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Hu P, Hao Y, Tang W, Diering GH, Zou F, Kafri T. Analysis of hepatic lentiviral vector transduction; implications for preclinical studies and clinical gene therapy protocols. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.20.608805. [PMID: 39229157 PMCID: PMC11370356 DOI: 10.1101/2024.08.20.608805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Lentiviral vector-transduced T-cells were approved by the FDA as gene therapy anti-cancer medications. Little is known about the host genetic variation effects on the safety and efficacy of the lentiviral vector gene delivery system. To narrow this knowledge-gap, we characterized hepatic gene delivery by lentiviral vectors across the Collaborative Cross (CC) mouse genetic reference population. For 24 weeks, we periodically measured hepatic luciferase expression from lentiviral vectors in 41 CC mouse strains. Hepatic and splenic vector copy numbers were determined. We report that CC mouse strains showed highly diverse outcomes following lentiviral gene delivery. For the first time, moderate correlation between mouse strain-specific sleeping patterns and transduction efficiency was observed. We associated two quantitative trait loci (QTLs) with intra-strain variations in transduction phenotypes, which mechanistically relates to the phenomenon of metastable epialleles. An additional QTL was associated with the kinetics of hepatic transgene expression. Genes comprised in the above QTLs are potential targets to personalize gene therapy protocols. Importantly, we identified two mouse strains that open new directions in characterizing continuous viral vector silencing and HIV latency. Our findings suggest that wide-range patient-specific outcomes of viral vector-based gene therapy should be expected. Thus, novel escalating dose-based clinical protocols should be considered.
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Affiliation(s)
- Peirong Hu
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- These authors contributed equally
| | - Yajing Hao
- Department of Biostatistics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- These authors contributed equally
| | - Wei Tang
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
| | - Graham H Diering
- Department of Cell Biology and Physiology and UNC Neuroscience Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Carolina Institute for developmental disabilities, 27510 Carrboro, North Carolina
| | - Fei Zou
- Department of Biostatistics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Department of Genetics, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
| | - Tal Kafri
- Gene Therapy Center, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, 27599 Chapel Hill, North Carolina
- Lineberger Comprehensive Cancer Center, 27599 Chapel Hill, North Carolina
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2
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Shi G, Pang Q, Lin Z, Zhang X, Huang K. Repetitive Sequence Stability in Embryonic Stem Cells. Int J Mol Sci 2024; 25:8819. [PMID: 39201503 PMCID: PMC11354519 DOI: 10.3390/ijms25168819] [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: 07/10/2024] [Revised: 08/07/2024] [Accepted: 08/12/2024] [Indexed: 09/02/2024] Open
Abstract
Repetitive sequences play an indispensable role in gene expression, transcriptional regulation, and chromosome arrangements through trans and cis regulation. In this review, focusing on recent advances, we summarize the epigenetic regulatory mechanisms of repetitive sequences in embryonic stem cells. We aim to bridge the knowledge gap by discussing DNA damage repair pathway choices on repetitive sequences and summarizing the significance of chromatin organization on repetitive sequences in response to DNA damage. By consolidating these insights, we underscore the critical relationship between the stability of repetitive sequences and early embryonic development, seeking to provide a deeper understanding of repetitive sequence stability and setting the stage for further research and potential therapeutic strategies in developmental biology and regenerative medicine.
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Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Qianwen Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Zhancheng Lin
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Xinyi Zhang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (Q.P.); (Z.L.); (X.Z.)
| | - Kaimeng Huang
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA;
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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3
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Morrissey A, Shi J, James DQ, Mahony S. Accurate allocation of multimapped reads enables regulatory element analysis at repeats. Genome Res 2024; 34:937-951. [PMID: 38986578 PMCID: PMC11293539 DOI: 10.1101/gr.278638.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/14/2024] [Indexed: 07/12/2024]
Abstract
Transposable elements (TEs) and other repetitive regions have been shown to contain gene regulatory elements, including transcription factor binding sites. However, regulatory elements harbored by repeats have proven difficult to characterize using short-read sequencing assays such as ChIP-seq or ATAC-seq. Most regulatory genomics analysis pipelines discard "multimapped" reads that align equally well to multiple genomic locations. Because multimapped reads arise predominantly from repeats, current analysis pipelines fail to detect a substantial portion of regulatory events that occur in repetitive regions. To address this shortcoming, we developed Allo, a new approach to allocate multimapped reads in an efficient, accurate, and user-friendly manner. Allo combines probabilistic mapping of multimapped reads with a convolutional neural network that recognizes the read distribution features of potential peaks, offering enhanced accuracy in multimapping read assignment. Allo also provides read-level output in the form of a corrected alignment file, making it compatible with existing regulatory genomics analysis pipelines and downstream peak-finders. In a demonstration application on CTCF ChIP-seq data, we show that Allo results in the discovery of thousands of new CTCF peaks. Many of these peaks contain the expected cognate motif and/or serve as TAD boundaries. We additionally apply Allo to a diverse collection of ENCODE ChIP-seq data sets, resulting in multiple previously unidentified interactions between transcription factors and repetitive element families. Finally, we show that Allo may be particularly beneficial in identifying ChIP-seq peaks at centromeres, near segmentally duplicated genes, and in younger TEs, enabling new regulatory analyses in these regions.
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Affiliation(s)
- Alexis Morrissey
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Jeffrey Shi
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Daniela Q James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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4
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Stötzel M, Cheng CY, IIik IA, Kumar AS, Omgba PA, van der Weijden VA, Zhang Y, Vingron M, Meissner A, Aktaş T, Kretzmer H, Bulut-Karslioğlu A. TET activity safeguards pluripotency throughout embryonic dormancy. Nat Struct Mol Biol 2024:10.1038/s41594-024-01313-7. [PMID: 38783076 DOI: 10.1038/s41594-024-01313-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 04/10/2024] [Indexed: 05/25/2024]
Abstract
Dormancy is an essential biological process for the propagation of many life forms through generations and stressful conditions. Early embryos of many mammals are preservable for weeks to months within the uterus in a dormant state called diapause, which can be induced in vitro through mTOR inhibition. Cellular strategies that safeguard original cell identity within the silent genomic landscape of dormancy are not known. Here we show that the protection of cis-regulatory elements from silencing is key to maintaining pluripotency in the dormant state. We reveal a TET-transcription factor axis, in which TET-mediated DNA demethylation and recruitment of methylation-sensitive transcription factor TFE3 drive transcriptionally inert chromatin adaptations during dormancy transition. Perturbation of TET activity compromises pluripotency and survival of mouse embryos under dormancy, whereas its enhancement improves survival rates. Our results reveal an essential mechanism for propagating the cellular identity of dormant cells, with implications for regeneration and disease.
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Affiliation(s)
- Maximilian Stötzel
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Chieh-Yu Cheng
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Ibrahim A IIik
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Abhishek Sampath Kumar
- Institute of Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Persia Akbari Omgba
- Stem Cell Chromatin Lab, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | | | - Yufei Zhang
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Alexander Meissner
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Tuğçe Aktaş
- Otto Warburg Laboratories, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
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5
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Irastorza-Azcarate I, Kukalev A, Kempfer R, Thieme CJ, Mastrobuoni G, Markowski J, Loof G, Sparks TM, Brookes E, Natarajan KN, Sauer S, Fisher AG, Nicodemi M, Ren B, Schwarz RF, Kempa S, Pombo A. Extensive folding variability between homologous chromosomes in mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.591087. [PMID: 38766012 PMCID: PMC11100664 DOI: 10.1101/2024.05.08.591087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Genetic variation and 3D chromatin structure have major roles in gene regulation. Due to challenges in mapping chromatin conformation with haplotype-specific resolution, the effects of genetic sequence variation on 3D genome structure and gene expression imbalance remain understudied. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (mESC) line with high density of single nucleotide polymorphisms (SNPs). GAM resolved haplotype-specific 3D genome structures with high sensitivity, revealing extensive allelic differences in chromatin compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts, and CTCF loops. Architectural differences often coincide with allele-specific differences in gene expression, mediated by Polycomb repression. We show that histone genes are expressed with allelic imbalance in mESCs, are involved in haplotype-specific chromatin contact marked by H3K27me3, and are targets of Polycomb repression through conditional knockouts of Ezh2 or Ring1b. Our work reveals highly distinct 3D folding structures between homologous chromosomes, and highlights their intricate connections with allelic gene expression.
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6
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Eggermann T. Human Reproduction and Disturbed Genomic Imprinting. Genes (Basel) 2024; 15:163. [PMID: 38397153 PMCID: PMC10888310 DOI: 10.3390/genes15020163] [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: 01/02/2024] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Genomic imprinting is a specific mode of gene regulation which particularly accounts for the factors involved in development. Its disturbance affects the fetus, the course of pregnancy and even the health of the mother. In children, aberrant imprinting signatures are associated with imprinting disorders (ImpDis). These alterations also affect the function of the placenta, which has consequences for the course of the pregnancy. The molecular causes of ImpDis comprise changes at the DNA level and methylation disturbances (imprinting defects/ImpDefs), and there is an increasing number of reports of both pathogenic fetal and maternal DNA variants causing ImpDefs. These ImpDefs can be inherited, but prediction of the pregnancy complications caused is difficult, as they can cause miscarriages, aneuploidies, health issues for the mother and ImpDis in the child. Due to the complexity of imprinting regulation, each pregnancy or patient with suspected altered genomic imprinting requires a specific workup to identify the precise molecular cause and also careful clinical documentation. This review will cover the current knowledge on the molecular causes of aberrant imprinting signatures and illustrate the need to identify this basis as the prerequisite for personalized genetic and reproductive counselling of families.
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Affiliation(s)
- Thomas Eggermann
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH University Aachen, Pauwelsstr. 3, D-52074 Aachen, Germany
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7
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Ramsoomair CK, Ceccarelli M, Heiss JD, Shah AH. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 2023; 21:893. [PMID: 38071304 PMCID: PMC10709919 DOI: 10.1186/s12967-023-04725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.
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Affiliation(s)
- Christian K Ramsoomair
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
- Medical Scientist Training Program, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1550 N.W. 10Th Avenue, Miami, FL, 33136, USA
| | - John D Heiss
- Surgical Neurology Branch, Disorders and Stroke, National Institute of Neurological, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish H Shah
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
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8
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Zhang G, Mao Y, Zhang Y, Huang H, Pan J. Assisted reproductive technology and imprinting errors: analyzing underlying mechanisms from epigenetic regulation. HUM FERTIL 2023; 26:864-878. [PMID: 37929309 DOI: 10.1080/14647273.2023.2261628] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 08/11/2023] [Indexed: 11/07/2023]
Abstract
With the increasing maturity and widespread application of assisted reproductive technology (ART), more attention has been paid to the health outcomes of offspring following ART. It is well established that children born from ART treatment are at an increased risk of imprinting errors and imprinting disorders. The disturbances of genetic imprinting are attributed to the overlap of ART procedures and important epigenetic reprogramming events during the development of gametes and early embryos, but the detailed mechanisms are hitherto obscure. In this review, we summarized the DNA methylation-dependent and independent mechanisms that control the dynamic epigenetic regulation of imprinted genes throughout the life cycle of a mammal, including erasure, establishment, and maintenance. In addition, we systematically described the dysregulation of imprinted genes in embryos conceived through ART and discussed the corresponding underlying mechanisms according to findings in animal models. This work is conducive to evaluating and improving the safety of ART.
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Affiliation(s)
- Gaochen Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Yiting Mao
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Yu Zhang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Hefeng Huang
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jiexue Pan
- Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
- Key Laboratory of Reproductive Genetics (Ministry of Education), Department of Reproductive Endocrinology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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9
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Felley-Bosco E. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy. Cancers (Basel) 2023; 15:cancers15112969. [PMID: 37296931 DOI: 10.3390/cancers15112969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Recent high-throughput RNA sequencing technologies have confirmed that a large part of the non-coding genome is transcribed. The priority for further investigations is nevertheless generally given in cancer to coding sequences, due to the obvious interest of finding therapeutic targets. In addition, several RNA-sequencing pipelines eliminate repetitive sequences, which are difficult to analyze. In this review, we shall focus on endogenous retroviruses. These sequences are remnants of ancestral germline infections by exogenous retroviruses. These sequences represent 8% of human genome, meaning four-fold the fraction of the genome encoding for proteins. These sequences are generally mostly repressed in normal adult tissues, but pathological conditions lead to their de-repression. Specific mesothelioma-associated endogenous retrovirus expression and their association to clinical outcome is discussed.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, Zürich University Hospital, 8091 Zurich, Switzerland
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10
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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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11
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Cossec JC, Traboulsi T, Sart S, Loe-Mie Y, Guthmann M, Hendriks IA, Theurillat I, Nielsen ML, Torres-Padilla ME, Baroud CN, Dejean A. Transient suppression of SUMOylation in embryonic stem cells generates embryo-like structures. Cell Rep 2023; 42:112380. [PMID: 37061916 PMCID: PMC10157296 DOI: 10.1016/j.celrep.2023.112380] [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: 08/12/2022] [Revised: 02/08/2023] [Accepted: 03/26/2023] [Indexed: 04/17/2023] Open
Abstract
Recent advances in synthetic embryology have opened new avenues for understanding the complex events controlling mammalian peri-implantation development. Here, we show that mouse embryonic stem cells (ESCs) solely exposed to chemical inhibition of SUMOylation generate embryo-like structures comprising anterior neural and trunk-associated regions. HypoSUMOylation-instructed ESCs give rise to spheroids that self-organize into gastrulating structures containing cell types spatially and functionally related to embryonic and extraembryonic compartments. Alternatively, spheroids cultured in a droplet microfluidic device form elongated structures that undergo axial organization reminiscent of natural embryo morphogenesis. Single-cell transcriptomics reveals various cellular lineages, including properly positioned anterior neuronal cell types and paraxial mesoderm segmented into somite-like structures. Transient SUMOylation suppression gradually increases DNA methylation genome wide and repressive mark deposition at Nanog. Interestingly, cell-to-cell variations in SUMOylation levels occur during early embryogenesis. Our approach provides a proof of principle for potentially powerful strategies to explore early embryogenesis by targeting chromatin roadblocks of cell fate change.
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Affiliation(s)
- Jack-Christophe Cossec
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
| | - Tatiana Traboulsi
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France
| | - Sébastien Sart
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France; Physical Microfluidics and Bioengineering Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Yann Loe-Mie
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics HUB, 75015 Paris, France
| | - Manuel Guthmann
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany
| | - Ivo A Hendriks
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Ilan Theurillat
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France; Sorbonne Université, Collège Doctoral, 75005 Paris, France
| | - Michael L Nielsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, 81377 München, Germany; Faculty of Biology, Ludwig-Maximilians-Universität, 81377 München, Germany
| | - Charles N Baroud
- LadHyX, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France; Physical Microfluidics and Bioengineering Unit, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Anne Dejean
- Nuclear Organization and Oncogenesis Unit, Department of Cell Biology and Infection, Equipe Labellisée Ligue Nationale Contre le Cancer, Institut Pasteur, Université Paris Cité, 75015 Paris, France; INSERM, U993, 75015 Paris, France.
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12
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Shutta KH, Weighill D, Burkholz R, Guebila M, DeMeo DL, Zacharias HU, Quackenbush J, Altenbuchinger M. DRAGON: Determining Regulatory Associations using Graphical models on multi-Omic Networks. Nucleic Acids Res 2022; 51:e15. [PMID: 36533448 PMCID: PMC9943674 DOI: 10.1093/nar/gkac1157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
The increasing quantity of multi-omic data, such as methylomic and transcriptomic profiles collected on the same specimen or even on the same cell, provides a unique opportunity to explore the complex interactions that define cell phenotype and govern cellular responses to perturbations. We propose a network approach based on Gaussian Graphical Models (GGMs) that facilitates the joint analysis of paired omics data. This method, called DRAGON (Determining Regulatory Associations using Graphical models on multi-Omic Networks), calibrates its parameters to achieve an optimal trade-off between the network's complexity and estimation accuracy, while explicitly accounting for the characteristics of each of the assessed omics 'layers.' In simulation studies, we show that DRAGON adapts to edge density and feature size differences between omics layers, improving model inference and edge recovery compared to state-of-the-art methods. We further demonstrate in an analysis of joint transcriptome - methylome data from TCGA breast cancer specimens that DRAGON can identify key molecular mechanisms such as gene regulation via promoter methylation. In particular, we identify Transcription Factor AP-2 Beta (TFAP2B) as a potential multi-omic biomarker for basal-type breast cancer. DRAGON is available as open-source code in Python through the Network Zoo package (netZooPy v0.8; netzoo.github.io).
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Affiliation(s)
| | | | - Rebekka Burkholz
- CISPA Helmholtz Center for Information Security, Saarbrücken, Germany
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital, and Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Helena U Zacharias
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany,Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany,Peter L. Reichertz Institute for Medical Informatics of TU Braunschweig and Hannover Medical School, Hannover, Germany
| | | | - Michael Altenbuchinger
- To whom correspondence should be addressed. Tel: +49 551 39 61788; Fax: +49 551 39 61783;
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Di Risi T, Cuomo M, Vinciguerra R, Ferraro S, Della Monica R, Costabile D, Buonaiuto M, Trio F, Capoluongo E, Visconti R, Riccio E, Pisani A, Chiariotti L. Methylome Profiling in Fabry Disease in Clinical Practice: A Proof of Concept. Int J Mol Sci 2022; 23:ijms232012110. [PMID: 36292965 PMCID: PMC9602470 DOI: 10.3390/ijms232012110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/04/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Anderson−Fabry disease (FD) is an X-linked disease caused by a functional deficit of the α-galactosidase A enzyme. FD diagnosis relies on the clinical manifestations and research of GLA gene mutations. However, because of the lack of a clear genotype/phenotype correlation, FD diagnosis can be challenging. Recently, several studies have highlighted the importance of investigating DNA methylation patterns for confirming the correct diagnosis of different rare Mendelian diseases, but to date, no such studies have been reported for FD. Thus, in the present investigation, we analyzed for the first time the genome-wide methylation profile of a well-characterized cohort of patients with Fabry disease. We profiled the methylation status of about 850,000 CpG sites in 5 FD patients, all carrying the same mutation in the GLA gene (exon 6 c.901C>G) and presenting comparable low levels of α-Gal A activity. We found that, although the whole methylome profile did not discriminate the FD group from the unaffected one, several genes were significantly differentially methylated in Fabry patients. Thus, we provide here a proof of concept, to be tested in patients with different mutations and in a larger cohort, that the methylation state of specific genes can potentially identify Fabry patients and possibly predict organ involvement and disease evolution.
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Affiliation(s)
- Teodolinda Di Risi
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Mariella Cuomo
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | | | - Sara Ferraro
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Davide Costabile
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- SEMM-European School of Molecular Medicine, University Federico II, 80145 Naples, Italy
| | - Michela Buonaiuto
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
| | - Federica Trio
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
| | - Ettore Capoluongo
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Department of Clinical Pathology and Genomics, Azienda Ospedaliera per L’Emergenza Cannizzaro, 95126 Catania, Italy
| | - Roberta Visconti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Institute for the Experimental Endocrinology and Oncology, Italian National Council of Research, 80131 Naples, Italy
| | - Eleonora Riccio
- Institute for Biomedical Research and Innovation, Italian National Research Council, 90146 Palermo, Italy
| | - Antonio Pisani
- Department of Public Health, University Federico II, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- CEINGE, Biotecnologie Avanzate, Via Gaetano Salvatore, 80145 Naples, Italy
- Department of Molecular Medicine and Medical Biotechnologies, University Federico II, 80131 Naples, Italy
- Correspondence:
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14
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Dopkins N, O’Mara MM, Lawrence E, Fei T, Sandoval-Motta S, Nixon DF, Bendall ML. A field guide to endogenous retrovirus regulatory networks. Mol Cell 2022; 82:3763-3768. [DOI: 10.1016/j.molcel.2022.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 11/06/2022]
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15
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Kaplun DS, Kaluzhny DN, Prokhortchouk EB, Zhenilo SV. DNA Methylation: Genomewide Distribution, Regulatory Mechanism and Therapy Target. Acta Naturae 2022; 14:4-19. [PMID: 36694897 PMCID: PMC9844086 DOI: 10.32607/actanaturae.11822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/29/2022] [Indexed: 01/22/2023] Open
Abstract
DNA methylation is the most important epigenetic modification involved in the regulation of transcription, imprinting, establishment of X-inactivation, and the formation of a chromatin structure. DNA methylation in the genome is often associated with transcriptional repression and the formation of closed heterochromatin. However, the results of genome-wide studies of the DNA methylation pattern and transcriptional activity of genes have nudged us toward reconsidering this paradigm, since the promoters of many genes remain active despite their methylation. The differences in the DNA methylation distribution in normal and pathological conditions allow us to consider methylation as a diagnostic marker or a therapy target. In this regard, the need to investigate the factors affecting DNA methylation and those involved in its interpretation becomes pressing. Recently, a large number of protein factors have been uncovered, whose ability to bind to DNA depends on their methylation. Many of these proteins act not only as transcriptional activators or repressors, but also affect the level of DNA methylation. These factors are considered potential therapeutic targets for the treatment of diseases resulting from either a change in DNA methylation or a change in the interpretation of its methylation level. In addition to protein factors, a secondary DNA structure can also affect its methylation and can be considered as a therapy target. In this review, the latest research into the DNA methylation landscape in the genome has been summarized to discuss why some DNA regions avoid methylation and what factors can affect its level or interpretation and, therefore, can be considered a therapy target.
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Affiliation(s)
- D. S. Kaplun
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - D. N. Kaluzhny
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
| | - S. V. Zhenilo
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, 119071 Russia
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119071 Russia
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16
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Acurzio B, Cecere F, Giaccari C, Verma A, Russo R, Valletta M, Hay Mele B, Angelini C, Chambery A, Riccio A. The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex. Epigenetics Chromatin 2022; 15:27. [PMID: 35918739 PMCID: PMC9344765 DOI: 10.1186/s13072-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00462-7.
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Affiliation(s)
- Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Rosita Russo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", 80126, Naples, Italy
| | - Claudia Angelini
- Istituto Per Le Applicazioni del Calcolo "Mauro Picone" (IAC), CNR, 80131, Naples, Italy
| | - Angela Chambery
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy.
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17
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Kojima S, Shiochi N, Sato K, Yamaura M, Ito T, Yamamura N, Goto N, Odamoto M, Kobayashi S, Kimura T, Sekita Y. Epigenome editing reveals core DNA methylation for imprinting control in the Dlk1-Dio3 imprinted domain. Nucleic Acids Res 2022; 50:5080-5094. [PMID: 35544282 PMCID: PMC9122602 DOI: 10.1093/nar/gkac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/03/2022] [Accepted: 04/24/2022] [Indexed: 11/12/2022] Open
Abstract
The Dlk1-Dio3 imprinted domain is controlled by an imprinting control region (ICR) called IG-DMR that is hypomethylated on the maternal allele and hypermethylated on the paternal allele. Although several genetic mutation experiments have shown that IG-DMR is essential for imprinting control of the domain, how DNA methylation itself functions has not been elucidated. Here, we performed both gain and loss of DNA methylation experiments targeting IG-DMR by transiently introducing CRISPR/Cas9 based-targeted DNA methylation editing tools along with one guide RNA into mouse ES cells. Altered DNA methylation, particularly at IG-DMR-Rep, which is a tandem repeat containing ZFP57 methylated DNA-binding protein binding motifs, affected the imprinting state of the whole domain, including DNA methylation, imprinted gene expression, and histone modifications. Moreover, the altered imprinting states were persistent through neuronal differentiation. Our results suggest that the DNA methylation state at IG-DMR-Rep, but not other sites in IG-DMR, is a master element to determine whether the allele behaves as the intrinsic maternal or paternal allele. Meanwhile, this study provides a robust strategy and methodology to study core DNA methylation in cis-regulatory elements, such as ICRs and enhancers.
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Affiliation(s)
- Shin Kojima
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoya Shiochi
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Kazuki Sato
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mamiko Yamaura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Toshiaki Ito
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Nodoka Yamamura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Naoki Goto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Mika Odamoto
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Shin Kobayashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koutou-ku, Tokyo 135-0064, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Yoichi Sekita
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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18
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Subnuclear localisation is associated with gene expression more than parental origin at the imprinted Dlk1-Dio3 locus. PLoS Genet 2022; 18:e1010186. [PMID: 35482825 PMCID: PMC9129038 DOI: 10.1371/journal.pgen.1010186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 05/24/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
At interphase, de-condensed chromosomes have a non-random three-dimensional architecture within the nucleus, however, little is known about the extent to which nuclear organisation might influence expression or vice versa. Here, using imprinting as a model, we use 3D RNA- and DNA-fluorescence-in-situ-hybridisation in normal and mutant mouse embryonic stem cell lines to assess the relationship between imprinting control, gene expression and allelic distance from the nuclear periphery. We compared the two parentally inherited imprinted domains at the Dlk1-Dio3 domain and find a small but reproducible trend for the maternally inherited domain to be further away from the periphery however we did not observe an enrichment of inactive alleles in the immediate vicinity of the nuclear envelope. Using Zfp57KO ES cells, which harbour a paternal to maternal epigenotype switch, we observe that expressed alleles are significantly further away from the nuclear periphery. However, within individual nuclei, alleles closer to the periphery are equally likely to be expressed as those further away. In other words, absolute position does not predict expression. Taken together, this suggests that whilst stochastic activation can cause subtle shifts in localisation for this locus, there is no dramatic relocation of alleles upon gene activation. Our results suggest that transcriptional activity, rather than the parent-of-origin, defines subnuclear localisation at an endogenous imprinted domain. Genomic imprinting is an epigenetically regulated process that results in the preferential expression of a subset of developmentally regulated genes from either the maternally or the paternally inherited chromosomes. We have used imprinted genes as a model system to investigate the relationship between the parental origin of the chromosomes, the localisation of genes within the cell nucleus and their active expression. By assessing the location of the Dlk1-Dio3 region and the expression of the Gtl2/Meg3 gene within it, we find that there is a small preference for the paternal chromosome to be closer to the periphery but a significant correlation between transcription and distance to the edge of the nucleus for the Gtl2/Meg3 gene. Furthermore, a chromosome nearer the periphery is just as likely to express the gene as the chromosome further away. These findings suggest that the parental origin of the chromosome may not be as important as the transcription of the gene in defining the position of the imprinted region within the nucleus.
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Silver MJ, Saffari A, Kessler NJ, Chandak GR, Fall CHD, Issarapu P, Dedaniya A, Betts M, Moore SE, Routledge MN, Herceg Z, Cuenin C, Derakhshan M, James PT, Monk D, Prentice AM. Environmentally sensitive hotspots in the methylome of the early human embryo. eLife 2022; 11:e72031. [PMID: 35188105 PMCID: PMC8912923 DOI: 10.7554/elife.72031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/18/2022] [Indexed: 11/26/2022] Open
Abstract
In humans, DNA methylation marks inherited from gametes are largely erased following fertilisation, prior to construction of the embryonic methylome. Exploiting a natural experiment of seasonal variation including changes in diet and nutritional status in rural Gambia, we analysed three datasets covering two independent child cohorts and identified 259 CpGs showing consistent associations between season of conception (SoC) and DNA methylation. SoC effects were most apparent in early infancy, with evidence of attenuation by mid-childhood. SoC-associated CpGs were enriched for metastable epialleles, parent-of-origin-specific methylation and germline differentially methylated regions, supporting a periconceptional environmental influence. Many SoC-associated CpGs overlapped enhancers or sites of active transcription in H1 embryonic stem cells and fetal tissues. Half were influenced but not determined by measured genetic variants that were independent of SoC. Environmental 'hotspots' providing a record of environmental influence at periconception constitute a valuable resource for investigating epigenetic mechanisms linking early exposures to lifelong health and disease.
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Affiliation(s)
- Matt J Silver
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Ayden Saffari
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Noah J Kessler
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Gririraj R Chandak
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Caroline HD Fall
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General HospitalSouthamptonUnited Kingdom
| | - Prachand Issarapu
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Akshay Dedaniya
- Genomic Research on Complex Diseases, CSIR-Centre for Cellular and Molecular BiologyHyderabadIndia
| | - Modupeh Betts
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Sophie E Moore
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
- Department of Women and Children's Health, King's College LondonLondonUnited Kingdom
| | - Michael N Routledge
- School of Medicine, University of LeedsLeedsUnited Kingdom
- School of Food and Biological Engineering, Jiangsu UniversityZhenjiangChina
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency For Research On CancerLyonFrance
| | - Maria Derakhshan
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - Philip T James
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
| | - David Monk
- Biomedical Research Centre, University of East AngliaNorwichUnited Kingdom
- Bellvitge Institute for Biomedical ResearchBarcelonaSpain
| | - Andrew M Prentice
- Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical MedicineGambiaUnited Kingdom
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20
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Hawe JS, Wilson R, Schmid KT, Zhou L, Lakshmanan LN, Lehne BC, Kühnel B, Scott WR, Wielscher M, Yew YW, Baumbach C, Lee DP, Marouli E, Bernard M, Pfeiffer L, Matías-García PR, Autio MI, Bourgeois S, Herder C, Karhunen V, Meitinger T, Prokisch H, Rathmann W, Roden M, Sebert S, Shin J, Strauch K, Zhang W, Tan WLW, Hauck SM, Merl-Pham J, Grallert H, Barbosa EGV, Illig T, Peters A, Paus T, Pausova Z, Deloukas P, Foo RSY, Jarvelin MR, Kooner JS, Loh M, Heinig M, Gieger C, Waldenberger M, Chambers JC. Genetic variation influencing DNA methylation provides insights into molecular mechanisms regulating genomic function. Nat Genet 2022; 54:18-29. [PMID: 34980917 DOI: 10.1038/s41588-021-00969-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/18/2021] [Indexed: 02/07/2023]
Abstract
We determined the relationships between DNA sequence variation and DNA methylation using blood samples from 3,799 Europeans and 3,195 South Asians. We identify 11,165,559 SNP-CpG associations (methylation quantitative trait loci (meQTL), P < 10-14), including 467,915 meQTL that operate in trans. The meQTL are enriched for functionally relevant characteristics, including shared chromatin state, High-throuhgput chromosome conformation interaction, and association with gene expression, metabolic variation and clinical traits. We use molecular interaction and colocalization analyses to identify multiple nuclear regulatory pathways linking meQTL loci to phenotypic variation, including UBASH3B (body mass index), NFKBIE (rheumatoid arthritis), MGA (blood pressure) and COMMD7 (white cell counts). For rs6511961 , chromatin immunoprecipitation followed by sequencing (ChIP-seq) validates zinc finger protein (ZNF)333 as the likely trans acting effector protein. Finally, we used interaction analyses to identify population- and lineage-specific meQTL, including rs174548 in FADS1, with the strongest effect in CD8+ T cells, thus linking fatty acid metabolism with immune dysregulation and asthma. Our study advances understanding of the potential pathways linking genetic variation to human phenotype.
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Affiliation(s)
- Johann S Hawe
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching bei München, Germany
| | - Rory Wilson
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Katharina T Schmid
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, Neuherberg, Germany
- Department of Informatics, Technical University of Munich, Garching bei München, Germany
| | - Li Zhou
- Lee Kong Chian School of Medicine, Singapore, Singapore
| | | | - Benjamin C Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Brigitte Kühnel
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - William R Scott
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
| | - Yik Weng Yew
- Lee Kong Chian School of Medicine, Singapore, Singapore
| | - Clemens Baumbach
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | | | - Eirini Marouli
- Centre for Genomic Health, Queen Mary University of London, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Manon Bernard
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Liliane Pfeiffer
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Pamela R Matías-García
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Matias I Autio
- Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Research Institute, National University Health Systems, National University of Singapore, Singapore, Singapore
| | - Stephane Bourgeois
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Christian Herder
- German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Ville Karhunen
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Holger Prokisch
- Institute of Human Genetics, Technical University Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Wolfgang Rathmann
- German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Michael Roden
- German Center for Diabetes Research (DZD), partner site Düsseldorf, Düsseldorf, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine University, Düsseldorf, Germany
- Division of Endocrinology and Diabetology, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department for Genomics of Common Diseases, School of Public Health, Imperial College London, London, UK
| | - Jean Shin
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Konstantin Strauch
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, Germany
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Johannes Gutenberg University, Mainz, Germany
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UK
| | | | - Stefanie M Hauck
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Centre for Environmental Health, Munich, Germany
| | - Juliane Merl-Pham
- Research Unit Protein Science, Helmholtz Zentrum München, German Research Centre for Environmental Health, Munich, Germany
| | - Harald Grallert
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Munich-Neuherberg, Germany
| | - Eudes G V Barbosa
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- Institute for Human Genetics, Hannover Medical School, Hannover, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Hannover, Germany
| | - Tomas Paus
- Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Canada
| | - Zdenka Pausova
- Departments of Physiology and Nutritional Sciences, University of Toronto, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Panos Deloukas
- Centre for Genomic Health, Queen Mary University of London, London, UK
- William Harvey Research Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Roger S Y Foo
- Genome Institute of Singapore, Singapore, Singapore
- Cardiovascular Research Institute, National University Health Systems, National University of Singapore, Singapore, Singapore
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jaspal S Kooner
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Marie Loh
- Lee Kong Chian School of Medicine, Singapore, Singapore.
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
| | - Matthias Heinig
- Institute of Computational Biology, Deutsches Forschungszentrum für Gesundheit und Umwelt, Helmholtz Zentrum München, Neuherberg, Germany.
- Department of Informatics, Technical University of Munich, Garching bei München, Germany.
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany.
| | - Melanie Waldenberger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany.
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Hannover, Germany.
| | - John C Chambers
- Lee Kong Chian School of Medicine, Singapore, Singapore.
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
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21
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Butz S, Schmolka N, Karemaker ID, Villaseñor R, Schwarz I, Domcke S, Uijttewaal ECH, Jude J, Lienert F, Krebs AR, de Wagenaar NP, Bao X, Zuber J, Elling U, Schübeler D, Baubec T. DNA sequence and chromatin modifiers cooperate to confer epigenetic bistability at imprinting control regions. Nat Genet 2022; 54:1702-1710. [PMID: 36333500 PMCID: PMC9649441 DOI: 10.1038/s41588-022-01210-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 09/19/2022] [Indexed: 11/06/2022]
Abstract
Genomic imprinting is regulated by parental-specific DNA methylation of imprinting control regions (ICRs). Despite an identical DNA sequence, ICRs can exist in two distinct epigenetic states that are memorized throughout unlimited cell divisions and reset during germline formation. Here, we systematically study the genetic and epigenetic determinants of this epigenetic bistability. By iterative integration of ICRs and related DNA sequences to an ectopic location in the mouse genome, we first identify the DNA sequence features required for maintenance of epigenetic states in embryonic stem cells. The autonomous regulatory properties of ICRs further enabled us to create DNA-methylation-sensitive reporters and to screen for key components involved in regulating their epigenetic memory. Besides DNMT1, UHRF1 and ZFP57, we identify factors that prevent switching from methylated to unmethylated states and show that two of these candidates, ATF7IP and ZMYM2, are important for the stability of DNA and H3K9 methylation at ICRs in embryonic stem cells.
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Affiliation(s)
- Stefan Butz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Nina Schmolka
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.7400.30000 0004 1937 0650Present Address: Institute of Experimental Immunology, University of Zurich, Zurich, Switzerland
| | - Ino D. Karemaker
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Rodrigo Villaseñor
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland ,grid.5252.00000 0004 1936 973XPresent Address: Division of Molecular Biology, Biomedical Center Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Isabel Schwarz
- grid.7400.30000 0004 1937 0650Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Silvia Domcke
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland ,grid.34477.330000000122986657Present Address: Department of Genome Sciences, University of Washington, Seattle, WA USA
| | - Esther C. H. Uijttewaal
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julian Jude
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Florian Lienert
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R. Krebs
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.4709.a0000 0004 0495 846XPresent Address: European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Nathalie P. de Wagenaar
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Xue Bao
- grid.5477.10000000120346234Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands
| | - Johannes Zuber
- grid.14826.390000 0000 9799 657XResearch Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- grid.473822.80000 0005 0375 3232Institute of Molecular Biotechnology Austria (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- grid.482245.d0000 0001 2110 3787Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland ,grid.6612.30000 0004 1937 0642Faculty of Science, University of Basel, Basel, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland. .,Division of Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Science Faculty, Utrecht University, Utrecht, the Netherlands.
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22
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Puri D, Koschorz B, Engist B, Onishi-Seebacher M, Ryan D, Soujanya M, Montavon T. Foxd3 controls heterochromatin-mediated repression of repeat elements and 2-cell state transcription. EMBO Rep 2021; 22:e53180. [PMID: 34605600 PMCID: PMC8647145 DOI: 10.15252/embr.202153180] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/18/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Repeat element transcription plays a vital role in early embryonic development. The expression of repeats such as MERVL characterises mouse embryos at the 2‐cell stage and defines a 2‐cell‐like cell (2CLC) population in a mouse embryonic stem cell culture. Repeat element sequences contain binding sites for numerous transcription factors. We identify the forkhead domain transcription factor FOXD3 as a regulator of major satellite repeats and MERVL transcription in mouse embryonic stem cells. FOXD3 binds to and recruits the histone methyltransferase SUV39H1 to MERVL and major satellite repeats, consequentially repressing the transcription of these repeats by the establishment of the H3K9me3 heterochromatin modification. Notably, depletion of FOXD3 leads to the de‐repression of MERVL and major satellite repeats as well as a subset of genes expressed in the 2‐cell state, shifting the balance between the stem cell and 2‐cell‐like population in culture. Thus, FOXD3 acts as a negative regulator of repeat transcription, ascribing a novel function to this transcription factor.
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Affiliation(s)
- Deepika Puri
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany.,National Centre for Cell Science, Savitribai Phule Pune University, Pune, India
| | - Birgit Koschorz
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Bettina Engist
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Megumi Onishi-Seebacher
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | - Devon Ryan
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
| | | | - Thomas Montavon
- Department of Epigenetics, Max Planck Institute for Immunobiology and Epigenetics, Freiburg, Germany
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23
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Zhang H, Li Y, Ma Y, Lai C, Yu Q, Shi G, Li J. Epigenetic integrity of paternal imprints enhances the developmental potential of androgenetic haploid embryonic stem cells. Protein Cell 2021; 13:102-119. [PMID: 34865203 PMCID: PMC8783938 DOI: 10.1007/s13238-021-00890-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/26/2021] [Indexed: 11/24/2022] Open
Abstract
The use of two inhibitors of Mek1/2 and Gsk3β (2i) promotes the generation of mouse diploid and haploid embryonic stem cells (ESCs) from the inner cell mass of biparental and uniparental blastocysts, respectively. However, a system enabling long-term maintenance of imprints in ESCs has proven challenging. Here, we report that the use of a two-step a2i (alternative two inhibitors of Src and Gsk3β, TSa2i) derivation/culture protocol results in the establishment of androgenetic haploid ESCs (AG-haESCs) with stable DNA methylation at paternal DMRs (differentially DNA methylated regions) up to passage 60 that can efficiently support generating mice upon oocyte injection. We also show coexistence of H3K9me3 marks and ZFP57 bindings with intact DMR methylations. Furthermore, we demonstrate that TSa2i-treated AG-haESCs are a heterogeneous cell population regarding paternal DMR methylation. Strikingly, AG-haESCs with late passages display increased paternal-DMR methylations and improved developmental potential compared to early-passage cells, in part through the enhanced proliferation of H19-DMR hypermethylated cells. Together, we establish AG-haESCs that can long-term maintain paternal imprints.
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Affiliation(s)
- Hongling Zhang
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuanyuan Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yongjian Ma
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Chongping Lai
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qian Yu
- Animal Core Facility, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Guangyong Shi
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jinsong Li
- State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
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24
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Aronson BE, Scourzic L, Shah V, Swanzey E, Kloetgen A, Polyzos A, Sinha A, Azziz A, Caspi I, Li J, Pelham-Webb B, Glenn RA, Vierbuchen T, Wichterle H, Tsirigos A, Dawlaty MM, Stadtfeld M, Apostolou E. A bipartite element with allele-specific functions safeguards DNA methylation imprints at the Dlk1-Dio3 locus. Dev Cell 2021; 56:3052-3065.e5. [PMID: 34710357 PMCID: PMC8628258 DOI: 10.1016/j.devcel.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/23/2022]
Abstract
Loss of imprinting (LOI) results in severe developmental defects, but the mechanisms preventing LOI remain incompletely understood. Here, we dissect the functional components of the imprinting control region of the essential Dlk1-Dio3 locus (called IG-DMR) in pluripotent stem cells. We demonstrate that the IG-DMR consists of two antagonistic elements: a paternally methylated CpG island that prevents recruitment of TET dioxygenases and a maternally unmethylated non-canonical enhancer that ensures expression of the Gtl2 lncRNA by counteracting de novo DNA methyltransferases. Genetic or epigenetic editing of these elements leads to distinct LOI phenotypes with characteristic alternations of allele-specific gene expression, DNA methylation, and 3D chromatin topology. Although repression of the Gtl2 promoter results in dysregulated imprinting, the stability of LOI phenotypes depends on the IG-DMR, suggesting a functional hierarchy. These findings establish the IG-DMR as a bipartite control element that maintains imprinting by allele-specific restriction of the DNA (de)methylation machinery.
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Affiliation(s)
- Boaz E Aronson
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Laurianne Scourzic
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Veevek Shah
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Emily Swanzey
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA; The Jackson Laboratory, Bar Harbor, ME, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Department of Computational Biology of Infection Research, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alexander Polyzos
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Abhishek Sinha
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Annabel Azziz
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA
| | - Inbal Caspi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jiexi Li
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA
| | - Bobbie Pelham-Webb
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY, USA
| | - Rachel A Glenn
- Weill Cornell Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Thomas Vierbuchen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hynek Wichterle
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, Neuroscience and Rehabilitation and Regenerative Medicine, Columbia University Irving Medical Center, Center for Motor Neuron Biology and Disease and Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Institute for Computational Medicine and Applied Bioinformatics Laboratories, New York University School of Medicine, New York, NY 10016, USA
| | - Meelad M Dawlaty
- Ruth L and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Bronx, NY 10461, USA; Department of Genetics, Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Matthias Stadtfeld
- Sanford I Weill Department of Medicine, Division of Regenerative Medicine, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Effie Apostolou
- Sanford I Weill Department of Medicine, Division of Hematology/Oncology, Sandra and Edward Meyer Cancer Center, New York, NY 10021, USA.
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25
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Identifying regulators of parental imprinting by CRISPR/Cas9 screening in haploid human embryonic stem cells. Nat Commun 2021; 12:6718. [PMID: 34795250 PMCID: PMC8602306 DOI: 10.1038/s41467-021-26949-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 10/28/2021] [Indexed: 12/13/2022] Open
Abstract
In mammals, imprinted genes are regulated by differentially methylated regions (DMRs) that are inherited from germ cells, leading to monoallelic expression in accordance with parent-of-origin. Yet, it is largely unknown how imprinted DMRs are maintained in human embryos despite global DNA demethylation following fertilization. Here, we explored the mechanisms involved in imprinting regulation by employing human parthenogenetic embryonic stem cells (hpESCs), which lack paternal alleles. We show that although global loss of DNA methylation in hpESCs affects most imprinted DMRs, many paternally-expressed genes (PEGs) remain repressed. To search for factors regulating PEGs, we performed a genome-wide CRISPR/Cas9 screen in haploid hpESCs. This revealed ATF7IP as an essential repressor of a set of PEGs, which we further show is also required for silencing sperm-specific genes. Our study reinforces an important role for histone modifications in regulating imprinted genes and suggests a link between parental imprinting and germ cell identity. Genetic imprinting ensures monoallelic gene expression critical for normal embryonic development. Here the authors take advantage of human haploid parthenogenic embryonic stem cells lacking paternal alleles to identify, by genome-wide screening, factors involved in the regulation of imprinted genes.
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26
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Senft AD, Macfarlan TS. Transposable elements shape the evolution of mammalian development. Nat Rev Genet 2021; 22:691-711. [PMID: 34354263 DOI: 10.1038/s41576-021-00385-1] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Transposable elements (TEs) promote genetic innovation but also threaten genome stability. Despite multiple layers of host defence, TEs actively shape mammalian-specific developmental processes, particularly during pre-implantation and extra-embryonic development and at the maternal-fetal interface. Here, we review how TEs influence mammalian genomes both directly by providing the raw material for genetic change and indirectly via co-evolving TE-binding Krüppel-associated box zinc finger proteins (KRAB-ZFPs). Throughout mammalian evolution, individual activities of ancient TEs were co-opted to enable invasive placentation that characterizes live-born mammals. By contrast, the widespread activity of evolutionarily young TEs may reflect an ongoing co-evolution that continues to impact mammalian development.
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Affiliation(s)
- Anna D Senft
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
| | - Todd S Macfarlan
- The Eunice Kennedy Shriver National Institute of Child Health and Human Development, The National Institutes of Health, Bethesda, MD, USA.
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27
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Robles-Matos N, Artis T, Simmons RA, Bartolomei MS. Environmental Exposure to Endocrine Disrupting Chemicals Influences Genomic Imprinting, Growth, and Metabolism. Genes (Basel) 2021; 12:1153. [PMID: 34440327 PMCID: PMC8393470 DOI: 10.3390/genes12081153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/26/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic imprinting is an epigenetic mechanism that results in monoallelic, parent-of-origin-specific expression of a small number of genes. Imprinted genes play a crucial role in mammalian development as their dysregulation result in an increased risk of human diseases. DNA methylation, which undergoes dynamic changes early in development, is one of the epigenetic marks regulating imprinted gene expression patterns during early development. Thus, environmental insults, including endocrine disrupting chemicals during critical periods of fetal development, can alter DNA methylation patterns, leading to inappropriate developmental gene expression and disease risk. Here, we summarize the current literature on the impacts of in utero exposure to endocrine disrupting chemicals on genomic imprinting and metabolism in humans and rodents. We evaluate how early-life environmental exposures are a potential risk factor for adult metabolic diseases. We also introduce our mouse model of phthalate exposure. Finally, we describe the potential of genomic imprinting to serve as an environmental sensor during early development and as a novel biomarker for postnatal health outcomes.
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Affiliation(s)
- Nicole Robles-Matos
- Epigenetics Institute, Center of Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-122 Smilow Center for Translational Research, Philadelphia, PA 19104, USA;
| | - Tre Artis
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
| | - Rebecca A. Simmons
- Center of Excellence in Environmental Toxicology, Department of Pediatrics, Children’s Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, 1308 Biomedical Research Building II/III, Philadelphia, PA 19104, USA;
| | - Marisa S. Bartolomei
- Epigenetics Institute, Center of Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-122 Smilow Center for Translational Research, Philadelphia, PA 19104, USA;
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Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs. Sci Rep 2021; 11:13802. [PMID: 34226608 PMCID: PMC8257706 DOI: 10.1038/s41598-021-93297-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/23/2021] [Indexed: 12/05/2022] Open
Abstract
ZFP57 is required to maintain the germline-marked differential methylation at imprinting control regions (ICRs) in mouse embryonic stem cells (ESCs). Although DNA methylation has a key role in genomic imprinting, several imprinted genes are controlled by different mechanisms, and a comprehensive study of the relationship between DMR methylation and imprinted gene expression is lacking. To address the latter issue, we differentiated wild-type and Zfp57-/- hybrid mouse ESCs into neural precursor cells (NPCs) and evaluated allelic expression of imprinted genes. In mutant NPCs, we observed a reduction of allelic bias of all the 32 genes that were imprinted in wild-type cells, demonstrating that ZFP57-dependent methylation is required for maintaining or acquiring imprinted gene expression during differentiation. Analysis of expression levels showed that imprinted genes expressed from the non-methylated chromosome were generally up-regulated, and those expressed from the methylated chromosome were down-regulated in mutant cells. However, expression levels of several imprinted genes acquiring biallelic expression were not affected, suggesting the existence of compensatory mechanisms that control their RNA level. Since neural differentiation was partially impaired in Zfp57-mutant cells, this study also indicates that imprinted genes and/or non-imprinted ZFP57-target genes are required for proper neurogenesis in cultured ESCs.
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29
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Abstract
Genomic imprinting is the monoallelic expression of a gene based on parent of origin and is a consequence of differential epigenetic marking between the male and female germlines. Canonically, genomic imprinting is mediated by allelic DNA methylation. However, recently it has been shown that maternal H3K27me3 can result in DNA methylation-independent imprinting, termed "noncanonical imprinting." In this review, we compare and contrast what is currently known about the underlying mechanisms, the role of endogenous retroviral elements, and the conservation of canonical and noncanonical genomic imprinting.
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Affiliation(s)
- Courtney W Hanna
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
| | - Gavin Kelsey
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom
- Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, United Kingdom
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30
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Stäubli A, Peters AHFM. Mechanisms of maternal intergenerational epigenetic inheritance. Curr Opin Genet Dev 2021; 67:151-162. [DOI: 10.1016/j.gde.2021.01.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 12/20/2022]
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31
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Galan C, Serra RW, Sun F, Rinaldi VD, Conine CC, Rando OJ. Stability of the cytosine methylome during post-testicular sperm maturation in mouse. PLoS Genet 2021; 17:e1009416. [PMID: 33661909 PMCID: PMC7963034 DOI: 10.1371/journal.pgen.1009416] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 03/16/2021] [Accepted: 02/14/2021] [Indexed: 12/28/2022] Open
Abstract
Beyond the haploid genome, mammalian sperm carry a payload of epigenetic information with the potential to modulate offspring phenotypes. Recent studies show that the small RNA repertoire of sperm is remodeled during post-testicular maturation in the epididymis. Epididymal maturation has also been linked to changes in the sperm methylome, suggesting that the epididymis might play a broader role in shaping the sperm epigenome. Here, we characterize the genome-wide methylation landscape in seven germ cell populations from throughout the male reproductive tract. We find very few changes in the cytosine methylation landscape between testicular germ cell populations and cauda epididymal sperm, demonstrating that the sperm methylome is stable throughout post-testicular maturation. Although our sequencing data suggested that caput epididymal sperm exhibit a highly unusual methylome, follow-up studies revealed that this resulted from contamination of caput sperm by extracellular DNA. Extracellular DNA formed web-like structures that ensnared sperm, and was present only in sperm samples obtained from the caput epididymis and vas deferens of virgin males. Curiously, contaminating extracellular DNA was associated with citrullinated histone H3, potentially resulting from a PAD-driven genome decondensation process. Taken together, our data emphasize the stability of cytosine methylation in mammalian sperm, and identify a surprising, albeit transient, period during which sperm are associated with extracellular DNA.
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Affiliation(s)
- Carolina Galan
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Ryan W. Serra
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Fengyun Sun
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Vera D. Rinaldi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Colin C. Conine
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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32
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Hao Y, Lee HJ, Baraboo M, Burch K, Maurer T, Somarelli JA, Conant GC. Baby Genomics: Tracing the Evolutionary Changes That Gave Rise to Placentation. Genome Biol Evol 2021; 12:35-47. [PMID: 32053193 PMCID: PMC7144826 DOI: 10.1093/gbe/evaa026] [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] [Accepted: 02/02/2020] [Indexed: 12/12/2022] Open
Abstract
It has long been challenging to uncover the molecular mechanisms behind striking morphological innovations such as mammalian pregnancy. We studied the power of a robust comparative orthology pipeline based on gene synteny to address such problems. We inferred orthology relations between human genes and genes from each of 43 other vertebrate genomes, resulting in ∼18,000 orthologous pairs for each genome comparison. By identifying genes that first appear coincident with origin of the placental mammals, we hypothesized that we would define a subset of the genome enriched for genes that played a role in placental evolution. We thus pinpointed orthologs that appeared before and after the divergence of eutherian mammals from marsupials. Reinforcing previous work, we found instead that much of the genetic toolkit of mammalian pregnancy evolved through the repurposing of preexisting genes to new roles. These genes acquired regulatory controls for their novel roles from a group of regulatory genes, many of which did in fact originate at the appearance of the eutherians. Thus, orthologs appearing at the origin of the eutherians are enriched in functions such as transcriptional regulation by Krüppel-associated box-zinc-finger proteins, innate immune responses, keratinization, and the melanoma-associated antigen protein class. Because the cellular mechanisms of invasive placentae are similar to those of metastatic cancers, we then used our orthology inferences to explore the association between placenta invasion and cancer metastasis. Again echoing previous work, we find that genes that are phylogenetically older are more likely to be implicated in cancer development.
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Affiliation(s)
- Yue Hao
- Bioinformatics Research Center, North Carolina State University
| | - Hyuk Jin Lee
- Division of Biological Sciences, University of Missouri-Columbia
| | | | | | | | - Jason A Somarelli
- Duke Cancer Institute, Duke University Medical Center.,Department of Medicine, Duke University School of Medicine
| | - Gavin C Conant
- Bioinformatics Research Center, North Carolina State University.,Division of Animal Sciences, University of Missouri-Columbia.,Program in Genetics, North Carolina State University.,Department of Biological Sciences, North Carolina State University
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33
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Monteagudo-Sánchez A, Hernandez Mora JR, Simon C, Burton A, Tenorio J, Lapunzina P, Clark S, Esteller M, Kelsey G, López-Siguero JP, de Nanclares GP, Torres-Padilla ME, Monk D. The role of ZFP57 and additional KRAB-zinc finger proteins in the maintenance of human imprinted methylation and multi-locus imprinting disturbances. Nucleic Acids Res 2020; 48:11394-11407. [PMID: 33053156 PMCID: PMC7672439 DOI: 10.1093/nar/gkaa837] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/10/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
Genomic imprinting is an epigenetic process regulated by germline-derived DNA methylation that is resistant to embryonic reprogramming, resulting in parental origin-specific monoallelic gene expression. A subset of individuals affected by imprinting disorders (IDs) displays multi-locus imprinting disturbances (MLID), which may result from aberrant establishment of imprinted differentially methylated regions (DMRs) in gametes or their maintenance in early embryogenesis. Here we investigated the extent of MLID in a family harbouring a ZFP57 truncating variant and characterize the interactions between human ZFP57 and the KAP1 co-repressor complex. By ectopically targeting ZFP57 to reprogrammed loci in mouse embryos using a dCas9 approach, we confirm that ZFP57 recruitment is sufficient to protect oocyte-derived methylation from reprogramming. Expression profiling in human pre-implantation embryos and oocytes reveals that unlike in mice, ZFP57 is only expressed following embryonic-genome activation, implying that other KRAB-zinc finger proteins (KZNFs) recruit KAP1 prior to blastocyst formation. Furthermore, we uncover ZNF202 and ZNF445 as additional KZNFs likely to recruit KAP1 to imprinted loci during reprogramming in the absence of ZFP57. Together, these data confirm the perplexing link between KZFPs and imprint maintenance and highlight the differences between mouse and humans in this respect.
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Affiliation(s)
- Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University and INCLIVA, Valencia, Spain.,Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, München, Germany
| | - Jair Tenorio
- Medical and Molecular Genetics Institute, University Hospital La Paz, Madrid, Spain.,CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - Pablo Lapunzina
- Medical and Molecular Genetics Institute, University Hospital La Paz, Madrid, Spain.,CIBERER, Centro de Investigacion Biomedica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability
| | - Stephen Clark
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge, UK
| | - Manel Esteller
- Josep Carreras Leukeamia Research Institute, Can Ruti, Cami de les Escoles, Badalona, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Babraham, Cambridge, UK.,Centre for Trophoblast Research, University of Cambridge, UK
| | | | - Guiomar Perez de Nanclares
- (Epi)Genetics Laboratory, BioAraba Research Health Institute, Araba University Hospital, Vitoria-Gasteiz, Alava, Spain
| | | | - David Monk
- Imprinting and Cancer group, Bellvitge Institute for Biomedical Research, Gran via, L'Hospitalet de Llobregat, Barcelona, Spain.,Biomedical Research Centre, University of East Anglia, Norwich Research Park, Norwich, UK
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34
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An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility. Nat Commun 2020; 11:5095. [PMID: 33037201 PMCID: PMC7547087 DOI: 10.1038/s41467-020-18863-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 09/14/2020] [Indexed: 12/17/2022] Open
Abstract
Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Nucleosome turnover is known to be universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently at intracisternal A-particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28-KAP1/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. Further, we find that Smarcad1 chromatin remodeler evicts nucleosomes generating accessible DNA. Free DNA is repackaged via DAXX-mediated nucleosome assembly with histone variant H3.3 in this dynamic heterochromatin state. Loss of H3.3 in mouse embryonic stem cells elicits a highly specific opening of interstitial heterochromatin with minimal effects on other silent or active regions of the genome. Nucleosome turnover concomitant with incorporation of the histone variant H3.3 is a hallmark of regulatory regions in the animal genome. Here, the authors demonstrate that fast histone turnover and H3.3 incorporation defines a dynamic heterochromatin state in pluripotent stem cells.
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35
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Strain-Specific Epigenetic Regulation of Endogenous Retroviruses: The Role of Trans-Acting Modifiers. Viruses 2020; 12:v12080810. [PMID: 32727076 PMCID: PMC7472028 DOI: 10.3390/v12080810] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Approximately 10 percent of the mouse genome consists of endogenous retroviruses (ERVs), relics of ancient retroviral infections that are classified based on their relatedness to exogenous retroviral genera. Because of the ability of ERVs to retrotranspose, as well as their cis-acting regulatory potential due to functional elements located within the elements, mammalian ERVs are generally subject to epigenetic silencing by DNA methylation and repressive histone modifications. The mobilisation and expansion of ERV elements is strain-specific, leading to ERVs being highly polymorphic between inbred mouse strains, hinting at the possibility of the strain-specific regulation of ERVs. In this review, we describe the existing evidence of mouse strain-specific epigenetic control of ERVs and discuss the implications of differential ERV regulation on epigenetic inheritance models. We consider Krüppel-associated box domain (KRAB) zinc finger proteins as likely candidates for strain-specific ERV modifiers, drawing on insights gained from the study of the strain-specific behaviour of transgenes. We conclude by considering the coevolution of KRAB zinc finger proteins and actively transposing ERV elements, and highlight the importance of cross-strain studies in elucidating the mechanisms and consequences of strain-specific ERV regulation.
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36
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Pisano MP, Grandi N, Tramontano E. High-Throughput Sequencing is a Crucial Tool to Investigate the Contribution of Human Endogenous Retroviruses (HERVs) to Human Biology and Development. Viruses 2020; 12:E633. [PMID: 32545287 PMCID: PMC7354619 DOI: 10.3390/v12060633] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 01/19/2023] Open
Abstract
Human Endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that represent a large fraction of our genome. Their transcriptional activity is finely regulated in early developmental stages and their expression is modulated in different cell types and tissues. Such activity has an impact on human physiology and pathology that is only partially understood up to date. Novel high-throughput sequencing tools have recently allowed for a great advancement in elucidating the various HERV expression patterns in different tissues as well as the mechanisms controlling their transcription, and overall, have helped in gaining better insights in an all-inclusive understanding of the impact of HERVs in biology of the host.
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Affiliation(s)
- Maria Paola Pisano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Nicole Grandi
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
| | - Enzo Tramontano
- Laboratory of Molecular Virology, Department of Life and Environmental Sciences, University of Cagliari, 09042 Cagliari, Italy; (M.P.P.); (N.G.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, 09042 Cagliari, Italy
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37
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Biwer C, Kawam B, Chapelle V, Silvestre F. The Role of Stochasticity in the Origin of Epigenetic Variation in Animal Populations. Integr Comp Biol 2020; 60:1544-1557. [PMID: 32470118 DOI: 10.1093/icb/icaa047] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Epigenetic mechanisms such as DNA methylation modulate gene expression in a complex fashion are consequently recognized as among the most important contributors to phenotypic variation in natural populations of plants, animals, and microorganisms. Interactions between genetics and epigenetics are multifaceted and epigenetic variation stands at the crossroad between genetic and environmental variance, which make these mechanisms prominent in the processes of adaptive evolution. DNA methylation patterns depend on the genotype and can be reshaped by environmental conditions, while transgenerational epigenetic inheritance has been reported in various species. On the other hand, DNA methylation can influence the genetic mutation rate and directly affect the evolutionary potential of a population. The origin of epigenetic variance can be attributed to genetic, environmental, or stochastic factors. Generally less investigated than the first two components, variation lacking any predictable order is nevertheless present in natural populations and stochastic epigenetic variation, also referred to spontaneous epimutations, can sustain phenotypic diversity. Here, potential sources of such stochastic epigenetic variability in animals are explored, with a focus on DNA methylation. To this day, quantifying the importance of stochasticity in epigenetic variability remains a challenge. However, comparisons between the mutation and the epimutation rates showed a high level of the latter, suggesting a significant role of spontaneous epimutations in adaptation. The implications of stochastic epigenetic variability are multifold: by affecting development and subsequently phenotype, random changes in epigenetic marks may provide additional phenotypic diversity, which can help natural populations when facing fluctuating environments. In isogenic lineages and asexually reproducing organisms, poor or absent genetic diversity can hence be tolerated. Further implication of stochastic epigenetic variability in adaptation is found in bottlenecked invasive species populations and populations using a bet-hedging strategy.
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Affiliation(s)
| | | | | | - F Silvestre
- Institute of Earth, Life and Environment (ILEE), University of Namur, 61 rue de Bruxelles, Namur, 5000, Belgium
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38
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Farhadova S, Gomez-Velazquez M, Feil R. Stability and Lability of Parental Methylation Imprints in Development and Disease. Genes (Basel) 2019; 10:genes10120999. [PMID: 31810366 PMCID: PMC6947649 DOI: 10.3390/genes10120999] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/25/2019] [Accepted: 11/27/2019] [Indexed: 02/06/2023] Open
Abstract
DNA methylation plays essential roles in mammals. Of particular interest are parental methylation marks that originate from the oocyte or the sperm, and bring about mono-allelic gene expression at defined chromosomal regions. The remarkable somatic stability of these parental imprints in the pre-implantation embryo—where they resist global waves of DNA demethylation—is not fully understood despite the importance of this phenomenon. After implantation, some methylation imprints persist in the placenta only, a tissue in which many genes are imprinted. Again here, the underlying epigenetic mechanisms are not clear. Mouse studies have pinpointed the involvement of transcription factors, covalent histone modifications, and histone variants. These and other features linked to the stability of methylation imprints are instructive as concerns their conservation in humans, in which different congenital disorders are caused by perturbed parental imprints. Here, we discuss DNA and histone methylation imprints, and why unravelling maintenance mechanisms is important for understanding imprinting disorders in humans.
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