1
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Malla S, Kumari K, García-Prieto CA, Caroli J, Nordin A, Phan TTT, Bhattarai DP, Martinez-Gamero C, Dorafshan E, Stransky S, Álvarez-Errico D, Saiki PA, Lai W, Lyu C, Lizana L, Gilthorpe JD, Wang H, Sidoli S, Mateus A, Lee DF, Cantù C, Esteller M, Mattevi A, Roman AC, Aguilo F. The scaffolding function of LSD1 controls DNA methylation in mouse ESCs. Nat Commun 2024; 15:7758. [PMID: 39237615 PMCID: PMC11377572 DOI: 10.1038/s41467-024-51966-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/21/2024] [Indexed: 09/07/2024] Open
Abstract
Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di- methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for mouse embryonic stem cell (ESC) self-renewal but is required for mouse ESC growth and differentiation. Reintroduction of a catalytically-impaired LSD1 (LSD1MUT) recovers the proliferation capability of mouse ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, increased H3K4me1 in Lsd1 knockout (KO) mouse ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUT results in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUT control protein stability of UHRF1 and DNMT1 through interaction with HDAC1 and the ubiquitin-specific peptidase 7 (USP7), consequently, facilitating the deacetylation and deubiquitination of DNMT1 and UHRF1. Our studies elucidate a mechanism by which LSD1 controls DNA methylation in mouse ESCs, independently of its lysine demethylase activity.
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Affiliation(s)
- Sandhya Malla
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Kanchan Kumari
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Jonatan Caroli
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Trinh T T Phan
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Devi Prasad Bhattarai
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Carlos Martinez-Gamero
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Paulina Avovome Saiki
- Department of Molecular Biology, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Weiyi Lai
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Cong Lyu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ludvig Lizana
- Department of Physics, Integrated Science Lab, Umeå University, Umeå, Sweden
| | | | - Hailin Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Andre Mateus
- Department of Chemistry, Umeå University, Umeå, Sweden
- The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå, Sweden
| | - Dung-Fang Lee
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
- Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, McWilliams School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Barcelona, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Angel-Carlos Roman
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Francesca Aguilo
- Department of Molecular Biology, Umeå University, Umeå, Sweden.
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
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2
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Bailey JK, Ma D, Clegg DO. Initial Characterization of WDR5B Reveals a Role in the Proliferation of Retinal Pigment Epithelial Cells. Cells 2024; 13:1189. [PMID: 39056772 PMCID: PMC11275010 DOI: 10.3390/cells13141189] [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: 05/10/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
The chromatin-associated protein WDR5 has been widely studied due to its role in histone modification and its potential as a pharmacological target for the treatment of cancer. In humans, the protein with highest sequence homology to WDR5 is encoded by the retrogene WDR5B, which remains unexplored. Here, we used CRISPR-Cas9 genome editing to generate WDR5B knockout and WDR5B-FLAG knock-in cell lines for further characterization. In contrast to WDR5, WDR5B exhibits low expression in pluripotent cells and is upregulated upon neural differentiation. Loss or shRNA depletion of WDR5B impairs cell growth and increases the fraction of non-viable cells in proliferating retinal pigment epithelial (RPE) cultures. CUT&RUN chromatin profiling in RPE and neural progenitors indicates minimal WDR5B enrichment at established WDR5 binding sites. These results suggest that WDR5 and WDR5B exhibit several divergent biological properties despite sharing a high degree of sequence homology.
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Affiliation(s)
- Jeffrey K. Bailey
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
| | - Dzwokai Ma
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
| | - Dennis O. Clegg
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA 93106, USA
- Center for Stem Cell Biology and Engineering, University of California, Santa Barbara, CA 93106, USA
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3
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Atac D, Maggi K, Feil S, Maggi J, Cuevas E, Sowden JC, Koller S, Berger W. Identification and Characterization of ATOH7-Regulated Target Genes and Pathways in Human Neuroretinal Development. Cells 2024; 13:1142. [PMID: 38994994 PMCID: PMC11240604 DOI: 10.3390/cells13131142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/13/2024] Open
Abstract
The proneural transcription factor atonal basic helix-loop-helix transcription factor 7 (ATOH7) is expressed in early progenitors in the developing neuroretina. In vertebrates, this is crucial for the development of retinal ganglion cells (RGCs), as mutant animals show an almost complete absence of RGCs, underdeveloped optic nerves, and aberrations in retinal vessel development. Human mutations are rare and result in autosomal recessive optic nerve hypoplasia (ONH) or severe vascular changes, diagnosed as autosomal recessive persistent hyperplasia of the primary vitreous (PHPVAR). To better understand the role of ATOH7 in neuroretinal development, we created ATOH7 knockout and eGFP-expressing ATOH7 reporter human induced pluripotent stem cells (hiPSCs), which were differentiated into early-stage retinal organoids. Target loci regulated by ATOH7 were identified by Cleavage Under Targets and Release Using Nuclease with sequencing (CUT&RUN-seq) and differential expression by RNA sequencing (RNA-seq) of wildtype and mutant organoid-derived reporter cells. Additionally, single-cell RNA sequencing (scRNA-seq) was performed on whole organoids to identify cell type-specific genes. Mutant organoids displayed substantial deficiency in axon sprouting, reduction in RGCs, and an increase in other cell types. We identified 469 differentially expressed target genes, with an overrepresentation of genes belonging to axon development/guidance and Notch signaling. Taken together, we consolidate the function of human ATOH7 in guiding progenitor competence by inducing RGC-specific genes while inhibiting other cell fates. Furthermore, we highlight candidate genes responsible for ATOH7-associated optic nerve and retinovascular anomalies, which sheds light to potential future therapy targets for related disorders.
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Affiliation(s)
- David Atac
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Kevin Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Elisa Cuevas
- UCL Great Ormond Street Institute of Child Health, University College London and NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Jane C Sowden
- UCL Great Ormond Street Institute of Child Health, University College London and NIHR Great Ormond Street Hospital Biomedical Research Centre, London WC1N 1EH, UK
| | - Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, 8057 Zurich, Switzerland
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4
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De Sá Fernandes C, Novoszel P, Gastaldi T, Krauß D, Lang M, Rica R, Kutschat AP, Holcmann M, Ellmeier W, Seruggia D, Strobl H, Sibilia M. The histone deacetylase HDAC1 controls dendritic cell development and anti-tumor immunity. Cell Rep 2024; 43:114308. [PMID: 38829740 DOI: 10.1016/j.celrep.2024.114308] [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: 10/23/2023] [Revised: 03/17/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Dendritic cell (DC) progenitors adapt their transcriptional program during development, generating different subsets. How chromatin modifications modulate these processes is unclear. Here, we investigate the impact of histone deacetylation on DCs by genetically deleting histone deacetylase 1 (HDAC1) or HDAC2 in hematopoietic progenitors and CD11c-expressing cells. While HDAC2 is not critical for DC development, HDAC1 deletion impairs pro-pDC and mature pDC generation and affects ESAM+cDC2 differentiation from tDCs and pre-cDC2s, whereas cDC1s are unchanged. HDAC1 knockdown in human hematopoietic cells also impairs cDC2 development, highlighting its crucial role across species. Multi-omics analyses reveal that HDAC1 controls expression, chromatin accessibility, and histone acetylation of the transcription factors IRF4, IRF8, and SPIB required for efficient development of cDC2 subsets. Without HDAC1, DCs switch immunologically, enhancing tumor surveillance through increased cDC1 maturation and interleukin-12 production, driving T helper 1-mediated immunity and CD8+ T cell recruitment. Our study reveals the importance of histone acetylation in DC development and anti-tumor immunity, suggesting DC-targeted therapeutic strategies for immuno-oncology.
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Affiliation(s)
- Cristiano De Sá Fernandes
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Philipp Novoszel
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Tommaso Gastaldi
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Dana Krauß
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Magdalena Lang
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Ramona Rica
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Ana P Kutschat
- St. Anna Children's Cancer Research Institute, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Martin Holcmann
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria
| | - Wilfried Ellmeier
- Institute of Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Davide Seruggia
- St. Anna Children's Cancer Research Institute, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Herbert Strobl
- Division of Immunology, Otto Loewi Research Center, Medical University of Graz, Graz, Austria
| | - Maria Sibilia
- Center for Cancer Research, Medical University of Vienna, Comprehensive Cancer Center, Vienna, Austria.
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5
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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6
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Nordin A, Pagella P, Zambanini G, Cantù C. Exhaustive identification of genome-wide binding events of transcriptional regulators. Nucleic Acids Res 2024; 52:e40. [PMID: 38499482 PMCID: PMC11040144 DOI: 10.1093/nar/gkae180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 03/20/2024] Open
Abstract
Genome-wide binding assays aspire to map the complete binding pattern of gene regulators. Common practice relies on replication-duplicates or triplicates-and high stringency statistics to favor false negatives over false positives. Here we show that duplicates and triplicates of CUT&RUN are not sufficient to discover the entire activity of transcriptional regulators. We introduce ICEBERG (Increased Capture of Enrichment By Exhaustive Replicate aGgregation), a pipeline that harnesses large numbers of CUT&RUN replicates to discover the full set of binding events and chart the line between false positives and false negatives. We employed ICEBERG to map the full set of H3K4me3-marked regions, the targets of the co-factor β-catenin, and those of the transcription factor TBX3, in human colorectal cancer cells. The ICEBERG datasets allow benchmarking of individual replicates, comparing the performance of peak calling and replication approaches, and expose the arbitrary nature of strategies to identify reproducible peaks. Instead of a static view of genomic targets, ICEBERG establishes a spectrum of detection probabilities across the genome for a given factor, underlying the intrinsic dynamicity of its mechanism of action, and permitting to distinguish frequent from rare regulation events. Finally, ICEBERG discovered instances, undetectable with other approaches, that underlie novel mechanisms of colorectal cancer progression.
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Affiliation(s)
- Anna Nordin
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Pierfrancesco Pagella
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Gianluca Zambanini
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
| | - Claudio Cantù
- Wallenberg Centre for Molecular Medicine, Linköping University, Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Division of Molecular Medicine and Virology, Faculty of Medicine and Health Sciences, Linköping University, Linköping, Sweden
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7
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Deochand DK, Dacic M, Bale MJ, Daman AW, Josefowicz SZ, Oliver D, Chinenov Y, Rogatsky I. Mechanisms of Epigenomic and Functional Convergence Between Glucocorticoid- and IL4-Driven Macrophage Programming. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.16.580560. [PMID: 38405750 PMCID: PMC10888924 DOI: 10.1101/2024.02.16.580560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Macrophages adopt distinct phenotypes in response to environmental cues, with type-2 cytokine interleukin-4 promoting a tissue-repair homeostatic state (M2IL4). Glucocorticoids, widely used anti-inflammatory therapeutics, reportedly impart a similar phenotype (M2GC), but how such disparate pathways may functionally converge is unknown. We show using integrative functional genomics that M2IL4 and M2GC transcriptomes share a striking overlap mirrored by a shift in chromatin landscape in both common and signal-specific gene subsets. This core homeostatic program is enacted by transcriptional effectors KLF4 and the GC receptor, whose genome-wide occupancy and actions are integrated in a stimulus-specific manner by the nuclear receptor cofactor GRIP1. Indeed, many of the M2IL4:M2GC-shared transcriptomic changes were GRIP1-dependent. Consistently, GRIP1 loss attenuated phagocytic activity of both populations in vitro and macrophage tissue-repair properties in the murine colitis model in vivo. These findings provide a mechanistic framework for homeostatic macrophage programming by distinct signals, to better inform anti-inflammatory drug design.
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Affiliation(s)
- Dinesh K Deochand
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Marija Dacic
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Michael J Bale
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Andrew W Daman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Steven Z Josefowicz
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - David Oliver
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Yurii Chinenov
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
| | - Inez Rogatsky
- Hospital for Special Surgery Research Institute, The David Rosenzweig Genomics Center, New York, NY, USA
- Graduate Program in Immunology and Microbial Pathogenesis, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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8
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de Mello FN, Tahira AC, Berzoti-Coelho MG, Verjovski-Almeida S. The CUT&RUN greenlist: genomic regions of consistent noise are effective normalizing factors for quantitative epigenome mapping. Brief Bioinform 2024; 25:bbad538. [PMID: 38279652 PMCID: PMC10818165 DOI: 10.1093/bib/bbad538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/14/2023] [Accepted: 12/25/2023] [Indexed: 01/28/2024] Open
Abstract
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a recent development for epigenome mapping, but its unique methodology can hamper proper quantitative analyses. As traditional normalization approaches have been shown to be inaccurate, we sought to determine endogenous normalization factors based on the human genome regions of constant nonspecific signal. This constancy was determined by applying Shannon's information entropy, and the set of normalizer regions, which we named the 'Greenlist', was extensively validated using publicly available datasets. We demonstrate here that the greenlist normalization outperforms the current top standards, and remains consistent across different experimental setups, cell lines and antibodies; the approach can even be applied to different species or to CUT&Tag. Requiring no additional experimental steps and no added cost, this approach can be universally applied to CUT&RUN experiments to greatly minimize the interference of technical variation over the biological epigenome changes of interest.
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Affiliation(s)
- Fabio N de Mello
- Cell Cycle Laboratory, Instituto Butantan, São Paulo, Brazil
- Interunit Bioinformatics Graduate Program, Universidade de São Paulo, São Paulo, Brazil
| | - Ana C Tahira
- Cell Cycle Laboratory, Instituto Butantan, São Paulo, Brazil
| | - Maria Gabriela Berzoti-Coelho
- Cell Cycle Laboratory, Instituto Butantan, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Cell Cycle Laboratory, Instituto Butantan, São Paulo, Brazil
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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9
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Mandemaker IK, Fessler E, Corujo D, Kotthoff C, Wegerer A, Rouillon C, Buschbeck M, Jae LT, Mattiroli F, Ladurner AG. The histone chaperone ANP32B regulates chromatin incorporation of the atypical human histone variant macroH2A. Cell Rep 2023; 42:113300. [PMID: 37858472 DOI: 10.1016/j.celrep.2023.113300] [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: 02/03/2023] [Revised: 08/25/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
All vertebrate genomes encode for three large histone H2A variants that have an additional metabolite-binding globular macrodomain module, macroH2A. MacroH2A variants impact heterochromatin organization and transcription regulation and establish a barrier for cellular reprogramming. However, the mechanisms of how macroH2A is incorporated into chromatin and the identity of any chaperones required for histone deposition remain elusive. Here, we develop a split-GFP-based assay for chromatin incorporation and use it to conduct a genome-wide mutagenesis screen in haploid human cells to identify proteins that regulate macroH2A dynamics. We show that the histone chaperone ANP32B is a regulator of macroH2A deposition. ANP32B associates with macroH2A in cells and in vitro binds to histones with low nanomolar affinity. In vitro nucleosome assembly assays show that ANP32B stimulates deposition of macroH2A-H2B and not of H2A-H2B onto tetrasomes. In cells, depletion of ANP32B strongly affects global macroH2A chromatin incorporation, revealing ANP32B as a macroH2A histone chaperone.
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Affiliation(s)
- Imke K Mandemaker
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Hubrecht Institute, Uppsalalaan 8, 3584CT Utrecht, the Netherlands.
| | - Evelyn Fessler
- Gene Center and Department of Biochemistry, LMU Munich, 81377 Munich, Germany
| | - David Corujo
- Applied Epigenetics Program, Myeloid Neoplasm Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Spain; Germans Trias I Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
| | - Christiane Kotthoff
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas Wegerer
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany
| | - Clément Rouillon
- Hubrecht Institute, Uppsalalaan 8, 3584CT Utrecht, the Netherlands
| | - Marcus Buschbeck
- Applied Epigenetics Program, Myeloid Neoplasm Program, Josep Carreras Leukaemia Research Institute (IJC), Campus ICO-GTP-UAB, 08916 Badalona, Barcelona, Spain; Germans Trias I Pujol Research Institute (IGTP), 08916 Badalona, Barcelona, Spain
| | - Lucas T Jae
- Gene Center and Department of Biochemistry, LMU Munich, 81377 Munich, Germany
| | | | - Andreas G Ladurner
- Biomedical Center (BMC), Department of Physiological Chemistry, Faculty of Medicine, LMU Munich, 82152 Planegg-Martinsried, Germany; Eisbach Bio GmbH, 82152 Planegg-Martinsried, Germany.
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Ogata JD, Mu W, Davis ES, Xue B, Harrell JC, Sheffield NC, Phanstiel DH, Love MI, Dozmorov MG. excluderanges: exclusion sets for T2T-CHM13, GRCm39, and other genome assemblies. Bioinformatics 2023; 39:btad198. [PMID: 37067481 PMCID: PMC10126321 DOI: 10.1093/bioinformatics/btad198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/16/2023] [Accepted: 04/12/2023] [Indexed: 04/18/2023] Open
Abstract
SUMMARY Exclusion regions are sections of reference genomes with abnormal pileups of short sequencing reads. Removing reads overlapping them improves biological signal, and these benefits are most pronounced in differential analysis settings. Several labs created exclusion region sets, available primarily through ENCODE and Github. However, the variety of exclusion sets creates uncertainty which sets to use. Furthermore, gap regions (e.g. centromeres, telomeres, short arms) create additional considerations in generating exclusion sets. We generated exclusion sets for the latest human T2T-CHM13 and mouse GRCm39 genomes and systematically assembled and annotated these and other sets in the excluderanges R/Bioconductor data package, also accessible via the BEDbase.org API. The package provides unified access to 82 GenomicRanges objects covering six organisms, multiple genome assemblies, and types of exclusion regions. For human hg38 genome assembly, we recommend hg38.Kundaje.GRCh38_unified_blacklist as the most well-curated and annotated, and sets generated by the Blacklist tool for other organisms. AVAILABILITY AND IMPLEMENTATION https://bioconductor.org/packages/excluderanges/. Package website: https://dozmorovlab.github.io/excluderanges/.
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Affiliation(s)
- Jonathan D Ogata
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, United States
| | - Wancen Mu
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, United States
| | - Eric S Davis
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Bingjie Xue
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, United States
| | - J Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23220, United States
| | - Nathan C Sheffield
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, United States
| | - Douglas H Phanstiel
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Thurston Arthritis Research Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States
| | - Michael I Love
- Department of Biostatistics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, United States
- Department of Genetics, University of North Carolina-Chapel Hill, Chapel Hill, NC 27514, United States
| | - Mikhail G Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA 23298, United States
- Department of Pathology, Virginia Commonwealth University, Richmond, VA 23284, United States
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