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Portillo-Ledesma S, Chung S, Hoffman J, Schlick T. Regulation of chromatin architecture by transcription factor binding. eLife 2024; 12:RP91320. [PMID: 38241351 PMCID: PMC10945602 DOI: 10.7554/elife.91320] [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] [Indexed: 01/21/2024] Open
Abstract
Transcription factors (TF) bind to chromatin and regulate the expression of genes. The pair Myc:Max binds to E-box regulatory DNA elements throughout the genome to control the transcription of a large group of specific genes. We introduce an implicit modeling protocol for Myc:Max binding to mesoscale chromatin fibers at nucleosome resolution to determine TF effect on chromatin architecture and shed light into its mechanism of gene regulation. We first bind Myc:Max to different chromatin locations and show how it can direct fiber folding and formation of microdomains, and how this depends on the linker DNA length. Second, by simulating increasing concentrations of Myc:Max binding to fibers that differ in the DNA linker length, linker histone density, and acetylation levels, we assess the interplay between Myc:Max and other chromatin internal parameters. Third, we study the mechanism of gene silencing by Myc:Max binding to the Eed gene loci. Overall, our results show how chromatin architecture can be regulated by TF binding. The position of TF binding dictates the formation of microdomains that appear visible only at the ensemble level. At the same time, the level of linker histone and tail acetylation, or different linker DNA lengths, regulates the concentration-dependent effect of TF binding. Furthermore, we show how TF binding can repress gene expression by increasing fiber folding motifs that help compact and occlude the promoter region. Importantly, this effect can be reversed by increasing linker histone density. Overall, these results shed light on the epigenetic control of the genome dictated by TF binding.
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Affiliation(s)
- Stephanie Portillo-Ledesma
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
| | - Suckwoo Chung
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Jill Hoffman
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
| | - Tamar Schlick
- Department of Chemistry, 100 Washington Square East, Silver Building, New York UniversityNew YorkUnited States
- Simons Center for Computational Physical Chemistry, 24 Waverly Place, Silver Building, New York UniversityNew YorkUnited States
- Courant Institute of Mathematical Sciences, New York UniversityNew YorkUnited States
- New York University-East China Normal University Center for Computational Chemistry, New York University ShanghaiShanghaiChina
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2
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Viner C, Ishak CA, Johnson J, Walker NJ, Shi H, Sjöberg-Herrera MK, Shen SY, Lardo SM, Adams DJ, Ferguson-Smith AC, De Carvalho DD, Hainer SJ, Bailey TL, Hoffman MM. Modeling methyl-sensitive transcription factor motifs with an expanded epigenetic alphabet. Genome Biol 2024; 25:11. [PMID: 38191487 PMCID: PMC10773111 DOI: 10.1186/s13059-023-03070-0] [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: 03/08/2023] [Accepted: 09/21/2023] [Indexed: 01/10/2024] Open
Abstract
BACKGROUND Transcription factors bind DNA in specific sequence contexts. In addition to distinguishing one nucleobase from another, some transcription factors can distinguish between unmodified and modified bases. Current models of transcription factor binding tend not to take DNA modifications into account, while the recent few that do often have limitations. This makes a comprehensive and accurate profiling of transcription factor affinities difficult. RESULTS Here, we develop methods to identify transcription factor binding sites in modified DNA. Our models expand the standard A/C/G/T DNA alphabet to include cytosine modifications. We develop Cytomod to create modified genomic sequences and we also enhance the MEME Suite, adding the capacity to handle custom alphabets. We adapt the well-established position weight matrix (PWM) model of transcription factor binding affinity to this expanded DNA alphabet. Using these methods, we identify modification-sensitive transcription factor binding motifs. We confirm established binding preferences, such as the preference of ZFP57 and C/EBPβ for methylated motifs and the preference of c-Myc for unmethylated E-box motifs. CONCLUSIONS Using known binding preferences to tune model parameters, we discover novel modified motifs for a wide array of transcription factors. Finally, we validate our binding preference predictions for OCT4 using cleavage under targets and release using nuclease (CUT&RUN) experiments across conventional, methylation-, and hydroxymethylation-enriched sequences. Our approach readily extends to other DNA modifications. As more genome-wide single-base resolution modification data becomes available, we expect that our method will yield insights into altered transcription factor binding affinities across many different modifications.
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Affiliation(s)
- Coby Viner
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James Johnson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicolas J Walker
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Hui Shi
- Department of Genetics, University of Cambridge, Cambridge, England
| | - Marcela K Sjöberg-Herrera
- Wellcome Sanger Institute, Cambridge, England
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Santana M Lardo
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | | | | | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Timothy L Bailey
- Department of Pharmacology, University of Nevada, Reno, Reno, NV, USA
| | - Michael M Hoffman
- Department of Computer Science, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada.
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3
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Yamamoto T, Wang H, Sato H, Honda S, Ikeda S, Minami N. MYC-MAX heterodimerization is essential for the induction of major zygotic genome activation and subsequent preimplantation development. Sci Rep 2023; 13:16011. [PMID: 37749153 PMCID: PMC10520005 DOI: 10.1038/s41598-023-43127-5] [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: 07/03/2023] [Accepted: 09/20/2023] [Indexed: 09/27/2023] Open
Abstract
In mouse preimplantation development, zygotic genome activation (ZGA), which synthesizes new transcripts in the embryo, begins in the S phase at the one-cell stage, with major ZGA occurring especially at the late two-cell stage. Myc is a transcription factor expressed in parallel with ZGA, but its direct association with major ZGA has not been clarified. In this study, we found that developmental arrest occurs at the two-cell stage when mouse embryos were treated with antisense oligonucleotides targeting Myc or MYC-specific inhibitors from the one-cell stage. To identify when MYC inhibition affects development, we applied time-limited inhibitor treatment and found that inhibition of MYC at the one-cell, four-cell, and morula stages had no effect on preimplantation development, whereas inhibitor treatment at the two-cell stage arrested development at the two-cell stage. Furthermore, transcriptome analysis revealed that when MYC function was inhibited, genes expressed in the major ZGA phase were suppressed. These results suggest that MYC is essential for the induction of major ZGA and subsequent preimplantation development. Revealing the function of MYC in preimplantation development is expected to contribute to advances in assisted reproductive technology.
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Affiliation(s)
- Takuto Yamamoto
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Haoxue Wang
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Hana Sato
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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4
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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5
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Gupta N, Yakhou L, Albert JR, Azogui A, Ferry L, Kirsh O, Miura F, Battault S, Yamaguchi K, Laisné M, Domrane C, Bonhomme F, Sarkar A, Delagrange M, Ducos B, Cristofari G, Ito T, Greenberg MVC, Defossez PA. A genome-wide screen reveals new regulators of the 2-cell-like cell state. Nat Struct Mol Biol 2023; 30:1105-1118. [PMID: 37488355 DOI: 10.1038/s41594-023-01038-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
In mammals, only the zygote and blastomeres of the early embryo are totipotent. This totipotency is mirrored in vitro by mouse '2-cell-like cells' (2CLCs), which appear at low frequency in cultures of embryonic stem cells (ESCs). Because totipotency is not completely understood, we carried out a genome-wide CRISPR knockout screen in mouse ESCs, searching for mutants that reactivate the expression of Dazl, a gene expressed in 2CLCs. Here we report the identification of four mutants that reactivate Dazl and a broader 2-cell-like signature: the E3 ubiquitin ligase adaptor SPOP, the Zinc-Finger transcription factor ZBTB14, MCM3AP, a component of the RNA processing complex TREX-2, and the lysine demethylase KDM5C. All four factors function upstream of DPPA2 and DUX, but not via p53. In addition, SPOP binds DPPA2, and KDM5C interacts with ncPRC1.6 and inhibits 2CLC gene expression in a catalytic-independent manner. These results extend our knowledge of totipotency, a key phase of organismal life.
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Affiliation(s)
- Nikhil Gupta
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France.
- Joint AZ CRUK Functional Genomics Centre, The Milner Therapeutics Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
| | - Lounis Yakhou
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | | | - Anaelle Azogui
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Laure Ferry
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Olivier Kirsh
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
| | - Sarah Battault
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Kosuke Yamaguchi
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Marthe Laisné
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Cécilia Domrane
- Epigenetics and Cell Fate, Université Paris Cité, CNRS, Paris, France
| | - Frédéric Bonhomme
- Epigenetic Chemical Biology, UMR3523, Institut Pasteur, Université Paris Cité, CNRS, Paris, France
| | - Arpita Sarkar
- IRCAN, Université Côte d'Azur, Inserm, CNRS, Nice, France
| | - Marine Delagrange
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | - Bertrand Ducos
- High Throughput qPCR Facility, Institut de Biologie de l'École Normale Supérieure (IBENS), Laboratoire de Physique de l'ENS CNRS UMR8023, PSL Research University, Paris, France
| | | | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, Japan
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6
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Astanina E, Doronzo G, Corà D, Neri F, Oliviero S, Genova T, Mussano F, Middonti E, Vallariello E, Cencioni C, Valdembri D, Serini G, Limana F, Foglio E, Ballabio A, Bussolino F. The TFEB-TGIF1 axis regulates EMT in mouse epicardial cells. Nat Commun 2022; 13:5191. [PMID: 36057632 PMCID: PMC9440911 DOI: 10.1038/s41467-022-32855-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 08/17/2022] [Indexed: 11/24/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a complex and pivotal process involved in organogenesis and is related to several pathological processes, including cancer and fibrosis. During heart development, EMT mediates the conversion of epicardial cells into vascular smooth muscle cells and cardiac interstitial fibroblasts. Here, we show that the oncogenic transcription factor EB (TFEB) is a key regulator of EMT in epicardial cells and that its genetic overexpression in mouse epicardium is lethal due to heart defects linked to impaired EMT. TFEB specifically orchestrates the EMT-promoting function of transforming growth factor (TGF) β, and this effect results from activated transcription of thymine-guanine-interacting factor (TGIF)1, a TGFβ/Smad pathway repressor. The Tgif1 promoter is activated by TFEB, and in vitro and in vivo findings demonstrate its increased expression when Tfeb is overexpressed. Furthermore, Tfeb overexpression in vitro prevents TGFβ-induced EMT, and this effect is abolished by Tgif1 silencing. Tfeb loss of function, similar to that of Tgif1, sensitizes cells to TGFβ, inducing an EMT response to low doses of TGFβ. Together, our findings reveal an unexpected function of TFEB in regulating EMT, which might provide insights into injured heart repair and control of cancer progression. Epithelial-mesenchymal transition (EMT) is a complex process involved in organogenesis. Here, the authors show that the transcription factor EB (TFEB) regulates EMT in epicardium during heart development by tuning sensitivity to TGFβ signaling.
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Affiliation(s)
- Elena Astanina
- Department of Oncology, University of Torino, Torino, Italy. .,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy.
| | - Gabriella Doronzo
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Università degli Studi del Piemonte Orientale, Novara, Italy
| | - Francesco Neri
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Tullio Genova
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | - Federico Mussano
- CIR Dental School, Department of Surgical Sciences, University of Torino, Via Nizza 230, 10126, Turin, Italy
| | - Emanuele Middonti
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Edoardo Vallariello
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Chiara Cencioni
- Institute for Systems Analysis and Computer Science "A. Ruberti", National Research Council (IASI-CNR), Rome, Italy
| | - Donatella Valdembri
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Guido Serini
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
| | - Federica Limana
- San Raffaele Open University, Rome, Italy.,Laboratory of Cellular and Molecular Pathology, IRCCS San Raffaele Pisana, Rome, Italy
| | - Eleonora Foglio
- Technoscience, Parco Scientifico e Tecnologico Pontino, 04100, Latina, Italy
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Federico Bussolino
- Department of Oncology, University of Torino, Torino, Italy.,Candiolo Cancer Institute-IRCCS-FPO, Candiolo, Italy
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7
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Divisato G, Chiariello AM, Esposito A, Zoppoli P, Zambelli F, Elia MA, Pesole G, Incarnato D, Passaro F, Piscitelli S, Oliviero S, Nicodemi M, Parisi S, Russo T. Hmga2 protein loss alters nuclear envelope and 3D chromatin structure. BMC Biol 2022; 20:171. [PMID: 35918713 PMCID: PMC9344646 DOI: 10.1186/s12915-022-01375-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 07/14/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The high-mobility group Hmga family of proteins are non-histone chromatin-interacting proteins which have been associated with a number of nuclear functions, including heterochromatin formation, replication, recombination, DNA repair, transcription, and formation of enhanceosomes. Due to its role based on dynamic interaction with chromatin, Hmga2 has a pathogenic role in diverse tumors and has been mainly studied in a cancer context; however, whether Hmga2 has similar physiological functions in normal cells remains less explored. Hmga2 was additionally shown to be required during the exit of embryonic stem cells (ESCs) from the ground state of pluripotency, to allow their transition into epiblast-like cells (EpiLCs), and here, we use that system to gain further understanding of normal Hmga2 function. RESULTS We demonstrated that Hmga2 KO pluripotent stem cells fail to develop into EpiLCs. By using this experimental system, we studied the chromatin changes that take place upon the induction of EpiLCs and we observed that the loss of Hmga2 affects the histone mark H3K27me3, whose levels are higher in Hmga2 KO cells. Accordingly, a sustained expression of polycomb repressive complex 2 (PRC2), responsible for H3K27me3 deposition, was observed in KO cells. However, gene expression differences between differentiating wt vs Hmga2 KO cells did not show any significant enrichments of PRC2 targets. Similarly, endogenous Hmga2 association to chromatin in epiblast stem cells did not show any clear relationships with gene expression modification observed in Hmga2 KO. Hmga2 ChIP-seq confirmed that this protein preferentially binds to the chromatin regions associated with nuclear lamina. Starting from this observation, we demonstrated that nuclear lamina underwent severe alterations when Hmga2 KO or KD cells were induced to exit from the naïve state and this phenomenon is accompanied by a mislocalization of the heterochromatin mark H3K9me3 within the nucleus. As nuclear lamina (NL) is involved in the organization of 3D chromatin structure, we explored the possible effects of Hmga2 loss on this phenomenon. The analysis of Hi-C data in wt and Hmga2 KO cells allowed us to observe that inter-TAD (topologically associated domains) interactions in Hmga2 KO cells are different from those observed in wt cells. These differences clearly show a peculiar compartmentalization of inter-TAD interactions in chromatin regions associated or not to nuclear lamina. CONCLUSIONS Overall, our results indicate that Hmga2 interacts with heterochromatic lamin-associated domains, and highlight a role for Hmga2 in the crosstalk between chromatin and nuclear lamina, affecting the establishment of inter-TAD interactions.
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Affiliation(s)
- Giuseppina Divisato
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Andrea M Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy
| | - Pietro Zoppoli
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Federico Zambelli
- Dipartimento di Bioscienze, Università di Milano Statale, Milan, Italy
| | - Maria Antonietta Elia
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Graziano Pesole
- Dipartimento Di Bioscienze, Biotecnologie e Biofarmaceutica, Università di Bari A. Moro and IBIOM CNR, Bari, Italy
| | - Danny Incarnato
- University of Groningen, GBB Institute, Groningen, The Netherlands
| | - Fabiana Passaro
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Silvia Piscitelli
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino and IIGM Candiolo, Turin, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Naples, Italy.,Berlin Institute for Medical Systems Biology, Max-Delbrück Centre for Molecular Medicine, Berlin, Germany.,CNR-SPIN, Naples, Italy
| | - Silvia Parisi
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy.
| | - Tommaso Russo
- Dipartimento di Medicina molecolare e biotecnologie mediche, Università di Napoli Federico II, Naples, Italy.
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8
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Acurzio B, Cecere F, Giaccari C, Verma A, Russo R, Valletta M, Hay Mele B, Angelini C, Chambery A, Riccio A. The mismatch-repair proteins MSH2 and MSH6 interact with the imprinting control regions through the ZFP57-KAP1 complex. Epigenetics Chromatin 2022; 15:27. [PMID: 35918739 PMCID: PMC9344765 DOI: 10.1186/s13072-022-00462-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 11/21/2022] Open
Abstract
Background Imprinting Control Regions (ICRs) are CpG-rich sequences acquiring differential methylation in the female and male germline and maintaining it in a parental origin-specific manner in somatic cells. Despite their expected high mutation rate due to spontaneous deamination of methylated cytosines, ICRs show conservation of CpG-richness and CpG-containing transcription factor binding sites in mammalian species. However, little is known about the mechanisms contributing to the maintenance of a high density of methyl CpGs at these loci. Results To gain functional insights into the mechanisms for maintaining CpG methylation, we sought to identify the proteins binding the methylated allele of the ICRs by determining the interactors of ZFP57 that recognizes a methylated hexanucleotide motif of these DNA regions in mouse ESCs. By using a tagged approach coupled to LC–MS/MS analysis, we identified several proteins, including factors involved in mRNA processing/splicing, chromosome organization, transcription and DNA repair processes. The presence of the post-replicative mismatch-repair (MMR) complex components MSH2 and MSH6 among the identified ZFP57 interactors prompted us to investigate their DNA binding profile by chromatin immunoprecipitation and sequencing. We demonstrated that MSH2 was enriched at gene promoters overlapping unmethylated CpG islands and at repeats. We also found that both MSH2 and MSH6 interacted with the methylated allele of the ICRs, where their binding to DNA was mediated by the ZFP57/KAP1 complex. Conclusions Our findings show that the MMR complex is concentrated on gene promoters and repeats in mouse ESCs, suggesting that maintaining the integrity of these regions is a primary function of highly proliferating cells. Furthermore, the demonstration that MSH2/MSH6 are recruited to the methylated allele of the ICRs through interaction with ZFP57/KAP1 suggests a role of the MMR complex in the maintenance of the integrity of these regulatory regions and evolution of genomic imprinting in mammalian species. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00462-7.
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Affiliation(s)
- Basilia Acurzio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Francesco Cecere
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Carlo Giaccari
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Ankit Verma
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy.,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy
| | - Rosita Russo
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Mariangela Valletta
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Bruno Hay Mele
- Department of Biology, Università Degli Studi Di Napoli "Federico II", 80126, Naples, Italy
| | - Claudia Angelini
- Istituto Per Le Applicazioni del Calcolo "Mauro Picone" (IAC), CNR, 80131, Naples, Italy
| | - Angela Chambery
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy
| | - Andrea Riccio
- Department of Environmental Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), Università Degli Studi Della Campania "Luigi Vanvitelli", 81100, Caserta, Italy. .,Institute of Genetics and Biophysics (IGB) "Adriano Buzzati-Traverso", Consiglio Nazionale Delle Ricerche (CNR), 80131, Naples, Italy.
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9
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Jiang Q, Ang JYJ, Lee AY, Cao Q, Li KY, Yip KY, Leung DCY. G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping. Cell Rep 2020; 33:108315. [PMID: 33113380 DOI: 10.1016/j.celrep.2020.108315] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 09/05/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
G9a is a lysine methyltransferase that regulates epigenetic modifications, transcription, and genome organization. However, whether these properties are dependent on one another or represent distinct functions of G9a remains unclear. In this study, we observe widespread DNA methylation loss in G9a depleted and catalytic mutant embryonic stem cells. Furthermore, we define how G9a regulates chromatin accessibility, epigenetic modifications, and transcriptional silencing in both catalytic-dependent and -independent manners. Reactivated retrotransposons provide alternative promoters and splice sites leading to the upregulation of neighboring genes and the production of chimeric transcripts. Moreover, while topologically associated domains and compartment A/B definitions are largely unaffected, the loss of G9a leads to altered chromatin states, aberrant CTCF and cohesin binding, and differential chromatin looping, especially at retrotransposons. Taken together, our findings reveal how G9a regulates the epigenome, transcriptome, and higher-order chromatin structures in distinct mechanisms.
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Affiliation(s)
- Qinghong Jiang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Julie Y J Ang
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Ah Young Lee
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Qin Cao
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Kelly Y Li
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong, China
| | - Danny C Y Leung
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.
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10
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Zorzan I, Pellegrini M, Arboit M, Incarnato D, Maldotti M, Forcato M, Tagliazucchi GM, Carbognin E, Montagner M, Oliviero S, Martello G. The transcriptional regulator ZNF398 mediates pluripotency and epithelial character downstream of TGF-beta in human PSCs. Nat Commun 2020; 11:2364. [PMID: 32398665 PMCID: PMC7217929 DOI: 10.1038/s41467-020-16205-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/17/2020] [Indexed: 12/16/2022] Open
Abstract
Human pluripotent stem cells (hPSCs) have the capacity to give rise to all differentiated cells of the adult. TGF-beta is used routinely for expansion of conventional hPSCs as flat epithelial colonies expressing the transcription factors POU5F1/OCT4, NANOG, SOX2. Here we report a global analysis of the transcriptional programme controlled by TGF-beta followed by an unbiased gain-of-function screening in multiple hPSC lines to identify factors mediating TGF-beta activity. We identify a quartet of transcriptional regulators promoting hPSC self-renewal including ZNF398, a human-specific mediator of pluripotency and epithelial character in hPSCs. Mechanistically, ZNF398 binds active promoters and enhancers together with SMAD3 and the histone acetyltransferase EP300, enabling transcription of TGF-beta targets. In the context of somatic cell reprogramming, inhibition of ZNF398 abolishes activation of pluripotency and epithelial genes and colony formation. Our findings have clear implications for the generation of bona fide hPSCs for regenerative medicine.
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Affiliation(s)
- Irene Zorzan
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Marco Pellegrini
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy.,UCL Great Ormond Street Institute of Child Health, Developmental Biology and Cancer, Stem Cells and Regenerative Medicine, 30 Guilford Street, WC1N 1EH, London, UK
| | - Mattia Arboit
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Danny Incarnato
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy.,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy.,Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, the Netherlands
| | - Mara Maldotti
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy.,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy
| | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Guidantonio Malagoli Tagliazucchi
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy.,UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Darwin Building, WC1E 6BT, London, UK
| | - Elena Carbognin
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Marco Montagner
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology and Molecular Biotechnology Center (MCB), University of Turin, 10126, Turin, Italy. .,Italian Institute for Genomic Medicine (IIGM), 10060, Candiolo (TO), Italy.
| | - Graziano Martello
- Department of Molecular Medicine, Medical School, University of Padua, 35121, Padua, Italy.
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11
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Blackledge NP, Fursova NA, Kelley JR, Huseyin MK, Feldmann A, Klose RJ. PRC1 Catalytic Activity Is Central to Polycomb System Function. Mol Cell 2020; 77:857-874.e9. [PMID: 31883950 PMCID: PMC7033600 DOI: 10.1016/j.molcel.2019.12.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 10/21/2019] [Accepted: 12/02/2019] [Indexed: 01/01/2023]
Abstract
The Polycomb repressive system is an essential chromatin-based regulator of gene expression. Despite being extensively studied, how the Polycomb system selects its target genes is poorly understood, and whether its histone-modifying activities are required for transcriptional repression remains controversial. Here, we directly test the requirement for PRC1 catalytic activity in Polycomb system function. To achieve this, we develop a conditional mutation system in embryonic stem cells that completely removes PRC1 catalytic activity. Using this system, we demonstrate that catalysis by PRC1 drives Polycomb chromatin domain formation and long-range chromatin interactions. Furthermore, we show that variant PRC1 complexes with DNA-binding activities occupy target sites independently of PRC1 catalytic activity, providing a putative mechanism for Polycomb target site selection. Finally, we discover that Polycomb-mediated gene repression requires PRC1 catalytic activity. Together these discoveries provide compelling evidence that PRC1 catalysis is central to Polycomb system function and gene regulation.
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Affiliation(s)
- Neil P Blackledge
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Nadezda A Fursova
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Jessica R Kelley
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Miles K Huseyin
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Angelika Feldmann
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, South Parks Rd., Oxford OX1 3QU, UK.
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12
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Fu X, Wu X, Djekidel MN, Zhang Y. Myc and Dnmt1 impede the pluripotent to totipotent state transition in embryonic stem cells. Nat Cell Biol 2019; 21:835-844. [PMID: 31209294 PMCID: PMC7137718 DOI: 10.1038/s41556-019-0343-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 05/09/2019] [Indexed: 12/26/2022]
Abstract
Totipotency refers to the ability of a cell to generate all of the cell types of an organism. Unlike pluripotency, the establishment of totipotency is poorly understood. In mouse embryonic stem cells, Dux drives a small percentage of cells into a totipotent state by expressing 2-cell-embryo-specific transcripts. To understand how this transition takes place, we performed single-cell RNA-seq, which revealed a two-step transcriptional reprogramming process characterized by downregulation of pluripotent genes in the first step and upregulation of the 2-cell-embryo-specific elements in the second step. To identify factors controlling the transition, we performed a CRISPR-Cas9-mediated screen, which revealed Myc and Dnmt1 as two factors preventing the transition. Mechanistic studies demonstrate that Myc prevents downregulation of pluripotent genes in the first step, while Dnmt1 impedes 2-cell-embryo-specific gene activation in the second step. Collectively, the findings of our study reveal insights into the establishment and regulation of the totipotent state in mouse embryonic stem cells.
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Affiliation(s)
- Xudong Fu
- Howard Hughes Medical Institute, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Xiaoji Wu
- Howard Hughes Medical Institute, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mohamed Nadhir Djekidel
- Howard Hughes Medical Institute, Boston, MA, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston, MA, USA.
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Harvard Stem Cell Institute, Boston, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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13
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Doronzo G, Astanina E, Corà D, Chiabotto G, Comunanza V, Noghero A, Neri F, Puliafito A, Primo L, Spampanato C, Settembre C, Ballabio A, Camussi G, Oliviero S, Bussolino F. TFEB controls vascular development by regulating the proliferation of endothelial cells. EMBO J 2018; 38:embj.201798250. [PMID: 30591554 PMCID: PMC6356157 DOI: 10.15252/embj.201798250] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/12/2018] [Accepted: 11/20/2018] [Indexed: 12/30/2022] Open
Abstract
Transcription factor TFEB is thought to control cellular functions—including in the vascular bed—primarily via regulation of lysosomal biogenesis and autophagic flux. Here, we report that TFEB also orchestrates a non‐canonical program that controls the cell cycle/VEGFR2 pathway in the developing vasculature. In endothelial cells, TFEB depletion halts proliferation at the G1‐S transition by inhibiting the CDK4/Rb pathway. TFEB‐deficient cells attempt to compensate for this limitation by increasing VEGFR2 levels at the plasma membrane via microRNA‐mediated mechanisms and controlled membrane trafficking. TFEB stimulates expression of the miR‐15a/16‐1 cluster, which limits VEGFR2 transcript stability and negatively modulates expression of MYO1C, a regulator of VEGFR2 trafficking to the cell surface. Altered levels of miR‐15a/16‐1 and MYO1C in TFEB‐depleted cells cause increased expression of plasma membrane VEGFR2, but in a manner associated with low signaling strength. An endothelium‐specific Tfeb‐knockout mouse model displays defects in fetal and newborn mouse vasculature caused by reduced endothelial proliferation and by anomalous function of the VEGFR2 pathway. These previously unrecognized functions of TFEB expand its role beyond regulation of the autophagic pathway in the vascular system.
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Affiliation(s)
- Gabriella Doronzo
- Department of Oncology, University of Turin, Candiolo, Italy .,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Elena Astanina
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Davide Corà
- Department of Translational Medicine, Piemonte Orientale University, Novara, Italy
| | - Giulia Chiabotto
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Valentina Comunanza
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Alessio Noghero
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Francesco Neri
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Alberto Puliafito
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Luca Primo
- Department of Oncology, University of Turin, Candiolo, Italy.,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
| | - Carmine Spampanato
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli (Naples), Italy.,Department of Translational Medicine, Federico II University, Naples, Italy.,Department of Molecular and Human Genetics, Ian and Dan Duncan Neurological Research Institute, Baylor College of Medicine, Houston, TX, USA
| | - Giovanni Camussi
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Federico Bussolino
- Department of Oncology, University of Turin, Candiolo, Italy .,Candiolo Cancer Institute-FPO-IRCCS, Candiolo, Italy
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14
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A molecular roadmap for the emergence of early-embryonic-like cells in culture. Nat Genet 2017; 50:106-119. [PMID: 29255263 PMCID: PMC5755687 DOI: 10.1038/s41588-017-0016-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 11/13/2017] [Indexed: 12/24/2022]
Abstract
Unlike pluripotent cells, which generate only embryonic tissues, totipotent cells can generate a full organism, including extraembryonic annexes. A rare population of cells resembling 2-cell stage embryos arises in pluripotent embryonic stem (ES) cell cultures. These 2-cell-like-cells display molecular features of totipotency and broader developmental plasticity. However, their specific nature and the process through which they arise remain outstanding questions. Here, we identify intermediate cellular states and molecular determinants during the emergence of 2-cell-like-cells. By deploying a quantitative single cell expression approach, we identified an intermediate population characterised by the expression of the transcription factor ZSCAN4 as precursor of 2-cell-like-cells. Using an siRNA screening, we uncovered novel epigenetic regulators of 2-cell-like-cell emergence, including the non-canonical PRC1 complex PRC1.6 and Ep400/Tip60. Our data shed light on the mechanisms underlying the exit from the ES cell state towards the formation of early-embryonic-like cells in culture and identify key epigenetic pathways that promote this transition.
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15
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Yesudhas D, Batool M, Anwar MA, Panneerselvam S, Choi S. Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes (Basel) 2017; 8:genes8080192. [PMID: 28763006 PMCID: PMC5575656 DOI: 10.3390/genes8080192] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 12/17/2022] Open
Abstract
Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression.
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Affiliation(s)
- Dhanusha Yesudhas
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Muhammad Ayaz Anwar
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Suresh Panneerselvam
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 443-749, Korea.
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16
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Fagnocchi L, Zippo A. Multiple Roles of MYC in Integrating Regulatory Networks of Pluripotent Stem Cells. Front Cell Dev Biol 2017; 5:7. [PMID: 28217689 PMCID: PMC5289991 DOI: 10.3389/fcell.2017.00007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/20/2017] [Indexed: 12/20/2022] Open
Abstract
Pluripotent stem cells (PSCs) are defined by their self-renewal potential, which permits their unlimited propagation, and their pluripotency, being able to generate cell of the three embryonic lineages. These properties render PSCs a valuable tool for both basic and medical research. To induce and stabilize the pluripotent state, complex circuitries involving signaling pathways, transcription regulators and epigenetic mechanisms converge on a core transcriptional regulatory network of PSCs, thus determining their cell identity. Among the transcription factors, MYC represents a central hub, which modulates and integrates multiple mechanisms involved both in the maintenance of pluripotency and in cell reprogramming. Indeed, it instructs the PSC-specific cell cycle, metabolism and epigenetic landscape, contributes to limit exit from pluripotency and modulates signaling cascades affecting the PSC identity. Moreover, MYC extends its regulation on pluripotency by controlling PSC-specific non-coding RNAs. In this report, we review the MYC-controlled networks, which support the pluripotent state and discuss how their perturbation could affect cell identity. We further discuss recent finding demonstrating a central role of MYC in triggering epigenetic memory in PSCs, which depends on the establishment of a WNT-centered self-reinforcing circuit. Finally, we comment on the therapeutic implications of the role of MYC in affecting PSCs. Indeed, PSCs are used for both disease and cancer modeling and to derive cells for regenerative medicine. For these reasons, unraveling the MYC-mediated mechanism in those cells is fundamental to exploit their full potential and to identify therapeutic targets.
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Affiliation(s)
- Luca Fagnocchi
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
| | - Alessio Zippo
- Department of Epigenetics, Fondazione Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi" (INGM)Milan, Italy; Division of Pathology, Fondazione IRCCS Ca' Granda, Ospedale Maggiore PoliclinicoMilan, Italy
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17
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Glanzner WG, Komninou ER, Mahendran A, Rissi VB, Gutierrez K, Bohrer RC, Collares T, Gonçalves PBD, Bordignon V. Exposure of Somatic Cells to Cytoplasm Extracts of Porcine Oocytes Induces Stem Cell-Like Colony Formation and Alters Expression of Pluripotency and Chromatin-Modifying Genes. Cell Reprogram 2016; 18:137-46. [PMID: 27253625 DOI: 10.1089/cell.2016.0009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Cell permeabilization followed by exposure to cytoplasmic extracts of oocytes has been proposed as an alternative to transduction of transcription factors for inducing pluripotency in cultured somatic cells. The main goal in this study was to investigate the effect of treating porcine fibroblast cells with cytoplasmic extracts of GV-stage oocyte (OEx) followed by inhibition of histone deacetylases with Scriptaid (Scrip) on the formation of stem cell-like colonies and expression of genes encoding pluripotency and chromatin-modifying enzymes. Stem cell-like colonies start developing ∼2 weeks after treatment in cells exposed to OEx or OEx + Scrip. The number of cell colonies at the first day of appearance and 48 hours later was also similar between OEx and OEx + Scrip treatments. Transcripts for Nanog, Rex1, and c-Myc genes were detected in most cell samples that were analyzed on different days after OEx treatment. However, Sox2 transcripts were not detected and only a small proportion of samples had detectable levels of Oct4 mRNA after OEx treatment. A similar pattern of transcripts for pluripotency genes was observed in cells treated with OEx alone or OEx + Scrip. Transcript levels for Dnmt1 and Ezh2 were reduced at Day 3 after treatment in cells exposed to OEx. These findings revealed that: (a) exposure to OEx can induce a partial reprogramming of fibroblast cells toward pluripotency, characterized by colony formation and activation of pluripotency genes; and (b) inhibition of histone deacetylases does not improve the reprogramming effect of OEx treatment.
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Affiliation(s)
- Werner Giehl Glanzner
- 1 Laboratory of Biotechnology and Animal Reproduction-BioRep, Federal University of Santa Maria (UFSM) , Santa Maria, Brazil
| | - Eliza R Komninou
- 2 Postgraduate Program in Biotechnology, Laboratory of Molecular Embryology and Transgenesis, Technology Development Center, Federal University of Pelotas (UFPEL) , Pelotas, Brazil
| | - Ashwini Mahendran
- 3 Department of Animal Science, McGill University , Ste-Anne-De-Bellevue, Canada
| | - Vitor B Rissi
- 1 Laboratory of Biotechnology and Animal Reproduction-BioRep, Federal University of Santa Maria (UFSM) , Santa Maria, Brazil
| | - Karina Gutierrez
- 3 Department of Animal Science, McGill University , Ste-Anne-De-Bellevue, Canada
| | - Rodrigo C Bohrer
- 3 Department of Animal Science, McGill University , Ste-Anne-De-Bellevue, Canada
| | - Tiago Collares
- 2 Postgraduate Program in Biotechnology, Laboratory of Molecular Embryology and Transgenesis, Technology Development Center, Federal University of Pelotas (UFPEL) , Pelotas, Brazil
| | - Paulo B D Gonçalves
- 1 Laboratory of Biotechnology and Animal Reproduction-BioRep, Federal University of Santa Maria (UFSM) , Santa Maria, Brazil
| | - Vilceu Bordignon
- 3 Department of Animal Science, McGill University , Ste-Anne-De-Bellevue, Canada
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18
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Kin K, Chen X, Gonzalez-Garay M, Fakhouri WD. The effect of non-coding DNA variations on P53 and cMYC competitive inhibition at cis-overlapping motifs. Hum Mol Genet 2016; 25:1517-27. [PMID: 26908612 DOI: 10.1093/hmg/ddw030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/01/2016] [Indexed: 01/22/2023] Open
Abstract
Non-coding DNA variations play a critical role in increasing the risk for development of common complex diseases, and account for the majority of SNPs highly associated with cancer. However, it remains a challenge to identify etiologic variants and to predict their pathological effects on target gene expression for clinical purposes. Cis-overlapping motifs (COMs) are elements of enhancer regions that impact gene expression by enabling competitive binding and switching between transcription factors. Mutations within COMs are especially important when the involved transcription factors have opposing effects on gene regulation, like P53 tumor suppressor and cMYC proto-oncogene. In this study, genome-wide analysis of ChIP-seq data from human cancer and mouse embryonic cells identified a significant number of putative regulatory elements with signals for both P53 and cMYC. Each co-occupied element contains, on average, two COMs, and one common SNP every two COMs. Gene ontology of predicted target genes for COMs showed that the majority are involved in DNA damage, apoptosis, cell cycle regulation, and RNA processing. EMSA results showed that both cMYC and P53 bind to cis-overlapping motifs within a ChIP-seq co-occupied region in Chr12. In vitro functional analysis of selected co-occupied elements verified enhancer activity, and also showed that the occurrence of SNPs within three COMs significantly altered enhancer activity. We identified a list of COM-associated functional SNPs that are in close proximity to SNPs associated with common diseases in large population studies. These results suggest a potential molecular mechanism to identify etiologic regulatory mutations associated with common diseases.
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Affiliation(s)
- Katherine Kin
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
| | - Xi Chen
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
| | - Manuel Gonzalez-Garay
- Center for Molecular Imaging, The Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Walid D Fakhouri
- Department of Diagnostic and Biomedical Sciences, Center for Craniofacial Research, University of Texas Health Science Center at Houston School of Dentistry, Houston, TX 77054, USA and
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19
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The role of the polycomb repressive complex pathway in T and NK cell lymphoma: biological and prognostic implications. Tumour Biol 2015; 37:2037-47. [PMID: 26337274 DOI: 10.1007/s13277-015-3977-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 08/24/2015] [Indexed: 01/16/2023] Open
Abstract
Polycomb repressive complex 2 (PRC2; formed by EZH2, SUZ12, and EED protein subunits) and PRC1 (BMI1 protein) induce gene silencing through histone modification, primarily H3K27me3, and deregulation of PRC pathways leads to tumorigenesis. In the present study, activation of PRC2, H3K27me3, and BMI1 was investigated by immunohistochemistry in 175 cases of T and natural killer (NK) cell lymphoma. Activation of PRC proteins was analyzed according to c-MYC activation, Epstein-Barr virus (EBV) infection, CD30 activation, and survival. Among all T and NK cell lymphomas, high expression rates of 54.7 % for EZH2, 33.3 % for SUZ12, 85.7 % for EED, 40.5 % for H3K27me3, and 30.9 % for BMI1 were discovered. Activation of PRC2, H3K27me3, and BMI1 showed positive correlations (P < 0.05). Activation of c-MYC was associated with activation of SUZ12 and triple coactivation of all PRC2 protein subunits (EZH2(high)/SUZ12(high)/EED(high)) (P < 0.05). In EBV-positive tumors, activation of EZH2 and H3K27me3 showed greater association (P < 0.05). H3K27me3 and BMI1 showed a negative association in tumors expressing CD30 (P < 0.05). With respect to survival, BMI1 activation was independently associated with poor prognosis in T and NK cell lymphomas (P = 0.002). In conclusion, T and NK cell lymphomas were associated with activation of PRC pathway markers, for which c-MYC activation and EBV infection could be suggested as possible causes. PRC pathway markers may be potential therapeutic targets and prognostic markers in T and NK cell lymphoma.
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Neri F, Incarnato D, Krepelova A, Dettori D, Rapelli S, Maldotti M, Parlato C, Anselmi F, Galvagni F, Oliviero S. TET1 is controlled by pluripotency-associated factors in ESCs and downmodulated by PRC2 in differentiated cells and tissues. Nucleic Acids Res 2015; 43:6814-26. [PMID: 25925565 PMCID: PMC4538807 DOI: 10.1093/nar/gkv392] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 04/14/2015] [Indexed: 12/22/2022] Open
Abstract
Ten-eleven translocation (Tet) genes encode for a family of hydroxymethylase enzymes involved in regulating DNA methylation dynamics. Tet1 is highly expressed in mouse embryonic stem cells (ESCs) where it plays a critical role the pluripotency maintenance. Tet1 is also involved in cell reprogramming events and in cancer progression. Although the functional role of Tet1 has been largely studied, its regulation is poorly understood. Here we show that Tet1 gene is regulated, both in mouse and human ESCs, by the stemness specific factors Oct3/4, Nanog and by Myc. Thus Tet1 is integrated in the pluripotency transcriptional network of ESCs. We found that Tet1 is switched off by cell proliferation in adult cells and tissues with a consequent genome-wide reduction of 5hmC, which is more evident in hypermethylated regions and promoters. Tet1 downmodulation is mediated by the Polycomb repressive complex 2 (PRC2) through H3K27me3 histone mark deposition. This study expands the knowledge about Tet1 involvement in stemness circuits in ESCs and provides evidence for a transcriptional relationship between Tet1 and PRC2 in adult proliferating cells improving our understanding of the crosstalk between the epigenetic events mediated by these factors.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Daniela Dettori
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Stefania Rapelli
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Mara Maldotti
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy
| | - Federico Galvagni
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, Torino, 10126, Italy Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Via Aldo Moro 2, 53100, Siena, Italy
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Galvagni F, Neri F. Snai1 represses Nanog to promote embryonic stem cell differentiation. GENOMICS DATA 2015; 4:82-3. [PMID: 26484184 PMCID: PMC4535745 DOI: 10.1016/j.gdata.2015.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 11/18/2022]
Abstract
Embryonic stem cell (ESC) self-renewal and pluripotency is maintained by an external signaling pathways and intrinsic regulatory networks involving ESC-specific transcriptional complexes (mainly formed by OCT3/4, Sox2 and Nanog proteins), the Polycomb repressive complex 2 (PRC2) and DNA methylation [1], [2], [3], [4], [5], [6], [7], [8]. Among these, Nanog represents the more ESC specific factor and its repression correlates with the loss of pluripotency and ESC differentiation [9], [10], [11]. During ESC early differentiation, many development-associated genes become upregulated and although, in general, much is known about the pluripotency self-renewal circuitry, the molecular events that lead ESCs to exit from pluripotency and begin differentiation are largely unknown. Snai1 is one the most early induced genes during ESC differentiation in vitro and in vivo [12], [13]. Here we show that Snai1 is able to directly repress several stemness-associated genes including Nanog. We use a ESC stable-line expressing a inducible Snai1 protein. We here show microarray analysis of embryonic stem cells (ESC) expressing Snail-ER at various time points of induction with 4-OH. Data were deposited in Gene Expression Omnibus (GEO) datasets under reference GSE57854 and here: http://epigenetics.hugef-research.org/data.php.
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Affiliation(s)
- F. Galvagni
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, 53100 Siena, Italy
| | - F. Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
- Next Generation Intelligence (NGI), Torino, Italy
- Corresponding author at: via Nizza 52, Torino, 10126, Italy.
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Neri F, Incarnato D, Krepelova A, Rapelli S, Anselmi F, Parlato C, Medana C, Dal Bello F, Oliviero S. Single-Base Resolution Analysis of 5-Formyl and 5-Carboxyl Cytosine Reveals Promoter DNA Methylation Dynamics. Cell Rep 2015; 10:674-683. [PMID: 25660018 DOI: 10.1016/j.celrep.2015.01.008] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/24/2014] [Accepted: 12/30/2014] [Indexed: 12/20/2022] Open
Abstract
Ten eleven translocation (Tet) proteins oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC can be further excised by thymine-DNA glycosylase (Tdg). Here, we present a genome-wide approach, named methylation-assisted bisulfite sequencing (MAB-seq), that enables single-base resolution mapping of 5fC and 5caC and measures their abundance. Application of this method to mouse embryonic stem cells (ESCs) shows the occurrence of 5fC and 5caC residues on the hypomethylated promoters of highly expressed genes, which is increased upon Tdg silencing, revealing active DNA demethylation on these promoters. Genome-wide mapping of Tdg reveals extensive colocalization with Tet1 on active promoters. These regions were found to be methylated by Dnmt1 and Dnmt3a and demethylated by a Tet-dependent mechanism. Our work demonstrates the DNA methylation dynamics that occurs on the promoters of the expressed genes and provides a genomic reference map of 5fC and 5caC in ESCs.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, via Fiorentina 1, 53100 Siena, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, via Fiorentina 1, 53100 Siena, Italy
| | - Francesca Anselmi
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Claudio Medana
- Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università di Torino, Via Pietro Giuria 5, 10125 Torino, Italy
| | - Federica Dal Bello
- Dipartimento di Biotecnologie Molecolari e Scienze per la Salute, Università di Torino, Via Pietro Giuria 5, 10125 Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino, Via Accademia Albertina 13, 10123 Torino, Italy.
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High-throughput whole-genome sequencing of E14 mouse embryonic stem cells. GENOMICS DATA 2014; 3:6-7. [PMID: 26484140 PMCID: PMC4535964 DOI: 10.1016/j.gdata.2014.10.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 10/30/2014] [Accepted: 10/30/2014] [Indexed: 11/24/2022]
Abstract
Mouse E14 embryonic stem cells (ESCs) are the most used ESC line, often employed for genome-wide studies involving next generation sequencing analysis [1], [2], [3], [4], [5]. More than 2 × 10 E9 sequences made on Illumina platform derived from the genome of E14 embryonic stem cells cultured in our laboratory were used to build a database of about 2.7 × 10 E6 single nucleotide variant [6]. The database was validated using other two sequencing datasets from other laboratory and high overlap was observed. The identified variants are enriched on intergenic regions, but several thousands reside on gene exons and regulatory regions, such as promoters, enhancers, splicing site and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly including the new identified variants and used it to map reads from next generation sequencing data generated in our laboratory or in others on E14 cell line. We observed an increase in the number of mapped reads of about 5%. CpG dinucleotide showed the higher variation frequency, probably because it could be a target of DNA methylation. Data were deposited in GEO datasets under reference GSM1283021 and here: http://epigenetics.hugef-research.org/data.php.
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Neri F, Dettori D, Incarnato D, Krepelova A, Rapelli S, Maldotti M, Parlato C, Paliogiannis P, Oliviero S. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene 2014; 34:4168-76. [PMID: 25362856 DOI: 10.1038/onc.2014.356] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/22/2014] [Accepted: 09/16/2014] [Indexed: 12/17/2022]
Abstract
Ten eleven translocation (TET) enzymes catalyse the oxidative reactions of 5-methylcytosine (5mC) to promote the demethylation process. The reaction intermediate 5-hydroxymethylcytosine (5hmC) has been shown to be abundant in embryonic stem cells and tissues but strongly depleted in human cancers. Genetic mutations of TET2 gene were associated with leukaemia, whereas TET1 downregulation has been shown to promote malignancy in breast cancer. Here we report that TET1 is downregulated in colon tumours from the initial stage. TET1 silencing in primary epithelial colon cells increase their cellular proliferation while its re-expression in colon cancer cells inhibits their proliferation and the growth of tumour xenografts even at later stages. We found that TET1 binds to the promoter of the DKK gene inhibitors of the WNT signalling to maintain them hypomethylated. Downregulation of TET1 during colon cancer initiation leads to repression, by DNA methylation, the promoters of the inhibitors of the WNT pathway resulting in a constitutive activation of the WNT pathway. Thus the DNA hydroxymethylation mediated by TET1 controlling the WNT signalling is a key player of tumour growth. These results provide new insights for understanding how tumours escape cellular controls.
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Affiliation(s)
- F Neri
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Dettori
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Incarnato
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - A Krepelova
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - S Rapelli
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - M Maldotti
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - C Parlato
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - P Paliogiannis
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche, Università di Sassari, Sassari, Italy
| | - S Oliviero
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino Torino, Italy
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Incarnato D, Krepelova A, Neri F. High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly. Genomics 2014; 104:121-7. [PMID: 25004115 DOI: 10.1016/j.ygeno.2014.06.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/24/2014] [Accepted: 06/27/2014] [Indexed: 11/18/2022]
Abstract
Mouse E14 embryonic stem cells (ESCs) are a well-characterized and widespread used ESC line, often employed for genome-wide studies involving next generation sequencing analysis. More than 2×10(9) sequences made on Illumina platform derived from the genome of E14 ESCs were used to build a database of about 2.7×10(6) single nucleotide variants (SNVs). The identified variants are enriched in intergenic regions, but several thousands reside in gene exons and regulatory regions, such as promoters, enhancers, splicing sites and untranslated regions of RNA, thus indicating high probability of an important functional impact on the molecular biology of these cells. We created a new E14 genome assembly reference that increases the number of mapped reads of about 5%. We performed a Reduced Representation Bisulfite Sequencing on E14 ESCs and we obtained an increase of about 120,000 called CpGs and avoided about 20,000 wrong CpG calls with respect to the mm9 genome reference.
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Affiliation(s)
- Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy; Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via Fiorentina 1, 53100 Siena, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy
| | - Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126 Torino, Italy.
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