1
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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 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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2
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MacFawn I, Farris J, Pifer P, Margaryan NV, Akhter H, Wang L, Dziadowicz S, Denvir J, Hu G, Frisch SM. Grainyhead-like-2, an epithelial master programmer, promotes interferon induction and suppresses breast cancer recurrence. Mol Immunol 2024; 170:156-169. [PMID: 38692097 PMCID: PMC11106721 DOI: 10.1016/j.molimm.2024.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 04/22/2024] [Accepted: 04/22/2024] [Indexed: 05/03/2024]
Abstract
Type-I and -III interferons play a central role in immune rejection of pathogens and tumors, thus promoting immunogenicity and suppressing tumor recurrence. Double strand RNA is an important ligand that stimulates tumor immunity via interferon responses. Differentiation of embryonic stem cells to pluripotent epithelial cells activates the interferon response during development, raising the question of whether epithelial vs. mesenchymal gene signatures in cancer potentially regulate the interferon pathway as well. Here, using genomics and signaling approaches, we show that Grainyhead-like-2 (GRHL2), a master programmer of epithelial cell identity, promotes type-I and -III interferon responses to double-strand RNA. GRHL2 enhanced the activation of IRF3 and relA/NF-kB and the expression of IRF1; a functional GRHL2 binding site in the IFNL1 promoter was also identified. Moreover, time to recurrence in breast cancer correlated positively with GRHL2 protein expression, indicating that GRHL2 is a tumor recurrence suppressor, consistent with its enhancement of interferon responses. These observations demonstrate that epithelial cell identity supports interferon responses in the context of cancer.
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Affiliation(s)
- Ian MacFawn
- Department of Immunology, University of Pittsburgh, 5051 Centre Avenue, Pittsburgh, PA 15213, USA; UPMC Hillman Cancer Center, 5115 Centre Avenue, Pittsburgh, PA 15232, USA
| | - Joshua Farris
- Wake Forest University, Department of Radiation Oncology, 1 Medical Center Blvd., Winston-Salem, NC 27157, USA
| | - Phillip Pifer
- Department of Radiation Oncology, WVU Cancer Institute, 1 Medical Drive, Morgantown, WV, USA
| | - Naira V Margaryan
- WVU Cancer Institute, West Virginia University, 64 Medical Center Drive, Morgantown, WV 26506, USA
| | - Halima Akhter
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - Lei Wang
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - Sebastian Dziadowicz
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA
| | - James Denvir
- Byrd Biotechnology Center, Marshall University, One John Marshall Drive, Huntington, WV 25701, USA
| | - Gangqing Hu
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, 64 Medical Center Drive, Box 9142, Morgantown, WV 26505, USA.
| | - Steven M Frisch
- Department of Biochemistry and Molecular Medicine, 64 Medical Center Drive, Box 9142, West Virginia University, Morgantown, WV 26506.
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3
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Stoeber S, Godin H, Xu C, Bai L. Pioneer factors: nature or nurture? Crit Rev Biochem Mol Biol 2024:1-15. [PMID: 38778580 DOI: 10.1080/10409238.2024.2355885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
Chromatin is densely packed with nucleosomes, which limits the accessibility of many chromatin-associated proteins. Pioneer factors (PFs) are usually viewed as a special group of sequence-specific transcription factors (TFs) that can recognize nucleosome-embedded motifs, invade compact chromatin, and generate open chromatin regions. Through this process, PFs initiate a cascade of events that play key roles in gene regulation and cell differentiation. A current debate in the field is if PFs belong to a unique subset of TFs with intrinsic "pioneering activity", or if all TFs have the potential to function as PFs within certain cellular contexts. There are also different views regarding the key feature(s) that define pioneering activity. In this review, we present evidence from the literature related to these alternative views and discuss how to potentially reconcile them. It is possible that both intrinsic properties, like tight nucleosome binding and structural compatibility, and cellular conditions, like concentration and co-factor availability, are important for PF function.
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Affiliation(s)
- Shane Stoeber
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Holly Godin
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Cheng Xu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
| | - Lu Bai
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
- Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA, USA
- Department of Physics, The Pennsylvania State University, University Park, PA, USA
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4
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Ertl HA, Bayala EX, Siddiq MA, Wittkopp PJ. Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588430. [PMID: 38645200 PMCID: PMC11030446 DOI: 10.1101/2024.04.07.588430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level. SUMMARY STATEMENT Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.
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5
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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 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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6
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Taskiran II, Spanier KI, Dickmänken H, Kempynck N, Pančíková A, Ekşi EC, Hulselmans G, Ismail JN, Theunis K, Vandepoel R, Christiaens V, Mauduit D, Aerts S. Cell-type-directed design of synthetic enhancers. Nature 2024; 626:212-220. [PMID: 38086419 PMCID: PMC10830415 DOI: 10.1038/s41586-023-06936-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/05/2023] [Indexed: 01/19/2024]
Abstract
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes1. It has been a long-standing goal in the field to decode the regulatory logic of an enhancer and to understand the details of how spatiotemporal gene expression is encoded in an enhancer sequence. Here we show that deep learning models2-6, can be used to efficiently design synthetic, cell-type-specific enhancers, starting from random sequences, and that this optimization process allows detailed tracing of enhancer features at single-nucleotide resolution. We evaluate the function of fully synthetic enhancers to specifically target Kenyon cells or glial cells in the fruit fly brain using transgenic animals. We further exploit enhancer design to create 'dual-code' enhancers that target two cell types and minimal enhancers smaller than 50 base pairs that are fully functional. By examining the state space searches towards local optima, we characterize enhancer codes through the strength, combination and arrangement of transcription factor activator and transcription factor repressor motifs. Finally, we apply the same strategies to successfully design human enhancers, which adhere to enhancer rules similar to those of Drosophila enhancers. Enhancer design guided by deep learning leads to better understanding of how enhancers work and shows that their code can be exploited to manipulate cell states.
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Affiliation(s)
- Ibrahim I Taskiran
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Katina I Spanier
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Hannah Dickmänken
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Niklas Kempynck
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Alexandra Pančíková
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB-KULeuven Center for Cancer Biology, Leuven, Belgium
| | - Eren Can Ekşi
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- UK Dementia Research Institute at Imperial College London, London, UK
| | - Koen Theunis
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Roel Vandepoel
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, VIB Center for AI & Computational Biology (VIB.AI), Leuven, Belgium.
- VIB-KULeuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
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7
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de Almeida BP, Schaub C, Pagani M, Secchia S, Furlong EEM, Stark A. Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo. Nature 2024; 626:207-211. [PMID: 38086418 PMCID: PMC10830412 DOI: 10.1038/s41586-023-06905-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/28/2023] [Indexed: 01/19/2024]
Abstract
Enhancers control gene expression and have crucial roles in development and homeostasis1-3. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo: the central nervous system, epidermis, gut, muscle and brain. We first train convolutional neural networks using genome-wide single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq) datasets and then fine-tune the convolutional neural networks with smaller-scale data from in vivo enhancer activity assays, yielding models with 13% to 76% positive predictive value according to cross-validation. We designed and experimentally assessed 40 synthetic enhancers (8 per tissue) in vivo, of which 31 (78%) were active and 27 (68%) functioned in the target tissue (100% for central nervous system and muscle). The strategy of combining genome-wide and small-scale functional datasets by transfer learning is generally applicable and should enable the design of tissue-, cell type- and cell state-specific enhancers in any system.
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Affiliation(s)
- Bernardo P de Almeida
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- InstaDeep, Paris, France
| | - Christoph Schaub
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria.
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria.
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8
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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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9
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Bravo González-Blas C, Matetovici I, Hillen H, Taskiran II, Vandepoel R, Christiaens V, Sansores-García L, Verboven E, Hulselmans G, Poovathingal S, Demeulemeester J, Psatha N, Mauduit D, Halder G, Aerts S. Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. Nat Cell Biol 2024; 26:153-167. [PMID: 38182825 PMCID: PMC10791584 DOI: 10.1038/s41556-023-01316-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 11/15/2023] [Indexed: 01/07/2024]
Abstract
In the mammalian liver, hepatocytes exhibit diverse metabolic and functional profiles based on their location within the liver lobule. However, it is unclear whether this spatial variation, called zonation, is governed by a well-defined gene regulatory code. Here, using a combination of single-cell multiomics, spatial omics, massively parallel reporter assays and deep learning, we mapped enhancer-gene regulatory networks across mouse liver cell types. We found that zonation affects gene expression and chromatin accessibility in hepatocytes, among other cell types. These states are driven by the repressors TCF7L1 and TBX3, alongside other core hepatocyte transcription factors, such as HNF4A, CEBPA, FOXA1 and ONECUT1. To examine the architecture of the enhancers driving these cell states, we trained a hierarchical deep learning model called DeepLiver. Our study provides a multimodal understanding of the regulatory code underlying hepatocyte identity and their zonation state that can be used to engineer enhancers with specific activity levels and zonation patterns.
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Affiliation(s)
- Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Irina Matetovici
- VIB Center for Brain & Disease Research, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
- VIB Tech Watch, VIB Headquarters, Ghent, Belgium
| | - Hanne Hillen
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Roel Vandepoel
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Leticia Sansores-García
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Elisabeth Verboven
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | | | - Jonas Demeulemeester
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Nikoleta Psatha
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - David Mauduit
- VIB Center for Brain & Disease Research, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium
| | - Georg Halder
- VIB Center for Cancer Biology, Leuven, Belgium
- Department of Oncology, KU Leuven, Leuven, Belgium
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium.
- Department of Human Genetics, KU Leuven, Leuven, Belgium.
- VIB Center for AI and Computational Biology (VIB.AI), Leuven, Belgium.
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10
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Fukagawa A, Hama N, Totoki Y, Nakamura H, Arai Y, Saito-Adachi M, Maeshima A, Matsui Y, Yachida S, Ushiku T, Shibata T. Genomic and epigenomic integrative subtypes of renal cell carcinoma in a Japanese cohort. Nat Commun 2023; 14:8383. [PMID: 38104198 PMCID: PMC10725467 DOI: 10.1038/s41467-023-44159-1] [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: 06/06/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023] Open
Abstract
Renal cell carcinoma (RCC) comprises several histological types characterised by different genomic and epigenomic aberrations; however, the molecular pathogenesis of each type still requires further exploration. We perform whole-genome sequencing of 128 Japanese RCC cases of different histology to elucidate the significant somatic alterations and mutagenesis processes. We also perform transcriptomic and epigenomic sequencing to identify distinguishing features, including assay for transposase-accessible chromatin sequencing (ATAC-seq) and methyl sequencing. Genomic analysis reveals that the mutational signature differs among the histological types, suggesting that different carcinogenic factors drive each histology. From the ATAC-seq results, master transcription factors are identified for each histology. Furthermore, clear cell RCC is classified into three epi-subtypes, one of which expresses highly immune checkpoint molecules with frequent loss of chromosome 14q. These genomic and epigenomic features may lead to the development of effective therapeutic strategies for RCC.
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Affiliation(s)
- Akihiko Fukagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Yasuhito Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Maeshima
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiyuki Matsui
- Department of Urology, National Cancer Center Hospital, Tokyo, Japan
| | - Shinichi Yachida
- Department of Cancer Genome Informatics, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.
- Laboratory of Molecular Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
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11
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Spiegl B, Kapidzic F, Röner S, Kircher M, Speicher M. GCparagon: evaluating and correcting GC biases in cell-free DNA at the fragment level. NAR Genom Bioinform 2023; 5:lqad102. [PMID: 38025047 PMCID: PMC10657415 DOI: 10.1093/nargab/lqad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/18/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Analyses of cell-free DNA (cfDNA) are increasingly being employed for various diagnostic and research applications. Many technologies aim to increase resolution, e.g. for detecting early-stage cancer or minimal residual disease. However, these efforts may be confounded by inherent base composition biases of cfDNA, specifically the over - and underrepresentation of guanine (G) and cytosine (C) sequences. Currently, there is no universally applicable tool to correct these effects on sequencing read-level data. Here, we present GCparagon, a two-stage algorithm for computing and correcting GC biases in cfDNA samples. In the initial step, length and GC base count parameters are determined. Here, our algorithm minimizes the inclusion of known problematic genomic regions, such as low-mappability regions, in its calculations. In the second step, GCparagon computes weights counterbalancing the distortion of cfDNA attributes (correction matrix). These fragment weights are added to a binary alignment map (BAM) file as alignment tags for individual reads. The GC correction matrix or the tagged BAM file can be used for downstream analyses. Parallel computing allows for a GC bias estimation below 1 min. We demonstrate that GCparagon vastly improves the analysis of regulatory regions, which frequently show specific GC composition patterns and will contribute to standardized cfDNA applications.
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Affiliation(s)
- Benjamin Spiegl
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Faruk Kapidzic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
| | - Sebastian Röner
- Exploratory Diagnostic Sciences, Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Martin Kircher
- Exploratory Diagnostic Sciences, Berlin Institute of Health (BIH) at Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Institute of Human Genetics, University Medical Center Schleswig-Holstein (UKSH), University of Lübeck, 23562 Lübeck, Germany
| | - Michael R Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
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12
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Sun J, Zhang C, Gao F, Stathopoulos A. Single-cell transcriptomics illuminates regulatory steps driving anterior-posterior patterning of Drosophila embryonic mesoderm. Cell Rep 2023; 42:113289. [PMID: 37858470 DOI: 10.1016/j.celrep.2023.113289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/29/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Single-cell technologies promise to uncover how transcriptional programs orchestrate complex processes during embryogenesis. Here, we apply a combination of single-cell technology and genetic analysis to investigate the dynamic transcriptional changes associated with Drosophila embryo morphogenesis at gastrulation. Our dataset encompassing the blastoderm-to-gastrula transition provides a comprehensive single-cell map of gene expression across cell lineages validated by genetic analysis. Subclustering and trajectory analyses revealed a surprising stepwise progression in patterning to transition zygotic gene expression and specify germ layers as well as uncovered an early role for ecdysone signaling in epithelial-to-mesenchymal transition in the mesoderm. We also show multipotent progenitors arise prior to gastrulation by analyzing the transcription trajectory of caudal mesoderm cells, including a derivative that ultimately incorporates into visceral muscles of the midgut and hindgut. This study provides a rich resource of gastrulation and elucidates spatially regulated temporal transitions of transcription states during the process.
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Affiliation(s)
- Jingjing Sun
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Chen Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Fan Gao
- Bioinformatics Resource Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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13
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Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023; 58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
Abstract
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive accessibility and those that do not. Deep learning models that learn complex sequence rules provide an unprecedented opportunity to dissect this problem. Using zygotic genome activation in Drosophila as a model, we analyzed high-resolution TF binding and chromatin accessibility data with interpretable deep learning and performed genetic validation experiments. We identify a hierarchical relationship between the pioneer TF Zelda and the TFs involved in axis patterning. Zelda consistently pioneers chromatin accessibility proportional to motif affinity, whereas patterning TFs augment chromatin accessibility in sequence contexts where they mediate enhancer activation. We conclude that chromatin accessibility occurs in two tiers: one through pioneering, which makes enhancers accessible but not necessarily active, and the second when the correct combination of TFs leads to enhancer activation.
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Affiliation(s)
- Kaelan J Brennan
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Melanie Weilert
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Sabrina Krueger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anusri Pampari
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA
| | - Hsiao-Yun Liu
- Department of Biology, New York University, New York, NY 10003, USA
| | - Ally W H Yang
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Jason A Morrison
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Timothy R Hughes
- Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
| | | | - Anshul Kundaje
- Department of Computer Science, Stanford University, Palo Alto, CA 94305, USA; Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Julia Zeitlinger
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology & Laboratory Medicine, The University of Kansas Medical Center, Kansas City, KS 66160, USA.
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14
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Jacobs J, Pagani M, Wenzl C, Stark A. Widespread regulatory specificities between transcriptional co-repressors and enhancers in Drosophila. Science 2023; 381:198-204. [PMID: 37440660 DOI: 10.1126/science.adf6149] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 06/13/2023] [Indexed: 07/15/2023]
Abstract
Gene expression is controlled by the precise activation and repression of transcription. Repression is mediated by specialized transcription factors (TFs) that recruit co-repressors (CoRs) to silence transcription, even in the presence of activating cues. However, whether CoRs can dominantly silence all enhancers or display distinct specificities is unclear. In this work, we report that most enhancers in Drosophila can be repressed by only a subset of CoRs, and enhancers classified by CoR sensitivity show distinct chromatin features, function, TF motifs, and binding. Distinct TF motifs render enhancers more resistant or sensitive to specific CoRs, as we demonstrate by motif mutagenesis and addition. These CoR-enhancer compatibilities constitute an additional layer of regulatory specificity that allows differential regulation at close genomic distances and is indicative of distinct mechanisms of transcriptional repression.
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Affiliation(s)
- Jelle Jacobs
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Michaela Pagani
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Christoph Wenzl
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
| | - Alexander Stark
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Campus-Vienna-Biocenter 1, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria
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15
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Saini M, Schmidleitner L, Moreno HD, Donato E, Falcone M, Bartsch JM, Klein C, Vogel V, Würth R, Pfarr N, Espinet E, Lehmann M, Königshoff M, Reitberger M, Haas S, Graf E, Schwarzmayr T, Strom TM, Spaich S, Sütterlin M, Schneeweiss A, Weichert W, Schotta G, Reichert M, Aceto N, Sprick MR, Trumpp A, Scheel CH. Resistance to mesenchymal reprogramming sustains clonal propagation in metastatic breast cancer. Cell Rep 2023; 42:112533. [PMID: 37257449 DOI: 10.1016/j.celrep.2023.112533] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 10/04/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
The acquisition of mesenchymal traits is considered a hallmark of breast cancer progression. However, the functional relevance of epithelial-to-mesenchymal transition (EMT) remains controversial and context dependent. Here, we isolate epithelial and mesenchymal populations from human breast cancer metastatic biopsies and assess their functional potential in vivo. Strikingly, progressively decreasing epithelial cell adhesion molecule (EPCAM) levels correlate with declining disease propagation. Mechanistically, we find that persistent EPCAM expression marks epithelial clones that resist EMT induction and propagate competitively. In contrast, loss of EPCAM defines clones arrested in a mesenchymal state, with concomitant suppression of tumorigenicity and metastatic potential. This dichotomy results from distinct clonal trajectories impacting global epigenetic programs that are determined by the interplay between human ZEB1 and its target GRHL2. Collectively, our results indicate that susceptibility to irreversible EMT restrains clonal propagation, whereas resistance to mesenchymal reprogramming sustains disease spread in multiple models of human metastatic breast cancer, including patient-derived cells in vivo.
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Affiliation(s)
- Massimo Saini
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland.
| | - Laura Schmidleitner
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany; Translational Pancreatic Cancer Research Center, Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Garching, Germany; Center for Organoid Systems (COS), Technical University of Munich (TUM), Garching, Germany; Munich Institute of Biomedical Engineering (MIBE), Technical University of Munich (TUM), Garching, Germany
| | - Helena Domínguez Moreno
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University of Munich (LMU), Munich, Germany
| | - Elisa Donato
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Mattia Falcone
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Johanna M Bartsch
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany
| | - Corinna Klein
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Vanessa Vogel
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Roberto Würth
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Mareike Lehmann
- Institute for Lung Health and Immunity (LHI) and Comprehensive Pneumology Center (CPC), Helmholtz Center Munich, Member of the German Center for Lung Research (DZL), Munich, Germany; Institute for Lung Research, Philipps-University Marburg, Member of the German Center for Lung Research (DZL), Marburg, Germany
| | - Melanie Königshoff
- Research Unit Lung Repair and Regeneration, Helmholtz Center Munich, Member of the German Center of Lung Research (DZL), Munich, Germany
| | - Manuel Reitberger
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
| | - Simon Haas
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Elisabeth Graf
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Thomas Schwarzmayr
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Tim-Matthias Strom
- Institute of Human Genetics, Helmholtz Center Munich, Neuherberg, Germany
| | - Saskia Spaich
- Department of Gynaecology and Obstetrics, University Women's Clinic, University Medical Centre Mannheim, Mannheim, Germany
| | - Marc Sütterlin
- Department of Gynaecology and Obstetrics, University Women's Clinic, University Medical Centre Mannheim, Mannheim, Germany
| | - Andreas Schneeweiss
- National Center for Tumor Diseases, University Hospital and German Cancer Research Center, Heidelberg, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich, Germany; German Cancer Consortium (DKTK), Germany
| | - Gunnar Schotta
- Division of Molecular Biology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilian University of Munich (LMU), Munich, Germany
| | - Maximilian Reichert
- Translational Pancreatic Cancer Research Center, Klinik und Poliklinik für Innere Medizin II, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany; Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Garching, Germany; Center for Organoid Systems (COS), Technical University of Munich (TUM), Garching, Germany; Munich Institute of Biomedical Engineering (MIBE), Technical University of Munich (TUM), Garching, Germany; German Cancer Consortium (DKTK), Germany
| | - Nicola Aceto
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, Switzerland
| | - Martin R Sprick
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; German Cancer Consortium (DKTK), Germany.
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), and DKFZ-ZMBH Alliance, Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany; German Cancer Consortium (DKTK), Germany.
| | - Christina H Scheel
- Institute of Stem Cell Research, Helmholtz Center Munich, Neuherberg, Germany.
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16
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Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023; 19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [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: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023] Open
Abstract
We use ATAC-seq to examine chromatin accessibility for four different tissues in Drosophila melanogaster: adult female brain, ovaries, and both wing and eye-antennal imaginal discs from males. Each tissue is assayed in eight different inbred strain genetic backgrounds, seven associated with a reference quality genome assembly. We develop a method for the quantile normalization of ATAC-seq fragments and test for differences in coverage among genotypes, tissues, and their interaction at 44099 peaks throughout the euchromatic genome. For the strains with reference quality genome assemblies, we correct ATAC-seq profiles for read mis-mapping due to nearby polymorphic structural variants (SVs). Comparing coverage among genotypes without accounting for SVs results in a highly elevated rate (55%) of identifying false positive differences in chromatin state between genotypes. After SV correction, we identify 1050, 30383, and 4508 regions whose peak heights are polymorphic among genotypes, among tissues, or exhibit genotype-by-tissue interactions, respectively. Finally, we identify 3988 candidate causative variants that explain at least 80% of the variance in chromatin state at nearby ATAC-seq peaks.
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Affiliation(s)
- Khoi Huynh
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
- Center for Computational Biology, University of Kansas, Lawrence, Kansas, United States of America
| | - Anthony D. Long
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, United States of America
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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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Collier AE, Piekos SN, Liu A, Pattison JM, Felix F, Bailetti AA, Sedov E, Gaddam S, Zhen H, Oro AE. GRHL2 and AP2a coordinate early surface ectoderm lineage commitment during development. iScience 2023; 26:106125. [PMID: 36843855 PMCID: PMC9950457 DOI: 10.1016/j.isci.2023.106125] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/09/2022] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Ectodermal dysplasias including skin abnormalities and cleft lip/palate result from improper surface ectoderm (SE) patterning. However, the connection between SE gene regulatory networks and disease remains poorly understood. Here, we dissect human SE differentiation with multiomics and establish GRHL2 as a key mediator of early SE commitment, which acts by skewing cell fate away from the neural lineage. GRHL2 and master SE regulator AP2a balance early cell fate output, with GRHL2 facilitating AP2a binding to SE loci. In turn, AP2a restricts GRHL2 DNA binding away from de novo chromatin contacts. Integration of these regulatory sites with ectodermal dysplasia-associated genomic variants annotated within the Biomedical Data Commons identifies 55 loci previously implicated in craniofacial disorders. These include ABCA4/ARHGAP29 and NOG regulatory regions where disease-linked variants directly affect GRHL2/AP2a binding and gene transcription. These studies elucidate the logic underlying SE commitment and deepen our understanding of human oligogenic disease pathogenesis.
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Affiliation(s)
- Ann E. Collier
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Samantha N. Piekos
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | - Angela Liu
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Franco Felix
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
| | | | - Egor Sedov
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Sadhana Gaddam
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Hanson Zhen
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
| | - Anthony E. Oro
- Program in Epithelial Biology, Stanford University, Stanford, CA USA
- Stem Cell Biology and Regenerative Medicine Graduate Program, Stanford University, Stanford, CA USA
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19
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Chen M, Gao E, Lin G, Shen J, Wang D. The transcription factor optomotor-blind restricts apterous expression through TrxG and PcG genes. Dev Biol 2023; 497:59-67. [PMID: 36907311 DOI: 10.1016/j.ydbio.2023.03.002] [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: 11/19/2022] [Revised: 01/20/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023]
Abstract
The establishment of body pattern is a fundamental process in developmental biology. In Drosophila, the wing disc is subdivided into dorsal (D) and ventral (V) compartments by the D/V boundary. The dorsal fate is adopted by expressing the selector gene apterous (ap). ap expression is regulated by three combinational cis-regulatory modules which are activated by EGFR pathway, Ap-Vg auto-regulatory and epigenetic mechanisms. Here, we found that the Tbx family transcription factor Optomotor-blind (Omb) restricted ap expression in the ventral compartment. Loss of omb induced autonomous initiation of ap expression in the middle third instar larvae in the ventral compartment. Oppositely, over-activation of omb inhibited ap in the medial pouch. All three enhancers apE, apDV and apP were upregulated in omb null mutants, indicating a combinational regulation of ap modulators. However, Omb affected ap expression neither by directly regulating EGFR signaling, nor via Vg regulation. Therefore, a genetic screen of epigenetic regulators, including the Trithorax group (TrxG) and Polycomb group (PcG) genes was performed. We found that knocking down the TrxG gene kohtalo (kto), domino (dom) or expressing the PcG gene grainy head (grh), the ectopic ap in omb mutants was repressed. The inhibition of apDV by kto knockdown and grh activation could contribute to ap repression. Moreover, Omb and the EGFR pathway are genetically parallel in ap regulation in the ventral compartment. Collectively, Omb is a repressive signal for ap expression in the ventral compartment, which requires TrxG and PcG genes.
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Affiliation(s)
- Min Chen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China; Yantai Academy of Agricultural Sciences, Yantai, 265500, China
| | - Erqing Gao
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Guangze Lin
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Jie Shen
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Dan Wang
- Department of Plant Biosecurity and MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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20
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Ling L, Mühling B, Jaenichen R, Gompel N. Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila. SCIENCE ADVANCES 2023; 9:eade6529. [PMID: 36800429 PMCID: PMC9937571 DOI: 10.1126/sciadv.ade6529] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in developmental gene expression. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may be silenced through changes in chromatin accessibility or the emergence of repressive elements. Here, we show that increased chromatin accessibility at the gene yellow, combined with the gain of a repressor site, underlies the loss of a wing spot pigmentation pattern in a Drosophila species. The gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.
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21
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Galupa R, Alvarez-Canales G, Borst NO, Fuqua T, Gandara L, Misunou N, Richter K, Alves MRP, Karumbi E, Perkins ML, Kocijan T, Rushlow CA, Crocker J. Enhancer architecture and chromatin accessibility constrain phenotypic space during Drosophila development. Dev Cell 2023; 58:51-62.e4. [PMID: 36626871 PMCID: PMC9860173 DOI: 10.1016/j.devcel.2022.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/18/2022] [Accepted: 12/07/2022] [Indexed: 01/11/2023]
Abstract
Developmental enhancers bind transcription factors and dictate patterns of gene expression during development. Their molecular evolution can underlie phenotypical evolution, but the contributions of the evolutionary pathways involved remain little understood. Here, using mutation libraries in Drosophila melanogaster embryos, we observed that most point mutations in developmental enhancers led to changes in gene expression levels but rarely resulted in novel expression outside of the native pattern. In contrast, random sequences, often acting as developmental enhancers, drove expression across a range of cell types; random sequences including motifs for transcription factors with pioneer activity acted as enhancers even more frequently. Our findings suggest that the phenotypic landscapes of developmental enhancers are constrained by enhancer architecture and chromatin accessibility. We propose that the evolution of existing enhancers is limited in its capacity to generate novel phenotypes, whereas the activity of de novo elements is a primary source of phenotypic novelty.
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Affiliation(s)
- Rafael Galupa
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| | | | | | - Timothy Fuqua
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Lautaro Gandara
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Natalia Misunou
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Kerstin Richter
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Esther Karumbi
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Tin Kocijan
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | | | - Justin Crocker
- European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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22
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Ertl HA, Hill MS, Wittkopp PJ. Differential Grainy head binding correlates with variation in chromatin structure and gene expression in Drosophila melanogaster. BMC Genomics 2022; 23:854. [PMID: 36575386 PMCID: PMC9795675 DOI: 10.1186/s12864-022-09082-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022] Open
Abstract
Phenotypic evolution is often caused by variation in gene expression resulting from altered gene regulatory mechanisms. Genetic variation affecting chromatin remodeling has been identified as a potential source of variable gene expression; however, the roles of specific chromatin remodeling factors remain unclear. Here, we address this knowledge gap by examining the relationship between variation in gene expression, variation in chromatin structure, and variation in binding of the pioneer factor Grainy head between imaginal wing discs of two divergent strains of Drosophila melanogaster and their F1 hybrid. We find that (1) variation in Grainy head binding is mostly due to sequence changes that act in cis but are located outside of the canonical Grainy head binding motif, (2) variation in Grainy head binding correlates with changes in chromatin accessibility, and (3) this variation in chromatin accessibility, coupled with variation in Grainy head binding, correlates with variation in gene expression in some cases but not others. Interactions among these three molecular layers is complex, but these results suggest that genetic variation affecting the binding of pioneer factors contributes to variation in chromatin remodeling and the evolution of gene expression.
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Affiliation(s)
- Henry A. Ertl
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mark S. Hill
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA ,grid.83440.3b0000000121901201Present address: Cancer Evolution and Genome Instability Laboratory, University College London Cancer Institute and The Francis Crick Institute, London, UK
| | - Patricia J. Wittkopp
- grid.214458.e0000000086837370Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109 USA ,grid.214458.e0000000086837370Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109 USA
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23
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Pinto PB, Domsch K, Lohmann I. Hox function and specificity – A tissue centric view. Semin Cell Dev Biol 2022:S1084-9521(22)00353-6. [PMID: 36517344 DOI: 10.1016/j.semcdb.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/11/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022]
Abstract
Since their discovery, the Hox genes, with their incredible power to reprogram the identity of complete body regions, a phenomenon called homeosis, have captured the fascination of many biologists. Recent research has provided new insights into the function of Hox proteins in different germ layers and the mechanisms they employ to control tissue morphogenesis. We focus in this review on the ectoderm and mesoderm to highlight new findings and discuss them with regards to established concepts of Hox target gene regulation. Furthermore, we highlight the molecular mechanisms involved the transcriptional repression of specific groups of Hox target genes, and summarize the role of Hox mediated gene silencing in tissue development. Finally, we reflect on recent findings identifying a large number of tissue-specific Hox interactor partners, which open up new avenues and directions towards a better understanding of Hox function and specificity in different tissues.
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24
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GRHL2 Enhances Phosphorylated Estrogen Receptor (ER) Chromatin Binding and Regulates ER-Mediated Transcriptional Activation and Repression. Mol Cell Biol 2022; 42:e0019122. [PMID: 36036613 PMCID: PMC9584124 DOI: 10.1128/mcb.00191-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation of estrogen receptor α (ER) at serine 118 (pS118-ER) is induced by estrogen and is the most abundant posttranslational mark associated with a transcriptionally active receptor. Cistromic analysis of pS118-ER from our group revealed enrichment of the GRHL2 motif near pS118-ER binding sites. In this study, we used cistromic and transcriptomic analyses to interrogate the relationship between GRHL2 and pS118-ER. We found that GRHL2 is bound to chromatin at pS118-ER/GRHL2 co-occupancy sites prior to ligand treatment, and GRHL2 binding is required for maximal pS118-ER recruitment. pS118-ER/GRHL2 co-occupancy sites were enriched at active enhancers marked by H3K27ac and H3K4me1, along with FOXA1 and p300, compared to sites where each factor binds independently. Transcriptomic analysis yielded four subsets of ER/GRHL2-coregulated genes revealing that GRHL2 can both enhance and antagonize E2-mediated ER transcriptional activity. Gene ontology analysis indicated that coregulated genes are involved in cell migration. Accordingly, knockdown of GRHL2, combined with estrogen treatment, resulted in increased cell migration but no change in proliferation. These results support a model in which GRHL2 binds to selected enhancers and facilitates pS118-ER recruitment to chromatin, which then results in differential activation and repression of genes that control estrogen-regulated ER-positive breast cancer cell migration.
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25
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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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26
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Loker R, Mann RS. Divergent expression of paralogous genes by modification of shared enhancer activity through a promoter-proximal silencer. Curr Biol 2022; 32:3545-3555.e4. [PMID: 35853455 PMCID: PMC9398998 DOI: 10.1016/j.cub.2022.06.069] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/18/2022] [Accepted: 06/22/2022] [Indexed: 11/16/2022]
Abstract
The duplication of genes and their associated cis-regulatory elements, or enhancers, is a key contributor to genome evolution and biological complexity. Moreover, many paralogs, particularly tandem duplicates, are fixed for long periods of time under the control of shared enhancers. However, in most cases, the mechanism by which gene expression and function diverge following duplication is not known. Here, we dissect the regulation and function of the paralogous nubbin/pdm2 genes during wing development in Drosophila melanogaster. We show that these paralogs play a redundant role in the wing and that their expression relies on a single shared wing enhancer. However, the two genes differ in their ability to respond to this enhancer, with nub responding in all wing progenitor cells and pdm2 only in a small subset. This divergence is a result of a pdm2-specific silencer element at the pdm2 promoter that receives repressive input from the transcription factor Rotund. Repression through this silencer also depends on nub, allowing pdm2 to fully respond to the wing enhancer when nub expression is perturbed and functional compensation to occur. Thus, expression divergence downstream of a shared enhancer arises as a consequence of silencing the promoter of one paralog.
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Affiliation(s)
- Ryan Loker
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA; Department of Neuroscience, Department of Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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27
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Huang H, Liu J, Li M, Guo H, Zhu J, Zhu L, Wu S, Mo K, Huang Y, Tan J, Chen C, Wang B, Yu Y, Wang L, Liu Y, Ouyang H. Cis-regulatory chromatin loops analysis identifies GRHL3 as a master regulator of surface epithelium commitment. SCIENCE ADVANCES 2022; 8:eabo5668. [PMID: 35857527 PMCID: PMC9278850 DOI: 10.1126/sciadv.abo5668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Understanding the regulatory network of cell fate acquisition remains a major challenge. Using the induction of surface epithelium (SE) from human embryonic stem cells as a paradigm, we show that the dynamic changes in morphology-related genes (MRGs) closely correspond to SE fate transitions. The marked remodeling of cytoskeleton indicates the initiation of SE differentiation. By integrating promoter interactions, epigenomic features, and transcriptome, we delineate an SE-specific cis-regulatory network and identify grainyhead-like 3 (GRHL3) as an initiation factor sufficient to drive SE commitment. Mechanically, GRHL3 primes the SE chromatin accessibility landscape and activates SE-initiating gene expression. In addition, the evaluation of GRHL3-mediated promoter interactions unveils a positive feedback loop of GRHL3 and bone morphogenetic protein 4 on SE fate decisions. Our work proposes a concept that MRGs could be used to identify cell fate transitions and provides insights into regulatory principles of SE lineage development and stem cell-based regenerative medicine.
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Affiliation(s)
- Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jin Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Liqiong Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Kunlun Mo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Ying Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Jieying Tan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Chaoqun Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Bofeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yankun Yu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou 510060, China
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510060, China
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28
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Sipani R, Joshi R. Hox genes collaborate with helix-loop-helix factor Grainyhead to promote neuroblast apoptosis along the anterior-posterior axis of the Drosophila larval central nervous system. Genetics 2022; 222:6632667. [DOI: 10.1093/genetics/iyac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/21/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Hox genes code for a family of a homeodomain (HD) containing transcription factors that use TALE-HD containing factors Pbx/Exd and Meis/Hth to specify the development of the anterior-posterior (AP) axis of an organism. However, the absence of TALE-HD containing factors from specific tissues emphasizes the need to identify and validate new Hox cofactors. In Drosophila central nervous system (CNS), Hox execute segment-specific apoptosis of neural stem cells (neuroblasts-NBs) and neurons. In abdominal segments of larval CNS, Hox gene Abdominal-A (AbdA) mediates NB apoptosis with the help of Exd and bHLH factor Grainyhead (Grh) using a 717 bp apoptotic enhancer. In this study, we show that this enhancer is critical for abdominal NB apoptosis and relies on two separable set of DNA binding motifs responsible for its initiation and maintenance. Our results also show that AbdA and Grh interact through their highly conserved DNA binding domains, and the DNA binding specificity of AbdA-HD is important for it to interact with Grh and essential for it to execute NB apoptosis in CNS. We also establish that Grh is required for Hox-dependent NB apoptosis in Labial and Sex Combs Reduced (Scr) expressing regions of the CNS, and it can physically interact with all the Hox proteins in vitro. Our biochemical and functional data collectively support the idea that Grh can function as a Hox cofactor and help them carry out their in vivo roles during development.
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Affiliation(s)
- Rashmi Sipani
- Laboratory of Drosophila Neural Development, Centre for DNA Fingerprinting and Diagnostics (CDFD) , Inner Ring Road, Uppal, Hyderabad-500039. India
- Graduate Studies, Manipal Academy of Higher Education , Manipal 576104, India
| | - Rohit Joshi
- Laboratory of Drosophila Neural Development, Centre for DNA Fingerprinting and Diagnostics (CDFD) , Inner Ring Road, Uppal, Hyderabad-500039. India
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29
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Arruabarrena-Aristorena A, Toska E. Epigenetic Mechanisms Influencing Therapeutic Response in Breast Cancer. Front Oncol 2022; 12:924808. [PMID: 35774123 PMCID: PMC9239340 DOI: 10.3389/fonc.2022.924808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022] Open
Abstract
The majority of breast cancers are estrogen receptor (ER)+ and agents targeting the ER signaling pathway have markedly increased survival for women with breast cancer for decades. However, therapeutic resistance eventually emerges, especially in the metastatic setting. In the past decade disrupted epigenetic regulatory processes have emerged as major contributors to carcinogenesis in many cancer types. Aberrations in chromatin modifiers and transcription factors have also been recognized as mediators of breast cancer development and therapeutic outcome, and new epigenetic-based therapies in combination with targeted therapies have been proposed. Here we will discuss recent progress in our understanding of the chromatin-based mechanisms of breast tumorigenesis, how these mechanisms affect therapeutic response to standard of care treatment, and discuss new strategies towards therapeutic intervention to overcome resistance.
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Affiliation(s)
- Amaia Arruabarrena-Aristorena
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Traslational Prostate Cancer Research Lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
- *Correspondence: Amaia Arruabarrena-Aristorena, ; Eneda Toska,
| | - Eneda Toska
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biochemistry and Molecular Biology, Johns Hopkins School of Public Health, Baltimore, MD, United States
- *Correspondence: Amaia Arruabarrena-Aristorena, ; Eneda Toska,
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30
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Perry BW, Gopalan SS, Pasquesi GIM, Schield DR, Westfall AK, Smith CF, Koludarov I, Chippindale PT, Pellegrino MW, Chuong EB, Mackessy SP, Castoe TA. Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways. Genome Res 2022; 32:1058-1073. [PMID: 35649579 PMCID: PMC9248877 DOI: 10.1101/gr.276251.121] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 04/11/2022] [Indexed: 11/25/2022]
Abstract
Understanding how regulatory mechanisms evolve is critical for understanding the processes that give rise to novel phenotypes. Snake venom systems represent a valuable and tractable model for testing hypotheses related to the evolution of novel regulatory networks, yet the regulatory mechanisms underlying venom production remain poorly understood. Here, we use functional genomics approaches to investigate venom regulatory architecture in the prairie rattlesnake and identify cis-regulatory sequences (enhancers and promoters), trans-regulatory transcription factors, and integrated signaling cascades involved in the regulation of snake venom genes. We find evidence that two conserved vertebrate pathways, the extracellular signal-regulated kinase and unfolded protein response pathways, were co-opted to regulate snake venom. In one large venom gene family (snake venom serine proteases), this co-option was likely facilitated by the activity of transposable elements. Patterns of snake venom gene enhancer conservation, in some cases spanning 50 million yr of lineage divergence, highlight early origins and subsequent lineage-specific adaptations that have accompanied the evolution of venom regulatory architecture. We also identify features of chromatin structure involved in venom regulation, including topologically associated domains and CTCF loops that underscore the potential importance of novel chromatin structure to coevolve when duplicated genes evolve new regulatory control. Our findings provide a model for understanding how novel regulatory systems may evolve through a combination of genomic processes, including tandem duplication of genes and regulatory sequences, cis-regulatory sequence seeding by transposable elements, and diverse transcriptional regulatory proteins controlled by a co-opted regulatory cascade.
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Affiliation(s)
- Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA.,School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Siddharth S Gopalan
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Giulia I M Pasquesi
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Drew R Schield
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Aundrea K Westfall
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Ivan Koludarov
- Animal Venomics Group, Justus Liebig University, Giessen, 35390, Germany
| | - Paul T Chippindale
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Mark W Pellegrino
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
| | - Edward B Chuong
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, Colorado 80639, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, Texas 76019, USA
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31
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Fischer F, Grigolon G, Benner C, Ristow M. Evolutionarily conserved transcription factors as regulators of longevity and targets for geroprotection. Physiol Rev 2022; 102:1449-1494. [PMID: 35343830 DOI: 10.1152/physrev.00017.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Aging is the single largest risk factor for many debilitating conditions, including heart diseases, stroke, cancer, diabetes, and neurodegenerative disorders. While far from understood in its full complexity, it is scientifically well-established that aging is influenced by genetic and environmental factors, and can be modulated by various interventions. One of aging's early hallmarks are aberrations in transcriptional networks, controlling for example metabolic homeostasis or the response to stress. Evidence in different model organisms abounds that a number of evolutionarily conserved transcription factors, which control such networks, can affect lifespan and healthspan across species. These transcription factors thus potentially represent conserved regulators of longevity and are emerging as important targets in the challenging quest to develop treatments to mitigate age-related diseases, and possibly even to slow aging itself. This review provides an overview of evolutionarily conserved transcription factors that impact longevity or age-related diseases in at least one multicellular model organism (nematodes, flies, or mice), and/or are tentatively linked to human aging. Discussed is the general evidence for transcriptional regulation of aging and disease, followed by a more detailed look at selected transcription factor families, the common metabolic pathways involved, and the targeting of transcription factors as a strategy for geroprotective interventions.
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Affiliation(s)
- Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Christoph Benner
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, Switzerland
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32
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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: 84] [Impact Index Per Article: 42.0] [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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33
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Gasperoni JG, Fuller JN, Darido C, Wilanowski T, Dworkin S. Grainyhead-like (Grhl) Target Genes in Development and Cancer. Int J Mol Sci 2022; 23:ijms23052735. [PMID: 35269877 PMCID: PMC8911041 DOI: 10.3390/ijms23052735] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/12/2022] Open
Abstract
Grainyhead-like (GRHL) factors are essential, highly conserved transcription factors (TFs) that regulate processes common to both natural cellular behaviours during embryogenesis, and de-regulation of growth and survival pathways in cancer. Serving to drive the transcription, and therefore activation of multiple co-ordinating pathways, the three GRHL family members (GRHL1-3) are a critical conduit for modulating the molecular landscape that guides cellular decision-making processes during proliferation, epithelial-mesenchymal transition (EMT) and migration. Animal models and in vitro approaches harbouring GRHL loss or gain-of-function are key research tools to understanding gene function, which gives confidence that resultant phenotypes and cellular behaviours may be translatable to humans. Critically, identifying and characterising the target genes to which these factors bind is also essential, as they allow us to discover and understand novel genetic pathways that could ultimately be used as targets for disease diagnosis, drug discovery and therapeutic strategies. GRHL1-3 and their transcriptional targets have been shown to drive comparable cellular processes in Drosophila, C. elegans, zebrafish and mice, and have recently also been implicated in the aetiology and/or progression of a number of human congenital disorders and cancers of epithelial origin. In this review, we will summarise the state of knowledge pertaining to the role of the GRHL family target genes in both development and cancer, primarily through understanding the genetic pathways transcriptionally regulated by these factors across disparate disease contexts.
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Affiliation(s)
- Jemma G. Gasperoni
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
| | - Jarrad N. Fuller
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
| | - Charbel Darido
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC 3000, Australia;
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Sebastian Dworkin
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Melbourne, VIC 3086, Australia; (J.G.G.); (J.N.F.)
- Correspondence:
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34
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Holm I, Nardini L, Pain A, Bischoff E, Anderson CE, Zongo S, Guelbeogo WM, Sagnon N, Gohl DM, Nowling RJ, Vernick KD, Riehle MM. Comprehensive Genomic Discovery of Non-Coding Transcriptional Enhancers in the African Malaria Vector Anopheles coluzzii. Front Genet 2022; 12:785934. [PMID: 35082832 PMCID: PMC8784733 DOI: 10.3389/fgene.2021.785934] [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: 09/29/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Almost all regulation of gene expression in eukaryotic genomes is mediated by the action of distant non-coding transcriptional enhancers upon proximal gene promoters. Enhancer locations cannot be accurately predicted bioinformatically because of the absence of a defined sequence code, and thus functional assays are required for their direct detection. Here we used a massively parallel reporter assay, Self-Transcribing Active Regulatory Region sequencing (STARR-seq), to generate the first comprehensive genome-wide map of enhancers in Anopheles coluzzii, a major African malaria vector in the Gambiae species complex. The screen was carried out by transfecting reporter libraries created from the genomic DNA of 60 wild A. coluzzii from Burkina Faso into A. coluzzii 4a3A cells, in order to functionally query enhancer activity of the natural population within the homologous cellular context. We report a catalog of 3,288 active genomic enhancers that were significant across three biological replicates, 74% of them located in intergenic and intronic regions. The STARR-seq enhancer screen is chromatin-free and thus detects inherent activity of a comprehensive catalog of enhancers that may be restricted in vivo to specific cell types or developmental stages. Testing of a validation panel of enhancer candidates using manual luciferase assays confirmed enhancer function in 26 of 28 (93%) of the candidates over a wide dynamic range of activity from two to at least 16-fold activity above baseline. The enhancers occupy only 0.7% of the genome, and display distinct composition features. The enhancer compartment is significantly enriched for 15 transcription factor binding site signatures, and displays divergence for specific dinucleotide repeats, as compared to matched non-enhancer genomic controls. The genome-wide catalog of A. coluzzii enhancers is publicly available in a simple searchable graphic format. This enhancer catalogue will be valuable in linking genetic and phenotypic variation, in identifying regulatory elements that could be employed in vector manipulation, and in better targeting of chromosome editing to minimize extraneous regulation influences on the introduced sequences. Importance: Understanding the role of the non-coding regulatory genome in complex disease phenotypes is essential, but even in well-characterized model organisms, identification of regulatory regions within the vast non-coding genome remains a challenge. We used a large-scale assay to generate a genome wide map of transcriptional enhancers. Such a catalogue for the important malaria vector, Anopheles coluzzii, will be an important research tool as the role of non-coding regulatory variation in differential susceptibility to malaria infection is explored and as a public resource for research on this important insect vector of disease.
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Affiliation(s)
- Inge Holm
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Luisa Nardini
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Adrien Pain
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France.,Institut Pasteur, Université de Paris, Hub de Bioinformatique et Biostatistique, Paris, France
| | - Emmanuel Bischoff
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Cameron E Anderson
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Soumanaba Zongo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - Wamdaogo M Guelbeogo
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - N'Fale Sagnon
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ministry of Health, Ouagadougou, Burkina Faso
| | - Daryl M Gohl
- University of Minnesota Genomics Center, Minneapolis, MN, United States.,Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, United States
| | - Ronald J Nowling
- Department of Electrical Engineering and Computer Science, Milwaukee School of Engineering (MSOE), Milwaukee, WI, United States
| | - Kenneth D Vernick
- Institut Pasteur, Université de Paris, CNRS UMR 2000, Unit of Insect Vector Genetics and Genomics, Department of Parasites and Insect Vectors, Paris, France
| | - Michelle M Riehle
- Department of Microbiology and Immunology, Medical College of Wisconsin, Milwaukee, WI, United States
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Kervarrec T, Pissaloux D, Poilane J, Tirode F, Tallet A, Collin C, Tallegas M, Berthon P, Gaboriaud P, Sohier P, Calonje E, Luzar B, Goto K, Cokelaere K, Lamant L, Balme B, Wild R, Neuville A, Deschamps L, Auberger E, Paumier V, Bonte H, Moulonguet I, Plantier F, Cales V, Pinsolle V, Roblet D, Dupuy F, Dallot A, Seris A, Jouary T, Houben R, Schrama D, Hesbacher S, Macagno N, Battistella M, Cribier B, Vergier B, Fouchardière A, Jullie M. Recurrent
FOXK1
::
GRHL
and
GPS2
::
GRHL
fusions in trichogerminoma. J Pathol 2022; 257:96-108. [DOI: 10.1002/path.5872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 12/14/2021] [Accepted: 01/17/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Thibault Kervarrec
- Department of Pathology Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
- “Biologie des infections à polyomavirus” team, UMR INRA ISP 1282 Université de Tours Tours France
- CARADERM Network
| | - Daniel Pissaloux
- Department of Biopathology Center Léon Bérard Lyon France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer Lyon France
| | - Jeremie Poilane
- Department of Pathology Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
- Platform of Somatic Tumor Molecular Genetics Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
- Department of Pathology Centre Hospitalier Universitaire de Angers Angers France
| | - Franck Tirode
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer Lyon France
| | - Anne Tallet
- Platform of Somatic Tumor Molecular Genetics Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
| | - Christine Collin
- Platform of Somatic Tumor Molecular Genetics Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
| | - Matthias Tallegas
- Department of Pathology Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
- Platform of Somatic Tumor Molecular Genetics Université de Tours, Centre Hospitalier Universitaire de Tours Tours France
| | - Patricia Berthon
- “Biologie des infections à polyomavirus” team, UMR INRA ISP 1282 Université de Tours Tours France
| | - Pauline Gaboriaud
- “Biologie des infections à polyomavirus” team, UMR INRA ISP 1282 Université de Tours Tours France
| | - Pierre Sohier
- CARADERM Network
- Faculté de Médecine Paris Centre Santé University of Paris Paris France
- Department of Pathology Hôpital Cochin, AP‐HP Centre‐Université de Paris Paris France
| | - Eduardo Calonje
- Department of Dermatopathology St John's Institute of Dermatology, St Thomas's Hospital London UK
| | - Boštjan Luzar
- Institute of Pathology Medical Faculty University of Ljubljana Ljubljana Slovenia
| | - Keisuke Goto
- Department of Pathology Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital Tokyo Japan
- Department of Diagnostic Pathology Shizuoka Cancer Center Hospital, Sunto Japan
- Department of Diagnostic Pathology and Cytology Osaka International Cancer Institute Osaka Japan
- Department of Dermatology Hyogo Cancer Center Akashi Japan
| | | | - Laurence Lamant
- CARADERM Network
- Department of Pathology, CHU Toulouse, Institut Universitaire du Cancer Toulouse Oncopole Université Toulouse III Paul Sabatier Toulouse France
| | - Brigitte Balme
- CARADERM Network
- Department of Pathology Centre Hospitalier Universitaire de Lyon Lyon France
| | | | - Agnes Neuville
- Contades Office of Pathological Anatomy and Cytology Strasbourg France
| | - Lydia Deschamps
- CARADERM Network
- Department of Pathology, APHP Bichat Hospital Paris France
| | - Elisabeth Auberger
- Service d'anatomie et cytologie pathologiques Hopital Simone Veil Eaubonne France
| | | | | | | | - Françoise Plantier
- Department of Pathology Hôpital Cochin, AP‐HP Centre‐Université de Paris Paris France
- Cabinet Mathurin Moreau Paris France
| | - Valérie Cales
- Department of Pathology Centre hospitalier de Pau Pau France
| | - Vincent Pinsolle
- Department of plastic and reconstructive surgery Hôpital Haut‐Lévêque, Centre hospitalier universitaire de Bordeaux Pessac France
| | - Denis Roblet
- Department of Pathology Centre hospitalier d'Angouleme Saint Michel France
| | - Frantz Dupuy
- Laboratoire de cytologie et d'anatomie pathologiques», le Bouscat France
| | - Alexiane Dallot
- Centre national de Dermatopathologie‐La Roquette Paris France
| | | | - Thomas Jouary
- CARADERM Network
- Department of Dermatology Centre Hospitalier de Pau Pau France
| | - Roland Houben
- Department of Dermatology, Venereology and Allergology University Hospital Würzburg, Josef‐Schneider‐Straße 2 Würzburg Germany
| | - David Schrama
- Department of Dermatology, Venereology and Allergology University Hospital Würzburg, Josef‐Schneider‐Straße 2 Würzburg Germany
| | - Sonja Hesbacher
- Department of Dermatology, Venereology and Allergology University Hospital Würzburg, Josef‐Schneider‐Straße 2 Würzburg Germany
| | - Nicolas Macagno
- CARADERM Network
- Department of Biopathology Center Léon Bérard Lyon France
- Department of Pathology Timone University Hospital Marseille France
| | - Maxime Battistella
- CARADERM Network
- Department of Pathology, APHP Hôpital Saint Louis Université Paris 7 Paris France
| | - Bernard Cribier
- CARADERM Network
- Dermatology Clinic, Hôpitaux Universitaires & Université de Strasbourg, Hôpital Civil Strasbourg France
| | - Beatrice Vergier
- Department of Pathology, Hôpital Haut‐Lévêque, CHU de Bordeaux Pessac France
| | - Arnaud Fouchardière
- CARADERM Network
- Department of Biopathology Center Léon Bérard Lyon France
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Cancer Research Center of Lyon, Equipe Labellisée Ligue contre le Cancer Lyon France
| | - Marie‐Laure Jullie
- CARADERM Network
- Department of Pathology, Hôpital Haut‐Lévêque, CHU de Bordeaux Pessac France
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Grigolon G, Araldi E, Erni R, Wu JY, Thomas C, La Fortezza M, Laube B, Pöhlmann D, Stoffel M, Zarse K, Carreira EM, Ristow M, Fischer F. Grainyhead 1 acts as a drug-inducible conserved transcriptional regulator linked to insulin signaling and lifespan. Nat Commun 2022; 13:107. [PMID: 35013237 PMCID: PMC8748497 DOI: 10.1038/s41467-021-27732-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 12/06/2021] [Indexed: 12/13/2022] Open
Abstract
Aging is impacted by interventions across species, often converging on metabolic pathways. Transcription factors regulate longevity yet approaches for their pharmacological modulation to exert geroprotection remain sparse. We show that increased expression of the transcription factor Grainyhead 1 (GRH-1) promotes lifespan and pathogen resistance in Caenorhabditis elegans. A compound screen identifies FDA-approved drugs able to activate human GRHL1 and promote nematodal GRH-1-dependent longevity. GRHL1 activity is regulated by post-translational lysine methylation and the phosphoinositide (PI) 3-kinase C2A. Consistently, nematodal longevity following impairment of the PI 3-kinase or insulin/IGF-1 receptor requires grh-1. In BXD mice, Grhl1 expression is positively correlated with lifespan and insulin sensitivity. In humans, GRHL1 expression positively correlates with insulin receptor signaling and also with lifespan. Fasting blood glucose levels, including in individuals with type 2 diabetes, are negatively correlated with GRHL1 expression. Thereby, GRH-1/GRHL1 is identified as a pharmacologically malleable transcription factor impacting insulin signaling and lifespan. Life- and healthspan of organisms can be modulated by dietary, genetic, or pharmacological interventions, which often affect metabolic pathways. Here the authors report that Grainyhead 1 is an evolutionarily conserved, drug-inducible transcription factor that promotes longevity in C. elegans, and thus a potential target for the development of geroprotective drugs.
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Affiliation(s)
- Giovanna Grigolon
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Elisa Araldi
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.,Metabolism and Metabolic Disease Laboratory, Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Reto Erni
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Jia Yee Wu
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Carolin Thomas
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Marco La Fortezza
- Evolutionary Biology Laboratory, Department of Environmental Systems Science, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8092, Switzerland
| | - Beate Laube
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Doris Pöhlmann
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Markus Stoffel
- Metabolism and Metabolic Disease Laboratory, Institute for Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Kim Zarse
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
| | - Erick M Carreira
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH) Zurich, Zurich, CH-8093, Switzerland
| | - Michael Ristow
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland.
| | - Fabian Fischer
- Energy Metabolism Laboratory, Institute of Translational Medicine, Department of Health Sciences and Technology, Swiss Federal Institute of Technology (ETH) Zurich, Schwerzenbach, CH-8603, Switzerland
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37
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Janssens J, Aibar S, Taskiran II, Ismail JN, Gomez AE, Aughey G, Spanier KI, De Rop FV, González-Blas CB, Dionne M, Grimes K, Quan XJ, Papasokrati D, Hulselmans G, Makhzami S, De Waegeneer M, Christiaens V, Southall T, Aerts S. Decoding gene regulation in the fly brain. Nature 2022; 601:630-636. [PMID: 34987221 DOI: 10.1038/s41586-021-04262-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 11/17/2021] [Indexed: 12/13/2022]
Abstract
The Drosophila brain is a frequently used model in neuroscience. Single-cell transcriptome analysis1-6, three-dimensional morphological classification7 and electron microscopy mapping of the connectome8,9 have revealed an immense diversity of neuronal and glial cell types that underlie an array of functional and behavioural traits in the fly. The identities of these cell types are controlled by gene regulatory networks (GRNs), involving combinations of transcription factors that bind to genomic enhancers to regulate their target genes. Here, to characterize GRNs at the cell-type level in the fly brain, we profiled the chromatin accessibility of 240,919 single cells spanning 9 developmental timepoints and integrated these data with single-cell transcriptomes. We identify more than 95,000 regulatory regions that are used in different neuronal cell types, of which 70,000 are linked to developmental trajectories involving neurogenesis, reprogramming and maturation. For 40 cell types, uniquely accessible regions were associated with their expressed transcription factors and downstream target genes through a combination of motif discovery, network inference and deep learning, creating enhancer GRNs. The enhancer architectures revealed by DeepFlyBrain lead to a better understanding of neuronal regulatory diversity and can be used to design genetic driver lines for cell types at specific timepoints, facilitating their characterization and manipulation.
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Affiliation(s)
- Jasper Janssens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Sara Aibar
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Joy N Ismail
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Gabriel Aughey
- Department of Life Sciences, Imperial College London, London, UK
| | - Katina I Spanier
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Florian V De Rop
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Carmen Bravo González-Blas
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Marc Dionne
- Department of Life Sciences, Imperial College London, London, UK
| | - Krista Grimes
- Department of Life Sciences, Imperial College London, London, UK
| | - Xiao Jiang Quan
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Dafni Papasokrati
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Gert Hulselmans
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Samira Makhzami
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Maxime De Waegeneer
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- VIB Center for Brain & Disease Research, Leuven, Belgium.,Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tony Southall
- Department of Life Sciences, Imperial College London, London, UK
| | - Stein Aerts
- VIB Center for Brain & Disease Research, Leuven, Belgium. .,Department of Human Genetics, KU Leuven, Leuven, Belgium.
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38
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Waters CT, Gisselbrecht SS, Sytnikova YA, Cafarelli TM, Hill DE, Bulyk ML. Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue. Genome Biol 2021; 22:348. [PMID: 34930411 PMCID: PMC8686523 DOI: 10.1186/s13059-021-02574-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/10/2021] [Indexed: 11/16/2022] Open
Abstract
Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.
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Affiliation(s)
- Colin T Waters
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yuliya A Sytnikova
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Tiziana M Cafarelli
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - David E Hill
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, 02138, USA.
- Center for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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39
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Loker R, Sanner JE, Mann RS. Cell-type-specific Hox regulatory strategies orchestrate tissue identity. Curr Biol 2021; 31:4246-4255.e4. [PMID: 34358443 PMCID: PMC8511240 DOI: 10.1016/j.cub.2021.07.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/17/2021] [Accepted: 07/13/2021] [Indexed: 01/25/2023]
Abstract
Hox proteins are homeodomain transcription factors that diversify serially homologous segments along the animal body axis, as revealed by the classic bithorax phenotype of Drosophila melanogaster, in which mutations in Ultrabithorax (Ubx) transform the third thoracic segment into the likeness of the second thoracic segment. To specify segment identity, we show that Ubx both increases and decreases chromatin accessibility, coinciding with its dual role as both an activator and repressor of transcription. However, the choice of transcriptional activity executed by Ubx is spatially regulated and depends on the availability of cofactors, with Ubx acting as a repressor in some populations and as an activator in others. Ubx-mediated changes to chromatin accessibility positively and negatively affect the binding of Scalloped (Sd), a transcription factor that is required for appendage development in both segments. These findings illustrate how a single Hox protein can modify complex gene regulatory networks to transform the identity of an entire tissue.
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Affiliation(s)
- Ryan Loker
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, USA; Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Jordyn E Sanner
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA; Department of Neuroscience, Columbia University Irving Medical Center, New York, NY, USA; Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
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40
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Ray-Jones H, Spivakov M. Transcriptional enhancers and their communication with gene promoters. Cell Mol Life Sci 2021; 78:6453-6485. [PMID: 34414474 PMCID: PMC8558291 DOI: 10.1007/s00018-021-03903-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022]
Abstract
Transcriptional enhancers play a key role in the initiation and maintenance of gene expression programmes, particularly in metazoa. How these elements control their target genes in the right place and time is one of the most pertinent questions in functional genomics, with wide implications for most areas of biology. Here, we synthesise classic and recent evidence on the regulatory logic of enhancers, including the principles of enhancer organisation, factors that facilitate and delimit enhancer-promoter communication, and the joint effects of multiple enhancers. We show how modern approaches building on classic insights have begun to unravel the complexity of enhancer-promoter relationships, paving the way towards a quantitative understanding of gene control.
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Affiliation(s)
- Helen Ray-Jones
- MRC London Institute of Medical Sciences, London, W12 0NN, UK
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK
| | - Mikhail Spivakov
- MRC London Institute of Medical Sciences, London, W12 0NN, UK.
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College, London, W12 0NN, UK.
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41
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Kashgari G, Venkatesh S, Refuerzo S, Pham B, Bayat A, Klein RH, Ramos R, Ta AP, Plikus MV, Wang PH, Andersen B. GRHL3 activates FSCN1 to relax cell-cell adhesions between migrating keratinocytes during wound reepithelialization. JCI Insight 2021; 6:e142577. [PMID: 34494554 PMCID: PMC8492311 DOI: 10.1172/jci.insight.142577] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/21/2021] [Indexed: 01/23/2023] Open
Abstract
The migrating keratinocyte wound front is required for skin wound closure. Despite significant advances in wound healing research, we do not fully understand the molecular mechanisms that orchestrate collective keratinocyte migration. Here, we show that, in the wound front, the epidermal transcription factor Grainyhead like-3 (GRHL3) mediates decreased expression of the adherens junction protein E-cadherin; this results in relaxed adhesions between suprabasal keratinocytes, thus promoting collective cell migration and wound closure. Wound fronts from mice lacking GRHL3 in epithelial cells (Grhl3-cKO) have lower expression of Fascin-1 (FSCN1), a known negative regulator of E-cadherin. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) on wounded keratinocytes shows decreased wound-induced chromatin accessibility near the Fscn1 gene in Grhl3-cKO mice, a region enriched for GRHL3 motifs. These data reveal a wound-induced GRHL3/FSCN1/E-cadherin pathway that regulates keratinocyte-keratinocyte adhesion during wound-front migration; this pathway is activated in acute human wounds and is altered in diabetic wounds in mice, suggesting translational relevance.
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Affiliation(s)
| | | | | | - Brandon Pham
- Department of Biological Chemistry, School of Medicine
| | - Anita Bayat
- Department of Biological Chemistry, School of Medicine
| | | | - Raul Ramos
- Department of Developmental & Cell Biology, School of Biological Sciences, and
| | - Albert Paul Ta
- Department of Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine (UCI), California, USA
| | - Maksim V Plikus
- Department of Developmental & Cell Biology, School of Biological Sciences, and
| | - Ping H Wang
- Department of Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine (UCI), California, USA
| | - Bogi Andersen
- Department of Biological Chemistry, School of Medicine.,Department of Medicine, Division of Endocrinology, School of Medicine, University of California, Irvine (UCI), California, USA
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42
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Tachmatzidi EC, Galanopoulou O, Talianidis I. Transcription Control of Liver Development. Cells 2021; 10:cells10082026. [PMID: 34440795 PMCID: PMC8391549 DOI: 10.3390/cells10082026] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023] Open
Abstract
During liver organogenesis, cellular transcriptional profiles are constantly reshaped by the action of hepatic transcriptional regulators, including FoxA1-3, GATA4/6, HNF1α/β, HNF4α, HNF6, OC-2, C/EBPα/β, Hex, and Prox1. These factors are crucial for the activation of hepatic genes that, in the context of compact chromatin, cannot access their targets. The initial opening of highly condensed chromatin is executed by a special class of transcription factors known as pioneer factors. They bind and destabilize highly condensed chromatin and facilitate access to other "non-pioneer" factors. The association of target genes with pioneer and non-pioneer transcription factors takes place long before gene activation. In this way, the underlying gene regulatory regions are marked for future activation. The process is called "bookmarking", which confers transcriptional competence on target genes. Developmental bookmarking is accompanied by a dynamic maturation process, which prepares the genomic loci for stable and efficient transcription. Stable hepatic expression profiles are maintained during development and adulthood by the constant availability of the main regulators. This is achieved by a self-sustaining regulatory network that is established by complex cross-regulatory interactions between the major regulators. This network gradually grows during liver development and provides an epigenetic memory mechanism for safeguarding the optimal expression of the regulators.
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Affiliation(s)
- Evangelia C. Tachmatzidi
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Ourania Galanopoulou
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Department of Biology, University of Crete, 70013 Herakleion, Crete, Greece
| | - Iannis Talianidis
- Institute of Molecular Biology and Biotechnology, FORTH, 70013 Herakleion, Crete, Greece; (E.C.T.); (O.G.)
- Correspondence:
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43
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He Y, Gan M, Wang Y, Huang T, Wang J, Han T, Yu B. EGFR-ERK induced activation of GRHL1 promotes cell cycle progression by up-regulating cell cycle related genes in lung cancer. Cell Death Dis 2021; 12:430. [PMID: 33931584 PMCID: PMC8087693 DOI: 10.1038/s41419-021-03721-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/06/2021] [Accepted: 04/08/2021] [Indexed: 11/09/2022]
Abstract
Grainyhead-like 1 (GRHL1) is a transcription factor involved in embryonic development. However, little is known about the biological functions of GRHL1 in cancer. In this study, we found that GRHL1 was upregulated in non-small cell lung cancer (NSCLC) and correlated with poor survival of patients. GRHL1 overexpression promoted the proliferation of NSCLC cells and knocking down GRHL1 inhibited the proliferation. RNA sequencing showed that a series of cell cycle-related genes were altered when knocking down GRHL1. We further demonstrated that GRHL1 could regulate the expression of cell cycle-related genes by binding to the promoter regions and increasing the transcription of the target genes. Besides, we also found that EGF stimulation could activate GRHL1 and promoted its nuclear translocation. We identified the key phosphorylation site at Ser76 on GRHL1 that is regulated by the EGFR-ERK axis. Taken together, these findings elucidate a new function of GRHL1 on regulating the cell cycle progression and point out the potential role of GRHL1 as a drug target in NSCLC.
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Affiliation(s)
- Yiming He
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China.,Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China
| | - Mingxi Gan
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, P. R. China
| | - Yanan Wang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, P. R. China
| | - Tong Huang
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China
| | - Jianbin Wang
- School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, P. R. China.
| | - Tianyu Han
- Jiangxi Institute of Respiratory Disease, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China.
| | - Bentong Yu
- Department of Thoracic Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, P. R. China.
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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: 39] [Impact Index Per Article: 13.0] [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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Deng Z, Cangkrama M, Butt T, Jane SM, Carpinelli MR. Grainyhead-like transcription factors: guardians of the skin barrier. Vet Dermatol 2021; 32:553-e152. [PMID: 33843098 DOI: 10.1111/vde.12956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/24/2020] [Accepted: 12/14/2020] [Indexed: 01/02/2023]
Abstract
There has been selective pressure to maintain a skin barrier since terrestrial animals evolved 360 million years ago. These animals acquired an unique integumentary system with a keratinized, stratified, squamous epithelium surface barrier. The barrier protects against dehydration and entry of microbes and toxins. The skin barrier centres on the stratum corneum layer of the epidermis and consists of cornified envelopes cemented by the intercorneocyte lipid matrix. Multiple components of the barrier undergo cross-linking by transglutaminase (TGM) enzymes, while keratins provide additional mechanical strength. Cellular tight junctions also are crucial for barrier integrity. The grainyhead-like (GRHL) transcription factors regulate the formation and maintenance of the integument in diverse species. GRHL3 is essential for formation of the skin barrier during embryonic development, whereas GRHL1 maintains the skin barrier postnatally. This is achieved by transactivation of Tgm1 and Tgm5, respectively. In addition to its barrier function, GRHL3 plays key roles in wound repair and as an epidermal tumour suppressor. In its former role, GRHL3 activates the planar cell polarity signalling pathway to mediate wound healing by providing directional migration cues. In squamous epithelium, GRHL3 regulates the balance between proliferation and differentiation, and its loss induces squamous cell carcinoma (SCC). In the skin, this is mediated through increased expression of MIR21, which reduces the expression levels of GRHL3 and its direct target, PTEN, leading to activation of the PI3K-AKT signalling pathway. These data position the GRHL family as master regulators of epidermal homeostasis across a vast gulf of evolutionary history.
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Affiliation(s)
- Zihao Deng
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Michael Cangkrama
- Department of Biology, Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Tariq Butt
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Stephen M Jane
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
| | - Marina R Carpinelli
- Department of Medicine, Central Clinical School, Monash University, Melbourne, Australia
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46
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Atak ZK, Taskiran II, Demeulemeester J, Flerin C, Mauduit D, Minnoye L, Hulselmans G, Christiaens V, Ghanem GE, Wouters J, Aerts S. Interpretation of allele-specific chromatin accessibility using cell state-aware deep learning. Genome Res 2021; 31:1082-1096. [PMID: 33832990 PMCID: PMC8168584 DOI: 10.1101/gr.260851.120] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2021] [Indexed: 12/26/2022]
Abstract
Genomic sequence variation within enhancers and promoters can have a significant impact on the cellular state and phenotype. However, sifting through the millions of candidate variants in a personal genome or a cancer genome, to identify those that impact cis-regulatory function, remains a major challenge. Interpretation of noncoding genome variation benefits from explainable artificial intelligence to predict and interpret the impact of a mutation on gene regulation. Here we generate phased whole genomes with matched chromatin accessibility, histone modifications, and gene expression for 10 melanoma cell lines. We find that training a specialized deep learning model, called DeepMEL2, on melanoma chromatin accessibility data can capture the various regulatory programs of the melanocytic and mesenchymal-like melanoma cell states. This model outperforms motif-based variant scoring, as well as more generic deep learning models. We detect hundreds to thousands of allele-specific chromatin accessibility variants (ASCAVs) in each melanoma genome, of which 15%-20% can be explained by gains or losses of transcription factor binding sites. A considerable fraction of ASCAVs are caused by changes in AP-1 binding, as confirmed by matched ChIP-seq data to identify allele-specific binding of JUN and FOSL1. Finally, by augmenting the DeepMEL2 model with ChIP-seq data for GABPA, the TERT promoter mutation, as well as additional ETS motif gains, can be identified with high confidence. In conclusion, we present a new integrative genomics approach and a deep learning model to identify and interpret functional enhancer mutations with allelic imbalance of chromatin accessibility and gene expression.
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Affiliation(s)
- Zeynep Kalender Atak
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Ibrahim Ihsan Taskiran
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Jonas Demeulemeester
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium.,Cancer Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Christopher Flerin
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - David Mauduit
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Liesbeth Minnoye
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Gert Hulselmans
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Valerie Christiaens
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Ghanem-Elias Ghanem
- Institut Jules Bordet, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Jasper Wouters
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
| | - Stein Aerts
- VIB-KU Leuven Center for Brain and Disease Research, 3000 Leuven, Belgium.,KU Leuven, Department of Human Genetics KU Leuven, 3000 Leuven, Belgium
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47
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Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally 'accessible', the genome-wide profiling of chromatin accessibility can be used to identify candidate regulatory genomic regions in a tissue or cell type. Multiple biochemical methods have been developed to profile chromatin accessibility, both in bulk and at the single-cell level. Depending on the method, enzymatic cleavage, transposition or DNA methyltransferases are used, followed by high-throughput sequencing, providing a view of genome-wide chromatin accessibility. In this Primer, we discuss these biochemical methods, as well as bioinformatics tools for analysing and interpreting the generated data, and insights into the key regulators underlying developmental, evolutionary and disease processes. We outline standards for data quality, reproducibility and deposition used by the genomics community. Although chromatin accessibility profiling is invaluable to study gene regulation, alone it provides only a partial view of this complex process. Orthogonal assays facilitate the interpretation of accessible regions with respect to enhancer-promoter proximity, functional transcription factor binding and regulatory function. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
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Affiliation(s)
- Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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48
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Li M, Huang H, Li L, He C, Zhu L, Guo H, Wang L, Liu J, Wu S, Liu J, Xu T, Mao Z, Cao N, Zhang K, Lan F, Ding J, Yuan J, Liu Y, Ouyang H. Core transcription regulatory circuitry orchestrates corneal epithelial homeostasis. Nat Commun 2021; 12:420. [PMID: 33462242 PMCID: PMC7814021 DOI: 10.1038/s41467-020-20713-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 12/12/2020] [Indexed: 12/20/2022] Open
Abstract
Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restricted epigenetic and transcriptional regulatory networks. Here, by integrating super-enhancer and chromatin accessibility landscapes, we delineate core transcription regulatory circuitries (CRCs) of limbal stem/progenitor cells (LSCs) and find that RUNX1 and SMAD3 are required for maintenance of corneal epithelial identity and homeostasis. RUNX1 or SMAD3 depletion inhibits PAX6 and induces LSCs to differentiate into epidermal-like epithelial cells. RUNX1, PAX6, and SMAD3 (RPS) interact with each other and synergistically establish a CRC to govern the lineage-specific cis-regulatory atlas. Moreover, RUNX1 shapes LSC chromatin architecture via modulating H3K27ac deposition. Disturbance of RPS cooperation results in cell identity switching and dysfunction of the corneal epithelium, which is strongly linked to various human corneal diseases. Our work highlights CRC TF cooperativity for establishment of stem cell identity and lineage commitment, and provides comprehensive regulatory principles for human stratified epithelial homeostasis and pathogenesis. Corneal epithelium shares similar molecular signatures to other stratified epithelia. Here, the authors map super-enhancers and accessible chromatin in corneal epithelium, identifying a transcription regulatory circuit, including RUNX1, PAX6, and SMAD3, required for corneal epithelial identity and homeostasis.
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Affiliation(s)
- Mingsen Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Huaxing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lingyu Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chenxi He
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences; Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Liqiong Zhu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Huizhen Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Li Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Jiafeng Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Siqi Wu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Jingxin Liu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, 510080, Guangzhou, China
| | - Tao Xu
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, 510080, Guangzhou, China
| | - Zhen Mao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Nan Cao
- Program of Stem Cells and Regenerative Medicine, Fifth Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-Sen University, Guangdong, China
| | - Kang Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China.,Center for Biomedicine and Innovations, Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Fei Lan
- Key Laboratory of Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences; Liver Cancer Institute, Zhongshan Hospital, Fudan University, 200032, Shanghai, China
| | - Junjun Ding
- Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, 510080, Guangzhou, China
| | - Jin Yuan
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Yizhi Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Research Units of Ocular Development and Regeneration, Chinese Academy of Medical Sciences, Beijing, China.
| | - Hong Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 510060, Guangzhou, China.
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49
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Loss of FOXC1 contributes to the corneal epithelial fate switch and pathogenesis. Signal Transduct Target Ther 2021; 6:5. [PMID: 33414365 PMCID: PMC7791103 DOI: 10.1038/s41392-020-00378-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/01/2020] [Accepted: 07/31/2020] [Indexed: 11/08/2022] Open
Abstract
Forkhead box C1 (FOXC1) is required for neural crest and ocular development, and mutations in FOXC1 lead to inherited Axenfeld-Rieger syndrome. Here, we find that FOXC1 and paired box 6 (PAX6) are co-expressed in the human limbus and central corneal epithelium. Deficiency of FOXC1 and alternation in epithelial features occur in patients with corneal ulcers. FOXC1 governs the fate of the corneal epithelium by directly binding to lineage-specific open promoters or enhancers marked by H3K4me2. FOXC1 depletion not only activates the keratinization pathway and reprograms corneal epithelial cells into skin-like epithelial cells, but also disrupts the collagen metabolic process and interferon signaling pathways. Loss of interferon regulatory factor 1 and PAX6 induced by FOXC1 dysfunction is linked to the corneal ulcer. Collectively, our results reveal a FOXC1-mediated regulatory network responsible for corneal epithelial homeostasis and provide a potential therapeutic target for corneal ulcer.
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50
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Abstract
The evolutionary emergence of the mesenchymal phenotype greatly increased the complexity of tissue architecture and composition in early Metazoan species. At the molecular level, an epithelial-to-mesenchymal transition (EMT) was permitted by the innovation of specific transcription factors whose expression is sufficient to repress the epithelial transcriptional program. The reverse process, mesenchymal-to-epithelial transition (MET), involves direct inhibition of EMT transcription factors by numerous mechanisms including tissue-specific MET-inducing transcription factors (MET-TFs), micro-RNAs, and changes to cell and tissue architecture, thus providing an elegant solution to the need for tight temporal and spatial control over EMT and MET events during development and adult tissue homeostasis.
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Affiliation(s)
- John-Poul Ng-Blichfeldt
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
| | - Katja Röper
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
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