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Corleone G, Sorino C, Caforio M, Di Giovenale S, De Nicola F, Goeman F, Bertaina V, Pitisci A, Cortile C, Locatelli F, Folgiero V, Fanciulli M. Enhancer engagement sustains oncogenic transformation and progression of B-cell precursor acute lymphoblastic leukemia. J Exp Clin Cancer Res 2024; 43:179. [PMID: 38926853 PMCID: PMC11210131 DOI: 10.1186/s13046-024-03075-y] [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: 04/11/2024] [Accepted: 05/18/2024] [Indexed: 06/28/2024] Open
Abstract
BACKGROUND Enhancer reprogramming plays a significant role in the heterogeneity of cancer. However, we have limited knowledge about the impact of chromatin remodeling in B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) patients, and how it affects tumorigenesis and drug response. Our research focuses on investigating the role of enhancers in sustaining oncogenic transformation in children with BCP-ALL. METHODS We used ATAC-seq to study the accessibility of chromatin in pediatric BCP-ALL at three different stages-onset, remission, and relapse. Using a combination of computational and experimental methods, we were able to analyze the accessibility landscape and focus on the most significant cis-regulatory sites. These sites were then functionally validated through the use of Promoter capture Hi-C in a primary cell line model called LAL-B, followed by RNA-seq and genomic deletion of target sites using CRISPR-Cas9 editing. RESULTS We found that enhancer activity changes during cancer progression and is mediated by the production of enhancer RNAs (eRNAs). CRISPR-Cas9-mediated validation of previously unknown eRNA productive enhancers demonstrated their capability to control the oncogenic activities of the MYB and DCTD genes. CONCLUSIONS Our findings directly support the notion that productive enhancer engagement is a crucial determinant of the BCP-ALL and highlight the potential of enhancers as therapeutic targets in pediatric BCP-ALL.
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Affiliation(s)
- Giacomo Corleone
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Cristina Sorino
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Matteo Caforio
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Stefano Di Giovenale
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
- Department of Computer, Control, and Management, Engineering Antonio Ruberti, Sapienza University of Rome, Rome, 00161, Italy
| | - Francesca De Nicola
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Frauke Goeman
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Valentina Bertaina
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Angela Pitisci
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
| | - Clelia Cortile
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy
| | - Franco Locatelli
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy
- Department of Life Sciences and Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - Valentina Folgiero
- Department of Pediatric Hematology-Oncology and Cell and Gene Therapy, IRCCS Bambino Gesù Children's Hospital, Viale Di San Paolo 12, Rome, 00146, Italy.
| | - Maurizio Fanciulli
- IRCCS Regina Elena National Cancer Institute, Via Chianesi 53, Rome, 00144, Italy.
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Kotb NM, Ulukaya G, Chavan A, Nguyen SC, Proskauer L, Joyce EF, Hasson D, Jagannathan M, Rangan P. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis. Genes Dev 2024; 38:436-454. [PMID: 38866556 PMCID: PMC11216175 DOI: 10.1101/gad.351402.123] [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: 12/10/2023] [Accepted: 05/21/2024] [Indexed: 06/14/2024]
Abstract
Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ cell genes during differentiation, and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we found that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ cell genes into a silenced state and activating a group of oocyte genes and nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, cross-talk between genome architecture and NPCs is essential for successful cell fate transitions.
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Affiliation(s)
- Noor M Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany State University of New York (SUNY), Albany, New York 12202, USA
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
| | - Gulay Ulukaya
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Ankita Chavan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Son C Nguyen
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Lydia Proskauer
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, New York 12202, USA
| | - Eric F Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dan Hasson
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA
- Bioinformatics for Next-Generation Sequencing (BiNGS) Core, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Madhav Jagannathan
- Institute of Biochemistry, Department of Biology, Eidgenössische Technische Hochschule (ETH) Zürich, 8092 Zürich, Switzerland
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NewYork 10029, USA;
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3
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Abrar M, Ali S, Hussain I, Khatoon H, Batool F, Ghazanfar S, Corcoran D, Kawakami Y, Abbasi AA. Cis-regulatory control of mammalian Trps1 gene expression. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2024. [PMID: 38369890 DOI: 10.1002/jez.b.23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/20/2024]
Abstract
TRPS1 serves as the causative gene for tricho-rhino phalangeal syndrome, known for its craniofacial and skeletal abnormalities. The Trps1 gene encodes a protein that represses Wnt signaling through strong interactions with Wnt signaling inhibitors. The identification of genomic cis-acting regulatory sequences governing Trps1 expression is crucial for understanding its role in embryogenesis. Nevertheless, to date, no investigations have been conducted concerning these aspects of Trps1. To identify deeply conserved noncoding elements (CNEs) within the Trps1 locus, we employed a comparative genomics approach, utilizing slowly evolving fish such as coelacanth and spotted gar. These analyses resulted in the identification of eight CNEs in the intronic region of the Trps1 gene. Functional characterization of these CNEs in zebrafish revealed their regulatory potential in various tissues, including pectoral fins, heart, and pharyngeal arches. RNA in-situ hybridization experiments revealed concordance between the reporter expression pattern induced by the identified set of CNEs and the spatial expression pattern of the trps1 gene in zebrafish. Comparative in vivo data from zebrafish and mice for CNE7/hs919 revealed conserved functions of these enhancers. Each of these eight CNEs was further investigated in cell line-based reporter assays, revealing their repressive potential. Taken together, in vivo and in vitro assays suggest a context-dependent dual functionality for the identified set of Trps1-associated CNE enhancers. This functionally characterized set of CNE-enhancers will contribute to a more comprehensive understanding of the developmental roles of Trps1 and can aid in the identification of noncoding DNA variants associated with human diseases.
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Affiliation(s)
- Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
- Center of Regenerative Medicine and Stem Cells Research, Aga Khan University Hospital, Karachi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shakira Ghazanfar
- National Institute for Genomics Advanced Biotechnology, National Agriculture Research Centre (NARC), Islamabad, Pakistan
| | - Dylan Corcoran
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Yasuhiko Kawakami
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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Kotb NM, Ulukaya G, Chavan A, Nguyen SC, Proskauer L, Joyce E, Hasson D, Jagannathan M, Rangan P. Genome organization regulates nuclear pore complex formation and promotes differentiation during Drosophila oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.15.567233. [PMID: 38014330 PMCID: PMC10680722 DOI: 10.1101/2023.11.15.567233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Genome organization can regulate gene expression and promote cell fate transitions. The differentiation of germline stem cells (GSCs) to oocytes in Drosophila involves changes in genome organization mediated by heterochromatin and the nuclear pore complex (NPC). Heterochromatin represses germ-cell genes during differentiation and NPCs anchor these silenced genes to the nuclear periphery, maintaining silencing to allow for oocyte development. Surprisingly, we find that genome organization also contributes to NPC formation, mediated by the transcription factor Stonewall (Stwl). As GSCs differentiate, Stwl accumulates at boundaries between silenced and active gene compartments. Stwl at these boundaries plays a pivotal role in transitioning germ-cell genes into a silenced state and activating a group of oocyte genes and Nucleoporins (Nups). The upregulation of these Nups during differentiation is crucial for NPC formation and further genome organization. Thus, crosstalk between genome architecture and NPCs is essential for successful cell fate transitions.
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Affiliation(s)
- Noor M. Kotb
- Department of Biomedical Sciences/Wadsworth Center, University at Albany SUNY, Albany, NY 12202
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gulay Ulukaya
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core
| | - Ankita Chavan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich
| | - Son C. Nguyen
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
| | - Lydia Proskauer
- Department of Biological Sciences/RNA Institute, University at Albany SUNY, Albany, NY 12202
- Current address: Biochemistry and Molecular Biology Department, University of Massachusetts Amherst, Amherst, MA 01003
| | - Eric Joyce
- Department of Genetics, University of Pennsylvania, Philadelphia, PA 19104
| | - Dan Hasson
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madhav Jagannathan
- Department of Biology, Institute of Biochemistry, ETH Zurich, 8092 Zurich
| | - Prashanth Rangan
- Department of Cell, Developmental, and Regenerative Biology, Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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5
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Gao GF, Li P, Leonard WJ. Co-localization of clusters of TCR-regulated genes with TAD rearrangements. BMC Genomics 2023; 24:650. [PMID: 37898735 PMCID: PMC10613383 DOI: 10.1186/s12864-023-09693-8] [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: 05/18/2023] [Accepted: 09/21/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Gene expression has long been known to be influenced by the relative proximity of DNA regulatory elements. Topologically associating domains (TADs) are self-interacting genomic regions involved in regulating gene expression by controlling the proximity of these elements. Prior studies of TADs and their biological roles have revealed correlations between TAD changes and cellular differentiation. Here, we used Hi-C and RNA-seq data to correlate TCR-induced changes in TAD structure and gene expression in human CD4+ T cells. RESULTS We developed a pipeline, Differentially Expressed Gene Enrichment Finder (DEGEF), that identifies regions of differentially expressed gene enrichment. Using DEGEF, we found that TCR-regulated genes cluster non-uniformly across the genome and that these clusters preferentially localized in regions of TAD rearrangement. Interestingly, clusters of upregulated genes preferentially formed new Hi-C contacts compared to downregulated clusters, suggesting that TCR-activated CD4+ T cells may regulate genes by changing stimulatory contacts rather than inhibitory contacts. CONCLUSIONS Our observations support a significant relationship between TAD rearrangements and changes in local gene expression. These findings indicate potentially important roles for TAD rearrangements in shaping their local regulatory environments and thus driving differential expression of nearby genes during CD4+ T cell activation. Moreover, they provide new insights into global mechanisms that regulate gene expression.
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Affiliation(s)
- Galen F Gao
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Peng Li
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA
| | - Warren J Leonard
- Laboratory of Molecular Immunology and the Immunology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892-1674, USA.
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6
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Mcdonald BR, Picard C, Brabb IM, Savenkova MI, Schmitz RJ, Jacobsen SE, Duttke SH. Enhancers associated with unstable RNAs are rare in plants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559415. [PMID: 37808859 PMCID: PMC10557634 DOI: 10.1101/2023.09.25.559415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Unstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating ("nascent") transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many "distal" elements in plants initiate tissue-specific stable transcripts and are likely bone fide promoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer "enhancers" or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
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Affiliation(s)
- Bayley R. Mcdonald
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Colette Picard
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Ian M. Brabb
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Marina I. Savenkova
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | | | - Steven E. Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA
- Howard Hughes Medical Institute, University of California at Los Angeles, Los Angeles, CA, USA
| | - Sascha H. Duttke
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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Single-molecule tracking (SMT): a window into live-cell transcription biochemistry. Biochem Soc Trans 2023; 51:557-569. [PMID: 36876879 DOI: 10.1042/bst20221242] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 03/07/2023]
Abstract
How molecules interact governs how they move. Single-molecule tracking (SMT) thus provides a unique window into the dynamic interactions of biomolecules within live cells. Using transcription regulation as a case study, we describe how SMT works, what it can tell us about molecular biology, and how it has changed our perspective on the inner workings of the nucleus. We also describe what SMT cannot yet tell us and how new technical advances seek to overcome its limitations. This ongoing progress will be imperative to address outstanding questions about how dynamic molecular machines function in live cells.
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Lee R, Kang MK, Kim YJ, Yang B, Shim H, Kim S, Kim K, Yang CM, Min BG, Jung WJ, Lee EC, Joo JS, Park G, Cho WK, Kim HP. CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates. Nucleic Acids Res 2021; 50:207-226. [PMID: 34931241 PMCID: PMC8855298 DOI: 10.1093/nar/gkab1242] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 11/22/2021] [Accepted: 12/03/2021] [Indexed: 12/31/2022] Open
Abstract
CTCF is crucial to the organization of mammalian genomes into loop structures. According to recent studies, the transcription apparatus is compartmentalized and concentrated at super-enhancers to form phase-separated condensates and drive the expression of cell-identity genes. However, it remains unclear whether and how transcriptional condensates are coupled to higher-order chromatin organization. Here, we show that CTCF is essential for RNA polymerase II (Pol II)-mediated chromatin interactions, which occur as hyperconnected spatial clusters at super-enhancers. We also demonstrate that CTCF clustering, unlike Pol II clustering, is independent of liquid-liquid phase-separation and resistant to perturbation of transcription. Interestingly, clusters of Pol II, BRD4, and MED1 were found to dissolve upon CTCF depletion, but were reinstated upon restoration of CTCF, suggesting a potent instructive function for CTCF in the formation of transcriptional condensates. Overall, we provide evidence suggesting that CTCF-mediated chromatin looping acts as an architectural prerequisite for the assembly of phase-separated transcriptional condensates.
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Affiliation(s)
- Ryanggeun Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea.,College of Natural Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Moo-Koo Kang
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Yong-Jin Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Bobae Yang
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Hwanyong Shim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Sugyung Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyungwoo Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Chul Min Yang
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Byeong-Gyu Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Woong-Jae Jung
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Eun-Chong Lee
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Jung-Sik Joo
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Gunhee Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Won-Ki Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea.,KI for Health Science and Technology (KIHST), Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Hyoung-Pyo Kim
- Department of Environmental Medical Biology, Institute of Tropical Medicine, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea.,Yonsei Genome Center, Yonsei University College of Medicine, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
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Fallatah B, Shuaib M, Adroub S, Paytuví-Gallart A, Della Valle F, Nadeef S, Lanzuolo C, Orlando V. Ago1 controls myogenic differentiation by regulating eRNA-mediated CBP-guided epigenome reprogramming. Cell Rep 2021; 37:110066. [PMID: 34852230 DOI: 10.1016/j.celrep.2021.110066] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/05/2021] [Accepted: 11/08/2021] [Indexed: 01/03/2023] Open
Abstract
The role of chromatin-associated RNAi components in the nucleus of mammalian cells and in particular in the context of developmental programs remains to be elucidated. Here, we investigate the function of nuclear Argonaute 1 (Ago1) in gene expression regulation during skeletal muscle differentiation. We show that Ago1 is required for activation of the myogenic program by supporting chromatin modification mediated by developmental enhancer activation. Mechanistically, we demonstrate that Ago1 directly controls global H3K27 acetylation (H3K27ac) by regulating enhancer RNA (eRNA)-CREB-binding protein (CBP) acetyltransferase interaction, a key step in enhancer-driven gene activation. In particular, we show that Ago1 is specifically required for myogenic differentiation 1 (MyoD) and downstream myogenic gene activation, whereas its depletion leads to failure of CBP acetyltransferase activation and blocking of the myogenic program. Our work establishes a role of the mammalian enhancer-associated RNAi component Ago1 in epigenome regulation and activation of developmental programs.
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Affiliation(s)
- Bodor Fallatah
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Muhammad Shuaib
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Sabir Adroub
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | | | - Francesco Della Valle
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Seba Nadeef
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia
| | - Chiara Lanzuolo
- Institute of Biomedical Technologies, National Research Council, 20090 Milan, Italy; National Institute of Molecular Genetics (INGM) "Romeo ed Enrica Invernizzi," Chromatin and Nuclear Architecture Laboratory, 20122 Milan, Italy
| | - Valerio Orlando
- King Abdullah University of Science and Technology, KAUST Environmental Epigenetics Research Program, Biological and Environmental Sciences and Engineering Division, Thuwal 23955, Saudi Arabia.
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