1
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Luck C, Jacobs KA, Okimoto RA. The Capicua C1 Domain is Required for Full Activity of the CIC::DUX4 Fusion Oncoprotein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597815. [PMID: 38895482 PMCID: PMC11185703 DOI: 10.1101/2024.06.06.597815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Rearrangements between genes can yield neomorphic fusions that drive oncogenesis. Fusion oncogenes are made up of fractional segments of the partner genes that comprise them, with each partner potentially contributing some of its own function to the nascent fusion oncoprotein. Clinically, fusion oncoproteins driving one diagnostic entity are typically clustered into a single molecular subset and are often treated a similar fashion. However, knowledge of where specific fusion breakpoints occur in partner genes, and the resulting retention of functional domains in the fusion, is an important determinant of fusion oncoprotein activity and may differ between patients. This study investigates this phenomena through the example of CIC::DUX4, a fusion between the transcriptional repressor capicua (CIC) and the double homeobox 4 gene (DUX4), which drives an aggressive subset of undifferentiated round cell sarcoma. Using a harmonized dataset of over 100 patient fusion breakpoints from the literature, we show that most bona fide CIC::DUX4 fusions retain the C1 domain, which is known to contribute to DNA binding by wild type CIC. Mechanistically, deletion or mutation of the C1 domain reduces, but does not eliminate, activation of CIC target genes by CIC::DUX4. We also find that expression of C1-deleted CIC::DUX4 is capable of exerting intermediate transformation-related phenotypes compared with those imparted by full-length CIC::DUX4, but was not sufficient for tumorigenesis in a subcutaneous mouse model. In summary, our results suggest a supercharging role for the C1 domain in the activity of CIC::DUX4.
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Affiliation(s)
- Cuyler Luck
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Kyle A. Jacobs
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Cell and Tissue Biology, University of California, San Francisco, CA, USA
| | - Ross A. Okimoto
- Department of Medicine, University of California, San Francisco, CA, USA
- Helen Diller Comprehensive Cancer Center, University of California, San Francisco, CA, USA
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2
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Friedman MJ, Wagner T, Lee H, Rosenfeld MG, Oh S. Enhancer-promoter specificity in gene transcription: molecular mechanisms and disease associations. Exp Mol Med 2024; 56:772-787. [PMID: 38658702 PMCID: PMC11058250 DOI: 10.1038/s12276-024-01233-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 04/26/2024] Open
Abstract
Although often located at a distance from their target gene promoters, enhancers are the primary genomic determinants of temporal and spatial transcriptional specificity in metazoans. Since the discovery of the first enhancer element in simian virus 40, there has been substantial interest in unraveling the mechanism(s) by which enhancers communicate with their partner promoters to ensure proper gene expression. These research efforts have benefited considerably from the application of increasingly sophisticated sequencing- and imaging-based approaches in conjunction with innovative (epi)genome-editing technologies; however, despite various proposed models, the principles of enhancer-promoter interaction have still not been fully elucidated. In this review, we provide an overview of recent progress in the eukaryotic gene transcription field pertaining to enhancer-promoter specificity. A better understanding of the mechanistic basis of lineage- and context-dependent enhancer-promoter engagement, along with the continued identification of functional enhancers, will provide key insights into the spatiotemporal control of gene expression that can reveal therapeutic opportunities for a range of enhancer-related diseases.
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Affiliation(s)
- Meyer J Friedman
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Tobias Wagner
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Haram Lee
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea
| | - Michael G Rosenfeld
- Department and School of Medicine, University of California, San Diego, La Jolla, CA, USA.
| | - Soohwan Oh
- College of Pharmacy Korea University, 2511 Sejong-ro, Sejong, 30019, Republic of Korea.
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3
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Hawley RG, Hawley TS. CRISPR-Cas9-Mediated Bioluminescent Tagging of Endogenous Proteins by Fluorescent Protein-Assisted Cell Sorting. Methods Mol Biol 2024; 2779:273-286. [PMID: 38526790 DOI: 10.1007/978-1-0716-3738-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Oncogenic fusion genes are attractive therapeutic targets because of their tumor-specific expression and central "driver" roles in various human cancers. However, oncogenic fusions involving transcription factors such as PAX3-FOXO1 in alveolar fusion gene-positive rhabdomyosarcoma (FP-RMS) have been difficult to inhibit due to the apparent lack of tractable drug-like binding sites comparable to that recognized by Gleevec (imatinib mesylate) on the BCR-ABL1 tyrosine kinase fusion protein. Toward the identification of novel small molecules that selectively target PAX3-FOXO1, we used CRISPR-Cas9-mediated knock-in to append the pro-luminescent HiBiT tag onto the carboxy terminus of the endogenous PAX3-FOXO1 fusion protein in two human FP-RMS cell lines (RH4 and SCMC). HiBiT is an 11-amino acid peptide derived from the NanoLuc luciferase that produces a luminescence signal which is ~100-fold brighter than firefly or Renilla luciferases through high-affinity binding to a complementary NanoLuc peptide fragment called LgBiT. To facilitate single-cell clonal isolation of knock-ins, the homology-directed repair template encoding HiBiT was followed by a P2A self-cleaving peptide for coexpression of an mCherry fluorescent protein as a fluorescence-activated cell sorter (FACS)-selectable marker. HiBiT tagging thus allows highly sensitive luminescence detection of endogenous PAX3-FOXO1 levels permitting quantitative high-throughput screening of large compound libraries for the discovery of PAX3-FOXO1 inhibitors and degraders.
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Affiliation(s)
- Robert G Hawley
- Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA.
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4
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Searcy MB, Larsen RK, Stevens BT, Zhang Y, Jin H, Drummond CJ, Langdon CG, Gadek KE, Vuong K, Reed KB, Garcia MR, Xu B, Kimbrough DW, Adkins GE, Djekidel N, Porter SN, Schreiner PA, Pruett-Miller SM, Abraham BJ, Rehg JE, Hatley ME. PAX3-FOXO1 dictates myogenic reprogramming and rhabdomyosarcoma identity in endothelial progenitors. Nat Commun 2023; 14:7291. [PMID: 37968277 PMCID: PMC10651858 DOI: 10.1038/s41467-023-43044-1] [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: 12/12/2022] [Accepted: 10/27/2023] [Indexed: 11/17/2023] Open
Abstract
Fusion-positive rhabdomyosarcoma (FP-RMS) driven by the expression of the PAX3-FOXO1 (P3F) fusion oncoprotein is an aggressive subtype of pediatric rhabdomyosarcoma. FP-RMS histologically resembles developing muscle yet occurs throughout the body in areas devoid of skeletal muscle highlighting that FP-RMS is not derived from an exclusively myogenic cell of origin. Here we demonstrate that P3F reprograms mouse and human endothelial progenitors to FP-RMS. We show that P3F expression in aP2-Cre expressing cells reprograms endothelial progenitors to functional myogenic stem cells capable of regenerating injured muscle fibers. Further, we describe a FP-RMS mouse model driven by P3F expression and Cdkn2a loss in endothelial cells. Additionally, we show that P3F expression in TP53-null human iPSCs blocks endothelial-directed differentiation and guides cells to become myogenic cells that form FP-RMS tumors in immunocompromised mice. Together these findings demonstrate that FP-RMS can originate from aberrant development of non-myogenic cells driven by P3F.
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Affiliation(s)
- Madeline B Searcy
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Randolph K Larsen
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Bradley T Stevens
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Yang Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Catherine J Drummond
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Casey G Langdon
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Katherine E Gadek
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kyna Vuong
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Kristin B Reed
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Matthew R Garcia
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Beisi Xu
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Darden W Kimbrough
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- Rhodes College, Memphis, TN, 38112, USA
| | - Grace E Adkins
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
- St. Jude Graduate School of Biomedical Sciences, Memphis, TN, 38105, USA
| | - Nadhir Djekidel
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Patrick A Schreiner
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Brian J Abraham
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Mark E Hatley
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA.
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5
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Ibarra J, Hershenhouse T, Almassalha L, Walterhouse D, Backman V, MacQuarrie KL. Differentiation-dependent chromosomal organization changes in normal myogenic cells are absent in rhabdomyosarcoma cells. Front Cell Dev Biol 2023; 11:1293891. [PMID: 38020905 PMCID: PMC10662331 DOI: 10.3389/fcell.2023.1293891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Myogenesis, the progression of proliferating skeletal myoblasts to terminally differentiated myotubes, regulates thousands of target genes. Uninterrupted linear arrays of such genes are differentially associated with specific chromosomes, suggesting chromosome specific regulatory roles in myogenesis. Rhabdomyosarcoma (RMS), a tumor of skeletal muscle, shares common features with normal muscle cells. We hypothesized that RMS and myogenic cells possess differences in chromosomal organization related to myogenic gene arrangement. We compared the organizational characteristics of chromosomes 2 and 18, chosen for their difference in myogenic gene arrangement, in cultured RMS cell lines and normal myoblasts and myotubes. We found chromosome-specific differences in organization during normal myogenesis, with increased area occupied and a shift in peripheral localization specifically for chromosome 2. Most strikingly, we found a differentiation-dependent difference in positioning of chromosome 2 relative to the nuclear axis, with preferential positioning along the major nuclear axis present only in myotubes. RMS cells demonstrated no preference for such axial positioning, but induced differentiation through transfection of the pro-myogenic miRNA miR-206 resulted in an increase of major axial positioning of chromosome 2. Our findings identify both a differentiation-dependent, chromosome-specific change in organization in normal myogenesis, and highlight the role of chromosomal spatial organization in myogenic differentiation.
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Affiliation(s)
- Joe Ibarra
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Tyler Hershenhouse
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Luay Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Northwestern University, Chicago, IL, United States
| | - David Walterhouse
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, United States
| | - Kyle L. MacQuarrie
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL, United States
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6
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Allou L, Mundlos S. Disruption of regulatory domains and novel transcripts as disease-causing mechanisms. Bioessays 2023; 45:e2300010. [PMID: 37381881 DOI: 10.1002/bies.202300010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023]
Abstract
Deletions, duplications, insertions, inversions, and translocations, collectively called structural variations (SVs), affect more base pairs of the genome than any other sequence variant. The recent technological advancements in genome sequencing have enabled the discovery of tens of thousands of SVs per human genome. These SVs primarily affect non-coding DNA sequences, but the difficulties in interpreting their impact limit our understanding of human disease etiology. The functional annotation of non-coding DNA sequences and methodologies to characterize their three-dimensional (3D) organization in the nucleus have greatly expanded our understanding of the basic mechanisms underlying gene regulation, thereby improving the interpretation of SVs for their pathogenic impact. Here, we discuss the various mechanisms by which SVs can result in altered gene regulation and how these mechanisms can result in rare genetic disorders. Beyond changing gene expression, SVs can produce novel gene-intergenic fusion transcripts at the SV breakpoints.
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Affiliation(s)
- Lila Allou
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Mundlos
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Berlin, Germany
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7
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Wang M, Sreenivas P, Sunkel BD, Wang L, Ignatius M, Stanton B. The 3D chromatin landscape of rhabdomyosarcoma. NAR Cancer 2023; 5:zcad028. [PMID: 37325549 PMCID: PMC10261698 DOI: 10.1093/narcan/zcad028] [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: 12/12/2022] [Revised: 04/27/2023] [Accepted: 05/24/2023] [Indexed: 06/17/2023] Open
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue cancer with a lack of precision therapy options for patients. We hypothesized that with a general paucity of known mutations in RMS, chromatin structural driving mechanisms are essential for tumor proliferation. Thus, we carried out high-depth in situ Hi-C in representative cell lines and patient-derived xenografts (PDXs) to define chromatin architecture in each major RMS subtype. We report a comprehensive 3D chromatin structural analysis and characterization of fusion-positive (FP-RMS) and fusion-negative RMS (FN-RMS). We have generated spike-in in situ Hi-C chromatin interaction maps for the most common FP-RMS and FN-RMS cell lines and compared our data with PDX models. In our studies, we uncover common and distinct structural elements in large Mb-scale chromatin compartments, tumor-essential genes within variable topologically associating domains and unique patterns of structural variation. Our high-depth chromatin interactivity maps and comprehensive analyses provide context for gene regulatory events and reveal functional chromatin domains in RMS.
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Affiliation(s)
- Meng Wang
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
| | - Prethish Sreenivas
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Benjamin D Sunkel
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
| | - Long Wang
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Myron Ignatius
- Greehey Children’s Cancer Research Institute, Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, TX 78229, USA
| | - Benjamin Z Stanton
- Nationwide Children’s Hospital, Center for Childhood Cancer, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH 43205, USA
- Department of Biological Chemistry and Pharmacology, The Ohio State University College of Medicine, Columbus, OH 43210, USA
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8
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Ibarra J, Hershenhouse T, Almassalha L, MacQuarrie KL. Differentiation-dependent chromosomal organization changes in normal myogenic cells are absent in rhabdomyosarcoma cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540394. [PMID: 37214969 PMCID: PMC10197681 DOI: 10.1101/2023.05.11.540394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Myogenesis, the progression of proliferating skeletal myoblasts to terminally differentiated myotubes, regulates thousands of target genes. Uninterrupted linear arrays of such genes are differentially associated with specific chromosomes, suggesting chromosome specific regulatory roles in myogenesis. Rhabdomyosarcoma (RMS), a tumor of skeletal muscle, shares common features with normal muscle cells. We hypothesized that RMS and myogenic cells possess differences in chromosomal organization related to myogenic gene arrangement. We compared the organizational characteristics of chromosomes 2 and 18, chosen for their difference in myogenic gene arrangement, in cultured RMS cell lines and normal myoblasts and myotubes. We found chromosome-specific differences in organization during normal myogenesis, with increased area occupied and a shift in peripheral localization specifically for chromosome 2. Most strikingly, we found a differentiation-dependent difference in positioning of chromosome 2 relative to the nuclear axis, with preferential positioning along the major nuclear axis present only in myotubes. RMS cells demonstrated no preference for such axial positioning, but induced differentiation through transfection of the pro-myogenic miRNA miR-206 resulted in an increase of major axial positioning of chromosome 2. Our findings identify both a differentiation-dependent, chromosome-specific change in organization in normal myogenesis, and highlight the role of chromosomal spatial organization in myogenic differentiation.
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Affiliation(s)
- Joe Ibarra
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children's Hospital of Chicago, IL
| | - Tyler Hershenhouse
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children's Hospital of Chicago, IL
| | - Luay Almassalha
- Department of Gastroenterology and Hepatology, Northwestern Memorial Hospital, Northwestern University, Chicago, IL
| | - Kyle L MacQuarrie
- Division of Hematology, Oncology, and Stem Cell Transplantation, Department of Pediatrics, Feinberg School of Medicine, Northwestern University and Ann & Robert H. Lurie Children's Hospital of Chicago, IL
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9
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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10
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Chua EHZ, Yasar S, Harmston N. The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong! Biol Open 2022; 11:274931. [PMID: 35377406 PMCID: PMC9002814 DOI: 10.1242/bio.059091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The expression of a large number of genes is regulated by regulatory elements that are located far away from their promoters. Identifying which gene is the target of a specific regulatory element or is affected by a non-coding mutation is often accomplished by assigning these regions to the nearest gene in the genome. However, this heuristic ignores key features of genome organisation and gene regulation; in that the genome is partitioned into regulatory domains, which at some loci directly coincide with the span of topologically associated domains (TADs), and that genes are regulated by enhancers located throughout these regions, even across intervening genes. In this review, we examine the results from genome-wide studies using chromosome conformation capture technologies and from those dissecting individual gene regulatory domains, to highlight that the phenomenon of enhancer skipping is pervasive and affects multiple types of genes. We discuss how simply assigning a genomic region of interest to its nearest gene is problematic and often leads to incorrect predictions and highlight that where possible information on both the conservation and topological organisation of the genome should be used to generate better hypotheses. The article has an associated Future Leader to Watch interview. Summary: Identifying which gene is the target of an enhancer is often accomplished by assigning it to the nearest gene, here we discuss how this heuristic can lead to incorrect predictions.
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Affiliation(s)
| | - Samen Yasar
- Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Nathan Harmston
- Science Division, Yale-NUS College, Singapore 138527, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore
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11
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Tena JJ, Santos-Pereira JM. Topologically Associating Domains and Regulatory Landscapes in Development, Evolution and Disease. Front Cell Dev Biol 2021; 9:702787. [PMID: 34295901 PMCID: PMC8290416 DOI: 10.3389/fcell.2021.702787] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/17/2021] [Indexed: 01/02/2023] Open
Abstract
Animal genomes are folded in topologically associating domains (TADs) that have been linked to the regulation of the genes they contain by constraining regulatory interactions between cis-regulatory elements and promoters. Therefore, TADs are proposed as structural scaffolds for the establishment of regulatory landscapes (RLs). In this review, we discuss recent advances in the connection between TADs and gene regulation, their relationship with gene RLs and their dynamics during development and differentiation. Moreover, we describe how restructuring TADs may lead to pathological conditions, which explains their high evolutionary conservation, but at the same time it provides a substrate for the emergence of evolutionary innovations that lay at the origin of vertebrates and other phylogenetic clades.
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Affiliation(s)
- Juan J. Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
| | - José M. Santos-Pereira
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide, Seville, Spain
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12
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Gonzalez Curto G, Der Vartanian A, Frarma YEM, Manceau L, Baldi L, Prisco S, Elarouci N, Causeret F, Korenkov D, Rigolet M, Aurade F, De Reynies A, Contremoulins V, Relaix F, Faklaris O, Briscoe J, Gilardi-Hebenstreit P, Ribes V. The PAX-FOXO1s trigger fast trans-differentiation of chick embryonic neural cells into alveolar rhabdomyosarcoma with tissue invasive properties limited by S phase entry inhibition. PLoS Genet 2020; 16:e1009164. [PMID: 33175861 PMCID: PMC7682867 DOI: 10.1371/journal.pgen.1009164] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 11/23/2020] [Accepted: 10/02/2020] [Indexed: 12/18/2022] Open
Abstract
The chromosome translocations generating PAX3-FOXO1 and PAX7-FOXO1 chimeric proteins are the primary hallmarks of the paediatric fusion-positive alveolar subtype of Rhabdomyosarcoma (FP-RMS). Despite the ability of these transcription factors to remodel chromatin landscapes and promote the expression of tumour driver genes, they only inefficiently promote malignant transformation in vivo. The reason for this is unclear. To address this, we developed an in ovo model to follow the response of spinal cord progenitors to PAX-FOXO1s. Our data demonstrate that PAX-FOXO1s, but not wild-type PAX3 or PAX7, trigger the trans-differentiation of neural cells into FP-RMS-like cells with myogenic characteristics. In parallel, PAX-FOXO1s remodel the neural pseudo-stratified epithelium into a cohesive mesenchyme capable of tissue invasion. Surprisingly, expression of PAX-FOXO1s, similar to wild-type PAX3/7, reduce the levels of CDK-CYCLIN activity and increase the fraction of cells in G1. Introduction of CYCLIN D1 or MYCN overcomes this PAX-FOXO1-mediated cell cycle inhibition and promotes tumour growth. Together, our findings reveal a mechanism that can explain the apparent limited oncogenicity of PAX-FOXO1 fusion transcription factors. They are also consistent with certain clinical reports indicative of a neural origin of FP-RMS. The fusion-positive subtype of rhabdomyosarcoma (FP-RMS) is a rare malignant paediatric cancer, whose induction and evolution still remain to be deciphered. Out of the gross genetic aberrations found in these cancers, t(2:13) and t(1,13) chromosome translocations are the first to appear and lead to the expression of fusion proteins made of the DNA binding domains of either PAX3 or PAX7 and the transactivation domain of FOXO1. Both PAX3-FOXO1 and PAX7-FOXO1 have a strong impact on gene transcription, yet they only inefficiently promote the transformation of healthy cells into tumorigenic cells. To address this issue, we have used chick embryos to monitor in vivo the early response of cells to PAX-FOXO1 chimeric proteins. We showed that both proteins, but not the normal PAX3 and PAX7, transform neural cells into cells with FP-RMS molecular features. The PAX-FOXO1s also force polarized epithelial neural cells to adopt a mesenchymal phenotype with tissue invasive properties. However, the PAX-FOXO1s inhibit cell division and hence tumour growth. Genetically re-activating core cell cycle regulators rescues PAX-FOXO1 mediated cell cycle inhibition. Together, our findings bring further support to the idea that the PAX-FOXO1s are stricto sensu oncoproteins, whose oncogenicity is limited by negative effects on cell cycle.
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Affiliation(s)
| | | | | | - Line Manceau
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Lorenzo Baldi
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Selene Prisco
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Nabila Elarouci
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Frédéric Causeret
- Université de Paris, Imagine Institute, Team Genetics and Development of the Cerebral Cortex, Paris, France
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Paris, France
| | - Daniil Korenkov
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
| | - Muriel Rigolet
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Frédéric Aurade
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
- Sorbonne Université, INSERM, UMRS974, Center for Research in Myology, Paris, France
| | - Aurélien De Reynies
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre le Cancer, Paris, France
| | - Vincent Contremoulins
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - Frédéric Relaix
- Univ Paris Est Créteil, INSERM, EnVA, EFS, IMRB, Créteil, France
| | - Orestis Faklaris
- ImagoSeine core facility of Institut Jacques Monod and member of France-BioImaging, France
| | - James Briscoe
- The Francis Crick Institute, 1 Midland Road, London, United Kingdom
| | | | - Vanessa Ribes
- Université de Paris, CNRS, Institut Jacques Monod, Paris, France
- * E-mail:
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13
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Wang WJ, Li LY, Cui JW. Chromosome structural variation in tumorigenesis: mechanisms of formation and carcinogenesis. Epigenetics Chromatin 2020; 13:49. [PMID: 33168103 PMCID: PMC7654176 DOI: 10.1186/s13072-020-00371-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/29/2020] [Indexed: 12/23/2022] Open
Abstract
With the rapid development of next-generation sequencing technology, chromosome structural variation has gradually gained increased clinical significance in tumorigenesis. However, the molecular mechanism(s) underlying this structural variation remain poorly understood. A search of the literature shows that a three-dimensional chromatin state plays a vital role in inducing structural variation and in the gene expression profiles in tumorigenesis. Structural variants may result in changes in copy number or deletions of coding sequences, as well as the perturbation of structural chromatin features, especially topological domains, and disruption of interactions between genes and their regulatory elements. This review focuses recent work aiming at elucidating how structural variations develop and misregulate oncogenes and tumor suppressors, to provide general insights into tumor formation mechanisms and to provide potential targets for future anticancer therapies.
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Affiliation(s)
- Wen-Jun Wang
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Ling-Yu Li
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China
| | - Jiu-Wei Cui
- Cancer Center, The First Hospital of Jilin University, Jilin University, Changchun, 130021, Jilin, China.
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14
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Hernández-Hernández O, Ávila-Avilés RD, Hernández-Hernández JM. Chromatin Landscape During Skeletal Muscle Differentiation. Front Genet 2020; 11:578712. [PMID: 33193700 PMCID: PMC7530293 DOI: 10.3389/fgene.2020.578712] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/31/2020] [Indexed: 12/02/2022] Open
Abstract
Cellular commitment and differentiation involve highly coordinated mechanisms by which tissue-specific genes are activated while others are repressed. These mechanisms rely on the activity of specific transcription factors, chromatin remodeling enzymes, and higher-order chromatin organization in order to modulate transcriptional regulation on multiple cellular contexts. Tissue-specific transcription factors are key mediators of cell fate specification with the ability to reprogram cell types into different lineages. A classic example of a master transcription factor is the muscle specific factor MyoD, which belongs to the family of myogenic regulatory factors (MRFs). MRFs regulate cell fate determination and terminal differentiation of the myogenic precursors in a multistep process that eventually culminate with formation of muscle fibers. This developmental progression involves the activation and proliferation of muscle stem cells, commitment, and cell cycle exit and fusion of mononucleated myoblast to generate myotubes and myofibers. Although the epigenetics of muscle regeneration has been extensively addressed and discussed over the recent years, the influence of higher-order chromatin organization in skeletal muscle regeneration is still a field of development. In this review, we will focus on the epigenetic mechanisms modulating muscle gene expression and on the incipient work that addresses three-dimensional genome architecture and its influence in cell fate determination and differentiation to achieve skeletal myogenesis. We will visit known alterations of genome organization mediated by chromosomal fusions giving rise to novel regulatory landscapes, enhancing oncogenic activation in muscle, such as alveolar rhabdomyosarcomas (ARMS).
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Affiliation(s)
- Oscar Hernández-Hernández
- Laboratory of Genomic Medicine, Department of Genetics, Instituto Nacional de Rehabilitación Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Rodolfo Daniel Ávila-Avilés
- Laboratory of Epigenetics of Skeletal Muscle Regeneration, Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
| | - J Manuel Hernández-Hernández
- Laboratory of Epigenetics of Skeletal Muscle Regeneration, Department of Genetics and Molecular Biology, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Mexico City, Mexico
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15
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Gryder BE, Wachtel M, Chang K, El Demerdash O, Aboreden NG, Mohammed W, Ewert W, Pomella S, Rota R, Wei JS, Song Y, Stanton BZ, Schäfer B, Vakoc CR, Khan J. Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage. iScience 2020; 23:101103. [PMID: 32416589 PMCID: PMC7226896 DOI: 10.1016/j.isci.2020.101103] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/31/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Core regulatory transcription factors (CR TFs) establish enhancers with logical ordering during embryogenesis and development. Here we report that in fusion-positive rhabdomyosarcoma, a cancer of the muscle lineage, the chief oncogene PAX3-FOXO1 is driven by a translocated FOXO1 super enhancer (SE) restricted to a late stage of myogenesis. Using chromatin conformation capture techniques, we demonstrate that the extensive FOXO1 cis-regulatory domain interacts with PAX3. Furthermore, RNA sequencing and chromatin immunoprecipitation sequencing data in tumors bearing rare PAX translocations implicate enhancer miswiring across all fusion-positive tumors. HiChIP of H3K27ac showed connectivity between the FOXO1 SE, additional intra-domain enhancers, and the PAX3 promoter. We show that PAX3-FOXO1 transcription is diminished when this network of enhancers is ablated by CRISPR. Our data reveal a hijacked enhancer network that disrupts the stepwise CR TF logic of normal skeletal muscle development (PAX3 to MYOD to MYOG), replacing it with an "infinite loop" enhancer logic that locks rhabdomyosarcoma in an undifferentiated stage.
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Affiliation(s)
- Berkley E Gryder
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | | | - Kenneth Chang
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Osama El Demerdash
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | | | - Wardah Mohammed
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | - Silvia Pomella
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Rossella Rota
- Department of Oncohematology, Ospedale Pediatrico Bambino Gesu' Research Institute, IRCCS, Rome, Italy
| | - Jun S Wei
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Young Song
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Benjamin Z Stanton
- Center for Childhood Cancer & Blood Diseases, The Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Beat Schäfer
- University Children's Hospital, Zurich, Switzerland
| | - Christopher R Vakoc
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Javed Khan
- Genetics Branch, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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16
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Zisis D, Krajewski P, Stam M, Weber B, Hövel I. Analysis of 4C-seq data: A comparison of methods. J Bioinform Comput Biol 2020; 18:2050001. [PMID: 32336253 DOI: 10.1142/s0219720020500018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The circular chromosome conformation capture technique followed by sequencing (4C-seq) has been used in a number of studies to investigate chromosomal interactions between DNA fragments. Computational pipelines have been developed and published that offer various possibilities of 4C-seq data processing and statistical analysis. Here, we present an overview of four of such pipelines (fourSig, FourCSeq, 4C-ker and w4Cseq) taking into account the most important stages of computations. We provide comparisons of the methods and discuss their advantages and possible weaknesses. We illustrate the results with the use of data obtained for two different species, in a study devoted to vernalization control in Arabidopsis thaliana by the FLOWERING LOCUS C (FLC) gene and to long-range chromatin interactions in mouse embryonic stem cells.
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Affiliation(s)
- Dimitrios Zisis
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 61-479 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 61-479 Poznań, Poland
| | - Maike Stam
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Blaise Weber
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
| | - Iris Hövel
- Swammerdam Institute for Life Sciences, University of Amsterdam, Sciencepark 904, 1098 XH Amsterdam, The Netherlands
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17
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Galupa R, Nora EP, Worsley-Hunt R, Picard C, Gard C, van Bemmel JG, Servant N, Zhan Y, El Marjou F, Johanneau C, Diabangouaya P, Le Saux A, Lameiras S, Pipoli da Fonseca J, Loos F, Gribnau J, Baulande S, Ohler U, Giorgetti L, Heard E. A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary. Mol Cell 2020; 77:352-367.e8. [PMID: 31759823 PMCID: PMC6964159 DOI: 10.1016/j.molcel.2019.10.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 09/08/2019] [Accepted: 10/17/2019] [Indexed: 12/11/2022]
Abstract
cis-Regulatory communication is crucial in mammalian development and is thought to be restricted by the spatial partitioning of the genome in topologically associating domains (TADs). Here, we discovered that the Xist locus is regulated by sequences in the neighboring TAD. In particular, the promoter of the noncoding RNA Linx (LinxP) acts as a long-range silencer and influences the choice of X chromosome to be inactivated. This is independent of Linx transcription and independent of any effect on Tsix, the antisense regulator of Xist that shares the same TAD as Linx. Unlike Tsix, LinxP is well conserved across mammals, suggesting an ancestral mechanism for random monoallelic Xist regulation. When introduced in the same TAD as Xist, LinxP switches from a silencer to an enhancer. Our study uncovers an unsuspected regulatory axis for X chromosome inactivation and a class of cis-regulatory effects that may exploit TAD partitioning to modulate developmental decisions.
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Affiliation(s)
- Rafael Galupa
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Elphège Pierre Nora
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Rebecca Worsley-Hunt
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Christel Picard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Chris Gard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Joke Gerarda van Bemmel
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Nicolas Servant
- Bioinformatics, Biostatistics, Epidemiology and Computational Systems Unit, Institut Curie, PSL Research University, INSERM U900, Paris, France; MINES ParisTech, PSL Research University, Centre for Computational Biology (CBIO), Paris, France
| | - Yinxiu Zhan
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; University of Basel, Basel, Switzerland
| | | | | | - Patricia Diabangouaya
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Agnès Le Saux
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France
| | - Sonia Lameiras
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | | | - Friedemann Loos
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Institut Curie, Paris, France
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Department of Biology, Humboldt University, Berlin, Germany
| | - Luca Giorgetti
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Edith Heard
- Mammalian Developmental Epigenetics Group, Genetics and Developmental Biology Unit, Institut Curie, PSL Research University, CNRS UMR3215, INSERM U934, Paris, France; Collège de France, Paris, France.
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18
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Helm BR, Zhan X, Pandya PH, Murray ME, Pollok KE, Renbarger JL, Ferguson MJ, Han Z, Ni D, Zhang J, Huang K. Gene Co-Expression Networks Restructured Gene Fusion in Rhabdomyosarcoma Cancers. Genes (Basel) 2019; 10:genes10090665. [PMID: 31480361 PMCID: PMC6770752 DOI: 10.3390/genes10090665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/07/2019] [Accepted: 08/19/2019] [Indexed: 01/28/2023] Open
Abstract
Rhabdomyosarcoma is subclassified by the presence or absence of a recurrent chromosome translocation that fuses the FOXO1 and PAX3 or PAX7 genes. The fusion protein (FOXO1-PAX3/7) retains both binding domains and becomes a novel and potent transcriptional regulator in rhabdomyosarcoma subtypes. Many studies have characterized and integrated genomic, transcriptomic, and epigenomic differences among rhabdomyosarcoma subtypes that contain the FOXO1-PAX3/7 gene fusion and those that do not; however, few investigations have investigated how gene co-expression networks are altered by FOXO1-PAX3/7. Although transcriptional data offer insight into one level of functional regulation, gene co-expression networks have the potential to identify biological interactions and pathways that underpin oncogenesis and tumorigenicity. Thus, we examined gene co-expression networks for rhabdomyosarcoma that were FOXO1-PAX3 positive, FOXO1-PAX7 positive, or fusion negative. Gene co-expression networks were mined using local maximum Quasi-Clique Merger (lmQCM) and analyzed for co-expression differences among rhabdomyosarcoma subtypes. This analysis observed 41 co-expression modules that were shared between fusion negative and positive samples, of which 17/41 showed significant up- or down-regulation in respect to fusion status. Fusion positive and negative rhabdomyosarcoma showed differing modularity of co-expression networks with fusion negative (n = 109) having significantly more individual modules than fusion positive (n = 53). Subsequent analysis of gene co-expression networks for PAX3 and PAX7 type fusions observed 17/53 were differentially expressed between the two subtypes. Gene list enrichment analysis found that gene ontology terms were poorly matched with biological processes and molecular function for most co-expression modules identified in this study; however, co-expressed modules were frequently localized to cytobands on chromosomes 8 and 11. Overall, we observed substantial restructuring of co-expression networks relative to fusion status and fusion type in rhabdomyosarcoma and identified previously overlooked genes and pathways that may be targeted in this pernicious disease.
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Affiliation(s)
- Bryan R Helm
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
| | - Xiaohui Zhan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Pankita H Pandya
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
| | - Mary E Murray
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
| | - Karen E Pollok
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, IN 46202-3082, USA
| | - Jamie L Renbarger
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
| | - Michael J Ferguson
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA
| | - Zhi Han
- Department of Pharmacology and Toxicology, Indiana University, Indianapolis, IN 46202-3082, USA
| | - Dong Ni
- National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA.
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202-3082, USA.
- Regenstrief Institute, Indianapolis, IN 46202, USA.
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19
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Franke M, Gómez-Skarmeta JL. An evolutionary perspective of regulatory landscape dynamics in development and disease. Curr Opin Cell Biol 2018; 55:24-29. [PMID: 30006052 DOI: 10.1016/j.ceb.2018.06.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 06/11/2018] [Accepted: 06/13/2018] [Indexed: 01/01/2023]
Abstract
The organization of animal genomes into topologically associating domains (TADs) provides a structural scaffold in which cis-regulatory elements (CREs) operate on their target genes. Determining the position of CREs and genes relative to TADs has become instrumental to trace gene expression changes during evolution and in diseases. Here we will review recent studies and discuss TADs as structural units with respect to their conservation and stability during genome reorganization. Furthermore, we describe how TAD restructuring contributed to morphological novelties during evolution but also their deleterious effects associated with disease. Despite considering TADs as structural units, the nested and dynamic scaffold within TADs contributes to tissue-specific gene expression, implying that such changes can also account for gene expression differences during evolution.
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Affiliation(s)
- Martin Franke
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain.
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo (CABD), Consejo Superior de Investigaciones Científicas/Universidad Pablo de Olavide/Junta de Andalucía, Sevilla, Spain.
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20
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Fishman VS, Salnikov PA, Battulin NR. Interpreting Chromosomal Rearrangements in the Context of 3-Dimentional Genome Organization: A Practical Guide for Medical Genetics. BIOCHEMISTRY (MOSCOW) 2018; 83:393-401. [PMID: 29626926 DOI: 10.1134/s0006297918040107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In this exciting era of "next-gen cytogenetics", the use of novel molecular methods such as comparative genome hybridization and whole genome and whole exome sequencing becomes more and more common in clinics. This results in generation of large amounts of high-resolution patient-specific data and challenges the development of new approaches for interpretation of obtained information. Usually, interpretation of chromosomal rearrangements is focused on alterations of linear genome sequence, underestimating the role of spatial chromatin organization. In this article, we describe the main features of 3-dimentional genome organization, emphasizing their role in normal and pathological development. We highlight some tips to help physicians estimating the impact of chromosomal rearrangements on the patient phenotype. A separate section describes available tools that can be used to visualize and analyze human genome architecture.
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Affiliation(s)
- V S Fishman
- Federal Research Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 63009, Russia.
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21
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Drummond CJ, Hanna JA, Garcia MR, Devine DJ, Heyrana AJ, Finkelstein D, Rehg JE, Hatley ME. Hedgehog Pathway Drives Fusion-Negative Rhabdomyosarcoma Initiated From Non-myogenic Endothelial Progenitors. Cancer Cell 2018; 33:108-124.e5. [PMID: 29316425 PMCID: PMC5790179 DOI: 10.1016/j.ccell.2017.12.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/30/2017] [Accepted: 11/30/2017] [Indexed: 12/19/2022]
Abstract
Rhabdomyosarcoma (RMS) is a pediatric soft tissue sarcoma that histologically resembles embryonic skeletal muscle. RMS occurs throughout the body and an exclusively myogenic origin does not account for RMS occurring in sites devoid of skeletal muscle. We previously described an RMS model activating a conditional constitutively active Smoothened mutant (SmoM2) with aP2-Cre. Using genetic fate mapping, we show SmoM2 expression in Cre-expressing endothelial progenitors results in myogenic transdifferentiation and RMS. We show that endothelium and skeletal muscle within the head and neck arise from Kdr-expressing progenitors, and that hedgehog pathway activation results in aberrant expression of myogenic specification factors as a potential mechanism driving RMS genesis. These findings suggest that RMS can originate from aberrant development of non-myogenic cells.
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Affiliation(s)
- Catherine J Drummond
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jason A Hanna
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Matthew R Garcia
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Daniel J Devine
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Alana J Heyrana
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jerold E Rehg
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mark E Hatley
- Department of Oncology, MS-352, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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Galupa R, Heard E. Topologically Associating Domains in Chromosome Architecture and Gene Regulatory Landscapes during Development, Disease, and Evolution. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2017; 82:267-278. [DOI: 10.1101/sqb.2017.82.035030] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
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