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Gallego A, Fernández-Justel JM, Martín-Vírgala S, Maslon MM, Gómez M. Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs. Genes (Basel) 2022; 13:genes13091652. [PMID: 36140819 PMCID: PMC9498810 DOI: 10.3390/genes13091652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/05/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.
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Affiliation(s)
- Alicia Gallego
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - José Miguel Fernández-Justel
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Sara Martín-Vírgala
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
| | - Magdalena M. Maslon
- Center for Advanced Technology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 10, 61-614 Poznań, Poland
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznań, Poland
| | - María Gómez
- Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid (CSIC/UAM), Nicolás Cabrera 1, 28049 Madrid, Spain
- Correspondence:
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Stavast CJ, van Zuijen I, Karkoulia E, Özçelik A, van Hoven-Beijen A, Leon LG, Voerman JSA, Janssen GMC, van Veelen PA, Burocziova M, Brouwer RWW, van IJcken WFJ, Maas A, Bindels EM, van der Velden VHJ, Schliehe C, Katsikis PD, Alberich-Jorda M, Erkeland SJ. The tumor suppressor MIR139 is silenced by POLR2M to promote AML oncogenesis. Leukemia 2022; 36:687-700. [PMID: 34741119 PMCID: PMC8885418 DOI: 10.1038/s41375-021-01461-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 12/03/2022]
Abstract
MIR139 is a tumor suppressor and is commonly silenced in acute myeloid leukemia (AML). However, the tumor-suppressing activities of miR-139 and molecular mechanisms of MIR139-silencing remain largely unknown. Here, we studied the poorly prognostic MLL-AF9 fusion protein-expressing AML. We show that MLL-AF9 expression in hematopoietic precursors caused epigenetic silencing of MIR139, whereas overexpression of MIR139 inhibited in vitro and in vivo AML outgrowth. We identified novel miR-139 targets that mediate the tumor-suppressing activities of miR-139 in MLL-AF9 AML. We revealed that two enhancer regions control MIR139 expression and found that the polycomb repressive complex 2 (PRC2) downstream of MLL-AF9 epigenetically silenced MIR139 in AML. Finally, a genome-wide CRISPR-Cas9 knockout screen revealed RNA Polymerase 2 Subunit M (POLR2M) as a novel MIR139-regulatory factor. Our findings elucidate the molecular control of tumor suppressor MIR139 and reveal a role for POLR2M in the MIR139-silencing mechanism, downstream of MLL-AF9 and PRC2 in AML. In addition, we confirmed these findings in human AML cell lines with different oncogenic aberrations, suggesting that this is a more common oncogenic mechanism in AML. Our results may pave the way for new targeted therapy in AML.
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Affiliation(s)
- Christiaan J Stavast
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - Iris van Zuijen
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - Elena Karkoulia
- Department of Hemato-Oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Childhood Leukemia Investigation Prague, Department of Pediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Arman Özçelik
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | | | - Leticia G Leon
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - Jane S A Voerman
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - George M C Janssen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Monika Burocziova
- Department of Hemato-Oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Rutger W W Brouwer
- Erasmus MC, University Medical Center Rotterdam, Center for Biomics, Rotterdam, the Netherlands
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Rotterdam, the Netherlands
| | - Wilfred F J van IJcken
- Erasmus MC, University Medical Center Rotterdam, Center for Biomics, Rotterdam, the Netherlands
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Rotterdam, the Netherlands
| | - Alex Maas
- Erasmus MC, University Medical Center Rotterdam, Department of Cell Biology, Rotterdam, the Netherlands
| | - Eric M Bindels
- Erasmus MC, University Medical Center Rotterdam, Department of Hematology, Rotterdam, the Netherlands
| | | | - Christopher Schliehe
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - Peter D Katsikis
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands
| | - Meritxell Alberich-Jorda
- Department of Hemato-Oncology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- Childhood Leukemia Investigation Prague, Department of Pediatric Haematology and Oncology, 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Stefan J Erkeland
- Erasmus MC, University Medical Center Rotterdam, Department of Immunology, Rotterdam, the Netherlands.
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Stavast CJ, van Zuijen I, Erkeland SJ. MicroRNA-139, an Emerging Gate-Keeper in Various Types of Cancer. Cells 2022; 11:cells11050769. [PMID: 35269391 PMCID: PMC8909004 DOI: 10.3390/cells11050769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/17/2022] [Accepted: 02/19/2022] [Indexed: 11/25/2022] Open
Abstract
Mounting data show that MIR139 is commonly silenced in solid cancer and hematological malignancies. MIR139 acts as a critical tumor suppressor by tuning the cellular response to different types of stress, including DNA damage, and by repressing oncogenic signaling pathways. Recently, novel insights into the mechanism of MIR139 silencing in tumor cells have been described. These include epigenetic silencing, inhibition of POL-II transcriptional activity on gene regulatory elements, enhanced expression of competing RNAs and post-transcriptional regulation by the microprocessor complex. Some of these MIR139-silencing mechanisms have been demonstrated in different types of cancer, suggesting that these are more general oncogenic events. Reactivation of MIR139 expression in tumor cells causes inhibition of tumor cell expansion and induction of cell death by the repression of oncogenic mRNA targets. In this review, we discuss the different aspects of MIR139 as a tumor suppressor gene and give an overview on different transcriptional mechanisms regulating MIR139 in oncogenic stress and across different types of cancer. The novel insights into the expression regulation and the tumor-suppressing activities of MIR139 may pave the way to new treatment options for cancer.
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Mantsoki A, Parussel K, Joshi A. Identification and Characterisation of Putative Enhancer Elements in Mouse Embryonic Stem Cells. Bioinform Biol Insights 2021; 15:1177932220974623. [PMID: 33623376 PMCID: PMC7876754 DOI: 10.1177/1177932220974623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 10/26/2020] [Indexed: 11/16/2022] Open
Abstract
Enhancer elements control mammalian transcription largely in a cell-type-specific
manner. The genome-wide identification of enhancer elements and their activity
status in a cellular context is therefore fundamental to understanding cell
identity and function. We determined enhancer activity in mouse embryonic stem
(ES) cells using chromatin modifications and characterised their global
properties. Specifically, we first grouped enhancers into 5 groups using
multiple H3K4me1, H3K27ac, and H3K27me3 modification data sets. Active enhancers
(simultaneous presence of H3K4me1 and H3K27ac) were enriched for binding of
pluripotency factors and were found near pluripotency-related genes. Although
both H3K4me1-only and active enhancers were enriched for super-enhancers and a
TATA box like motif, active enhancers were preferentially bound by RNA polII
(s2) and were enriched for bidirectional transcription, while H3K4me1-only
enhancers were enriched for RNA polII (8WG16) suggesting they were likely
poised. Bivalent enhancers (simultaneous presence of H3K4me1 and H3K27me3) were
preferentially in the vicinity of bivalent genes. They were enriched for binding
of components of polycomb complex as well as Tcf3 and Oct4. Moreover, a
‘CTTTCTC’ de-novo motif was enriched at bivalent enhancers, previously
identified at bivalent promoters in ES cells. Taken together, 3 histone
modifications successfully demarcated active, bivalent, and poised enhancers
with distinct sequence and binding features.
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Affiliation(s)
- Anna Mantsoki
- Division of Developmental Biology, The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Karla Parussel
- Division of Developmental Biology, The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Anagha Joshi
- Computational Biology Unit, Department of Clinical Science, University of Bergen, Bergen, Norway
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