1
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Drastichova Z, Trubacova R, Novotny J. Regulation of phosphosignaling pathways involved in transcription of cell cycle target genes by TRH receptor activation in GH1 cells. Biomed Pharmacother 2023; 168:115830. [PMID: 37931515 DOI: 10.1016/j.biopha.2023.115830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Thyrotropin-releasing hormone (TRH) is known to activate several cellular signaling pathway, but the activation of the TRH receptor (TRH-R) has not been reported to regulate gene transcription. The aim of this study was to identify phosphosignaling pathways and phosphoprotein complexes associated with gene transcription in GH1 pituitary cells treated with TRH or its analog, taltirelin (TAL), using label-free bottom-up mass spectrometry-based proteomics. Our detailed analysis provided insight into the mechanism through which TRH-R activation may regulate the transcription of genes related to the cell cycle and proliferation. It involves control of the signaling pathways for β-catenin/Tcf, Notch/RBPJ, p53/p21/Rbl2/E2F, Myc, and YY1/Rb1/E2F through phosphorylation and dephosphorylation of their key components. In many instances, the phosphorylation patterns of differentially phosphorylated phosphoproteins in TRH- or TAL-treated cells were identical or displayed a similar trend in phosphorylation. However, some phosphoproteins, especially components of the Wnt/β-catenin/Tcf and YY1/Rb1/E2F pathways, exhibited different phosphorylation patterns in TRH- and TAL-treated cells. This supports the notion that TRH and TAL may act, at least in part, as biased agonists. Additionally, the deficiency of β-arrestin2 resulted in a reduced number of alterations in phosphorylation, highlighting the critical role of β-arrestin2 in the signal transduction from TRH-R in the plasma membrane to transcription factors in the nucleus.
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Affiliation(s)
- Zdenka Drastichova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia
| | - Radka Trubacova
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia; Institute of Physiology, Czech Academy of Sciences, 142 20 Prague, Czechia
| | - Jiri Novotny
- Department of Physiology, Faculty of Science, Charles University, 128 00 Prague, Czechia.
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2
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Figiel M, Górka AK, Górecki A. Zinc Ions Modulate YY1 Activity: Relevance in Carcinogenesis. Cancers (Basel) 2023; 15:4338. [PMID: 37686614 PMCID: PMC10487186 DOI: 10.3390/cancers15174338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
YY1 is widely recognized as an intrinsically disordered transcription factor that plays a role in development of many cancers. In most cases, its overexpression is correlated with tumor progression and unfavorable patient outcomes. Our latest research focusing on the role of zinc ions in modulating YY1's interaction with DNA demonstrated that zinc enhances the protein's multimeric state and affinity to its operator. In light of these findings, changes in protein concentration appear to be just one element relevant to modulating YY1-dependent processes. Thus, alterations in zinc ion concentration can directly and specifically impact the regulation of gene expression by YY1, in line with reports indicating a correlation between zinc ion levels and advancement of certain tumors. This review concentrates on other potential consequences of YY1 interaction with zinc ions that may act by altering charge distribution, conformational state distribution, or oligomerization to influence its interactions with molecular partners that can disrupt gene expression patterns.
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Affiliation(s)
| | | | - Andrzej Górecki
- Faculty of Biochemistry, Biophysics and Biotechnology, Department of Physical Biochemistry, Jagiellonian University, Gronostajowa 7, 30-387 Kraków, Poland; (M.F.); (A.K.G.)
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3
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Roles of Polycomb Complexes in the Reconstruction of 3D Genome Architecture during Preimplantation Embryonic Development. Genes (Basel) 2022; 13:genes13122382. [PMID: 36553649 PMCID: PMC9778514 DOI: 10.3390/genes13122382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/29/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
The appropriate deployment of developmental programs depends on complex genetic information encoded by genomic DNA sequences and their positioning and contacts in the three-dimensional (3D) space within the nucleus. Current studies using novel techniques including, but not limited to, Hi-C, ChIA-PET, and Hi-ChIP reveal that regulatory elements (Res), such as enhancers and promoters, may participate in the precise regulation of expression of tissue-specific genes important for both embryogenesis and organogenesis by recruiting Polycomb Group (PcG) complexes. PcG complexes usually poise the transcription of developmental genes by forming Polycomb bodies to compact poised enhancers and promoters marked by H3K27me3 in the 3D space. Additionally, recent studies have also uncovered their roles in transcriptional activation. To better understand the full complexities in the mechanisms of how PcG complexes regulate transcription and long-range 3D contacts of enhancers and promoters during developmental programs, we outline novel insights regarding PcG-associated dramatic changes in the 3D chromatin conformation in developmental programs of early embryos and naïve-ground-state transitions of pluripotent embryonic stem cells (ESCs), and highlight the distinct roles of unique and common subunits of canonical and non-canonical PcG complexes in shaping genome architectures and transcriptional programs.
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4
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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Abstract
Immunity could be viewed as the common factor in neurodevelopmental disorders and cancer. The immune and nervous systems coevolve as the embryo develops. Immunity can release cytokines that activate MAPK signaling in neural cells. In specific embryonic brain cell types, dysregulated signaling that results from germline or embryonic mutations can promote changes in chromatin organization and gene accessibility, and thus expression levels of essential genes in neurodevelopment. In cancer, dysregulated signaling can emerge from sporadic somatic mutations during human life. Neurodevelopmental disorders and cancer share similarities. In neurodevelopmental disorders, immunity, and cancer, there appears an almost invariable involvement of small GTPases (e.g., Ras, RhoA, and Rac) and their pathways. TLRs, IL-1, GIT1, and FGFR signaling pathways, all can be dysregulated in neurodevelopmental disorders and cancer. Although there are signaling similarities, decisive differentiating factors are timing windows, and cell type specific perturbation levels, pointing to chromatin reorganization. Finally, we discuss drug discovery.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
- Corresponding author
| | - Chung-Jung Tsai
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Owen BM, Davidovich C. DNA binding by polycomb-group proteins: searching for the link to CpG islands. Nucleic Acids Res 2022; 50:4813-4839. [PMID: 35489059 PMCID: PMC9122586 DOI: 10.1093/nar/gkac290] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/25/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Polycomb group proteins predominantly exist in polycomb repressive complexes (PRCs) that cooperate to maintain the repressed state of thousands of cell-type-specific genes. Targeting PRCs to the correct sites in chromatin is essential for their function. However, the mechanisms by which PRCs are recruited to their target genes in mammals are multifactorial and complex. Here we review DNA binding by polycomb group proteins. There is strong evidence that the DNA-binding subunits of PRCs and their DNA-binding activities are required for chromatin binding and CpG targeting in cells. In vitro, CpG-specific binding was observed for truncated proteins externally to the context of their PRCs. Yet, the mere DNA sequence cannot fully explain the subset of CpG islands that are targeted by PRCs in any given cell type. At this time we find very little structural and biophysical evidence to support a model where sequence-specific DNA-binding activity is required or sufficient for the targeting of CpG-dinucleotide sequences by polycomb group proteins while they are within the context of their respective PRCs, either PRC1 or PRC2. We discuss the current knowledge and open questions on how the DNA-binding activities of polycomb group proteins facilitate the targeting of PRCs to chromatin.
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Affiliation(s)
- Brady M Owen
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia.,EMBL-Australia, Clayton, VIC, Australia
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7
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Melo GA, Calôba C, Brum G, Passos TO, Martinez GJ, Pereira RM. Epigenetic regulation of T cells by Polycomb group proteins. J Leukoc Biol 2022; 111:1253-1267. [DOI: 10.1002/jlb.2ri0122-039r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/10/2022] [Accepted: 04/01/2022] [Indexed: 11/12/2022] Open
Affiliation(s)
- Guilherme A. Melo
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Carolina Calôba
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gabrielle Brum
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Thaís O. Passos
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
| | - Gustavo J. Martinez
- Center for Cancer Cell Biology, Immunology and Infection, Discipline of Microbiology and Immunology Rosalind Franklin University of Medicine and Science Chicago Illinois USA
| | - Renata M. Pereira
- Instituto de Microbiologia Paulo de Góes, Departamento de Imunologia Universidade Federal do Rio de Janeiro Rio de Janeiro RJ Brazil
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8
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Dong X, Guo R, Ji T, Zhang J, Xu J, Li Y, Sheng Y, Wang Y, Fang K, Wen Y, Liu B, Hu G, Deng H, Yao H. YY1 safeguard multidimensional epigenetic landscape associated with extended pluripotency. Nucleic Acids Res 2022; 50:12019-12038. [PMID: 35425987 PMCID: PMC9756953 DOI: 10.1093/nar/gkac230] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/21/2022] [Accepted: 03/27/2022] [Indexed: 12/24/2022] Open
Abstract
Although extended pluripotent stem cells (EPSCs) have the potential to form both embryonic and extraembryonic lineages, how their transcriptional regulatory mechanism differs from that of embryonic stem cells (ESCs) remains unclear. Here, we discovered that YY1 binds to specific open chromatin regions in EPSCs. Yy1 depletion in EPSCs leads to a gene expression pattern more similar to that of ESCs than control EPSCs. Moreover, Yy1 depletion triggers a series of epigenetic crosstalk activities, including changes in DNA methylation, histone modifications and high-order chromatin structures. Yy1 depletion in EPSCs disrupts the enhancer-promoter (EP) interactions of EPSC-specific genes, including Dnmt3l. Yy1 loss results in DNA hypomethylation and dramatically reduces the enrichment of H3K4me3 and H3K27ac on the promoters of EPSC-specific genes by upregulating the expression of Kdm5c and Hdac6 through facilitating the formation of CCCTC-binding factor (CTCF)-mediated EP interactions surrounding their loci. Furthermore, single-cell RNA sequencing (scRNA-seq) experiments revealed that YY1 is required for the derivation of extraembryonic endoderm (XEN)-like cells from EPSCs in vitro. Together, this study reveals that YY1 functions as a key regulator of multidimensional epigenetic crosstalk associated with extended pluripotency.
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Affiliation(s)
| | | | - Tianrong Ji
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Jun Xu
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yaoyi Li
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingliang Sheng
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yuxiang Wang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Ke Fang
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Yulin Wen
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,University of Chinese Academy of Sciences, Beijing 100049, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Bei Liu
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Gongcheng Hu
- CAS Key Laboratory of Regenerative Biology, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou 510530, China,Bioland Laboratory (Guangzhou Regenerative Medicine and Health GuangDong Laboratory), Guangzhou 510005, China,Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-CUHK Joint Research Laboratory on Stem Cell and Regenerative Medicine, State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,Institute of Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongkui Deng
- School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hongjie Yao
- To whom correspondence should be addressed. Tel: +86 20 32015279;
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Tang L, Hill MC, Ellinor PT, Li M. Bacon: a comprehensive computational benchmarking framework for evaluating targeted chromatin conformation capture-specific methodologies. Genome Biol 2022; 23:30. [PMID: 35063001 PMCID: PMC8780810 DOI: 10.1186/s13059-021-02597-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 12/30/2021] [Indexed: 01/10/2023] Open
Abstract
Chromatin conformation capture (3C)-based technologies have enabled the accurate detection of topological genomic interactions, and the adoption of ChIP techniques to 3C-based protocols makes it possible to identify long-range interactions. To analyze these large and complex datasets, computational methods are undergoing rapid and expansive evolution. Thus, a thorough evaluation of these analytical pipelines is necessary to identify which commonly used algorithms and processing pipelines need to be improved. Here we present a comprehensive benchmark framework, Bacon, to evaluate the performance of several computational methods. Finally, we provide practical recommendations for users working with HiChIP and/or ChIA-PET analyses.
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Affiliation(s)
- Li Tang
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China
| | - Matthew C Hill
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Patrick T Ellinor
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02129, USA
- Cardiovascular Disease Initiative, The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Min Li
- Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, 410083, China.
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10
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Blackledge NP, Klose RJ. The molecular principles of gene regulation by Polycomb repressive complexes. Nat Rev Mol Cell Biol 2021; 22:815-833. [PMID: 34400841 PMCID: PMC7612013 DOI: 10.1038/s41580-021-00398-y] [Citation(s) in RCA: 185] [Impact Index Per Article: 61.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Precise control of gene expression is fundamental to cell function and development. Although ultimately gene expression relies on DNA-binding transcription factors to guide the activity of the transcription machinery to genes, it has also become clear that chromatin and histone post-translational modification have fundamental roles in gene regulation. Polycomb repressive complexes represent a paradigm of chromatin-based gene regulation in animals. The Polycomb repressive system comprises two central protein complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which are essential for normal gene regulation and development. Our early understanding of Polycomb function relied on studies in simple model organisms, but more recently it has become apparent that this system has expanded and diverged in mammals. Detailed studies are now uncovering the molecular mechanisms that enable mammalian PRC1 and PRC2 to identify their target sites in the genome, communicate through feedback mechanisms to create Polycomb chromatin domains and control transcription to regulate gene expression. In this Review, we discuss and contextualize the emerging principles that define how this fascinating chromatin-based system regulates gene expression in mammals.
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Affiliation(s)
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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11
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Dong A, Cheung TH. Deciphering the chromatin organization and dynamics for muscle stem cell function. Curr Opin Cell Biol 2021; 73:124-132. [PMID: 34534837 DOI: 10.1016/j.ceb.2021.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/15/2021] [Accepted: 08/04/2021] [Indexed: 12/28/2022]
Abstract
The chromatin landscape represents a critical regulatory layer for precise transcriptional control. Chromosome architecture restrains the physical access to the DNA elements and is one of the determinants that specifies cell identity. Adult stem cells possess the unique ability to differentiate into a specific lineage. One of the underexplored areas in skeletal muscle biology is the molecular mechanism guiding the chromatin organization changes in muscle stem cell specification, myogenic determination, and differentiation. In this review, we focus on the regulatory network guiding the progression of muscle stem cells to differentiated progeny. We summarize recent findings regarding the mechanisms directing myogenic cell fate decision and differentiation, with a particular focus on three-dimensional chromosome architecture and long noncoding RNA-associated chromatin accessibility changes.
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Affiliation(s)
- Anqi Dong
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Tom H Cheung
- Division of Life Science, Center for Stem Cell Research, HKUST-Nan Fung Life Sciences Joint Laboratory, State Key Laboratory of Molecular Neuroscience, Molecular Neuroscience Center, The Hong Kong University of Science and Technology, Hong Kong, China; Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China; Guangdong Provincial Key Laboratory of Brain Science, Disease and Drug Development, Shenzhen-Hong Kong Institute of Brain Science, HKUST Shenzhen Research Institute, Shenzhen, China.
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12
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Emori C, Ito H, Fujii W, Naito K, Sugiura K. Oocytes suppress FOXL2 expression in cumulus cells in mice†. Biol Reprod 2021; 103:85-93. [PMID: 32307529 DOI: 10.1093/biolre/ioaa054] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/07/2020] [Accepted: 04/16/2020] [Indexed: 11/15/2022] Open
Abstract
Cumulus cells and mural granulosa cells (MGCs) play distinct roles during follicular development, and normal development of these cell lineages is critical for the female fertility. Transcriptomic diversification between the two cell lineages is obviously a critical mechanism for their functional diversification; however, the transcriptional regulators responsible for this event have not been fully defined. In this study, we sought to identify key transcriptional regulators responsible for the differential gene expression between the two cell lineages. In silico analysis of transcriptomic comparison between cumulus cells and MGCs identified several candidate regulators responsible for the diversification of the two cell lineages. Among them, we herein focused on forkhead box L2 (FOXL2) and showed that expressions of FOXL2 as well as its target transcripts were differentially regulated between cumulus cells and MGCs. The lower expression of FOXL2 in cumulus cells seemed to be due to the suppression by oocyte-derived paracrine signals. These results suggest that FOXL2 is one of the critical transcription factors that determine cumulus cell and MGC lineages under the control of oocytes.
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Affiliation(s)
- Chihiro Emori
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Haruka Ito
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Fujii
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Kunihiko Naito
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Koji Sugiura
- Department of Animal Resource Sciences, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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13
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Phase separation of OCT4 controls TAD reorganization to promote cell fate transitions. Cell Stem Cell 2021; 28:1868-1883.e11. [PMID: 34038708 DOI: 10.1016/j.stem.2021.04.023] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 08/06/2020] [Accepted: 04/19/2021] [Indexed: 02/05/2023]
Abstract
Topological-associated domains (TADs) are thought to be relatively stable across cell types, although some TAD reorganization has been observed during cellular differentiation. However, little is known about the mechanisms through which TAD reorganization affects cell fate or how master transcription factors affect TAD structures during cell fate transitions. Here, we show extensive TAD reorganization during somatic cell reprogramming, which is correlated with gene transcription and changes in cellular identity. Manipulating TAD reorganization promotes reprogramming, and the dynamics of concentrated chromatin loops in OCT4 phase separated condensates contribute to TAD reorganization. Disrupting OCT4 phase separation attenuates TAD reorganization and reprogramming, which can be rescued by fusing an intrinsically disordered region (IDR) to OCT4. We developed an approach termed TAD reorganization-based multiomics analysis (TADMAN), which identified reprogramming regulators. Together, these findings elucidate a role and mechanism of TAD reorganization, regulated by OCT4 phase separation, in cellular reprogramming.
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Pérez-Palacios R, Climent M, Santiago-Arcos J, Macías-Redondo S, Klar M, Muniesa P, Schoorlemmer J. YY2 in Mouse Preimplantation Embryos and in Embryonic Stem Cells. Cells 2021; 10:cells10051123. [PMID: 34066930 PMCID: PMC8148602 DOI: 10.3390/cells10051123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Yin Yang 2 encodes a mammalian-specific transcription factor (YY2) that shares high homology in the zinc finger region with both YY1 and REX1/ZFP42, encoded by the Yin Yang 1 and Reduced Expression Protein 1/Zinc Finger Protein 42 gene, respectively. In contrast to the well-established roles of the latter two in gene regulation, X chromosome inactivation and binding to specific transposable elements (TEs), much less is known about YY2, and its presence during mouse preimplantation development has not been described. As it has been reported that mouse embryonic stem cells (mESC) cannot be propagated in the absence of Yy2, the mechanistic understanding of how Yy2 contributes to mESC maintenance remains only very partially characterized. We describe Yy2 expression studies using RT-PCR and staining with a high-affinity polyclonal serum in mouse embryos and mESC. Although YY2 is expressed during preimplantation development, its presence appears dispensable for developmental progress in vitro until formation of the blastocyst. Attenuation of Yy2 levels failed to alter either Zscan4 levels in two-cell embryos or IAP and MERVL levels at later preimplantation stages. In contrast to previous claims that constitutively expressed shRNA against Yy2 in mESC prohibited the propagation of mESC in culture, we obtained colonies generated from mESC with attenuated Yy2 levels. Concomitant with a decreased number of undifferentiated colonies, Yy2-depleted mESC expressed higher levels of Zscan4 but no differences in the expression of TEs or other pluripotency markers including Sox2, Oct4, Nanog and Esrrb were observed. These results confirm the contribution of Yy2 to the maintenance of mouse embryonic stem cells and show the preimplantation expression of YY2. These functions are discussed in relation to mammalian-specific functions of YY1 and REX1.
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Affiliation(s)
- Raquel Pérez-Palacios
- Regenerative Medicine Program, Instituto Aragonés de Ciencias de la Salud, CIBA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain; (R.P.-P.); (S.M.-R.)
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/Miguel Servet 177, 50013 Zaragoza, Spain; (M.C.); (J.S.-A.); (P.M.)
| | - María Climent
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/Miguel Servet 177, 50013 Zaragoza, Spain; (M.C.); (J.S.-A.); (P.M.)
- Placental Pathophysiology and Fetal Programming Group, Fundación IISA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Javier Santiago-Arcos
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/Miguel Servet 177, 50013 Zaragoza, Spain; (M.C.); (J.S.-A.); (P.M.)
| | - Sofía Macías-Redondo
- Regenerative Medicine Program, Instituto Aragonés de Ciencias de la Salud, CIBA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain; (R.P.-P.); (S.M.-R.)
| | - Martin Klar
- Department of Neonatology, Charité—Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany;
| | - Pedro Muniesa
- Departamento de Anatomía, Embriología y Genética Animal, Facultad de Veterinaria, Universidad de Zaragoza, C/Miguel Servet 177, 50013 Zaragoza, Spain; (M.C.); (J.S.-A.); (P.M.)
- Placental Pathophysiology and Fetal Programming Group, Fundación IISA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Jon Schoorlemmer
- Regenerative Medicine Program, Instituto Aragonés de Ciencias de la Salud, CIBA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain; (R.P.-P.); (S.M.-R.)
- Placental Pathophysiology and Fetal Programming Group, Fundación IISA, Avenida San Juan Bosco 13, 50009 Zaragoza, Spain
- Fundación “Agencia Aragonesa para la Investigación y el Desarrollo” (ARAID), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-976-715-412 or +34-672-022-215
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Abstract
Accumulating evidence strongly indicates that the presence of cancer stem cells (CSCs) leads to the emergence of worse clinical scenarios, such as chemo- and radiotherapy resistance, metastasis, and cancer recurrence. CSCs are a highly tumorigenic population characterized by self-renewal capacity and differentiation potential. Thus, CSCs establish a hierarchical intratumor organization that enables tumor adaptation to evade the immune response and resist anticancer therapy. YY1 functions as a transcription factor, RNA-binding protein, and 3D chromatin regulator. Thus, YY1 has multiple effects and regulates several molecular processes. Emerging evidence indicates that the development of lethal YY1-mediated cancer phenotypes is associated with the presence of or enrichment in cancer stem-like cells. Therefore, it is necessary to investigate whether and to what extent YY1 regulates the CSC phenotype. Since CSCs mirror the phenotypic behavior of stem cells, we initially describe the roles played by YY1 in embryonic and adult stem cells. Next, we scrutinize evidence supporting the contributions of YY1 in CSCs from a number of various cancer types. Finally, we identify new areas for further investigation into the YY1-CSCs axis, including the participation of YY1 in the CSC niche.
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16
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YY1 regulated transcription-based stratification of gastric tumors and identification of potential therapeutic candidates. J Cell Commun Signal 2021; 15:251-267. [PMID: 33620645 DOI: 10.1007/s12079-021-00608-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/27/2021] [Indexed: 10/22/2022] Open
Abstract
Gastric cancer is one of the leading causes of cancer-related death worldwide. The transcription factor YY1 regulates diverse biological processes, including cell proliferation, development, DNA damage responses, and carcinogenesis. This study was designed to explore the role of YY1 regulated transcription in gastric cancer. YY1 silencing in gastric cancer cells has resulted in the inhibition of Wnt/β-catenin, JNK/MAPK, ERK/MAPK, ER, and HIF-1α signaling pathways. Genome-wide mRNA profiling upon silencing the expression YY1 gene in gastric cancer cells and comparison with the previously identified YY1 regulated genes from other lineages revealed a moderate overlap among the YY1 regulated genes. Despite the differing genes, all the YY1 regulated gene sets were expressed in most of the intestinal subtype gastric tumors and a subset of diffuse subtype gastric tumors. Integrative functional genomic analysis of the YY1 gene sets revealed an association among the pathways Wnt/β-catenin, Rapamycin, Cyclin-D1, Myc, E2F, PDGF, and AKT. Further, the drugs capable of inhibiting YY1 mediated transcription were identified as suitable targeted therapeutic candidates for gastric tumors with activated YY1. The data emerging from the investigation would pave the way for the development of YY1-based targeted therapeutics for gastric cancer.
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17
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Cheon YP, Choi D, Lee SH, Kim CG. YY1 and CP2c in Unidirectional Spermatogenesis and Stemness. Dev Reprod 2021; 24:249-262. [PMID: 33537512 PMCID: PMC7837418 DOI: 10.12717/dr.2020.24.4.249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 11/21/2020] [Accepted: 12/29/2020] [Indexed: 11/17/2022]
Abstract
Spermatogonial stem cells (SSCs) have stemness characteristics, including germ cell-specific imprints that allow them to form gametes. Spermatogenesis involves changes in gene expression such as a transition from expression of somatic to germ cell-specific genes, global repression of gene expression, meiotic sex chromosome inactivation, highly condensed packing of the nucleus with protamines, and morphogenesis. These step-by-step processes finally generate spermatozoa that are fertilization competent. Dynamic epigenetic modifications also confer totipotency to germ cells after fertilization. Primordial germ cells (PGCs) in embryos do not enter meiosis, remain in the proliferative stage, and are referred to as gonocytes, before entering quiescence. Gonocytes develop into SSCs at about 6 days after birth in rodents. Although chromatin structural modification by Polycomb is essential for gene silencing in mammals, and epigenetic changes are critical in spermatogenesis, a comprehensive understanding of transcriptional regulation is lacking. Recently, we evaluated the expression profiles of Yin Yang 1 (YY1) and CP2c in the gonads of E14.5 and 12-week-old mice. YY1 localizes at the nucleus and/or cytoplasm at specific stages of spermatogenesis, possibly by interaction with CP2c and YY1-interacting transcription factor. In the present article, we discuss the possible roles of YY1 and CP2c in spermatogenesis and stemness based on our results and a review of the relevant literature.
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Affiliation(s)
- Yong-Pil Cheon
- Division of Developmental Biology and Physiology, Institute for Basic Sciences, Sungshin University, Seoul 02844, Korea
| | - Donchan Choi
- Department of Life Science, College of Environmental Sciences, Yong-In University, Yongin 17092, Korea
| | - Sung-Ho Lee
- Department of Biotechnology, Sangmyung University, Seoul 03016, Korea
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, College of Natural Sciences, Hanyang University, Seoul 04763, Korea
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18
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Neve B, Jonckheere N, Vincent A, Van Seuningen I. Long non-coding RNAs: the tentacles of chromatin remodeler complexes. Cell Mol Life Sci 2021; 78:1139-1161. [PMID: 33001247 PMCID: PMC11072783 DOI: 10.1007/s00018-020-03646-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/01/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
Chromatin remodeler complexes regulate gene transcription, DNA replication and DNA repair by changing both nucleosome position and post-translational modifications. The chromatin remodeler complexes are categorized into four families: the SWI/SNF, INO80/SWR1, ISWI and CHD family. In this review, we describe the subunits of these chromatin remodeler complexes, in particular, the recently identified members of the ISWI family and novelties of the CHD family. Long non-coding (lnc) RNAs regulate gene expression through different epigenetic mechanisms, including interaction with chromatin remodelers. For example, interaction of lncBRM with BRM inhibits the SWI/SNF complex associated with a differentiated phenotype and favors assembly of a stem cell-related SWI/SNF complex. Today, over 50 lncRNAs have been shown to affect chromatin remodeler complexes and we here discuss the mechanisms involved.
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Affiliation(s)
- Bernadette Neve
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France.
| | - Nicolas Jonckheere
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Audrey Vincent
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
| | - Isabelle Van Seuningen
- UMR9020-U1277 - CANTHER - Cancer Heterogeneity, Plasticity and Resistance to Therapies, Univ. Lille, CNRS, Inserm, CHU Lille, 59000, Lille, France
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19
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Yang Y, Wang C, Wei N, Hong T, Sun Z, Xiao J, Yao J, Li Z, Liu T. Identification of prognostic chromatin-remodeling genes in clear cell renal cell carcinoma. Aging (Albany NY) 2020; 12:25614-25642. [PMID: 33232269 PMCID: PMC7803503 DOI: 10.18632/aging.104170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/28/2020] [Indexed: 12/16/2022]
Abstract
The aim of this study was to investigate the effects of chromatin-remodeling genes on the prognosis of patients with clear cell renal cell carcinoma (ccRCC). In TCGA-KIRC patients, two subgroups based on 86 chromatin-remodeling genes were established. The random forest algorithm was used for feature selection to identify BPTF, SIN3A and CNOT1 as characterized chromatin remodelers in ccRCC with good prognostic value. YY1 was indicated to be a transcription factor of genes highly related to BPTF, SIN3A and CNOT1. Functional annotations indicated that BPTF, SIN3A, CNOT1 and YY1 are all involved in the ubiquitin-mediated proteolysis process and that high expression of any of the five associated E3 ubiquitin ligases found in the pathway suggests a good prognosis. Protein network analysis indicated that BPTF has a targeted regulatory effect on YY1. Another independent dataset from International Cancer Genome Consortium (ICGC) showed a strong consistency with results in TCGA. In conclusion, we demonstrate that BPTF, SIN3A and CNOT1 are novel prognostic factors that predict good survival in ccRCC. We predicted that the good prognostic value of chromatin-remodeling genes BPTF and SIN3A is related to the regulation of YY1 and that YY1 regulates E3 ubiquitin ligases for further degradation of oncoproteins in ccRCC.
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Affiliation(s)
- Yujing Yang
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Chengyuan Wang
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ningde Wei
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Ting Hong
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zuyu Sun
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Jiawen Xiao
- Department of Medical Oncology, Shenyang Fifth People Hospital, Tiexi District, Shenyang 110001, P.R. China
| | - Jiaxi Yao
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Zhi Li
- Department of Medical Oncology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
| | - Tao Liu
- Department of Urology, The First Affiliated Hospital of China Medical University, Shenyang 110001, P.R. China
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20
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Schutt C, Hallmann A, Hachim S, Klockner I, Valussi M, Atzberger A, Graumann J, Braun T, Boettger T. Linc-MYH configures INO80 to regulate muscle stem cell numbers and skeletal muscle hypertrophy. EMBO J 2020; 39:e105098. [PMID: 32960481 PMCID: PMC7667881 DOI: 10.15252/embj.2020105098] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 08/20/2020] [Accepted: 08/24/2020] [Indexed: 12/16/2022] Open
Abstract
Chromatin remodeling complexes have functions in transcriptional regulation and chromosome maintenance, but it is mostly unknown how the function of these normally ubiquitous complexes is specified in the cellular context. Here, we describe that the evolutionary conserved long non‐coding RNA linc‐MYH regulates the composition of the INO80 chromatin remodeler complex in muscle stem cells and prevents interaction with WDR5 and the transcription factor YY1. Linc‐MYH acts as a selective molecular switch in trans that governs the pro‐proliferative function of the ubiquitous INO80 complex but does not affect its role in maintaining genomic stability. The molecular switch is essential for restricting generation of quiescent MuSCs and proliferation of myoblasts in homeostasis and regeneration. Since linc‐MYH is expressed in proliferating myoblasts but not in quiescent MuSCs, we reason that the extent of myoblast proliferation has decisive effects on the size of the quiescent MuSC pool.
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Affiliation(s)
- Christian Schutt
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Alix Hallmann
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Salma Hachim
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Ina Klockner
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Melissa Valussi
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Ann Atzberger
- Max Planck Institute for Heart- and Lung Research, FACS Service Group, Bad Nauheim, Germany
| | - Johannes Graumann
- Max Planck Institute for Heart- and Lung Research, Mass Spectrometry Service Group, Bad Nauheim, Germany
| | - Thomas Braun
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
| | - Thomas Boettger
- Department of Cardiac Development and Remodelling, Max Planck Institute for Heart- and Lung Research, Bad Nauheim, Germany
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21
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Prendergast L, McClurg UL, Hristova R, Berlinguer-Palmini R, Greener S, Veitch K, Hernandez I, Pasero P, Rico D, Higgins JMG, Gospodinov A, Papamichos-Chronakis M. Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability. Nat Commun 2020; 11:4534. [PMID: 32913330 PMCID: PMC7484789 DOI: 10.1038/s41467-020-18306-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 08/18/2020] [Indexed: 02/04/2023] Open
Abstract
Collisions between the DNA replication machinery and co-transcriptional R-loops can impede DNA synthesis and are a major source of genomic instability in cancer cells. How cancer cells deal with R-loops to proliferate is poorly understood. Here we show that the ATP-dependent chromatin remodelling INO80 complex promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells. Depletion of INO80 in prostate cancer PC3 cells leads to increased R-loops. Overexpression of the RNA:DNA endonuclease RNAse H1 rescues the DNA synthesis defects and suppresses DNA damage caused by INO80 depletion. R-loops co-localize with and promote recruitment of INO80 to chromatin. Artificial tethering of INO80 to a LacO locus enabled turnover of R-loops in cis. Finally, counteracting R-loops by INO80 promotes proliferation and averts DNA damage-induced death in cancer cells. Our work suggests that INO80-dependent resolution of R-loops promotes DNA replication in the presence of transcription, thus enabling unlimited proliferation in cancers.
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Affiliation(s)
- Lisa Prendergast
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne, NE2 4HH, UK
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Urszula L McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rossitsa Hristova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Sarah Greener
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Katie Veitch
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Inmaculada Hernandez
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UMR9002 and University of Montpellier, Equipe Labéllisée Ligue Contre le Cancer, 34090, Montpellier, France
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Manolis Papamichos-Chronakis
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK.
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22
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The YY1/miR-548t-5p/CXCL11 signaling axis regulates cell proliferation and metastasis in human pancreatic cancer. Cell Death Dis 2020; 11:294. [PMID: 32341359 PMCID: PMC7186231 DOI: 10.1038/s41419-020-2475-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 04/07/2020] [Accepted: 04/08/2020] [Indexed: 01/18/2023]
Abstract
Pancreatic cancer (PC) is a malignant tumor with a poor prognosis and high mortality. However, the biological role of miR-548t-5p in PC has not been reported. In this study, we found that miR-548t-5p expression was significantly decreased in PC tissues compared with adjacent tissues, and that low miR-548t-5p expression was associated with malignant PC behavior. In addition, high miR-548t-5p expression inhibited the proliferation, migration, and invasion of PC cell lines. Regarding the molecular mechanism, the luciferase reporter gene, chromatin immunoprecipitation (ChIP), and functional recovery assays revealed that YY1 binds to the miR-548t-5p promoter and positively regulates the expression and function of miR-548t-5p. miR-548t-5p also directly regulates CXCL11 to inhibit its expression. A high level of CXCL11 was associated with worse Tumor Node Metastasis (TNM) staging in patients with PC, enhancing proliferation and metastasis in PC cells. Our study shows that the YY1/miR-548t-5p/CXCL11 axis plays an important role in PC and provides a new potential candidate for the treatment of PC.
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23
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Hui Y, Zhang Y, Wang K, Pan C, Chen H, Qu L, Song X, Lan X. Goat DNMT3B: An indel mutation detection, association analysis with litter size and mRNA expression in gonads. Theriogenology 2020; 147:108-115. [PMID: 32122684 DOI: 10.1016/j.theriogenology.2020.02.025] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 02/10/2020] [Accepted: 02/16/2020] [Indexed: 12/20/2022]
Abstract
DNA methyltransferase 3β (DNMT3B) is a gene encoding a de novo methylation enzyme that is required for DNA methylation during mammalian embryo development. Previous genome-wide association analysis suggested DNMT3B is a candidate gene for goat fertility, but there is no study on the effect of DNMT3B on litter size in goat. The aim of this study was to identify possible insertion/deletion (indel) mutations associated with litter size. Seven putative indels were designed to study their association with litter size, but just one 11-bp insertion variant of intron 22 (the last intron) was found in healthy female Shaanbei white cashmere goats (SBWC goats) (n = 1534). Statistical analysis showed that the 11-bp insertion was related to the first-born litter size (P < 0.01) and the goats with the deletion/deletion genotype had a higher average first-born litter size (P < 0.01). In addition, the expression profile of the DNMT3B mRNA in goat was detected, which revealed significant differences in DNMT3B mRNA expression in the gonads. Additionally, the results of western blotting revealed that the ovaries of mothers of multi-lamb (MML) had a higher level of DNMT3B protein than the ovaries of mothers of single-lamb (MSL). Furthermore, the mRNA of DNMT3B was widely expressed in male goats. Differences in mRNA expression levels were observed in the ovaries of MSL and MML. These findings indicated that the 11-bp indel in DNMT3B was significantly associated with first-born litter size, which can be used for marker-assisted selection (MAS) of goats for breeding.
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Affiliation(s)
- Yiqing Hui
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
| | - Yanghai Zhang
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
| | - Ke Wang
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
| | - Chuanying Pan
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
| | - Hong Chen
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; College of Life Sciences, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Xianyong Lan
- College of Animals Science and Technology, Northwest A&F University, No.22 Xinong Road, Yangling, Shaanxi, 712100, P.R. China.
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24
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Qian S, Wang W, Li M. Transcriptional factor Yin Yang 1 facilitates the stemness of ovarian cancer via suppressing miR-99a activity through enhancing its deacetylation level. Biomed Pharmacother 2020; 126:110085. [PMID: 32199224 DOI: 10.1016/j.biopha.2020.110085] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 02/08/2023] Open
Abstract
The promoting effects of transcriptional factor Yin Yang 1 (YY1) have been confirmed in various tumors, however, its roles in ovarian cancer (OC) progression are still unclear. Here, Kaplan-Meier Plotter analysis was used to determine the correlation between YY1 expression and the survival of OC patients. It was found that YY1 expression was negatively correlated with the overall survival, progression-free survival and post-progression survival of OC patients. Functional experiments indicated that overexpression of YY1 facilitated the stemness of OC cells, while YY1 knockdown reduced it. MiRNAs-based RNA-sequencing analysis showed that miR-99a was the mostly upregulated miRNA in RNA extracted from OC cells with YY1 knockdown. Mechanistic studies revealed that YY1 recruited (Histone deacetylase) HDAC5 to the promoter of miR-99a, and subsequently enhanced miR-99a deacetylation level and decreased miR-99a level. Additionally, overexpression of miR-99a or knockdown of HDAC5 attenuated the promoting effects of YY1 on the stemness of OC cells. This work firstly indicated a novel YY1/miR-99a axis, which promotes the stemness of OC cells.
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Affiliation(s)
- Sumin Qian
- The Second Department of Gynecology, Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China.
| | - Wei Wang
- The Second Department of Gynecology, Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China
| | - Meng Li
- The Fifth Department of Neurology, The Brain Hospital of Cangzhou Central Hospital, 16 Xinhua West Road, Cangzhou, 061000, China
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25
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Yang S, Wang J, Guo S, Huang D, Lorigados IB, Nie X, Lou D, Li Y, Liu M, Kang Y, Zhou W, Song W. Transcriptional activation of USP16 gene expression by NFκB signaling. Mol Brain 2019; 12:120. [PMID: 31888715 PMCID: PMC6937840 DOI: 10.1186/s13041-019-0535-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 12/11/2019] [Indexed: 12/22/2022] Open
Abstract
Ubiquitin Specific Peptidase 16 (USP16) has been reported to contribute to somatic stem-cell defects in Down syndrome. However, how this gene being regulated is largely unknown. To study the mechanism underlying USP16 gene expression, USP16 gene promoter was cloned and analyzed by luciferase assay. We identified that the 5′ flanking region (− 1856 bp ~ + 468 bp) of the human USP16 gene contained the functional promotor to control its transcription. Three bona fide NFκB binding sites were found in USP16 promoter. We showed that p65 overexpression enhanced endogenous USP16 mRNA level. Furthermore, LPS and TNFα, strong activators of the NFκB pathway, upregulated the USP16 transcription. Our data demonstrate that USP16 gene expression is tightly regulated at transcription level. NFκB signaling regulates the human USP16 gene expression through three cis-acting elements. The results provide novel insights into a potential role of dysregulation of USP16 expression in Alzheimer’s dementia in Down Syndrome.
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Affiliation(s)
- Shou Yang
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Juelu Wang
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Shipeng Guo
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Daochao Huang
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Isabel Bestard Lorigados
- Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Xing Nie
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Dandan Lou
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yanhua Li
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Mingjing Liu
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Yu Kang
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China
| | - Weihui Zhou
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China.
| | - Weihong Song
- Chongqing City Key Lab of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, and Ministry of Education Key Lab of Child Development and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, 400014, China. .,Townsend Family Laboratories, Department of Psychiatry, The University of British Columbia, 2255 Wesbrook Mall, Vancouver, BC, V6T 1Z3, Canada.
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26
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Hou J, Wang X. The polycomb group proteins functions in epithelial to mesenchymal transition in lung cancer. Semin Cell Dev Biol 2019; 90:138-143. [DOI: 10.1016/j.semcdb.2018.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/08/2018] [Indexed: 12/29/2022]
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27
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Hartl D, Krebs AR, Grand RS, Baubec T, Isbel L, Wirbelauer C, Burger L, Schübeler D. CG dinucleotides enhance promoter activity independent of DNA methylation. Genome Res 2019; 29:554-563. [PMID: 30709850 PMCID: PMC6442381 DOI: 10.1101/gr.241653.118] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/24/2019] [Indexed: 11/24/2022]
Abstract
Most mammalian RNA polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the transcriptional activity of a large number of chromosomally integrated promoter constructs and monitored binding of transcription factors assumed to play a role in CpG island activity. This revealed that CpG density significantly improves motif-based prediction of transcription factor binding. Our experiments also show that high CpG density alone is insufficient for transcriptional activity, yet results in increased transcriptional output when combined with particular transcription factor motifs. However, this CpG contribution to promoter activity is independent of DNA methyltransferase activity. Together, this refines our understanding of mammalian promoter regulation as it shows that high CpG density within CpG islands directly contributes to an environment permissive for full transcriptional activity.
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Affiliation(s)
- Dominik Hartl
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, CH 4003 Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Tuncay Baubec
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland
| | | | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Swiss Institute of Bioinformatics, CH 4058 Basel, Switzerland
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, CH 4058 Basel, Switzerland.,Faculty of Sciences, University of Basel, CH 4003 Basel, Switzerland
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28
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Du J, Kirk B, Zeng J, Ma J, Wang Q. Three classes of response elements for human PRC2 and MLL1/2-Trithorax complexes. Nucleic Acids Res 2018; 46:8848-8864. [PMID: 29992232 PMCID: PMC6158500 DOI: 10.1093/nar/gky595] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 06/19/2018] [Accepted: 06/21/2018] [Indexed: 12/15/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are essential for maintaining epigenetic memory in both embryonic stem cells and differentiated cells. To date, how they are localized to hundreds of specific target genes within a vertebrate genome had remained elusive. Here, by focusing on short cis-acting DNA elements of single functions, we discovered three classes of response elements in human genome: Polycomb response elements (PREs), Trithorax response elements (TREs) and Polycomb/Trithorax response elements (P/TREs). In particular, the four PREs (PRE14, 29, 39 and 48) are the first set of, to our knowledge, bona fide vertebrate PREs ever discovered, while many previously reported Drosophila or vertebrate PREs are likely P/TREs. We further demonstrated that YY1 and CpG islands are specifically enriched in the four TREs (PRE30, 41, 44 and 55), but not in the PREs. The three classes of response elements as unraveled in this study should guide further global investigation and open new doors for a deeper understanding of PcG and TrxG mechanisms in vertebrates.
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Affiliation(s)
- Junqing Du
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Brian Kirk
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jia Zeng
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jianpeng Ma
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
- Department of Bioengineering, Rice University, 6500 Main Street, Houston, TX 77030, USA
| | - Qinghua Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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29
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Patten DK, Corleone G, Győrffy B, Perone Y, Slaven N, Barozzi I, Erdős E, Saiakhova A, Goddard K, Vingiani A, Shousha S, Pongor LS, Hadjiminas DJ, Schiavon G, Barry P, Palmieri C, Coombes RC, Scacheri P, Pruneri G, Magnani L. Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Nat Med 2018; 24:1469-1480. [PMID: 30038216 PMCID: PMC6130800 DOI: 10.1038/s41591-018-0091-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/14/2018] [Indexed: 12/31/2022]
Abstract
The degree of intrinsic and interpatient phenotypic heterogeneity and its role in tumor evolution is poorly understood. Phenotypic drifts can be transmitted via inheritable transcriptional programs. Cell-type specific transcription is maintained through the activation of epigenetically defined regulatory regions including promoters and enhancers. Here we have annotated the epigenome of 47 primary and metastatic estrogen-receptor (ERα)-positive breast cancer clinical specimens and inferred phenotypic heterogeneity from the regulatory landscape, identifying key regulatory elements commonly shared across patients. Shared regions contain a unique set of regulatory information including the motif for transcription factor YY1. We identify YY1 as a critical determinant of ERα transcriptional activity promoting tumor growth in most luminal patients. YY1 also contributes to the expression of genes mediating resistance to endocrine treatment. Finally, we used H3K27ac levels at active enhancer elements as a surrogate of intra-tumor phenotypic heterogeneity to track the expansion and contraction of phenotypic subpopulations throughout breast cancer progression. By tracking the clonality of SLC9A3R1-positive cells, a bona fide YY1-ERα-regulated gene, we show that endocrine therapies select for phenotypic clones under-represented at diagnosis. Collectively, our data show that epigenetic mechanisms significantly contribute to phenotypic heterogeneity and evolution in systemically treated breast cancer patients.
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Affiliation(s)
- Darren K Patten
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- Semmelweis University, 2nd Deptartment of Pediatrics, Budapest, Hungary
| | - Ylenia Perone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Neil Slaven
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Edina Erdős
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kate Goddard
- Department of Breast and General Surgery, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Andrea Vingiani
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Sami Shousha
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | - Lőrinc Sándor Pongor
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dimitri J Hadjiminas
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | | | - Peter Barry
- Department of Breast Surgery, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Carlo Palmieri
- Institute of Translational Medicine University of Liverpool, Clatterbridge Cancer Centre, NHS Foundation Trust, and Royal Liverpool University Hospital, Liverpool, Merseyside, UK
| | - Raul C Coombes
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Giancarlo Pruneri
- Pathology Department, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.
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30
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van Bömmel A, Love MI, Chung HR, Vingron M. coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PLoS Comput Biol 2018; 14:e1006372. [PMID: 30142147 PMCID: PMC6126874 DOI: 10.1371/journal.pcbi.1006372] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 09/06/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
Cell-type specific gene expression is regulated by the combinatorial action of transcription factors (TFs). In this study, we predict transcription factor (TF) combinations that cooperatively bind in a cell-type specific manner. We first divide DNase hypersensitive sites into cell-type specifically open vs. ubiquitously open sites in 64 cell types to describe possible cell-type specific enhancers. Based on the pattern contrast between these two groups of sequences we develop "co-occurring TF predictor on Cell-Type specific Enhancers" (coTRaCTE) - a novel statistical method to determine regulatory TF co-occurrences. Contrasting the co-binding of TF pairs between cell-type specific and ubiquitously open chromatin guarantees the high cell-type specificity of the predictions. coTRaCTE predicts more than 2000 co-occurring TF pairs in 64 cell types. The large majority (70%) of these TF pairs is highly cell-type specific and overlaps in TF pair co-occurrence are highly consistent among related cell types. Furthermore, independently validated co-occurring and directly interacting TFs are significantly enriched in our predictions. Focusing on the regulatory network derived from the predicted co-occurring TF pairs in embryonic stem cells (ESCs) we find that it consists of three subnetworks with distinct functions: maintenance of pluripotency governed by OCT4, SOX2 and NANOG, regulation of early development governed by KLF4, STAT3, ZIC3 and ZNF148 and general functions governed by MYC, TCF3 and YY1. In summary, coTRaCTE predicts highly cell-type specific co-occurring TFs which reveal new insights into transcriptional regulatory mechanisms.
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Affiliation(s)
- Alena van Bömmel
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michael I. Love
- Department of Biostatistics, Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Ho-Ryun Chung
- Otto Warburg Laboratory, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Philipps-Universität Marburg, Fachbereich Medizin, Institut für Medizinische Bioinformatik und Biostatistik, Marburg, Germany
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
- * E-mail:
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31
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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32
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Zhang Y, He S, Mei R, Kang Y, Duan J, Wei R, Xiang C, Wu Y, Lu X, Cai Z, Xiong L. miR‑29a suppresses IL‑13‑induced cell invasion by inhibiting YY1 in the AKT pathway in lung adenocarcinoma A549 cells. Oncol Rep 2018; 39:2613-2623. [PMID: 29620222 PMCID: PMC5983933 DOI: 10.3892/or.2018.6352] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/29/2018] [Indexed: 12/15/2022] Open
Abstract
IL‑13 is a proinflammatory cytokine associated with multiple pathological conditions and the promotion of metastasis in lung cancer. Previous studies have demonstrated that IL‑13 and YY1 are associated with PI3K/AKT signaling. In addition, miR‑29a has been found to play a critical role in cell invasion in lung cancer. However, the molecular mechanism of miR‑29a underlying its involvement in IL‑13‑induced lung cancer cell invasion remains largely unknown. In the present study, we aimed to investigate the role of miR‑29a in cell invasion mediated by IL‑13 in lung cancer. By using MTT and wound‑scratch assays, we assessed cell proliferation and migration induced by IL‑13, and identified activation of the PI3K/AKT/YY1 pathway. Inhibition of PI3K/AKT by LY294002 downregulated IL‑13‑induced YY1 expression. Furthermore, we found that miR‑29a directly targets YY1 and suppressed its expression in lung cancer. By using MTT, flow cytometry and Transwell assays, overexpression of miR‑29a restricted both YY1 and N‑cadherin expression, and inhibited IL‑13‑induced invasion of lung cancer A549 cells. Taken together, these findings demonstrate that PI3K/AKT/YY1 is involved in the regulation of lung cancer cell behavior induced by IL‑13, and miR‑29a represents a promising therapeutic target.
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Affiliation(s)
- Yu Zhang
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Shujin He
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Renmei Mei
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yurong Kang
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Jing Duan
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Ran Wei
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Chuqi Xiang
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Yemeng Wu
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Xiangtong Lu
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Zhenyu Cai
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
| | - Lixia Xiong
- Department of Pathophysiology, Medical College, Nanchang University, Nanchang, Jiangxi 330006, P.R. China
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33
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Liu D, Zhang J, Wu Y, Shi G, Yuan H, Lu Z, Zhu Q, Wu P, Lu C, Guo F, Chen J, Jiang K, Miao Y. YY1 suppresses proliferation and migration of pancreatic ductal adenocarcinoma by regulating the CDKN3/MdM2/P53/P21 signaling pathway. Int J Cancer 2018; 142:1392-1404. [PMID: 29168185 DOI: 10.1002/ijc.31173] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/08/2017] [Accepted: 11/16/2017] [Indexed: 01/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the malignant lethal tumors. It has been reported that the transcriptional regulator Yin Yang-1 (YY1) suppressed the invasion and metastasis of PDAC. However, the function of YY1 on proliferation and migration of pancreatic cancer remains to be clarified. In this study, we found that YY1 overexpression or knockdown can inhibit or promote the proliferation and migration of pancreatic cancer cells. Digital gene expression sequencing indicates that cyclin-dependent kinase inhibitor 3 (CDKN3) may be the candidate target gene of YY1. Then we found that YY1 can downregulate the expression of CDKN3 by directly binding to the promoter region of CDKN3. Silencing CDKN3 expression could inhibit the ability of cell proliferation and migration and overexpression of CDKN3 could restore the effects induced by YY1 overexpression in pancreatic cancer cells. The expression levels of YY1 and CDKN3 were negatively correlated in pancreatic cancer tissues and PDAC patients with higher levels of CDKN3 have poor prognosis. Vitro and vivo study show that CDKN3 can form a complex with MdM2-P53, thus leading to inhibiting the expression of P21, which is the target gene of P53, and finally facilitates the cell cycle to promote the proliferation of pancreatic cancer cells. Hence, YY1 can directly regulate the expression of CDKN3 and participate in the cycle of pancreatic cancer cells, which can inhibit the progression of pancreatic cancer. These results reveal that YY1-CDKN3-MDM2/P53-P21 axis is involved in pancreatic tumorigenesis, which may develop new methods for human pancreatic cancer therapy.
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Affiliation(s)
- Dongfang Liu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jingjing Zhang
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yang Wu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Guodong Shi
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Hao Yuan
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Zipeng Lu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Qicong Zhu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Pengfei Wu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Cheng Lu
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Feng Guo
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Jianmin Chen
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Kuirong Jiang
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
| | - Yi Miao
- Pancreas Center, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, People's Republic of China
- Pancreas Institute of Nanjing Medical University, Nanjing, People's Republic of China
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34
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Wang J, Wu X, Wei C, Huang X, Ma Q, Huang X, Faiola F, Guallar D, Fidalgo M, Huang T, Peng D, Chen L, Yu H, Li X, Sun J, Liu X, Cai X, Chen X, Wang L, Ren J, Wang J, Ding J. YY1 Positively Regulates Transcription by Targeting Promoters and Super-Enhancers through the BAF Complex in Embryonic Stem Cells. Stem Cell Reports 2018; 10:1324-1339. [PMID: 29503092 PMCID: PMC5998734 DOI: 10.1016/j.stemcr.2018.02.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 12/20/2022] Open
Abstract
Yin Yang 1 (YY1) regulates early embryogenesis and adult tissue formation. However, the role of YY1 in stem cell regulation remains unclear. YY1 has a Polycomb group (PcG) protein-dependent role in mammalian cells. The PcG-independent functions of YY1 are also reported, although their underlying mechanism is still undefined. This paper reports the role of YY1 and BAF complex in the OCT4-mediated pluripotency network in mouse embryonic stem cells (mESCs). The interaction between YY1 and BAF complex promotes mESC proliferation and pluripotency. Knockdown of Yy1 or Smarca4, the core component of the BAF complex, downregulates pluripotency markers and upregulates several differentiation markers. Moreover, YY1 enriches at both promoter and super-enhancer regions to stimulate transcription. Thus, this study elucidates the role of YY1 in regulating pluripotency through its interaction with OCT4 and the BAF complex and the role of BAF complex in integrating YY1 into the core pluripotency network. YY1 is integrated into the core pluripotency network through the BAF complex YY1 and the BAF complex promote ESC proliferation YY1 activates gene expression through the BAF complex to maintain pluripotency YY1 is enriched at the ESC-specific super-enhancers to promote gene expression
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Affiliation(s)
- Jia Wang
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xingui Wu
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Chao Wei
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xin Huang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Qian Ma
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaona Huang
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Diana Guallar
- Centro de Investigaciónen Medicina Molecular e EnfermidadesCronicas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Miguel Fidalgo
- Centro de Investigaciónen Medicina Molecular e EnfermidadesCronicas, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Tingyuan Huang
- Guangzhou Center for Disease Control and Prevention, Guangzhou 510440, China
| | - Di Peng
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Li Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Haopeng Yu
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xingyu Li
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Junyi Sun
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xinyi Liu
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiaoxia Cai
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Xiao Chen
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Ling Wang
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Jian Ren
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510275, China
| | - Jianlong Wang
- The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Junjun Ding
- Program in Stem Cell and Regenerative Medicine, The Third Affiliated Hospital of Sun Yat-Sen University, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China; Center for Stem Cell Biology and Tissue Engineering, Key Laboratory for Stem Cells and Tissue Engineering, Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, China; Department of Cell Biology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China.
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Vazquez-Martin A, Anatskaya OV, Giuliani A, Erenpreisa J, Huang S, Salmina K, Inashkina I, Huna A, Nikolsky NN, Vinogradov AE. Somatic polyploidy is associated with the upregulation of c-MYC interacting genes and EMT-like signature. Oncotarget 2018; 7:75235-75260. [PMID: 27655693 PMCID: PMC5342737 DOI: 10.18632/oncotarget.12118] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 09/05/2016] [Indexed: 12/30/2022] Open
Abstract
The dependence of cancer on overexpressed c-MYC and its predisposition for polyploidy represents a double puzzle. We address this conundrum by cross-species transcription analysis of c-MYC interacting genes in polyploid vs. diploid tissues and cells, including human vs. mouse heart, mouse vs. human liver and purified 4n vs. 2n mouse decidua cells. Gene-by-gene transcriptome comparison and principal component analysis indicated that c-MYC interactants are significantly overrepresented among ploidy-associated genes. Protein interaction networks and gene module analysis revealed that the most upregulated genes relate to growth, stress response, proliferation, stemness and unicellularity, as well as to the pathways of cancer supported by MAPK and RAS coordinated pathways. A surprising feature was the up-regulation of epithelial-mesenchymal transition (EMT) modules embodied by the N-cadherin pathway and EMT regulators from SNAIL and TWIST families. Metabolic pathway analysis also revealed the EMT-linked features, such as global proteome remodeling, oxidative stress, DNA repair and Warburg-like energy metabolism. Genes associated with apoptosis, immunity, energy demand and tumour suppression were mostly down-regulated. Noteworthy, despite the association between polyploidy and ample features of cancer, polyploidy does not trigger it. Possibly it occurs because normal polyploidy does not go that far in embryonalisation and linked genome destabilisation. In general, the analysis of polyploid transcriptome explained the evolutionary relation of c-MYC and polyploidy to cancer.
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Affiliation(s)
| | - Olga V Anatskaya
- Institute of Cytology, St-Petersburg, Russian Federation, Russia
| | | | | | - Sui Huang
- Systems Biology Institute, Seattle, USA
| | | | - Inna Inashkina
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Anda Huna
- Latvian Biomedical Research and Study Centre, Riga, Latvia
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36
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Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass. Nat Commun 2017; 8:1297. [PMID: 29101321 PMCID: PMC5670228 DOI: 10.1038/s41467-017-01415-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/15/2017] [Indexed: 12/11/2022] Open
Abstract
X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27. We further show that in UTX H3K27 histone demethylase mutant embryos, these genes are even more slowly reactivated, suggesting that these genes carry an epigenetic memory that may be actively lost. On the other hand, expression of rapidly reactivated genes may be driven by transcription factors. Thus, some X-linked genes have minimal epigenetic memory in the inner cell mass, whereas others may require active erasure of chromatin marks. X-chromosome inactivation is reversed in the mouse inner cell mass (ICM) through a mechanism that is not fully understood. Here, the authors investigate this process and characterize the contributions of the epigenetic landscape and transcription factors in X-linked gene reactivation dynamics.
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37
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Wu XN, Shi TT, He YH, Wang FF, Sang R, Ding JC, Zhang WJ, Shu XY, Shen HF, Yi J, Gao X, Liu W. Methylation of transcription factor YY2 regulates its transcriptional activity and cell proliferation. Cell Discov 2017; 3:17035. [PMID: 29098080 PMCID: PMC5665210 DOI: 10.1038/celldisc.2017.35] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 08/08/2017] [Indexed: 01/05/2023] Open
Abstract
Yin Yang 1 (YY1) is a multifunctional DNA-binding transcription factor shown to be critical in a variety of biological processes, and its activity and function have been shown to be regulated by multitude of mechanisms, which include but are not limited to post-translational modifications (PTMs), its associated proteins and cellular localization. YY2, the paralog of YY1 in mouse and human, has been proposed to function redundantly or oppositely in a context-specific manner compared with YY1. Despite its functional importance, how YY2’s DNA-binding activity and function are regulated, particularly by PTMs, remains completely unknown. Here we report the first PTM with functional characterization on YY2, namely lysine 247 monomethylation (K247me1), which was found to be dynamically regulated by SET7/9 and LSD1 both in vitro and in cultured cells. Functional study revealed that SET7/9-mediated YY2 methylation regulated its DNA-binding activity in vitro and in association with chromatin examined by chromatin immunoprecipitation coupled with sequencing (ChIP-seq) in cultured cells. Knockout of YY2, SET7/9 or LSD1 by CRISPR (clustered, regularly interspaced, short palindromic repeats)/Cas9-mediated gene editing followed by RNA sequencing (RNA-seq) revealed that a subset of genes was positively regulated by YY2 and SET7/9, but negatively regulated by LSD1, which were enriched with genes involved in cell proliferation regulation. Importantly, YY2-regulated gene transcription, cell proliferation and tumor growth were dependent, at least partially, on YY2 K247 methylation. Finally, somatic mutations on YY2 found in cancer, which are in close proximity to K247, altered its methylation, DNA-binding activity and gene transcription it controls. Our findings revealed the first PTM with functional implications imposed on YY2 protein, and linked YY2 methylation with its biological functions.
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Affiliation(s)
- Xiao-Nan Wu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Tao-Tao Shi
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Yao-Hui He
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Fei-Fei Wang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Rui Sang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Jian-Cheng Ding
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Wen-Juan Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Xing-Yi Shu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Hai-Feng Shen
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Jia Yi
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Xiang Gao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
| | - Wen Liu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Fujian, China
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38
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Gabriele M, Vulto-van Silfhout AT, Germain PL, Vitriolo A, Kumar R, Douglas E, Haan E, Kosaki K, Takenouchi T, Rauch A, Steindl K, Frengen E, Misceo D, Pedurupillay CRJ, Stromme P, Rosenfeld JA, Shao Y, Craigen WJ, Schaaf CP, Rodriguez-Buritica D, Farach L, Friedman J, Thulin P, McLean SD, Nugent KM, Morton J, Nicholl J, Andrieux J, Stray-Pedersen A, Chambon P, Patrier S, Lynch SA, Kjaergaard S, Tørring PM, Brasch-Andersen C, Ronan A, van Haeringen A, Anderson PJ, Powis Z, Brunner HG, Pfundt R, Schuurs-Hoeijmakers JHM, van Bon BWM, Lelieveld S, Gilissen C, Nillesen WM, Vissers LELM, Gecz J, Koolen DA, Testa G, de Vries BBA. YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction. Am J Hum Genet 2017; 100:907-925. [PMID: 28575647 DOI: 10.1016/j.ajhg.2017.05.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/04/2017] [Indexed: 01/06/2023] Open
Abstract
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and as an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, and various congenital malformations. Our combined clinical and molecular data define "YY1 syndrome" as a haploinsufficiency syndrome. Through immunoprecipitation of YY1-bound chromatin from affected individuals' cells with antibodies recognizing both ends of the protein, we show that YY1 deletions and missense mutations lead to a global loss of YY1 binding with a preferential retention at high-occupancy sites. Finally, we uncover a widespread loss of H3K27 acetylation in particular on the YY1-bound enhancers, underscoring a crucial role for YY1 in enhancer regulation. Collectively, these results define a clinical syndrome caused by haploinsufficiency of YY1 through dysregulation of key transcriptional regulators.
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Affiliation(s)
- Michele Gabriele
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | | | - Pierre-Luc Germain
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Alessandro Vitriolo
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy
| | - Raman Kumar
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Evelyn Douglas
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Eric Haan
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Toshiki Takenouchi
- Center for Medical Genetics, Keio University School of Medicine, 160-8582 Tokyo, Japan
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, 8952 Schlieren-Zurich, Switzerland
| | - Eirik Frengen
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | - Doriana Misceo
- Department of Medical Genetics, University of Oslo and Oslo University Hospital, 0315 Oslo, Norway
| | | | - Petter Stromme
- Division of Paediatric and Adolescent Medicine, Oslo University Hospital and University of Oslo, 0313 Oslo, Norway
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yunru Shao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - David Rodriguez-Buritica
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Laura Farach
- Division of Genetics, Department of Pediatrics, University of Texas Health, Houston, TX 77030, USA
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, and Rady Children's Hospital, San Diego, CA 92123, USA
| | - Perla Thulin
- Department of Neurology, University of Utah, San Diego, CA 92123, USA
| | - Scott D McLean
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Kimberly M Nugent
- Clinical Genetics Section, Children's Hospital of San Antonio, San Antonio, TX 78207, USA
| | - Jenny Morton
- Birmingham Women's Hospital, B15 2TG Birmingham, UK
| | - Jillian Nicholl
- SA Clinical Genetics Service, SA Pathology, Adelaide, SA 5000, Australia; School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
| | - Joris Andrieux
- Institut de Génétique Médicale, Hopital Jeanne de Flandre, 59000 Lille, France
| | | | - Pascal Chambon
- Laboratory of Cytogenetics, Rouen University Hospital, 76031 Rouen, France
| | - Sophie Patrier
- Service d'Anatomie Pathologique, Rouen University Hospital, 76031 Rouen, France
| | - Sally A Lynch
- National Centre for Medical Genetics, Our Lady's Children's Hospital, D12 V004 Dublin, Ireland
| | - Susanne Kjaergaard
- Department of Clinical Genetics, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Pernille M Tørring
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense, Denmark
| | | | - Anne Ronan
- Hunter Genetics, Waratah, NSW 2298, Australia
| | - Arie van Haeringen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 ZA Leiden, the Netherlands
| | - Peter J Anderson
- Australian Craniofacial Unit, Women's and Children's Hospital, North Adelaide, SA 5006, Australia
| | - Zöe Powis
- Ambry Genetics, Aliso Viejo, CA 92656, USA
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | | | - Bregje W M van Bon
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Stefan Lelieveld
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Willy M Nillesen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Jozef Gecz
- School of Medicine and Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - David A Koolen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands
| | - Giuseppe Testa
- Laboratory of Stem Cell Epigenetics, Department of Experimental Oncology, European Institute of Oncology, Milan 20139, Italy; Department of Oncology and Hemato-Oncology, University of Milan, 20122 Milan, Italy.
| | - Bert B A de Vries
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, the Netherlands.
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39
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Cao K, Collings CK, Marshall SA, Morgan MA, Rendleman EJ, Wang L, Sze CC, Sun T, Bartom ET, Shilatifard A. SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression. Genes Dev 2017; 31:787-801. [PMID: 28487406 PMCID: PMC5435891 DOI: 10.1101/gad.294744.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/12/2017] [Indexed: 01/16/2023]
Abstract
In this study, Cao et al. identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Their results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development. The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various processes in development, and misregulation of their expression is associated with human cancer. In the developing embryo, Hox genes are activated sequentially in time and space according to their genomic position within Hox gene clusters. Accumulating evidence implicates both enhancer elements and noncoding RNAs in controlling this spatiotemporal expression of Hox genes, but disentangling their relative contributions is challenging. Here, we identify two cis-regulatory elements (E1 and E2) functioning as shadow enhancers to regulate the early expression of the HoxA genes. Simultaneous deletion of these shadow enhancers in embryonic stem cells leads to impaired activation of HoxA genes upon differentiation, while knockdown of a long noncoding RNA overlapping E1 has no detectable effect on their expression. Although MLL/COMPASS (complex of proteins associated with Set1) family of histone methyltransferases is known to activate transcription of Hox genes in other contexts, we found that individual inactivation of the MLL1-4/COMPASS family members has little effect on early Hox gene activation. Instead, we demonstrate that SET1A/COMPASS is required for full transcriptional activation of multiple Hox genes but functions independently of the E1 and E2 cis-regulatory elements. Our results reveal multiple regulatory layers for Hox genes to fine-tune transcriptional programs essential for development.
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Affiliation(s)
- Kaixiang Cao
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Clayton K Collings
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Stacy A Marshall
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Marc A Morgan
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Emily J Rendleman
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Lu Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Christie C Sze
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Tianjiao Sun
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Elizabeth T Bartom
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, USA
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40
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Aberrant methylation patterns affect the molecular pathogenesis of rheumatoid arthritis. Int Immunopharmacol 2017; 46:141-145. [PMID: 28282578 DOI: 10.1016/j.intimp.2017.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2016] [Revised: 01/04/2017] [Accepted: 02/07/2017] [Indexed: 12/22/2022]
Abstract
This study aims to investigate DNA methylation signatures in fibroblast-like synoviocytes (FLS) from patients with rheumatoid arthritis (RA), and to explore the relationship with transcription factors (TFs) that help to distinguish RA from osteoarthritis (OA). Microarray dataset of GSE46346, including six FLS samples from patients with RA and five FLS samples from patients with OA, was downloaded from the Gene Expression Omnibus database. RA and OA samples were screened for differentially methylated loci (DMLs). The corresponding differentially methylated genes (DMGs) were identified, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) enrichment analysis. A transcriptional regulatory network was built with TFs and their corresponding DMGs. Overall, 280 hypomethylated loci and 561 hypermethylated loci were screened. Genes containing hypermethylated loci were enriched in pathways in cancer, ECM-receptor interaction, focal adhesion and neurotrophin signaling pathways. Genes containing hypomethylated loci were enriched in the neurotrophin signaling pathway. Moreover, we found that CCCTC-binding factor (CTCF), Yin Yang 1 (YY1), v-myc avian myelocytomatosis viral oncogene homolog (c-MYC), and early growth response 1 (EGR1) were important TFs in the transcriptional regulatory network. Therefore, DMGs might participate in the neurotrophin signaling pathway, pathways in cancer, ECM-receptor interaction and focal adhesion pathways in RA. Furthermore, CTCF, c-MYC, YY1, and EGR1 may play important roles in RA through regulating DMGs.
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41
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Inverse correlation between the metastasis suppressor RKIP and the metastasis inducer YY1: Contrasting roles in the regulation of chemo/immuno-resistance in cancer. Drug Resist Updat 2017; 30:28-38. [PMID: 28363333 DOI: 10.1016/j.drup.2017.01.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/28/2016] [Accepted: 01/04/2017] [Indexed: 02/06/2023]
Abstract
Several gene products have been postulated to mediate inherent and/or acquired anticancer drug resistance and tumor metastasis. Among these, the metastasis suppressor and chemo-immuno-sensitizing gene product, Raf Kinase Inhibitor Protein (RKIP), is poorly expressed in many cancers. In contrast, the metastasis inducer and chemo-immuno-resistant factor Yin Yang 1 (YY1) is overexpressed in many cancers. This inverse relationship between RKIP and YY1 expression suggests that these two gene products may be regulated via cross-talks of molecular signaling pathways, culminating in the expression of different phenotypes based on their targets. Analyses of the molecular regulation of the expression patterns of RKIP and YY1 as well as epigenetic, post-transcriptional, and post-translational regulation revealed the existence of several effector mechanisms and crosstalk pathways, of which five pathways of relevance have been identified and analyzed. The five examined cross-talk pathways include the following loops: RKIP/NF-κB/Snail/YY1, p38/MAPK/RKIP/GSK3β/Snail/YY1, RKIP/Smurf2/YY1/Snail, RKIP/MAPK/Myc/Let-7/HMGA2/Snail/YY1, as well as RKIP/GPCR/STAT3/miR-34/YY1. Each loop is comprised of multiple interactions and cascades that provide evidence for YY1's negative regulation of RKIP expression and vice versa. These loops elucidate potential prognostic motifs and targets for therapeutic intervention. Chiefly, these findings suggest that targeted inhibition of YY1 by specific small molecule inhibitors and/or the specific induction of RKIP expression and activity are potential therapeutic strategies to block tumor growth and metastasis in many cancers, as well as to overcome anticancer drug resistance. These strategies present potential alternatives for their synergistic uses in combination with low doses of conventional chemo-immunotherapeutics and hence, increasing survival, reducing toxicity, and improving quality of life.
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42
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Pérez-Rico YA, Boeva V, Mallory AC, Bitetti A, Majello S, Barillot E, Shkumatava A. Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. Genome Res 2016; 27:259-268. [PMID: 27965291 PMCID: PMC5287231 DOI: 10.1101/gr.203679.115] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 12/09/2016] [Indexed: 12/11/2022]
Abstract
Super-enhancers (SEs) are key transcriptional drivers of cellular, developmental, and disease states in mammals, yet the conservational and regulatory features of these enhancer elements in nonmammalian vertebrates are unknown. To define SEs in zebrafish and enable sequence and functional comparisons to mouse and human SEs, we used genome-wide histone H3 lysine 27 acetylation (H3K27ac) occupancy as a primary SE delineator. Our study determined the set of SEs in pluripotent state cells and adult zebrafish tissues and revealed both similarities and differences between zebrafish and mammalian SEs. Although the total number of SEs was proportional to the genome size, the genomic distribution of zebrafish SEs differed from that of the mammalian SEs. Despite the evolutionary distance separating zebrafish and mammals and the low overall SE sequence conservation, ∼42% of zebrafish SEs were located in close proximity to orthologs that also were associated with SEs in mouse and human. Compared to their nonassociated counterparts, higher sequence conservation was revealed for those SEs that have maintained orthologous gene associations. Functional dissection of two of these SEs identified conserved sequence elements and tissue-specific expression patterns, while chromatin accessibility analyses predicted transcription factors governing the function of pluripotent state zebrafish SEs. Our zebrafish annotations and comparative studies show the extent of SE usage and their conservation across vertebrates, permitting future gene regulatory studies in several tissues.
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Affiliation(s)
- Yuvia A Pérez-Rico
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,INSERM, U900, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Valentina Boeva
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France.,Institut Cochin, INSERM U1016, CNRS UMR 8104, Université Paris Descartes UMR-S1016, F-75014 Paris, France
| | - Allison C Mallory
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Angelo Bitetti
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, F-75005, Paris, France
| | - Sara Majello
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
| | - Emmanuel Barillot
- INSERM, U900, F-75005, Paris, France.,Institut Curie, Mines ParisTech, PSL Research University, F-75005, Paris, France
| | - Alena Shkumatava
- Institut Curie, PSL Research University, INSERM U934, CNRS UMR 3215, F-75005, Paris, France
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43
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Control of embryonic stem cell self-renewal and differentiation via coordinated alternative splicing and translation of YY2. Proc Natl Acad Sci U S A 2016; 113:12360-12367. [PMID: 27791185 DOI: 10.1073/pnas.1615540113] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Translational control of gene expression plays a key role during the early phases of embryonic development. Here we describe a transcriptional regulator of mouse embryonic stem cells (mESCs), Yin-yang 2 (YY2), that is controlled by the translation inhibitors, Eukaryotic initiation factor 4E-binding proteins (4E-BPs). YY2 plays a critical role in regulating mESC functions through control of key pluripotency factors, including Octamer-binding protein 4 (Oct4) and Estrogen-related receptor-β (Esrrb). Importantly, overexpression of YY2 directs the differentiation of mESCs into cardiovascular lineages. We show that the splicing regulator Polypyrimidine tract-binding protein 1 (PTBP1) promotes the retention of an intron in the 5'-UTR of Yy2 mRNA that confers sensitivity to 4E-BP-mediated translational suppression. Thus, we conclude that YY2 is a major regulator of mESC self-renewal and lineage commitment and document a multilayer regulatory mechanism that controls its expression.
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44
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Piunti A, Shilatifard A. Epigenetic balance of gene expression by Polycomb and COMPASS families. Science 2016; 352:aad9780. [PMID: 27257261 DOI: 10.1126/science.aad9780] [Citation(s) in RCA: 331] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epigenetic regulation of gene expression in metazoans is central for establishing cellular diversity, and its deregulation can result in pathological conditions. Although transcription factors are essential for implementing gene expression programs, they do not function in isolation and require the recruitment of various chromatin-modifying and -remodeling machineries. A classic example of developmental chromatin regulation is the balanced activities of the Polycomb group (PcG) proteins within the PRC1 and PRC2 complexes, and the Trithorax group (TrxG) proteins within the COMPASS family, which are highly mutated in a large number of human diseases. In this review, we will discuss the latest findings regarding the properties of the PcG and COMPASS families and the insight they provide into the epigenetic control of transcription under physiological and pathological settings.
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Affiliation(s)
- Andrea Piunti
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, 320 East Superior Street, Chicago, IL 60611, USA.
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45
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Abstract
Ying Yang 1 (YY1) is a ubiquitously expressed transcription factor shown to be essential for pro-B-cell development. However, the role of YY1 in other B-cell populations has never been investigated. Recent bioinformatics analysis data have implicated YY1 in the germinal center (GC) B-cell transcriptional program. In accord with this prediction, we demonstrated that deletion of YY1 by Cγ1-Cre completely prevented differentiation of GC B cells and plasma cells. To determine if YY1 was also required for the differentiation of other B-cell populations, we deleted YY1 with CD19-Cre and found that all peripheral B-cell subsets, including B1 B cells, require YY1 for their differentiation. Transitional 1 (T1) B cells were the most dependent upon YY1, being sensitive to even a half-dosage of YY1 and also to short-term YY1 deletion by tamoxifen-induced Cre. We show that YY1 exerts its effects, in part, by promoting B-cell survival and proliferation. ChIP-sequencing shows that YY1 predominantly binds to promoters, and pathway analysis of the genes that bind YY1 show enrichment in ribosomal functions, mitochondrial functions such as bioenergetics, and functions related to transcription such as mRNA splicing. By RNA-sequencing analysis of differentially expressed genes, we demonstrated that YY1 normally activates genes involved in mitochondrial bioenergetics, whereas it normally down-regulates genes involved in transcription, mRNA splicing, NF-κB signaling pathways, the AP-1 transcription factor network, chromatin remodeling, cytokine signaling pathways, cell adhesion, and cell proliferation. Our results show the crucial role that YY1 plays in regulating broad general processes throughout all stages of B-cell differentiation.
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46
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Entrevan M, Schuettengruber B, Cavalli G. Regulation of Genome Architecture and Function by Polycomb Proteins. Trends Cell Biol 2016; 26:511-525. [PMID: 27198635 DOI: 10.1016/j.tcb.2016.04.009] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 04/19/2016] [Accepted: 04/21/2016] [Indexed: 12/13/2022]
Abstract
Polycomb group (PcG) proteins dynamically define cellular identities through the epigenetic repression of key developmental regulatory genes. PcG proteins are recruited to specific regulatory elements to modify the chromatin surrounding them. In addition, they regulate the organization of their target genes in the 3D space of the nucleus, and this regulatory function of the 3D genome architecture is involved in cell differentiation and the maintenance of cellular memory. In this review we discuss recent advances in our understanding of how PcG proteins are recruited to chromatin to induce local and global changes in chromosome conformation and regulate their target genes.
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Affiliation(s)
- Marianne Entrevan
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France
| | - Bernd Schuettengruber
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS UPR1142 and University of Montpellier, 141 Rue de la Cardonille, 34396, Montpellier Cedex 5, France.
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47
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Aaronson Y, Livyatan I, Gokhman D, Meshorer E. Systematic identification of gene family regulators in mouse and human embryonic stem cells. Nucleic Acids Res 2016; 44:4080-9. [PMID: 27084933 PMCID: PMC4872113 DOI: 10.1093/nar/gkw259] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/01/2016] [Indexed: 01/22/2023] Open
Abstract
Pluripotent self-renewing embryonic stem cells (ESCs) have been the focus of a growing number of high-throughput experiments, revealing the genome-wide locations of hundreds of transcription factors and histone modifications. While most of these datasets were used in a specific context, all datasets combined offer a comprehensive view of chromatin characteristics and regulatory elements that govern cell states. Here, using hundreds of datasets in ESCs, we generated colocalization maps of chromatin proteins and modifications, and built a discovery pipeline for regulatory proteins of gene families. By comparing genome-wide binding data with over-expression and knockdown analysis of hundreds of genes, we discovered that the pluripotency-related factor NR5A2 separates mitochondrial from cytosolic ribosomal genes, regulating their expression. We further show that genes with a common chromatin profile are enriched for distinct Gene Ontology (GO) categories. Our approach can be generalized to reveal common regulators of any gene group; discover novel gene families, and identify common genomic elements based on shared chromatin features.
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Affiliation(s)
- Yair Aaronson
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - Ilana Livyatan
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel
| | - Eran Meshorer
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Jerusalem 91904, Israel The Edmond and Lily Center for Brain Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 91904, Israel
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48
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Nieborak A, Górecki A. Significance of the pathogenic mutation T372R in the Yin Yang 1 protein interaction with DNA--thermodynamic studies. FEBS Lett 2016; 590:838-47. [PMID: 26910132 DOI: 10.1002/1873-3468.12106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/13/2016] [Accepted: 02/11/2016] [Indexed: 02/01/2023]
Abstract
This work focuses on the pathogenic missense mutation in YY1 protein correlated with insulinomas. Based on in vitro studies, we demonstrate that the mutation does not affect the secondary structure of either zinc fingers or the N-terminal fragment (NTF) of the protein. Apart from a slight increase in the protein's compactness, no changes in the tertiary structure were observed. The introduced mutation significantly alters DNA-binding properties, both the affinity and enthalpy-entropy contribution of the process, which are highly dependent on the recognized sequence. Obtained results indicate concerted rather than a modular mode of sequence recognition by YY1 with the significant impact of a disordered NTF.
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Affiliation(s)
- Anna Nieborak
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Andrzej Górecki
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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49
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Chen L, Foreman DP, Sant'Angelo DB, Krangel MS. Yin Yang 1 Promotes Thymocyte Survival by Downregulating p53. THE JOURNAL OF IMMUNOLOGY 2016; 196:2572-82. [PMID: 26843327 DOI: 10.4049/jimmunol.1501916] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 01/07/2016] [Indexed: 12/13/2022]
Abstract
Yin Yang 1 (YY1) is a zinc finger protein that functions as a transcriptional activator or repressor and participates in multiple biological processes, including development and tumorigenesis. To investigate the role of YY1 in developing T cells, we used mouse models that depleted YY1 at two distinct stages of thymocyte development. When YY1 was depleted in CD4(-)CD8(-) double-negative thymocytes, development to the CD4(+)CD8(+) double-positive stage was impaired, due to increased apoptosis that prevented expansion of post-β-selection thymocytes. When YY1 was depleted in double-positive thymocytes, they underwent increased cell-autonomous apoptosis in vitro and displayed a shorter lifespan in vivo, as judged by their ability to undergo secondary Vα-to-Jα recombination. Mechanistically, we found that the increased apoptosis in YY1-deficient thymocytes was attributed to overexpression of p53, because concurrent loss of p53 completely rescued the developmental defects of YY1-deficient thymocytes. These results indicated that YY1 functions as a critical regulator of thymocyte survival and that it does so by suppressing the expression of p53.
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Affiliation(s)
- Liang Chen
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
| | - Daniel P Foreman
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
| | - Derek B Sant'Angelo
- Child Health Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ 08901
| | - Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, NC 27710; and
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50
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Di Giorgio E, Brancolini C. Regulation of class IIa HDAC activities: it is not only matter of subcellular localization. Epigenomics 2016; 8:251-69. [DOI: 10.2217/epi.15.106] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
In response to environmental cues, enzymes that influence the functions of proteins, through reversible post-translational modifications supervise the coordination of cell behavior like orchestral conductors. Class IIa histone deacetylases (HDACs) belong to this category. Even though in vertebrates these deacetylases have discarded the core enzymatic activity, class IIa HDACs can assemble into multiprotein complexes devoted to transcriptional reprogramming, including but not limited to epigenetic changes. Class IIa HDACs are subjected to variegated and interconnected layers of regulation, which reflect the wide range of biological responses under the scrutiny of this gene family. Here, we discuss about the key mechanisms that fine tune class IIa HDACs activities.
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Affiliation(s)
- Eros Di Giorgio
- Department of Medical & Biological Sciences, Università degli Studi di Udine., P.le Kolbe 4 - 33100 Udine, Italy
| | - Claudio Brancolini
- Department of Medical & Biological Sciences, Università degli Studi di Udine., P.le Kolbe 4 - 33100 Udine, Italy
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