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Kubo N, Chen PB, Hu R, Ye Z, Sasaki H, Ren B. H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. Mol Cell 2024; 84:1742-1752.e5. [PMID: 38513661 PMCID: PMC11069443 DOI: 10.1016/j.molcel.2024.02.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers. KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase activities are largely dispensable for transcription during early embryogenesis in mammals. To better understand the role of H3K4me1 in enhancer function, we analyze dynamic enhancer-promoter (E-P) interactions and gene expression during neural differentiation of the mouse embryonic stem cells. We found that KMT2C/D catalytic activities were only required for H3K4me1 and E-P contacts at a subset of candidate enhancers, induced upon neural differentiation. By contrast, a majority of enhancers retained H3K4me1 in KMT2C/D catalytic mutant cells. Surprisingly, H3K4me1 signals at these KMT2C/D-independent sites were reduced after acute depletion of KMT2B, resulting in aggravated transcriptional defects. Our observations therefore implicate KMT2B in the catalysis of H3K4me1 at enhancers and provide additional support for an active role of H3K4me1 in enhancer-promoter interactions and transcription in mammalian cells.
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Affiliation(s)
- Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 7 Engineering Drive 1, Singapore 117574, Singapore
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Zhen Ye
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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Gambetta MC, Furlong EEM. The Insulator Protein CTCF Is Required for Correct Hox Gene Expression, but Not for Embryonic Development in Drosophila. Genetics 2018; 210:129-136. [PMID: 30021792 PMCID: PMC6116963 DOI: 10.1534/genetics.118.301350] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023] Open
Abstract
Insulator binding proteins (IBPs) play an important role in regulating gene expression by binding to specific DNA sites to facilitate appropriate gene regulation. There are several IBPs in Drosophila, each defined by their ability to insulate target gene promoters in transgenic assays from the activating or silencing effects of neighboring regulatory elements. Of these, only CCCTC-binding factor (CTCF) has an obvious ortholog in mammals. CTCF is essential for mammalian cell viability and is an important regulator of genome architecture. In flies, CTCF is both maternally deposited and zygotically expressed. Flies lacking zygotic CTCF die as young adults with homeotic defects, suggesting that specific Hox genes are misexpressed in inappropriate body segments. The lack of any major embryonic defects was assumed to be due to the maternal supply of CTCF protein, as maternally contributed factors are often sufficient to progress through much of embryogenesis. Here, we definitively determined the requirement of CTCF for developmental progression in Drosophila We generated animals that completely lack both maternal and zygotic CTCF and found that, contrary to expectation, these mutants progress through embryogenesis and larval life. They develop to pharate adults, which fail to eclose from their pupal case. These mutants show exacerbated homeotic defects compared to zygotic mutants, misexpressing the Hox gene Abdominal-B outside of its normal expression domain early in development. Our results indicate that loss of Drosophila CTCF is not accompanied by widespread effects on gene expression, which may be due to redundant functions with other IBPs. Rather, CTCF is required for correct Hox gene expression patterns and for the viability of adult Drosophila.
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Affiliation(s)
| | - Eileen E M Furlong
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
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Abstract
Enhancers are short noncoding segments of DNA (100-1000 bp) that control the temporal and spatial activity of genes in an orientation-independent manner. They can be separated from their target genes by large distances and are thus known as distal regulatory elements. One consequence of the variability in the distance separating enhancers and their target promoters is that it is difficult to determine which elements are involved in the regulation of a particular gene. Moreover, enhancers can be found in clusters in which multiple regulatory elements control expression of the same target gene. However, little is known about how the individual elements contribute to gene expression. Here, we describe how chromatin conformation promotes and constraints enhancer activity. Further, we discuss enhancer clusters and what is known about the contribution of individual elements to the regulation of target genes. Finally, we examine the reliability of different methods used to identify enhancers.
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Affiliation(s)
- Valentina Snetkova
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA.,MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jane A Skok
- Department of Pathology, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA
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Fraser J, Ferrai C, Chiariello AM, Schueler M, Rito T, Laudanno G, Barbieri M, Moore BL, Kraemer DCA, Aitken S, Xie SQ, Morris KJ, Itoh M, Kawaji H, Jaeger I, Hayashizaki Y, Carninci P, Forrest ARR, Semple CA, Dostie J, Pombo A, Nicodemi M. Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation. Mol Syst Biol 2015; 11:852. [PMID: 26700852 PMCID: PMC4704492 DOI: 10.15252/msb.20156492] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher‐order organization remains elusive. Here, we investigate TAD higher‐order interactions with Hi‐C through neuronal differentiation and show that they form a hierarchy of domains‐within‐domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. We find that TAD interactions are well captured by tree‐like, hierarchical structures irrespective of cell type. metaTAD tree structures correlate with genetic, epigenomic and expression features, and structural tree rearrangements during differentiation are linked to transcriptional state changes. Using polymer modelling, we demonstrate that hierarchical folding promotes efficient chromatin packaging without the loss of contact specificity, highlighting a role far beyond the simple need for packing efficiency.
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Affiliation(s)
- James Fraser
- Department of Biochemistry, Goodman Cancer Centre, McGill University, Montréal, QC, Canada
| | - Carmelo Ferrai
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany Genome Function Group, MRC Clinical Sciences Centre, Imperial College London Hammersmith Hospital Campus, London, UK
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II INFN Napoli CNR-SPIN Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Markus Schueler
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Tiago Rito
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Giovanni Laudanno
- Dipartimento di Fisica, Università di Napoli Federico II INFN Napoli CNR-SPIN Complesso Universitario di Monte Sant'Angelo, Naples, Italy
| | - Mariano Barbieri
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Benjamin L Moore
- MRC Human Genetics Unit, MRC IGMM University of Edinburgh, Edinburgh, UK
| | - Dorothee C A Kraemer
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC IGMM University of Edinburgh, Edinburgh, UK
| | - Sheila Q Xie
- Genome Function Group, MRC Clinical Sciences Centre, Imperial College London Hammersmith Hospital Campus, London, UK
| | - Kelly J Morris
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany Genome Function Group, MRC Clinical Sciences Centre, Imperial College London Hammersmith Hospital Campus, London, UK
| | - Masayoshi Itoh
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako Saitama, Japan Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama Kanagawa, Japan
| | - Hideya Kawaji
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako Saitama, Japan Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama Kanagawa, Japan
| | - Ines Jaeger
- Stem Cell Neurogenesis Group, MRC Clinical Sciences Centre, Imperial College London Hammersmith Hospital Campus, London, UK
| | | | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama Kanagawa, Japan
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies, Yokohama Kanagawa, Japan
| | | | - Colin A Semple
- MRC Human Genetics Unit, MRC IGMM University of Edinburgh, Edinburgh, UK
| | - Josée Dostie
- Department of Biochemistry, Goodman Cancer Centre, McGill University, Montréal, QC, Canada
| | - Ana Pombo
- Epigenetic Regulation and Chromatin Architecture Group, Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin-Buch, Germany Genome Function Group, MRC Clinical Sciences Centre, Imperial College London Hammersmith Hospital Campus, London, UK
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II INFN Napoli CNR-SPIN Complesso Universitario di Monte Sant'Angelo, Naples, Italy
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