1
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Grand RS, Pregnolato M, Baumgartner L, Hoerner L, Burger L, Schübeler D. Genome access is transcription factor-specific and defined by nucleosome position. Mol Cell 2024; 84:3455-3468.e6. [PMID: 39208807 PMCID: PMC11420395 DOI: 10.1016/j.molcel.2024.08.009] [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: 07/28/2023] [Revised: 06/14/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024]
Abstract
Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable the binding of TFs with diverse tissue specificities, functions, and DNA-binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly phased nucleosome. The pluripotency factors OCT4-SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome-internal sites, a preference that also guides binding genome wide. By contrast, factors such as BANP, REST, or CTCF engage throughout, causing nucleosomal displacement. This supports that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF specific and influenced by nucleosome position in the cell.
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Affiliation(s)
- Ralph Stefan Grand
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marco Pregnolato
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland
| | - Lisa Baumgartner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Swiss Institute of Bioinformatics, 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4003 Basel, Switzerland.
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2
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Forero A, Pipicelli F, Moser S, Baumann N, Grätz C, Gonzalez Pisfil M, Pfaffl MW, Pütz B, Kielkowski P, Cernilogar FM, Maccarrone G, Di Giaimo R, Cappello S. Extracellular vesicle-mediated trafficking of molecular cues during human brain development. Cell Rep 2024; 43:114755. [PMID: 39302835 DOI: 10.1016/j.celrep.2024.114755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 07/03/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
Cellular crosstalk is an essential process influenced by numerous factors, including secreted vesicles that transfer nucleic acids, lipids, and proteins between cells. Extracellular vesicles (EVs) have been the center of many studies focusing on neurodegenerative disorders, but whether EVs display cell-type-specific features for cellular crosstalk during neurodevelopment is unknown. Here, using human-induced pluripotent stem cell-derived cerebral organoids, neural progenitors, neurons, and astrocytes, we identify heterogeneity in EV protein content and dynamics in a cell-type-specific and time-dependent manner. Our results support the trafficking of key molecules via EVs in neurodevelopment, such as the transcription factor YAP1, and their localization to differing cell compartments depending on the EV recipient cell type. This study sheds new light on the biology of EVs during human brain development.
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Affiliation(s)
- Andrea Forero
- Max Planck Institute of Psychiatry, Munich, Germany; Division of Physiological Genomics, Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University (LMU), Munich, Germany
| | - Fabrizia Pipicelli
- Max Planck Institute of Psychiatry, Munich, Germany; International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Sylvain Moser
- Max Planck Institute of Psychiatry, Munich, Germany; International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Natalia Baumann
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Christian Grätz
- Division of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig Maximilian University, Munich, Germany
| | - Michael W Pfaffl
- Division of Animal Physiology and Immunology, Technical University of Munich, Freising, Germany
| | - Benno Pütz
- Max Planck Institute of Psychiatry, Munich, Germany
| | - Pavel Kielkowski
- Department of Chemistry, Ludwig Maximilian University, Munich, Germany
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University, Munich, Germany; Department of Science and Technological Innovation, University of Piemonte Orientale, Alessandria, Italy
| | | | - Rossella Di Giaimo
- Max Planck Institute of Psychiatry, Munich, Germany; Department of Biology, University of Naples Federico II, Naples, Italy.
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Munich, Germany; Division of Physiological Genomics, Biomedical Center (BMC), Faculty of Medicine, Ludwig Maximilian University (LMU), Munich, Germany.
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3
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Freund MM, Harrison MM, Torres-Zelada EF. Exploring the reciprocity between pioneer factors and development. Development 2024; 151:dev201921. [PMID: 38958075 PMCID: PMC11266817 DOI: 10.1242/dev.201921] [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] [Indexed: 07/04/2024]
Abstract
Development is regulated by coordinated changes in gene expression. Control of these changes in expression is largely governed by the binding of transcription factors to specific regulatory elements. However, the packaging of DNA into chromatin prevents the binding of many transcription factors. Pioneer factors overcome this barrier owing to unique properties that enable them to bind closed chromatin, promote accessibility and, in so doing, mediate binding of additional factors that activate gene expression. Because of these properties, pioneer factors act at the top of gene-regulatory networks and drive developmental transitions. Despite the ability to bind target motifs in closed chromatin, pioneer factors have cell type-specific chromatin occupancy and activity. Thus, developmental context clearly shapes pioneer-factor function. Here, we discuss this reciprocal interplay between pioneer factors and development: how pioneer factors control changes in cell fate and how cellular environment influences pioneer-factor binding and activity.
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Affiliation(s)
- Meghan M. Freund
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
| | - Eliana F. Torres-Zelada
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 52706, USA
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4
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Kucinski JP, Calderon D, Kendall GC. Biological and therapeutic insights from animal modeling of fusion-driven pediatric soft tissue sarcomas. Dis Model Mech 2024; 17:dmm050704. [PMID: 38916046 PMCID: PMC11225592 DOI: 10.1242/dmm.050704] [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] [Indexed: 06/26/2024] Open
Abstract
Survival for children with cancer has primarily improved over the past decades due to refinements in surgery, radiation and chemotherapy. Although these general therapies are sometimes curative, the cancer often recurs, resulting in poor outcomes for patients. Fusion-driven pediatric soft tissue sarcomas are genetically defined by chromosomal translocations that create a chimeric oncogene. This distinctive, almost 'monogenic', genetic feature supports the generation of animal models to study the respective diseases in vivo. This Review focuses on a subset of fusion-driven pediatric soft tissue sarcomas that have transgenic animal tumor models, which includes fusion-positive and infantile rhabdomyosarcoma, synovial sarcoma, undifferentiated small round cell sarcoma, alveolar soft part sarcoma and clear cell sarcoma. Studies using the animal models of these sarcomas have highlighted that pediatric cancers require a specific cellular state or developmental stage to drive tumorigenesis, as the fusion oncogenes cause different outcomes depending on their lineage and timing of expression. Therefore, understanding these context-specific activities could identify targetable activities and mechanisms critical for tumorigenesis. Broadly, these cancers show dependencies on chromatin regulators to support oncogenic gene expression and co-opting of developmental pathways. Comparative analyses across lineages and tumor models will further provide biological and therapeutic insights to improve outcomes for these children.
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Affiliation(s)
- Jack P. Kucinski
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
| | - Delia Calderon
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
| | - Genevieve C. Kendall
- Center for Childhood Cancer Research, The Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH 43215, USA
- Molecular, Cellular, and Developmental Biology PhD Program, The Ohio State University, Columbus, OH 43210, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43215, USA
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5
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Wang L, Yi S, Cui X, Guo Z, Wang M, Kou X, Zhao Y, Wang H, Jiang C, Gao S, Yang G, Chen J, Gao R. Chromatin landscape instructs precise transcription factor regulome during embryonic lineage specification. Cell Rep 2024; 43:114136. [PMID: 38643480 DOI: 10.1016/j.celrep.2024.114136] [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: 11/29/2023] [Revised: 03/10/2024] [Accepted: 04/08/2024] [Indexed: 04/23/2024] Open
Abstract
Embryos, originating from fertilized eggs, undergo continuous cell division and differentiation, accompanied by dramatic changes in transcription, translation, and metabolism. Chromatin regulators, including transcription factors (TFs), play indispensable roles in regulating these processes. Recently, the trophoblast regulator TFAP2C was identified as crucial in initiating early cell fate decisions. However, Tfap2c transcripts persist in both the inner cell mass and trophectoderm of blastocysts, prompting inquiry into Tfap2c's function in post-lineage establishment. In this study, we delineate the dynamics of TFAP2C during the mouse peri-implantation stage and elucidate its collaboration with the key lineage regulators CDX2 and NANOG. Importantly, we propose that de novo formation of H3K9me3 in the extraembryonic ectoderm during implantation antagonizes TFAP2C binding to crucial developmental genes, thereby maintaining its lineage identity. Together, these results highlight the plasticity of the chromatin environment in designating the genomic binding of highly adaptable lineage-specific TFs and regulating embryonic cell fates.
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Affiliation(s)
- Liping Wang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shanru Yi
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xinyu Cui
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Zhenxiang Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mengting Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Cizhong Jiang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of the Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200065, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China; Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai East Hospital, Tongji University, Shanghai 200120, China.
| | - Guang Yang
- Shanghai Tenth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai 200072, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Rui Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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6
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Gibson TJ, Larson ED, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer factor binding and function. Nat Struct Mol Biol 2024; 31:548-558. [PMID: 38365978 PMCID: PMC11261375 DOI: 10.1038/s41594-024-01231-8] [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: 04/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type-specific binding and activity. The mechanisms governing pioneer factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of pioneering activity. Multiple factors regulate occupancy, including motif content, local chromatin and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.
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Affiliation(s)
- Tyler J Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
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7
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Barral A, Zaret KS. Pioneer factors: roles and their regulation in development. Trends Genet 2024; 40:134-148. [PMID: 37940484 PMCID: PMC10873006 DOI: 10.1016/j.tig.2023.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/06/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Pioneer factors are a subclass of transcription factors that can bind and initiate opening of silent chromatin regions. Pioneer factors subsequently regulate lineage-specific genes and enhancers and, thus, activate the zygotic genome after fertilization, guide cell fate transitions during development, and promote various forms of human cancers. As such, pioneer factors are useful in directed cell reprogramming. In this review, we define the structural and functional characteristics of pioneer factors, how they bind and initiate opening of closed chromatin regions, and the consequences for chromatin dynamics and gene expression during cell differentiation. We also discuss emerging mechanisms that modulate pioneer factors during development.
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Affiliation(s)
- Amandine Barral
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Boulevard, Philadelphia, PA 19104, USA.
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8
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Spencer TE, Lowke MT, Davenport KM, Dhakal P, Kelleher AM. Single-cell insights into epithelial morphogenesis in the neonatal mouse uterus. Proc Natl Acad Sci U S A 2023; 120:e2316410120. [PMID: 38019863 PMCID: PMC10710066 DOI: 10.1073/pnas.2316410120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The uterus is vital for successful reproduction in mammals, and two different types of epithelia (luminal and glandular) are essential for embryo implantation and pregnancy establishment. However, the essential cellular and molecular factors and pathways governing postnatal epithelium maturation, determination, and differentiation in developing uterus are yet to be elucidated. Here, the epithelium of the neonatal mouse uterus was isolated and subjected to single-cell transcriptome (scRNA-seq) analysis. Both the undifferentiated epithelium and determined luminal epithelium were heterogeneous and contained several different cell clusters based on single-cell transcription profiles. Substantial gene expression differences were evident as the epithelium matured and differentiated between postnatal days 1 to 15. Two new glandular epithelium-expressed genes (Gas6 and Cited4) were identified and validated by in situ hybridization. Trajectory analyses provided a framework for understanding epithelium maturation, lineage bifurcation, and differentiation. A candidate set of transcription factors and gene regulatory networks were identified that potentially direct epithelium lineage specification and morphogenesis. This atlas provides a foundation important to discover intrinsic cellular and molecular mechanisms directing uterine epithelium morphogenesis during a critical window of postnatal development.
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Affiliation(s)
- Thomas E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO65211
- Division of Obstetrics, Gynecology, and Women’s Health, University of Missouri, Columbia, MO65211
| | - Makenzie T. Lowke
- Division of Animal Sciences, University of Missouri, Columbia, MO65211
| | | | - Pramod Dhakal
- Division of Animal Sciences, University of Missouri, Columbia, MO65211
| | - Andrew M. Kelleher
- Division of Obstetrics, Gynecology, and Women’s Health, University of Missouri, Columbia, MO65211
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9
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Sun Z, Cernilogar FM, Horvatic H, Yeroslaviz A, Abdullah Z, Schotta G, Hornung V. β1 integrin signaling governs necroptosis via the chromatin-remodeling factor CHD4. Cell Rep 2023; 42:113322. [PMID: 37883227 DOI: 10.1016/j.celrep.2023.113322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/28/2023] Open
Abstract
Fibrosis, characterized by sustained activation of myofibroblasts and excessive extracellular matrix (ECM) deposition, is known to be associated with chronic inflammation. Receptor-interacting protein kinase 3 (RIPK3), the central kinase of necroptosis signaling, is upregulated in fibrosis and contributes to tumor necrosis factor (TNF)-mediated inflammation. In bile-duct-ligation-induced liver fibrosis, we found that myofibroblasts are the major cell type expressing RIPK3. Genetic ablation of β1 integrin, the major profibrotic ECM receptor in fibroblasts, not only abolished ECM fibrillogenesis but also blunted RIPK3 expression via a mechanism mediated by the chromatin-remodeling factor chromodomain helicase DNA-binding protein 4 (CHD4). While the function of CHD4 has been conventionally linked to the nucleosome-remodeling deacetylase (NuRD) and CHD4-ADNP-HP1(ChAHP) complexes, we found that CHD4 potently repressed a set of genes, including Ripk3, with high locus specificity but independent of either the NuRD or the ChAHP complex. Thus, our data uncover that β1 integrin intrinsically links fibrotic signaling to RIPK3-driven inflammation via a novel mode of action of CHD4.
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Affiliation(s)
- Zhiqi Sun
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Helena Horvatic
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Assa Yeroslaviz
- Computational Biology Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Zeinab Abdullah
- Institute of Molecular Medicine and Experimental Immunology, University Hospital Bonn, Bonn, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University of Munich, Munich, Germany
| | - Veit Hornung
- Gene Center and Department of Biochemistry, Ludwig Maximilian University of Munich, Munich, Germany; Research Group Molecular Mechanisms of Inflammation, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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10
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Arora S, Yang J, Akiyama T, James DQ, Morrissey A, Blanda TR, Badjatia N, Lai WK, Ko MS, Pugh BF, Mahony S. Joint sequence & chromatin neural networks characterize the differential abilities of Forkhead transcription factors to engage inaccessible chromatin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.06.561228. [PMID: 37873361 PMCID: PMC10592618 DOI: 10.1101/2023.10.06.561228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The DNA-binding activities of transcription factors (TFs) are influenced by both intrinsic sequence preferences and extrinsic interactions with cell-specific chromatin landscapes and other regulatory proteins. Disentangling the roles of these binding determinants remains challenging. For example, the FoxA subfamily of Forkhead domain (Fox) TFs are known pioneer factors that can bind to relatively inaccessible sites during development. Yet FoxA TF binding also varies across cell types, pointing to a combination of intrinsic and extrinsic forces guiding their binding. While other Forkhead domain TFs are often assumed to have pioneering abilities, how sequence and chromatin features influence the binding of related Fox TFs has not been systematically characterized. Here, we present a principled approach to compare the relative contributions of intrinsic DNA sequence preference and cell-specific chromatin environments to a TF's DNA-binding activities. We apply our approach to investigate how a selection of Fox TFs (FoxA1, FoxC1, FoxG1, FoxL2, and FoxP3) vary in their binding specificity. We over-express the selected Fox TFs in mouse embryonic stem cells, which offer a platform to contrast each TF's binding activity within the same preexisting chromatin background. By applying a convolutional neural network to interpret the Fox TF binding patterns, we evaluate how sequence and preexisting chromatin features jointly contribute to induced TF binding. We demonstrate that Fox TFs bind different DNA targets, and drive differential gene expression patterns, even when induced in identical chromatin settings. Despite the association between Forkhead domains and pioneering activities, the selected Fox TFs display a wide range of affinities for preexiting chromatin states. Using sequence and chromatin feature attribution techniques to interpret the neural network predictions, we show that differential sequence preferences combined with differential abilities to engage relatively inaccessible chromatin together explain Fox TF binding patterns at individual sites and genome-wide.
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Affiliation(s)
- Sonny Arora
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Jianyu Yang
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
- Current address: School of Medicine, Yokohama City University, Japan
| | - Daniela Q. James
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Alexis Morrissey
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Thomas R. Blanda
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - Nitika Badjatia
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
| | - William K.M. Lai
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | - Minoru S.H. Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo, Japan
| | - B. Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell University, NY, USA
| | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA
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11
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Grau J, Schmidt F, Schulz MH. Widespread effects of DNA methylation and intra-motif dependencies revealed by novel transcription factor binding models. Nucleic Acids Res 2023; 51:e95. [PMID: 37650641 PMCID: PMC10570048 DOI: 10.1093/nar/gkad693] [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: 03/01/2022] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 09/01/2023] Open
Abstract
Several studies suggested that transcription factor (TF) binding to DNA may be impaired or enhanced by DNA methylation. We present MeDeMo, a toolbox for TF motif analysis that combines information about DNA methylation with models capturing intra-motif dependencies. In a large-scale study using ChIP-seq data for 335 TFs, we identify novel TFs that show a binding behaviour associated with DNA methylation. Overall, we find that the presence of CpG methylation decreases the likelihood of binding for the majority of methylation-associated TFs. For a considerable subset of TFs, we show that intra-motif dependencies are pivotal for accurately modelling the impact of DNA methylation on TF binding. We illustrate that the novel methylation-aware TF binding models allow to predict differential ChIP-seq peaks and improve the genome-wide analysis of TF binding. Our work indicates that simplistic models that neglect the effect of DNA methylation on DNA binding may lead to systematic underperformance for methylation-associated TFs.
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Affiliation(s)
- Jan Grau
- Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Florian Schmidt
- Goethe-University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
- Systems Biology and Data Analytics, Genome Institute of Singapore, Singapore 13862, Singapore
- ImmunoScape Pte Ltd, Singapore 228208, Singapore
| | - Marcel H Schulz
- Goethe-University Frankfurt, Institute for Cardiovascular Regeneration, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
- Max Planck Institute for Informatics, Saarland Informatics Campus, Saarbrücken 66123, Germany
- German Center for Cardiovascular Research, Partner site Rhein-Main, 60590 Frankfurt am Main, Germany
- Cardio-Pulmonary Institute, Goethe University, Frankfurt am Main, Germany
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12
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Lyu X, Rowley MJ, Kulik MJ, Dalton S, Corces VG. Regulation of CTCF loop formation during pancreatic cell differentiation. Nat Commun 2023; 14:6314. [PMID: 37813869 PMCID: PMC10562423 DOI: 10.1038/s41467-023-41964-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/22/2023] [Indexed: 10/11/2023] Open
Abstract
Transcription reprogramming during cell differentiation involves targeting enhancers to genes responsible for establishment of cell fates. To understand the contribution of CTCF-mediated chromatin organization to cell lineage commitment, we analyzed 3D chromatin architecture during the differentiation of human embryonic stem cells into pancreatic islet organoids. We find that CTCF loops are formed and disassembled at different stages of the differentiation process by either recruitment of CTCF to new anchor sites or use of pre-existing sites not previously involved in loop formation. Recruitment of CTCF to new sites in the genome involves demethylation of H3K9me3 to H3K9me2, demethylation of DNA, recruitment of pioneer factors, and positioning of nucleosomes flanking the new CTCF sites. Existing CTCF sites not involved in loop formation become functional loop anchors via the establishment of new cohesin loading sites containing NIPBL and YY1 at sites between the new anchors. In both cases, formation of new CTCF loops leads to strengthening of enhancer promoter interactions and increased transcription of genes adjacent to loop anchors. These results suggest an important role for CTCF and cohesin in controlling gene expression during cell differentiation.
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Affiliation(s)
- Xiaowen Lyu
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
- State Key Laboratory of Cellular Stress Biology, Fujian Provincial Key Laboratory of Reproductive Health Research, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
- Fujian Provincial Key Laboratory of Organ and Tissue Regeneration, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, 361102, Xiamen, China.
| | - M Jordan Rowley
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Michael J Kulik
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
| | - Stephen Dalton
- Department of Biochemistry and Molecular Biology, The University of Georgia, Athens, GA, 30602, USA
- Center for Molecular Medicine, The University of Georgia, Athens, GA, 30602, USA
- School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, Hong Kong
| | - Victor G Corces
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
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13
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Wartewig T, Daniels J, Schulz M, Hameister E, Joshi A, Park J, Morrish E, Venkatasubramani AV, Cernilogar FM, van Heijster FHA, Hundshammer C, Schneider H, Konstantinidis F, Gabler JV, Klement C, Kurniawan H, Law C, Lee Y, Choi S, Guitart J, Forne I, Giustinani J, Müschen M, Jain S, Weinstock DM, Rad R, Ortonne N, Schilling F, Schotta G, Imhof A, Brenner D, Choi J, Ruland J. PD-1 instructs a tumor-suppressive metabolic program that restricts glycolysis and restrains AP-1 activity in T cell lymphoma. NATURE CANCER 2023; 4:1508-1525. [PMID: 37723306 PMCID: PMC10597841 DOI: 10.1038/s43018-023-00635-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 08/15/2023] [Indexed: 09/20/2023]
Abstract
The PDCD1-encoded immune checkpoint receptor PD-1 is a key tumor suppressor in T cells that is recurrently inactivated in T cell non-Hodgkin lymphomas (T-NHLs). The highest frequencies of PDCD1 deletions are detected in advanced disease, predicting inferior prognosis. However, the tumor-suppressive mechanisms of PD-1 signaling remain unknown. Here, using tractable mouse models for T-NHL and primary patient samples, we demonstrate that PD-1 signaling suppresses T cell malignancy by restricting glycolytic energy and acetyl coenzyme A (CoA) production. In addition, PD-1 inactivation enforces ATP citrate lyase (ACLY) activity, which generates extramitochondrial acetyl-CoA for histone acetylation to enable hyperactivity of activating protein 1 (AP-1) transcription factors. Conversely, pharmacological ACLY inhibition impedes aberrant AP-1 signaling in PD-1-deficient T-NHLs and is toxic to these cancers. Our data uncover genotype-specific vulnerabilities in PDCD1-mutated T-NHL and identify PD-1 as regulator of AP-1 activity.
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Affiliation(s)
- Tim Wartewig
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
| | - Jay Daniels
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Miriam Schulz
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Erik Hameister
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Abhinav Joshi
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Joonhee Park
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Emma Morrish
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Anuroop V Venkatasubramani
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Filippo M Cernilogar
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Frits H A van Heijster
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christian Hundshammer
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Heike Schneider
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Filippos Konstantinidis
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith V Gabler
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Henry Kurniawan
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Calvin Law
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Yujin Lee
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sara Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Joan Guitart
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Ignasi Forne
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Jérôme Giustinani
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
| | - Markus Müschen
- Center of Molecular and Cellular Oncology, Yale School of Medicine, Yale University, New Haven, CT, USA
- Department of Immunobiology, Yale University, New Haven, CT, USA
| | - Salvia Jain
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - David M Weinstock
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Merck Research Laboratories, Boston, MA, USA
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Medicine II, School of Medicine, Technical University of Munich, Munich, Germany
| | - Nicolas Ortonne
- Institut Mondor de Recherche Biomédicale, Inserm U955, Paris-Est Créteil University, Créteil, France
- Pathology Department, AP-HP Inserm U955, Henri Mondor Hospital, Créteil, France
| | - Franz Schilling
- Department of Nuclear Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - Gunnar Schotta
- Department of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Axel Imhof
- Protein Analysis Unit, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität Munich, Martinsried, Germany
| | - Dirk Brenner
- Experimental and Molecular Immunology, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-sur-Alzette, Luxembourg
- Immunology and Genetics, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Odense Research Center for Anaphylaxis, Department of Dermatology and Allergy Center, Odense University Hospital, University of Southern Denmark, Odense, Denmark
| | - Jaehyuk Choi
- Department of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Department of Dermatology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL, USA.
- Center for Genetic Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Human Immunobiology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA.
| | - Jürgen Ruland
- TranslaTUM, Center for Translational Cancer Research, Technical University of Munich, Munich, Germany.
- Institute of Clinical Chemistry and Pathobiochemistry, School of Medicine, Technical University of Munich, Munich, Germany.
- German Cancer Consortium (DKTK), Heidelberg, Germany.
- German Center for Infection Research (DZIF), partner site Munich, Munich, Germany.
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14
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Cooke CB, Barrington C, Baillie-Benson P, Nichols J, Moris N. Gastruloid-derived primordial germ cell-like cells develop dynamically within integrated tissues. Development 2023; 150:dev201790. [PMID: 37526602 PMCID: PMC10508693 DOI: 10.1242/dev.201790] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 07/24/2023] [Indexed: 08/02/2023]
Abstract
Primordial germ cells (PGCs) are the early embryonic precursors of gametes - sperm and egg cells. PGC-like cells (PGCLCs) can currently be derived in vitro from pluripotent cells exposed to signalling cocktails and aggregated into large embryonic bodies, but these do not recapitulate the native embryonic environment during PGC formation. Here, we show that mouse gastruloids, a three-dimensional in vitro model of gastrulation, contain a population of gastruloid-derived PGCLCs (Gld-PGCLCs) that resemble early PGCs in vivo. Importantly, the conserved organisation of mouse gastruloids leads to coordinated spatial and temporal localisation of Gld-PGCLCs relative to surrounding somatic cells, even in the absence of specific exogenous PGC-specific signalling or extra-embryonic tissues. In gastruloids, self-organised interactions between cells and tissues, including the endodermal epithelium, enables the specification and subsequent maturation of a pool of Gld-PGCLCs. As such, mouse gastruloids represent a new source of PGCLCs in vitro and, owing to their inherent co-development, serve as a novel model to study the dynamics of PGC development within integrated tissue environments.
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Affiliation(s)
- Christopher B. Cooke
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Abcam, Discovery Drive, Cambridge Biomedical Campus, Cambridge CB2 0AX, UK
| | | | - Peter Baillie-Benson
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Wellcome Trust – MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Jennifer Nichols
- Wellcome Trust – MRC Stem Cell Institute, University of Cambridge, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Cambridge CB2 0AW, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Tennis Court Road, Cambridge CB2 3EG, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
| | - Naomi Moris
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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15
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Brown JC. Backup transcription factor binding sites protect human genes from mutations in the promoter. PLoS One 2023; 18:e0281569. [PMID: 37651425 PMCID: PMC10470901 DOI: 10.1371/journal.pone.0281569] [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: 01/25/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023] Open
Abstract
This study was designed to test the idea that the regulatory regions of human genes have evolved to be resistant to the effects of mutations in their primary function, the control of gene expression. It is proposed that the transcription factor/transcription factor binding site (TF/TFBS) pair having the greatest effect on control of a gene is the one with the highest abundance among the regulatory elements. Other pairs would have the same effect on gene expression and would predominate in the event of a mutation in the most abundant pair. It is expected that the overall regulatory design proposed here will be highly resistant to mutagenic change that would otherwise affect expression of the gene. The idea was tested beginning with a database of 42 human genes highly specific for expression in brain. For each gene, the five most abundant TF/TFBS pairs were identified and compared in their TFBS occupancy as measured by their ChIP-seq signal. A similar signal was observed and interpreted as evidence that the TF/TFBS pairs can substitute for one another. TF/TFBS pairs were also compared in their ability to substitute for one another in their effect on the level of gene expression. The study of brain specific genes was complemented with the same analysis performed with 31 human liver specific genes. Like the study of brain genes, the liver results supported the view that TF/TFBS pairs in liver specific genes can substitute for one another in the event of mutagenic damage. Finally, the TFBSs in the brain specific and liver specific gene populations were compared with each other with the goal of identifying any brain selective or liver selective TFBSs. Of the 89 TFBSs in the pooled population, 58 were found only in brain specific but not liver specific genes, 8 only in liver specific but not brain specific genes and 23 were found in both brain and liver specific genes. The results were interpreted to emphasize the large number of TFBS in brain specific genes.
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Affiliation(s)
- Jay C. Brown
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, United States of America
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16
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Pipicelli F, Baumann N, Di Giaimo R, Forero-Echeverry A, Kyrousi C, Bonrath R, Maccarrone G, Jabaudon D, Cappello S. Non-cell-autonomous regulation of interneuron specification mediated by extracellular vesicles. SCIENCE ADVANCES 2023; 9:eadd8164. [PMID: 37205765 DOI: 10.1126/sciadv.add8164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
Disruption in neurogenesis and neuronal migration can influence the assembly of cortical circuits, affecting the excitatory-inhibitory balance and resulting in neurodevelopmental and neuropsychiatric disorders. Using ventral cerebral organoids and dorsoventral cerebral assembloids with mutations in the extracellular matrix gene LGALS3BP, we show that extracellular vesicles released into the extracellular environment regulate the molecular differentiation of neurons, resulting in alterations in migratory dynamics. To investigate how extracellular vesicles affect neuronal specification and migration dynamics, we collected extracellular vesicles from ventral cerebral organoids carrying a mutation in LGALS3BP, previously identified in individuals with cortical malformations and neuropsychiatric disorders. These results revealed differences in protein composition and changes in dorsoventral patterning. Proteins associated with cell fate decision, neuronal migration, and extracellular matrix composition were altered in mutant extracellular vesicles. Moreover, we show that treatment with extracellular vesicles changes the transcriptomic profile in neural progenitor cells. Our results indicate that neuronal molecular differentiation can be influenced by extracellular vesicles.
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Affiliation(s)
- Fabrizia Pipicelli
- Max Planck Institute of Psychiatry, Munich, Germany
- International Max Planck Research School for Translational Psychiatry, Munich, Germany
| | - Natalia Baumann
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Rossella Di Giaimo
- Max Planck Institute of Psychiatry, Munich, Germany
- Department of Biology, University of Naples Federico II, Naples, Italy
- Biomedical Center (BMC), Ludwig-Maximilians-Universitaet (LMU), Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | - Andrea Forero-Echeverry
- Max Planck Institute of Psychiatry, Munich, Germany
- Biomedical Center (BMC), Ludwig-Maximilians-Universitaet (LMU), Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
| | | | | | | | - Denis Jabaudon
- Department of Basic Neurosciences, University of Geneva, Geneva, Switzerland
| | - Silvia Cappello
- Max Planck Institute of Psychiatry, Munich, Germany
- Biomedical Center (BMC), Ludwig-Maximilians-Universitaet (LMU), Großhaderner Straße 9, 82152 Planegg-Martinsried, Germany
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17
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Gibson TJ, Harrison MM. Protein-intrinsic properties and context-dependent effects regulate pioneer-factor binding and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.18.533281. [PMID: 37066406 PMCID: PMC10103944 DOI: 10.1101/2023.03.18.533281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Chromatin is a barrier to the binding of many transcription factors. By contrast, pioneer factors access nucleosomal targets and promote chromatin opening. Despite binding to target motifs in closed chromatin, many pioneer factors display cell-type specific binding and activity. The mechanisms governing pioneer-factor occupancy and the relationship between chromatin occupancy and opening remain unclear. We studied three Drosophila transcription factors with distinct DNA-binding domains and biological functions: Zelda, Grainy head, and Twist. We demonstrated that the level of chromatin occupancy is a key determinant of pioneering activity. Multiple factors regulate occupancy, including motif content, local chromatin, and protein concentration. Regions outside the DNA-binding domain are required for binding and chromatin opening. Our results show that pioneering activity is not a binary feature intrinsic to a protein but occurs on a spectrum and is regulated by a variety of protein-intrinsic and cell-type-specific features.
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Affiliation(s)
- Tyler J. Gibson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI
| | - Melissa M. Harrison
- Department of Biomolecular Chemistry, University of Wisconsin-Madison Madison, WI
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18
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Păun O, Tan YX, Patel H, Strohbuecker S, Ghanate A, Cobolli-Gigli C, Llorian Sopena M, Gerontogianni L, Goldstone R, Ang SL, Guillemot F, Dias C. Pioneer factor ASCL1 cooperates with the mSWI/SNF complex at distal regulatory elements to regulate human neural differentiation. Genes Dev 2023; 37:218-242. [PMID: 36931659 PMCID: PMC10111863 DOI: 10.1101/gad.350269.122] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023]
Abstract
Pioneer transcription factors are thought to play pivotal roles in developmental processes by binding nucleosomal DNA to activate gene expression, though mechanisms through which pioneer transcription factors remodel chromatin remain unclear. Here, using single-cell transcriptomics, we show that endogenous expression of neurogenic transcription factor ASCL1, considered a classical pioneer factor, defines a transient population of progenitors in human neural differentiation. Testing ASCL1's pioneer function using a knockout model to define the unbound state, we found that endogenous expression of ASCL1 drives progenitor differentiation by cis-regulation both as a classical pioneer factor and as a nonpioneer remodeler, where ASCL1 binds permissive chromatin to induce chromatin conformation changes. ASCL1 interacts with BAF SWI/SNF chromatin remodeling complexes, primarily at targets where it acts as a nonpioneer factor, and we provide evidence for codependent DNA binding and remodeling at a subset of ASCL1 and SWI/SNF cotargets. Our findings provide new insights into ASCL1 function regulating activation of long-range regulatory elements in human neurogenesis and uncover a novel mechanism of its chromatin remodeling function codependent on partner ATPase activity.
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Affiliation(s)
- Oana Păun
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Yu Xuan Tan
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Harshil Patel
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Stephanie Strohbuecker
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Avinash Ghanate
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Clementina Cobolli-Gigli
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Miriam Llorian Sopena
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Lina Gerontogianni
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Robert Goldstone
- Bioinformatics and Biostatistics Science and Technology Platform, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Siew-Lan Ang
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom
| | - François Guillemot
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
| | - Cristina Dias
- Neural Stem Cell Biology Laboratory, the Francis Crick Institute, London NW1 1AT, United Kingdom;
- Medical and Molecular Genetics, School of Basic and Medical Biosciences, Faculty of Life Sciences and Medicine, King's College London, London SE1 9RT, United Kingdom
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19
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Delás MJ, Kalaitzis CM, Fawzi T, Demuth M, Zhang I, Stuart HT, Costantini E, Ivanovitch K, Tanaka EM, Briscoe J. Developmental cell fate choice in neural tube progenitors employs two distinct cis-regulatory strategies. Dev Cell 2023; 58:3-17.e8. [PMID: 36516856 PMCID: PMC7614300 DOI: 10.1016/j.devcel.2022.11.016] [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: 08/21/2022] [Revised: 10/10/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022]
Abstract
In many developing tissues, the patterns of gene expression that assign cell fate are organized by graded secreted signals. Cis-regulatory elements (CREs) interpret these signals to control gene expression, but how this is accomplished remains poorly understood. In the neural tube, a gradient of the morphogen sonic hedgehog (Shh) patterns neural progenitors. We identify two distinct ways in which CREs translate graded Shh into differential gene expression in mouse neural progenitors. In most progenitors, a common set of CREs control gene activity by integrating cell-type-specific inputs. By contrast, the most ventral progenitors use a unique set of CREs, established by the pioneer factor FOXA2. This parallels the role of FOXA2 in endoderm, where FOXA2 binds some of the same sites. Together, the data identify distinct cis-regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for FOXA2 across tissues.
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Affiliation(s)
| | | | - Tamara Fawzi
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Isabel Zhang
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Hannah T Stuart
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Elena Costantini
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | | | - Elly M Tanaka
- Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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20
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Andrenacci D, Cernilogar FM. Chromatin Preparation and Chromatin Immunoprecipitation from Drosophila Heads. Methods Mol Biol 2023; 2655:19-30. [PMID: 37212985 DOI: 10.1007/978-1-0716-3143-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Chromatin immunoprecipitation (ChIP) is a widely used method to map protein-DNA interactions in vivo. Formaldehyde cross-linked chromatin is fragmented, and the protein of interest is immunoprecipitated using a specific antibody. The co-immunoprecipitated DNA is then purified and analyzed by quantitative PCR (ChIP-qPCR) or next-generation sequencing (ChIP-seq). Therefore, from the amount of DNA recovered, it can be inferred the localization and abundance of the target protein at specific loci or throughout the entire genome. This protocol describes how to perform ChIP from Drosophila adult fly heads.
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Affiliation(s)
- Davide Andrenacci
- CNR Institute of Molecular Genetics "Luigi-Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy
- IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center (BMC), Ludwig-Maximilians-University (LMU) Munich, Planegg, Germany.
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21
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Yelagandula R, Stecher K, Novatchkova M, Michetti L, Michlits G, Wang J, Hofbauer P, Vainorius G, Pribitzer C, Isbel L, Mendjan S, Schübeler D, Elling U, Brennecke J, Bell O. ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers. Nat Cell Biol 2023; 25:42-55. [PMID: 36604593 PMCID: PMC10038669 DOI: 10.1038/s41556-022-01051-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/10/2022] [Indexed: 01/07/2023]
Abstract
ZNF462 haploinsufficiency is linked to Weiss-Kruszka syndrome, a genetic disorder characterized by neurodevelopmental defects, including autism. Though conserved in vertebrates and essential for embryonic development, the molecular functions of ZNF462 remain unclear. We identified its murine homologue ZFP462 in a screen for mediators of epigenetic gene silencing. Here we show that ZFP462 safeguards neural lineage specification of mouse embryonic stem cells (ESCs) by targeting the H3K9-specific histone methyltransferase complex G9A/GLP to silence meso-endodermal genes. ZFP462 binds to transposable elements that are potential enhancers harbouring pluripotency and meso-endoderm transcription factor binding sites. Recruiting G9A/GLP, ZFP462 seeds heterochromatin, restricting transcription factor binding. Loss of ZFP462 in ESCs results in increased chromatin accessibility at target sites and ectopic expression of meso-endodermal genes. Taken together, ZFP462 confers lineage and locus specificity to the broadly expressed epigenetic regulator G9A/GLP. Our results suggest that aberrant activation of lineage non-specific genes in the neuronal lineage underlies ZNF462-associated neurodevelopmental pathology.
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Affiliation(s)
- Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
| | - Karin Stecher
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Vienna, Austria
| | - Maria Novatchkova
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luca Michetti
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Università Vita-Salute San Raffaele, Milan, Italy
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Pablo Hofbauer
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Gintautas Vainorius
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Carina Pribitzer
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Sasha Mendjan
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA.
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22
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Frederick MA, Williamson KE, Fernandez Garcia M, Ferretti MB, McCarthy RL, Donahue G, Luzete Monteiro E, Takenaka N, Reynaga J, Kadoch C, Zaret KS. A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling. Nat Struct Mol Biol 2023; 30:31-37. [PMID: 36536103 PMCID: PMC10004348 DOI: 10.1038/s41594-022-00886-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
To determine how different pioneer transcription factors form a targeted, accessible nucleosome within compacted chromatin and collaborate with an ATP-dependent chromatin remodeler, we generated nucleosome arrays in vitro with a central nucleosome containing binding sites for the hematopoietic E-Twenty Six (ETS) factor PU.1 and Basic Leucine Zipper (bZIP) factors C/EBPα and C/EBPβ. Our long-read sequencing reveals that each factor can expose a targeted nucleosome on linker histone-compacted arrays, but with different nuclease sensitivity patterns. The DNA binding domain of PU.1 binds mononucleosomes, but requires an additional intrinsically disordered domain to bind and open compacted chromatin. The canonical mammalian SWI/SNF (cBAF) remodeler was unable to act upon two forms of locally open chromatin unless cBAF was enabled by a separate transactivation domain of PU.1. cBAF potentiates the PU.1 DNA binding domain to weakly open chromatin in the absence of the PU.1 disordered domain. Our findings reveal a hierarchy by which chromatin is opened and show that pioneer factors can provide specificity for action by nucleosome remodelers.
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Affiliation(s)
- Megan A Frederick
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kaylyn E Williamson
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Meilin Fernandez Garcia
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Max B Ferretti
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan L McCarthy
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Greg Donahue
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Edgar Luzete Monteiro
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Naomi Takenaka
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Janice Reynaga
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Department Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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23
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Abstract
The control of gene expression in eukaryotes relies on how transcription factors and RNA polymerases manipulate the structure of chromatin. These interactions are especially important in development as gene expression programs change. Chromatin generally limits the accessibility of DNA, and thus exposing sequences at regulatory elements is critical for gene expression. However, it is challenging to understand how transcription factors manipulate chromatin structure and the sequence of regulatory events. The Drosophila embryo has provided a powerful setting to directly observe the establishment and elaboration of chromatin features and experimentally test the causality of transcriptional events that are shared among many metazoans. The large embryo is tractable by live imaging, and a variety of well-developed tools allow the manipulation of factors during early development. The early embryo develops as a syncytium with rapid nuclear divisions and no zygotic transcription, with largely featureless chromatin. Thus, studies in this system have revealed the progression of genome activation triggered by pioneer factors that initiate DNA exposure at regulatory elements and the establishment of chromatin domains, including heterochromatin, the nucleolus, and nuclear bodies. The de novo emergence of nuclear structures in the early embryo reveals features of chromatin dynamics that are likely to be central to transcriptional regulation in all cells.
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Affiliation(s)
- Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, 1100 Fairview Ave. N., P.O. Box 19024, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road Chevy Chase, MD 20815-6789, USA
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24
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Zheng B, Seltzsam S, Wang C, Schierbaum L, Schneider S, Wu CHW, Dai R, Connaughton DM, Nakayama M, Mann N, Stajic N, Mane S, Bauer SB, Tasic V, Nam HJ, Shril S, Hildebrandt F. Whole-exome sequencing identifies FOXL2, FOXA2 and FOXA3 as candidate genes for monogenic congenital anomalies of the kidneys and urinary tract. Nephrol Dial Transplant 2022; 37:1833-1843. [PMID: 34473308 PMCID: PMC9755999 DOI: 10.1093/ndt/gfab253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Congenital anomalies of the kidneys and urinary tract (CAKUT) constitute the most common cause of chronic kidney disease in the first three decades of life. Variants in four Forkhead box (FOX) transcription factors have been associated with CAKUT. We hypothesized that other FOX genes, if highly expressed in developing kidneys, may also represent monogenic causes of CAKUT. METHODS We here performed whole-exome sequencing (WES) in 541 families with CAKUT and generated four lists of CAKUT candidate genes: (A) 36 FOX genes showing high expression during renal development, (B) 4 FOX genes known to cause CAKUT to validate list A, (C) 80 genes that we identified as unique potential novel CAKUT candidate genes when performing WES in 541 CAKUT families and (D) 175 genes identified from WES as multiple potential novel CAKUT candidate genes. RESULTS To prioritize potential novel CAKUT candidates in the FOX gene family, we overlapped 36 FOX genes (list A) with lists C and D of WES-derived CAKUT candidates. Intersection with list C identified a de novo FOXL2 in-frame deletion in a patient with eyelid abnormalities and ureteropelvic junction obstruction, and a homozygous FOXA2 missense variant in a patient with horseshoe kidney. Intersection with list D identified a heterozygous FOXA3 missense variant in a CAKUT family with multiple affected individuals. CONCLUSIONS We hereby identified FOXL2, FOXA2 and FOXA3 as novel monogenic candidate genes of CAKUT, supporting the utility of a paralog-based approach to discover mutated genes associated with human disease.
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Affiliation(s)
- Bixia Zheng
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Steve Seltzsam
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chunyan Wang
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca Schierbaum
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Sophia Schneider
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Chen-Han Wilfred Wu
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rufeng Dai
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Dervla M Connaughton
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Makiko Nakayama
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Nina Mann
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Natasa Stajic
- Department of Pediatric Nephrology, Institute for Mother and Child Health Care, Belgrade, Serbia
| | - Shrikant Mane
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Stuart B Bauer
- Department of Urology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Velibor Tasic
- Medical Faculty of Skopje, University Children's Hospital, Skopje, Macedonia
| | - Hyun Joo Nam
- Department of Biological and Environmental Science, Texas A&M University at Commerce, Commerce, TX, USA
| | - Shirlee Shril
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Friedhelm Hildebrandt
- Department of Pediatrics, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
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25
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Dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm. Nat Commun 2022; 13:5447. [PMID: 36123357 PMCID: PMC9485127 DOI: 10.1038/s41467-022-32978-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 08/25/2022] [Indexed: 12/03/2022] Open
Abstract
Silencing of endogenous retroviruses (ERVs) is largely mediated by repressive chromatin modifications H3K9me3 and DNA methylation. On ERVs, these modifications are mainly deposited by the histone methyltransferase Setdb1 and by the maintenance DNA methyltransferase Dnmt1. Knock-out of either Setdb1 or Dnmt1 leads to ERV de-repression in various cell types. However, it is currently not known if H3K9me3 and DNA methylation depend on each other for ERV silencing. Here we show that conditional knock-out of Setdb1 in mouse embryonic endoderm results in ERV de-repression in visceral endoderm (VE) descendants and does not occur in definitive endoderm (DE). Deletion of Setdb1 in VE progenitors results in loss of H3K9me3 and reduced DNA methylation of Intracisternal A-particle (IAP) elements, consistent with up-regulation of this ERV family. In DE, loss of Setdb1 does not affect H3K9me3 nor DNA methylation, suggesting Setdb1-independent pathways for maintaining these modifications. Importantly, Dnmt1 knock-out results in IAP de-repression in both visceral and definitive endoderm cells, while H3K9me3 is unaltered. Thus, our data suggest a dominant role of DNA methylation over H3K9me3 for IAP silencing in endoderm cells. Our findings suggest that Setdb1-meditated H3K9me3 is not sufficient for IAP silencing, but rather critical for maintaining high DNA methylation. Silencing of endogenous retroviruses is crucial for maintaining transcriptional and genomic integrity of cells and is maintained by histone H3K9 methylation and/or DNA methylation in various cell types. Here the authors show that loss of DNA methyltransferase DNMT1 in endoderm results in ERV derepression while H3K9me3 is unaltered.
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26
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Trinh LT, Osipovich AB, Sampson L, Wong J, Wright CV, Magnuson MA. Differential regulation of alternate promoter regions in Sox17 during endodermal and vascular endothelial development. iScience 2022; 25:104905. [PMID: 36046192 PMCID: PMC9421400 DOI: 10.1016/j.isci.2022.104905] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 04/06/2022] [Accepted: 08/05/2022] [Indexed: 11/20/2022] Open
Abstract
Sox17 gene expression is essential for both endothelial and endodermal cell differentiation. To better understand the genetic basis for the expression of multiple Sox17 mRNA forms, we identified and performed CRISPR/Cas9 mutagenesis of two evolutionarily conserved promoter regions (CRs). The deletion of the upstream and endothelial cell-specific CR1 caused only a modest increase in lympho-vasculogenesis likely via reduced Notch signaling downstream of SOX17. In contrast, the deletion of the downstream CR2 region, which functions in both endothelial and endodermal cells, impairs both vascular and endodermal development causing death by embryonic day 12.5. Analyses of 3D chromatin looping, transcription factor binding, histone modification, and chromatin accessibility data at the Sox17 locus and surrounding region further support differential regulation of the two promoters during the development.
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Affiliation(s)
- Linh T. Trinh
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Anna B. Osipovich
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leesa Sampson
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Jonathan Wong
- College of Arts and Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Chris V.E. Wright
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Mark A. Magnuson
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA
- Center for Stem Cell Biology, Vanderbilt University, Nashville, TN 37232, USA
- Program in Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
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27
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Sierra-Pagan JE, Garry DJ. The regulatory role of pioneer factors during cardiovascular lineage specification – A mini review. Front Cardiovasc Med 2022; 9:972591. [PMID: 36082116 PMCID: PMC9445115 DOI: 10.3389/fcvm.2022.972591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Cardiovascular disease (CVD) remains the number one cause of death worldwide. Ischemic heart disease contributes to heart failure and has considerable morbidity and mortality. Therefore, alternative therapeutic strategies are urgently needed. One class of epigenetic regulators known as pioneer factors has emerged as an important tool for the development of regenerative therapies for the treatment of CVD. Pioneer factors bind closed chromatin and remodel it to drive lineage specification. Here, we review pioneer factors within the cardiovascular lineage, particularly during development and reprogramming and highlight the implications this field of research has for the future development of cardiac specific regenerative therapies.
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Affiliation(s)
- Javier E. Sierra-Pagan
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
- *Correspondence: Daniel J. Garry
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28
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Luzete-Monteiro E, Zaret KS. Structures and consequences of pioneer factor binding to nucleosomes. Curr Opin Struct Biol 2022; 75:102425. [PMID: 35863165 PMCID: PMC9976633 DOI: 10.1016/j.sbi.2022.102425] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/15/2022]
Abstract
Pioneer transcription factors are able to bind a partially exposed motif on the surface of a nucleosome, enabling the proteins to target sites in silent regions of chromatin that have been compacted by linker histone. The targeting of nucleosomal DNA by pioneer factors has been observed in vitro and in vivo, where binding can promote local nucleosome exposure that allows other transcription factors, nucleosome remodelers, and histone modifiers to engage the chromatin and elicit gene activation or further repression. Pioneer factors thereby establish new gene expression programs during cell fate changes that occur during embryonic development, regeneration, and cancer. Here, we review recent biophysical studies that reveal the structural features and strategies used by pioneer factors to accomplish nucleosome binding and the consequential changes to nucleosomes that can lead to DNA accessibility.
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Affiliation(s)
- Edgar Luzete-Monteiro
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA.,Department of Biology, School of Arts and Sciences, University of Pennsylvania, 433 S University Ave, Philadelphia, PA 19104-4544
| | - Kenneth S. Zaret
- Institute for Regenerative Medicine, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, 9-131 SCTR, 3400 Civic Center Blvd., Philadelphia, PA 19104-5157, USA
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29
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Matsuo M, Yuan J, Kim YS, Dewar A, Fujita H, Dey SK, Sun X. Targeted depletion of uterine glandular Foxa2 induces embryonic diapause in mice. eLife 2022; 11:78277. [PMID: 35861728 PMCID: PMC9355561 DOI: 10.7554/elife.78277] [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: 02/28/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Embryonic diapause is a reproductive strategy in which embryo development and growth is temporarily arrested within the uterus to ensure the survival of neonates and mothers during unfavorable conditions. Pregnancy is reinitiated when conditions become favorable for neonatal survival. The mechanism of how the uterus enters diapause in various species remains unclear. Mice with uterine depletion of Foxa2, a transcription factor, are infertile. In this study, we show that dormant blastocysts are recovered from these mice on day 8 of pregnancy with persistent expression of uterine Msx1, a gene critical to maintaining the uterine quiescent state, suggesting that these mice enter embryonic diapause. Leukemia inhibitory factor (LIF) can resume implantation in these mice. Although estrogen is critical for implantation in progesterone-primed uterus, our current model reveals that FOXA2-independent estrogenic effects are detrimental to sustaining uterine quiescence. Interestingly, progesterone and anti-estrogen can prolong uterine quiescence in the absence of FOXA2. Although we find that Msx1 expression persists in the uterus deficient in Foxa2, the complex relationship of FOXA2 with Msx genes and estrogen receptors remains to be explored.
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Affiliation(s)
- Mitsunori Matsuo
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Jia Yuan
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Yeon Sun Kim
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Amanda Dewar
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Hidetoshi Fujita
- Department of Biomedical Engineering, Osaka Institute of Technology, Osaka, Japan
| | - Sudhansu K Dey
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
| | - Xiaofei Sun
- Division of Reproductive Sciences, Cincinnati Children's Hospital Medical Center, Cincinnati, United States
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30
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Li J, Wu X, Ke J, Lee M, Lan Q, Li J, Yu J, Huang Y, Sun DQ, Xie R. TET1 dioxygenase is required for FOXA2-associated chromatin remodeling in pancreatic beta-cell differentiation. Nat Commun 2022; 13:3907. [PMID: 35798741 PMCID: PMC9263144 DOI: 10.1038/s41467-022-31611-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/17/2022] [Indexed: 12/02/2022] Open
Abstract
Existing knowledge of the role of epigenetic modifiers in pancreas development has exponentially increased. However, the function of TET dioxygenases in pancreatic endocrine specification remains obscure. We set out to tackle this issue using a human embryonic stem cell (hESC) differentiation system, in which TET1/TET2/TET3 triple knockout cells display severe defects in pancreatic β-cell specification. The integrative whole-genome analysis identifies unique cell-type-specific hypermethylated regions (hyper-DMRs) displaying reduced chromatin activity and remarkable enrichment of FOXA2, a pioneer transcription factor essential for pancreatic endoderm specification. Intriguingly, TET depletion leads to significant changes in FOXA2 binding at the pancreatic progenitor stage, in which gene loci with decreased FOXA2 binding feature low levels of active chromatin modifications and enriches for bHLH motifs. Transduction of full-length TET1 but not the TET1-catalytic-domain in TET-deficient cells effectively rescues β-cell differentiation accompanied by restoring PAX4 hypomethylation. Taking these findings together with the defective generation of functional β-cells upon TET1-inactivation, our study unveils an essential role of TET1-dependent demethylation in establishing β-cell identity. Moreover, we discover a physical interaction between TET1 and FOXA2 in endodermal lineage intermediates, which provides a mechanistic clue regarding the complex crosstalk between TET dioxygenases and pioneer transcription factors in epigenetic regulation during pancreas specification. Here the authors show that TET1 is required for the generation of functional insulin-producing cells, FOXA2 physically interacts with TET1 and contributes to specific recruitment of TET1 to mediate chromatin opening at the regulatory elements of pancreatic lineage determinants.
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Affiliation(s)
- Jianfang Li
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China.,Guangzhou Laboratory, Guangzhou, 510005, China
| | - Xinwei Wu
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China.,Thoracic Epigenetics Section, Thoracic Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jie Ke
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Minjung Lee
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Qingping Lan
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China
| | - Jia Li
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.,State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
| | - Jianxiu Yu
- Department of Biochemistry and Molecular Cell Biology & Shanghai Key Laboratory of Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yun Huang
- Center for Epigenetics & Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - De-Qiang Sun
- Innovation Center for Advanced Interdisciplinary Medicine, the Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510530, China. .,Cardiology Department, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, China.
| | - Ruiyu Xie
- Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macau SAR, 999078, China. .,Ministry of Education Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, 999078, China.
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31
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Mesp1 controls the chromatin and enhancer landscapes essential for spatiotemporal patterning of early cardiovascular progenitors. Nat Cell Biol 2022; 24:1114-1128. [PMID: 35817961 PMCID: PMC7613098 DOI: 10.1038/s41556-022-00947-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 05/25/2022] [Indexed: 01/13/2023]
Abstract
The mammalian heart arises from various populations of Mesp1-expressing cardiovascular progenitors (CPs) that are specified during the early stages of gastrulation. Mesp1 is a transcription factor that acts as a master regulator of CP specification and differentiation. However, how Mesp1 regulates the chromatin landscape of nascent mesodermal cells to define the temporal and spatial patterning of the distinct populations of CPs remains unknown. Here, by combining ChIP-seq, RNA-seq and ATAC-seq during mouse pluripotent stem cell differentiation, we defined the dynamic remodelling of the chromatin landscape mediated by Mesp1. We identified different enhancers that are temporally regulated to erase the pluripotent state and specify the pools of CPs that mediate heart development. We identified Zic2 and Zic3 as essential cofactors that act with Mesp1 to regulate its transcription-factor activity at key mesodermal enhancers, thereby regulating the chromatin remodelling and gene expression associated with the specification of the different populations of CPs in vivo. Our study identifies the dynamics of the chromatin landscape and enhancer remodelling associated with temporal patterning of early mesodermal cells into the distinct populations of CPs that mediate heart development.
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32
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Hammelman J, Patel T, Closser M, Wichterle H, Gifford D. Ranking reprogramming factors for cell differentiation. Nat Methods 2022; 19:812-822. [PMID: 35710610 PMCID: PMC10460539 DOI: 10.1038/s41592-022-01522-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 05/13/2022] [Indexed: 12/16/2022]
Abstract
Transcription factor over-expression is a proven method for reprogramming cells to a desired cell type for regenerative medicine and therapeutic discovery. However, a general method for the identification of reprogramming factors to create an arbitrary cell type is an open problem. Here we examine the success rate of methods and data for differentiation by testing the ability of nine computational methods (CellNet, GarNet, EBseq, AME, DREME, HOMER, KMAC, diffTF and DeepAccess) to discover and rank candidate factors for eight target cell types with known reprogramming solutions. We compare methods that use gene expression, biological networks and chromatin accessibility data, and comprehensively test parameter and preprocessing of input data to optimize performance. We find the best factor identification methods can identify an average of 50-60% of reprogramming factors within the top ten candidates, and methods that use chromatin accessibility perform the best. Among the chromatin accessibility methods, complex methods DeepAccess and diffTF have higher correlation with the ranked significance of transcription factor candidates within reprogramming protocols for differentiation. We provide evidence that AME and diffTF are optimal methods for transcription factor recovery that will allow for systematic prioritization of transcription factor candidates to aid in the design of new reprogramming protocols.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, MIT, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA
| | - Tulsi Patel
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Michael Closser
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - Hynek Wichterle
- Departments of Pathology and Cell Biology, Neuroscience, Rehabilitation and Regenerative Medicine (in Neurology), Columbia University Irving Medical Center, New York, NY, USA
- Center for Motor Neuron Biology and Disease, Columbia University Irving Medical Center, New York, NY, USA
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY, USA
| | - David Gifford
- Computational and Systems Biology, MIT, Cambridge, MA, USA.
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA.
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33
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Heslop JA, Pournasr B, Duncan SA. Chromatin remodeling is restricted by transient GATA6 binding during iPSC differentiation to definitive endoderm. iScience 2022; 25:104300. [PMID: 35602939 PMCID: PMC9118154 DOI: 10.1016/j.isci.2022.104300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 03/22/2022] [Accepted: 04/21/2022] [Indexed: 11/06/2022] Open
Abstract
In addition to cooperatively driving transcriptional programs, emerging evidence supports transcription factors interacting with one another to modulate the outcome of binding events. As such, transcription factor interactions fine-tune the unique gene expression profiles required for developmental progression. Using human-induced pluripotent stem cells as a model of human endoderm lineage commitment, we reveal that GATA6 transiently co-localizes with EOMES at regions associated with non-endodermal lineages and is required for the repression of chromatin opening at these loci. Our results indicate that GATA6-dependent repression of chromatin remodeling, which is potentially mediated via the recruitment of NCOR1 to the EOMES interactome, contributes to definitive endoderm commitment. We anticipate that similar mechanisms are common during human development, furthering our understanding of the complex mechanisms that define cell fate decisions.
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Affiliation(s)
- James A. Heslop
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, USA
| | - Behshad Pournasr
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, USA
| | - Stephen A. Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, USA
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34
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Muruganandan S, Pierce R, Teguh DA, Perez RF, Bell N, Nguyen B, Hohl K, Snyder BD, Grinstaff MW, Alberico H, Woods D, Kong Y, Sima C, Bhagat S, Ho K, Rosen V, Gamer L, Ionescu AM. A FoxA2+ long-term stem cell population is necessary for growth plate cartilage regeneration after injury. Nat Commun 2022; 13:2515. [PMID: 35523895 PMCID: PMC9076650 DOI: 10.1038/s41467-022-30247-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 04/14/2022] [Indexed: 01/14/2023] Open
Abstract
Longitudinal bone growth, achieved through endochondral ossification, is accomplished by a cartilaginous structure, the physis or growth plate, comprised of morphologically distinct zones related to chondrocyte function: resting, proliferating and hypertrophic zones. The resting zone is a stem cell-rich region that gives rise to the growth plate, and exhibits regenerative capabilities in response to injury. We discovered a FoxA2+group of long-term skeletal stem cells, situated at the top of resting zone, adjacent the secondary ossification center, distinct from the previously characterized PTHrP+ stem cells. Compared to PTHrP+ cells, FoxA2+ cells exhibit higher clonogenicity and longevity. FoxA2+ cells exhibit dual osteo-chondro-progenitor activity during early postnatal development (P0-P28) and chondrogenic potential beyond P28. When the growth plate is injured, FoxA2+ cells expand in response to trauma, and produce physeal cartilage for growth plate tissue regeneration.
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Affiliation(s)
- Shanmugam Muruganandan
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Rachel Pierce
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Dian Astari Teguh
- Centre for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA
| | | | - Nicole Bell
- New York University College of Dentistry, 345 E.24th St, New York, NY, 10010, USA
| | - Brandon Nguyen
- Moderna Therapeutics, One Upland Rd, Norwood, Ohio, MA, 02062, USA
| | - Katherine Hohl
- Centre for Advanced Orthopedic Studies, Beth Israel Deaconess Medical Center, 330 Brookline Avenue, Boston, MA, 02215, USA.,Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, 590 Commonwealth Ave, SCI 518, Boston, MA, 02215, USA
| | - Brian D Snyder
- Department of Orthopedic Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Mark W Grinstaff
- Departments of Biomedical Engineering, Chemistry, and Medicine, Boston University, 590 Commonwealth Ave, SCI 518, Boston, MA, 02215, USA
| | - Hannah Alberico
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Dori Woods
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Yiwei Kong
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA
| | - Corneliu Sima
- Department of Oral Medicine, Infection, and Immunity, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA
| | - Sanket Bhagat
- Ultragenyx Pharmaceutical, 840 Memorial Drive, Cambridge, MA, 02139, USA
| | - Kailing Ho
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA
| | - Vicki Rosen
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA
| | - Laura Gamer
- Department of Developmental Biology, Harvard School of Dental Medicine, 188 Longwood Avenue, Boston, MA, 02115, USA
| | - Andreia M Ionescu
- Department of Biology, 134 Mugar Life Sciences Building, Northeastern University, 360 Huntington Ave, Boston, MA, 02115, USA.
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35
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Ouyang C, Fu Q, Xie Y, Xie J. Forkhead box A2 transcriptionally activates hsa-let-7 g to inhibit hypoxia-induced epithelial-mesenchymal transition by targeting c14orf28 in colorectal cancer. Arab J Gastroenterol 2022; 23:188-194. [PMID: 35514011 DOI: 10.1016/j.ajg.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/28/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND STUDY AIMS This study aimed to investigate the effect of Forkhead Box A2 (FOXA2) on migration, invasion, and epithelial-mesenchymal transition (EMT) of colorectal cancer (CRC) cells in hypoxia and explore its related molecular mechanisms. PATIENTS AND METHODS A cellular hypoxia model was established, and the FOXA2 overexpression vector was transfected into SW480 and HCT116 cells. Cell apoptosis, migration, and invasion were examined by flow cytometry, scratch test, and transwell-invasion assay. Next, the hsa-let-7 g gene expression was detected by quantitative reverse transcription-polymerase chain reaction. Relative protein levels of HIF-1, FOXA2, c14orf28, E-cadherin, N-cadherin, and Vimentin were detected by western blot. RESULTS Hypoxia-exposed CRC cells showed a significantly increased cell apoptosis rate, as well as enhanced cell invasion and migration abilities compared with the cells in normoxia. FOXA2 overexpression induced apoptosis and inhibited hypoxia-exposed CRC cell migration and invasion. Additionally, FOXA2 overexpression led to the significantly increased hsa-let-7 g and E-cadherin expression, as well as the decreased c14orf28, N-cadherin, and Vimentin expression in hypoxic CRC cells. CONCLUSIONS This study demonstrated that FOXA2 could affect the apoptosis, migration, invasion, and EMT of CRC cells under hypoxia conditions. FOXA2 transcriptionally activates hsa-let-7 g to inhibit hypoxia-induced EMT by targeting c14orf28.
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Affiliation(s)
- Canhui Ouyang
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Qubo Fu
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Yun Xie
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China
| | - Jun Xie
- Department of Gastroenterology, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi 341000, China.
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36
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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37
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McMahon R, Sibbritt T, Aryamanesh N, Masamsetti VP, Tam PPL. Loss of Foxd4 Impacts Neurulation and Cranial Neural Crest Specification During Early Head Development. Front Cell Dev Biol 2022; 9:777652. [PMID: 35178396 PMCID: PMC8843869 DOI: 10.3389/fcell.2021.777652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/30/2021] [Indexed: 11/19/2022] Open
Abstract
The specification of anterior head tissue in the late gastrulation mouse embryo relies on signaling cues from the visceral endoderm and anterior mesendoderm (AME). Genetic loss-of-function studies have pinpointed a critical requirement of LIM homeobox 1 (LHX1) transcription factor in these tissues for the formation of the embryonic head. Transcriptome analysis of embryos with gain-of-function LHX1 activity identified the forkhead box gene, Foxd4, as one downstream target of LHX1 in late-gastrulation E7.75 embryos. Our analysis of single-cell RNA-seq data show Foxd4 is co-expressed with Lhx1 and Foxa2 in the anterior midline tissue of E7.75 mouse embryos, and in the anterior neuroectoderm (ANE) at E8.25 alongside head organizer genes Otx2 and Hesx1. To study the role of Foxd4 during early development we used CRISPR-Cas9 gene editing in mouse embryonic stem cells (mESCs) to generate bi-allelic frameshift mutations in the coding sequence of Foxd4. In an in vitro model of the anterior neural tissues derived from Foxd4-loss of function (LOF) mESCs and extraembryonic endoderm cells, expression of head organizer genes as well as Zic1 and Zic2 was reduced, pointing to a need for FOXD4 in regulating early neuroectoderm development. Mid-gestation mouse chimeras harbouring Foxd4-LOF mESCs displayed craniofacial malformations and neural tube closure defects. Furthermore, our in vitro data showed a loss of FOXD4 impacts the expression of cranial neural crest markers Twist1 and Sox9. Our findings have demonstrated that FOXD4 is essential in the AME and later in the ANE for rostral neural tube closure and neural crest specification during head development.
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Affiliation(s)
- Riley McMahon
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
| | - Tennille Sibbritt
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - Nadar Aryamanesh
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia
| | - V Pragathi Masamsetti
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
| | - Patrick P L Tam
- Embryology Research Unit, Children's Medical Research Institute, Sydney, NSW, Australia.,School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Darlington, NSW, Australia
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38
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Krauß L, Urban BC, Hastreiter S, Schneider C, Wenzel P, Hassan Z, Wirth M, Lankes K, Terrasi A, Klement C, Cernilogar FM, Öllinger R, de Andrade Krätzig N, Engleitner T, Schmid RM, Steiger K, Rad R, Krämer OH, Reichert M, Schotta G, Saur D, Schneider G. HDAC2 Facilitates Pancreatic Cancer Metastasis. Cancer Res 2022; 82:695-707. [PMID: 34903606 PMCID: PMC9359718 DOI: 10.1158/0008-5472.can-20-3209] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 09/17/2021] [Accepted: 12/02/2021] [Indexed: 01/07/2023]
Abstract
The mortality of patients with pancreatic ductal adenocarcinoma (PDAC) is strongly associated with metastasis, a multistep process that is incompletely understood in this disease. Although genetic drivers of PDAC metastasis have not been defined, transcriptional and epigenetic rewiring can contribute to the metastatic process. The epigenetic eraser histone deacetylase 2 (HDAC2) has been connected to less differentiated PDAC, but the function of HDAC2 in PDAC has not been comprehensively evaluated. Using genetically defined models, we show that HDAC2 is a cellular fitness factor that controls cell cycle in vitro and metastasis in vivo, particularly in undifferentiated, mesenchymal PDAC cells. Unbiased expression profiling detected a core set of HDAC2-regulated genes. HDAC2 controlled expression of several prosurvival receptor tyrosine kinases connected to mesenchymal PDAC, including PDGFRα, PDGFRβ, and EGFR. The HDAC2-maintained program disabled the tumor-suppressive arm of the TGFβ pathway, explaining impaired metastasis formation of HDAC2-deficient PDAC. These data identify HDAC2 as a tractable player in the PDAC metastatic cascade. The complexity of the function of epigenetic regulators like HDAC2 implicates that an increased understanding of these proteins is needed for implementation of effective epigenetic therapies. SIGNIFICANCE HDAC2 has a context-specific role in undifferentiated PDAC and the capacity to disseminate systemically, implicating HDAC2 as targetable protein to prevent metastasis.
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Affiliation(s)
- Lukas Krauß
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Bettina C. Urban
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Sieglinde Hastreiter
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Carolin Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Patrick Wenzel
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Zonera Hassan
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Matthias Wirth
- Department of Hematology, Oncology and Tumor Immunology, Campus Benjamin Franklin, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, German
| | - Katharina Lankes
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Andrea Terrasi
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Christine Klement
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Filippo M. Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
| | - Roland M. Schmid
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
| | - Katja Steiger
- Institute of Pathology, Technische Universität München, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University of Mainz Medical Center, Mainz, Germany
| | - Maximilian Reichert
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, LMU Munich, Planegg-Martinsried, Germany
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-University, Planegg-Martinsried, Germany
| | - Dieter Saur
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute for Translational Cancer Research and Experimental Cancer Therapy, Technical University Munich, München, Germany
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, München, Germany
- German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, Göttingen, Germany
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39
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Noack F, Vangelisti S, Raffl G, Carido M, Diwakar J, Chong F, Bonev B. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. Nat Neurosci 2022; 25:154-167. [PMID: 35132236 PMCID: PMC8825286 DOI: 10.1038/s41593-021-01002-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022]
Abstract
How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex. By profiling multiple epigenetic layers and enhancer activity in vivo, the authors show a widespread remodeling of the regulatory landscape during mouse cortical development and identify Neurog2 as a key transcription factor driving this process.
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Affiliation(s)
- Florian Noack
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Silvia Vangelisti
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gerald Raffl
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Madalena Carido
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Jeisimhan Diwakar
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Faye Chong
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Boyan Bonev
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany. .,Physiological Genomics, Biomedical Center, Ludwig-Maximilians-Universität München, Munich, Germany.
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40
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Hammelman J, Krismer K, Gifford DK. spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions. Nucleic Acids Res 2022; 50:e52. [PMID: 35100401 PMCID: PMC9122533 DOI: 10.1093/nar/gkac036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 01/07/2022] [Accepted: 01/29/2022] [Indexed: 01/30/2023] Open
Abstract
Genomic interactions provide important context to our understanding of the state of the genome. One question is whether specific transcription factor interactions give rise to genome organization. We introduce spatzie, an R package and a website that implements statistical tests for significant transcription factor motif cooperativity between enhancer–promoter interactions. We conducted controlled experiments under realistic simulated data from ChIP-seq to confirm spatzie is capable of discovering co-enriched motif interactions even in noisy conditions. We then use spatzie to investigate cell type specific transcription factor cooperativity within recent human ChIA-PET enhancer–promoter interaction data. The method is available online at https://spatzie.mit.edu.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - David K Gifford
- Computational and Systems Biology Program, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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41
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Hammelman J, Gifford DK. Discovering differential genome sequence activity with interpretable and efficient deep learning. PLoS Comput Biol 2021; 17:e1009282. [PMID: 34370721 PMCID: PMC8376110 DOI: 10.1371/journal.pcbi.1009282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 08/19/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
Discovering sequence features that differentially direct cells to alternate fates is key to understanding both cellular development and the consequences of disease related mutations. We introduce Expected Pattern Effect and Differential Expected Pattern Effect, two black-box methods that can interpret genome regulatory sequences for cell type-specific or condition specific patterns. We show that these methods identify relevant transcription factor motifs and spacings that are predictive of cell state-specific chromatin accessibility. Finally, we integrate these methods into framework that is readily accessible to non-experts and available for download as a binary or installed via PyPI or bioconda at https://cgs.csail.mit.edu/deepaccess-package/.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, MIT, Cambridge, Massachusetts, United States of America
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts, United States of America
| | - David K. Gifford
- Computer Science and Artificial Intelligence Laboratory, MIT, Cambridge, Massachusetts, United States of America
- Department of Electrical Engineering & Computer Science, MIT, Cambridge, Massachusetts, United States of America
- Department of Biological Engineering, MIT, Cambridge, Massachusetts, United States of America
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42
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Scheibner K, Schirge S, Burtscher I, Büttner M, Sterr M, Yang D, Böttcher A, Ansarullah, Irmler M, Beckers J, Cernilogar FM, Schotta G, Theis FJ, Lickert H. Epithelial cell plasticity drives endoderm formation during gastrulation. Nat Cell Biol 2021; 23:692-703. [PMID: 34168324 PMCID: PMC8277579 DOI: 10.1038/s41556-021-00694-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/05/2021] [Indexed: 01/06/2023]
Abstract
It is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock-in reporter systems to combine time-resolved lineage labelling with high-resolution single-cell transcriptomics. This allowed us to resolve the morphogenetic programs that segregate the mesoderm from the endoderm germ layer. Strikingly, while the mesoderm is formed by classical EMT, the endoderm is formed independent of the key EMT transcription factor Snail1 by mechanisms of epithelial cell plasticity. Importantly, forkhead box transcription factor A2 (Foxa2) acts as an epithelial gatekeeper and EMT suppressor to shield the endoderm from undergoing a mesenchymal transition. Altogether, these results not only establish the morphogenetic details of germ layer formation, but also have broader implications for stem cell differentiation and cancer metastasis.
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Affiliation(s)
- Katharina Scheibner
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Silvia Schirge
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Maren Büttner
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
| | - Michael Sterr
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Dapeng Yang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Anika Böttcher
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Ansarullah
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany
- German Center for Diabetes Research (DZD), Munich, Germany
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum München, Munich, Germany
| | - Johannes Beckers
- German Center for Diabetes Research (DZD), Munich, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, Munich, Germany
- School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Filippo M Cernilogar
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University, Munich, Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig Maximilian University, Munich, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Munich, Germany
- Department of Mathematics, Technische Universität München, Munich, Germany
- School of Life Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research, Helmholtz Diabetes Center, Helmholtz Zentrum München, Munich, Germany.
- Institute of Stem Cell Research, Helmholtz Zentrum München, Munich, Germany.
- German Center for Diabetes Research (DZD), Munich, Germany.
- School of Medicine, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany.
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43
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Heslop JA, Pournasr B, Liu JT, Duncan SA. GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human-induced pluripotent stem cells. Cell Rep 2021; 35:109145. [PMID: 34010638 PMCID: PMC8202205 DOI: 10.1016/j.celrep.2021.109145] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/20/2021] [Accepted: 04/26/2021] [Indexed: 02/07/2023] Open
Abstract
In addition to driving specific gene expression profiles, transcriptional regulators are becoming increasingly recognized for their capacity to modulate chromatin structure. GATA6 is essential for the formation of definitive endoderm; however, the molecular basis defining the importance of GATA6 to endoderm commitment is poorly understood. The members of the GATA family of transcription factors have the capacity to bind and alter the accessibility of chromatin. Using pluripotent stem cells as a model of human development, we reveal that GATA6 is integral to the establishment of the endoderm enhancer network via the induction of chromatin accessibility and histone modifications. We additionally identify the chromatin-modifying complexes that interact with GATA6, defining the putative mechanisms by which GATA6 modulates chromatin architecture. The identified GATA6-dependent processes further our knowledge of the molecular mechanisms that underpin cell-fate decisions during formative development.
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Affiliation(s)
- James A Heslop
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Behshad Pournasr
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Jui-Tung Liu
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Stephen A Duncan
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA.
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44
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Larson ED, Marsh AJ, Harrison MM. Pioneering the developmental frontier. Mol Cell 2021; 81:1640-1650. [PMID: 33689750 PMCID: PMC8052302 DOI: 10.1016/j.molcel.2021.02.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/28/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022]
Abstract
Coordinated changes in gene expression allow a single fertilized oocyte to develop into a complex multi-cellular organism. These changes in expression are controlled by transcription factors that gain access to discrete cis-regulatory elements in the genome, allowing them to activate gene expression. Although nucleosomes present barriers to transcription factor occupancy, pioneer transcription factors have unique properties that allow them to bind DNA in the context of nucleosomes, define cis-regulatory elements, and facilitate the subsequent binding of additional factors that determine gene expression. In this capacity, pioneer factors act at the top of gene-regulatory networks to control developmental transitions. Developmental context also influences pioneer factor binding and activity. Here we discuss the interplay between pioneer factors and development, their role in driving developmental transitions, and the influence of the cellular environment on pioneer factor binding and activity.
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Affiliation(s)
- Elizabeth D Larson
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Audrey J Marsh
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA.
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45
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Abstract
This Outlook discusses the findings by Reizel et al. describing FOXA as a key, opening regions of chromatin during development, and as a doorstep, maintaining the established euchromatic structure in adult tissues. Pioneer factors are transcriptional regulators with the capacity to bind inactive regions of chromatin and induce changes in accessibility that underpin cell fate decisions. The FOXA family of transcription factors is well understood to have pioneer capacity. Indeed, researchers have uncovered numerous examples of FOXA-dependent epigenomic modulation in developmental and disease processes. Despite the presence of FOXA being essential for correct epigenetic patterning, the need for continued FOXA presence postchromatin modulation has been debated. In a recent study in this issue of Genes & Development, Reizel and colleagues (pp. 1039–1050) show that the tissue-specific ablation of FOXA1/2/3 in the adult mouse liver results in the collapse of the epigenetic profile that maintains the hepatic gene expression profile. Thus, FOXA functions as a key, opening regions of chromatin during development, and as a doorstep, maintaining the established euchromatic structure in adult tissue.
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46
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Elsayed AK, Younis I, Ali G, Hussain K, Abdelalim EM. Aberrant development of pancreatic beta cells derived from human iPSCs with FOXA2 deficiency. Cell Death Dis 2021; 12:103. [PMID: 33473118 PMCID: PMC7817686 DOI: 10.1038/s41419-021-03390-8] [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: 06/29/2020] [Revised: 12/27/2020] [Accepted: 12/29/2020] [Indexed: 01/30/2023]
Abstract
FOXA2 has been identified as an essential factor for pancreas development and emerging evidence supports an association between FOXA2 and diabetes. Although the role of FOXA2 during pancreatic development is well-studied in animal models, its role during human islet cell development remains unclear. Here, we generated induced pluripotent stem cells (iPSCs) from a patient with FOXA2 haploinsufficiency (FOXA2+/- iPSCs) followed by beta-cell differentiation to understand the role of FOXA2 during pancreatic beta-cell development. Our results showed that FOXA2 haploinsufficiency resulted in aberrant expression of genes essential for the differentiation and proper functioning of beta cells. At pancreatic progenitor (PP2) and endocrine progenitor (EPs) stages, transcriptome analysis showed downregulation in genes associated with pancreatic development and diabetes and upregulation in genes associated with nervous system development and WNT signaling pathway. Knockout of FOXA2 in control iPSCs (FOXA2-/- iPSCs) led to severe phenotypes in EPs and beta-cell stages. The expression of NGN3 and its downstream targets at EPs as well as INSUILIN and GLUCAGON at the beta-cell stage, were almost absent in the cells derived from FOXA2-/- iPSCs. These findings indicate that FOXA2 is crucial for human pancreatic endocrine development and its defect may lead to diabetes based on FOXA2 dosage.
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Affiliation(s)
- Ahmed K. Elsayed
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ihab Younis
- grid.418818.c0000 0001 0516 2170Biological Sciences Program, Carnegie Mellon University, Qatar Foundation, Education City, Doha, Qatar
| | - Gowher Ali
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha, Qatar
| | - Essam M. Abdelalim
- grid.452146.00000 0004 1789 3191Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar ,grid.418818.c0000 0001 0516 2170College of Health and Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation, Education City, Doha, Qatar
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47
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Srivastava D, Aydin B, Mazzoni EO, Mahony S. An interpretable bimodal neural network characterizes the sequence and preexisting chromatin predictors of induced transcription factor binding. Genome Biol 2021; 22:20. [PMID: 33413545 PMCID: PMC7788824 DOI: 10.1186/s13059-020-02218-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/03/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Transcription factor (TF) binding specificity is determined via a complex interplay between the transcription factor's DNA binding preference and cell type-specific chromatin environments. The chromatin features that correlate with transcription factor binding in a given cell type have been well characterized. For instance, the binding sites for a majority of transcription factors display concurrent chromatin accessibility. However, concurrent chromatin features reflect the binding activities of the transcription factor itself and thus provide limited insight into how genome-wide TF-DNA binding patterns became established in the first place. To understand the determinants of transcription factor binding specificity, we therefore need to examine how newly activated transcription factors interact with sequence and preexisting chromatin landscapes. RESULTS Here, we investigate the sequence and preexisting chromatin predictors of TF-DNA binding by examining the genome-wide occupancy of transcription factors that have been induced in well-characterized chromatin environments. We develop Bichrom, a bimodal neural network that jointly models sequence and preexisting chromatin data to interpret the genome-wide binding patterns of induced transcription factors. We find that the preexisting chromatin landscape is a differential global predictor of TF-DNA binding; incorporating preexisting chromatin features improves our ability to explain the binding specificity of some transcription factors substantially, but not others. Furthermore, by analyzing site-level predictors, we show that transcription factor binding in previously inaccessible chromatin tends to correspond to the presence of more favorable cognate DNA sequences. CONCLUSIONS Bichrom thus provides a framework for modeling, interpreting, and visualizing the joint sequence and chromatin landscapes that determine TF-DNA binding dynamics.
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Affiliation(s)
- Divyanshi Srivastava
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA
| | - Begüm Aydin
- Department of Biology, New York University, New York, NY, USA
| | | | - Shaun Mahony
- Center for Eukaryotic Gene Regulation, Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, USA.
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48
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Wang Y, Zolotarev N, Yang CY, Rambold A, Mittler G, Grosschedl R. A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin. Immunity 2020; 53:1151-1167.e6. [DOI: 10.1016/j.immuni.2020.10.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/14/2020] [Accepted: 10/14/2020] [Indexed: 01/08/2023]
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49
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Hammelman J, Krismer K, Banerjee B, Gifford DK, Sherwood RI. Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay. Genome Res 2020; 30:1468-1480. [PMID: 32973041 PMCID: PMC7605270 DOI: 10.1101/gr.263228.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
A key mechanism in cellular regulation is the ability of the transcriptional machinery to physically access DNA. Transcription factors interact with DNA to alter the accessibility of chromatin, which enables changes to gene expression during development or disease or as a response to environmental stimuli. However, the regulation of DNA accessibility via the recruitment of transcription factors is difficult to study in the context of the native genome because every genomic site is distinct in multiple ways. Here we introduce the multiplexed integrated accessibility assay (MIAA), an assay that measures chromatin accessibility of synthetic oligonucleotide sequence libraries integrated into a controlled genomic context with low native accessibility. We apply MIAA to measure the effects of sequence motifs on cell type-specific accessibility between mouse embryonic stem cells and embryonic stem cell-derived definitive endoderm cells, screening 7905 distinct DNA sequences. MIAA recapitulates differential accessibility patterns of 100-nt sequences derived from natively differential genomic regions, identifying E-box motifs common to epithelial-mesenchymal transition driver transcription factors in stem cell-specific accessible regions that become repressed in endoderm. We show that a single binding motif for a key regulatory transcription factor is sufficient to open chromatin, and classify sets of stem cell-specific, endoderm-specific, and shared accessibility-modifying transcription factor motifs. We also show that overexpression of two definitive endoderm transcription factors, T and Foxa2, results in changes to accessibility in DNA sequences containing their respective DNA-binding motifs and identify preferential motif arrangements that influence accessibility.
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Affiliation(s)
- Jennifer Hammelman
- Computational and Systems Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Konstantin Krismer
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Budhaditya Banerjee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David K Gifford
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Richard I Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA
- Hubrecht Institute, 3584 CT Utrecht, Netherlands
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50
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Abstract
Pioneer transcription factors have the intrinsic biochemical ability to scan partial DNA sequence motifs that are exposed on the surface of a nucleosome and thus access silent genes that are inaccessible to other transcription factors. Pioneer factors subsequently enable other transcription factors, nucleosome remodeling complexes, and histone modifiers to engage chromatin, thereby initiating the formation of an activating or repressive regulatory sequence. Thus, pioneer factors endow the competence for fate changes in embryonic development, are essential for cellular reprogramming, and rewire gene networks in cancer cells. Recent studies with reconstituted nucleosomes in vitro and chromatin binding in vivo reveal that pioneer factors can directly perturb nucleosome structure and chromatin accessibility in different ways. This review focuses on our current understanding of the mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to our ability to control cell fates at will.
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Affiliation(s)
- Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104-5157, USA;
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