associated with essential genome functions. However, computational methods for identifying reorganized TADs are still in the early stages of development. Here, we present DiffDomain, an algorithm leveraging high-dimensional random matrix theory to identify structurally reorganized TADs using high-throughput chromosome conformation capture (Hi-C) contact maps. Method comparison using multiple real Hi-C datasets reveals that DiffDomain outperforms alternative methods for false positive rates, true positive rates, and identifying a new subtype of reorganized TADs. Applying DiffDomain to Hi-C data from different cell types and disease states demonstrates its biological relevance. Identified reorganized TADs are associated with structural variations and epigenomic changes such as changes in CTCF binding sites. By applying to a single-cell Hi-C data from mouse neuronal development, DiffDomain can identify reorganized TADs between cell types with reasonable reproducibility using pseudo-bulk Hi-C data from as few as 100 cells per condition. Moreover, DiffDomain reveals differential cell-to-population variability and heterogeneous cell-to-cell variability in TADs. Therefore, DiffDomain is a statistically sound method for better comparative analysis of TADs using both Hi-C and single-cell Hi-C data.
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Affiliation(s)
- Dunming Hua
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Ming Gu
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Xiao Zhang
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yanyi Du
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Hangcheng Xie
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Li Qi
- Chongqing Municipal Center for Disease Control and Prevention, Chongqing, 400042, China
| | - Xiangjun Du
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Zhidong Bai
- KLASMOE & School of Mathematics and Statistics, Northeast Normal University, Changchun, Jilin, 130024, China
| | - Xiaopeng Zhu
- MyCellome LLC., Allison Park, PA, 15101, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Dechao Tian
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, 510275, China.
- Department of Biostatistics and Systems Biology, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China.
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8
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis. Genes Dev 2023; 37:829-843. [PMID: 37821107 PMCID: PMC10620047 DOI: 10.1101/gad.350896.123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/18/2023] [Indexed: 10/13/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brains from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we showed that imprinted chromatin structure precedes imprinted expression at the locus. Additionally, activation of a distal enhancer induced imprinted expression of Kcnk9 in an allelic chromatin structure-dependent manner. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Courtney M Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Amanda J Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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9
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Loftus D, Bae B, Whilden CM, Whipple AJ. Allelic chromatin structure primes imprinted expression of Kcnk9 during neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.09.544389. [PMID: 37333073 PMCID: PMC10274912 DOI: 10.1101/2023.06.09.544389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Differences in chromatin state inherited from the parental gametes influence the regulation of maternal and paternal alleles in offspring. This phenomenon, known as genomic imprinting, results in genes preferentially transcribed from one parental allele. While local epigenetic factors such as DNA methylation are known to be important for the establishment of imprinted gene expression, less is known about the mechanisms by which differentially methylated regions (DMRs) lead to differences in allelic expression across broad stretches of chromatin. Allele-specific higher-order chromatin structure has been observed at multiple imprinted loci, consistent with the observation of allelic binding of the chromatin-organizing factor CTCF at multiple DMRs. However, whether allelic chromatin structure impacts allelic gene expression is not known for most imprinted loci. Here we characterize the mechanisms underlying brain-specific imprinted expression of the Peg13-Kcnk9 locus, an imprinted region associated with intellectual disability. We performed region capture Hi-C on mouse brain from reciprocal hybrid crosses and found imprinted higher-order chromatin structure caused by the allelic binding of CTCF to the Peg13 DMR. Using an in vitro neuron differentiation system, we show that on the maternal allele enhancer-promoter contacts formed early in development prime the brain-specific potassium leak channel Kcnk9 for maternal expression prior to neurogenesis. In contrast, these enhancer-promoter contacts are blocked by CTCF on the paternal allele, preventing paternal Kcnk9 activation. This work provides a high-resolution map of imprinted chromatin structure and demonstrates that chromatin state established in early development can promote imprinted expression upon differentiation.
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Affiliation(s)
- Daniel Loftus
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Bongmin Bae
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Courtney M. Whilden
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
| | - Amanda J. Whipple
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138 USA
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