1
|
Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet 2024; 56:473-482. [PMID: 38361031 DOI: 10.1038/s41588-024-01658-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
Collapse
Affiliation(s)
- Satoko Ishii
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taishi Kakizuka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Tagawa
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Chiaki Sanbo
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Miyanari
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
- Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
| |
Collapse
|
2
|
Homma MK, Nakato R, Niida A, Bando M, Fujiki K, Yokota N, Yamamoto S, Shibata T, Takagi M, Yamaki J, Kozuka-Hata H, Oyama M, Shirahige K, Homma Y. Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes. Life Sci Alliance 2024; 7:e202302077. [PMID: 37907238 PMCID: PMC10618106 DOI: 10.26508/lsa.202302077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 11/02/2023] Open
Abstract
Nuclear expression of protein kinase CK2α is reportedly elevated in human carcinomas, but mechanisms underlying its variable localization in cells are poorly understood. This study demonstrates a functional connection between nuclear CK2 and gene expression in relation to cell proliferation. Growth stimulation of quiescent human normal fibroblasts and phospho-proteomic analysis identified a pool of CK2α that is highly phosphorylated at serine 7. Phosphorylated CK2α translocates into the nucleus, and this phosphorylation appears essential for nuclear localization and catalytic activity. Protein signatures associated with nuclear CK2 complexes reveal enrichment of apparently unique transcription factors and chromatin remodelers during progression through the G1 phase of the cell cycle. Chromatin immunoprecipitation-sequencing profiling demonstrated recruitment of CK2α to active gene loci, more abundantly in late G1 phase than in early G1, notably at transcriptional start sites of core histone genes, growth stimulus-associated genes, and ribosomal RNAs. Our findings reveal that nuclear CK2α complexes may be essential to facilitate progression of the cell cycle, by activating histone genes and triggering ribosomal biogenesis, specified in association with nuclear and nucleolar transcriptional regulators.
Collapse
Affiliation(s)
- Miwako Kato Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Ryuichiro Nakato
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - Atsushi Niida
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masashige Bando
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Katsunori Fujiki
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
| | - Naoko Yokota
- Laboratory of Computational Genomics, Institute for Quantitative Biosciences, University of Tokyo, Bunkyo, Japan
| | - So Yamamoto
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | | | - Motoki Takagi
- Translational Research Center, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Junko Yamaki
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, The Institute of Medical Science, The University of Tokyo, Minato, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo, Japan
- Department of Biosciences and Nutrition, Karolinska Institutet, Biomedicum, Stockholm, Sweden
- Department of Cell and Molecular Biology, Karolinska Institutet, Biomedicum, Stockholm, Sweden
| | - Yoshimi Homma
- Department of Biomolecular Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| |
Collapse
|
3
|
Zhang X, Wang Y, Lu J, Xiao L, Chen H, Li Q, Li YY, Xu P, Ruan C, Zhou H, Zhao Y. A conserved ZFX/WNT3 axis modulates the growth and imatinib response of chronic myeloid leukemia stem/progenitor cells. Cell Mol Biol Lett 2023; 28:83. [PMID: 37864206 PMCID: PMC10589942 DOI: 10.1186/s11658-023-00496-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 10/03/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Zinc finger protein X-linked (ZFX) has been shown to promote the growth of tumor cells, including leukemic cells. However, the role of ZFX in the growth and drug response of chronic myeloid leukemia (CML) stem/progenitor cells remains unclear. METHODS Real-time quantitative PCR (RT-qPCR) and immunofluorescence were used to analyze the expression of ZFX and WNT3 in CML CD34+ cells compared with normal control cells. Short hairpin RNAs (shRNAs) and clustered regularly interspaced short palindromic repeats/dead CRISPR-associated protein 9 (CRISPR/dCas9) technologies were used to study the role of ZFX in growth and drug response of CML cells. Microarray data were generated to compare ZFX-silenced CML CD34+ cells with their controls. Chromatin immunoprecipitation (ChIP) and luciferase reporter assays were performed to study the molecular mechanisms of ZFX to regulate WNT3 expression. RT-qPCR and western blotting were used to study the effect of ZFX on β-catenin signaling. RESULTS We showed that ZFX expression was significantly higher in CML CD34+ cells than in control cells. Overexpression and gene silencing experiments indicated that ZFX promoted the in vitro growth of CML cells, conferred imatinib mesylate (IM) resistance to these cells, and enhanced BCR/ABL-induced malignant transformation. Microarray data and subsequent validation revealed that WNT3 transcription was conservatively regulated by ZFX. WNT3 was highly expressed in CML CD34+ cells, and WNT3 regulated the growth and IM response of these cells similarly to ZFX. Moreover, WNT3 overexpression partially rescued ZFX silencing-induced growth inhibition and IM hypersensitivity. ZFX silencing decreased WNT3/β-catenin signaling, including c-MYC and CCND1 expression. CONCLUSION The present study identified a novel ZFX/WNT3 axis that modulates the growth and IM response of CML stem/progenitor cells.
Collapse
MESH Headings
- Humans
- Imatinib Mesylate/pharmacology
- Imatinib Mesylate/metabolism
- beta Catenin/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Stem Cells/metabolism
- Signal Transduction
- Drug Resistance, Neoplasm/genetics
- Neoplastic Stem Cells/metabolism
- Wnt3 Protein/metabolism
- Wnt3 Protein/pharmacology
Collapse
Affiliation(s)
- Xiuyan Zhang
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China.
- Jiangsu Institute of Hematology, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| | - Yu Wang
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China
| | - Jinchang Lu
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China
| | - Lun Xiao
- Department of Vascular Surgery, The Affiliated Drum Tower Hospital, Nanjing University Medical School, Nanjing, 210008, China
| | - Hui Chen
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China
| | - Quanxue Li
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Yuan-Yuan Li
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, 200237, China
| | - Peng Xu
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China
| | - Changgeng Ruan
- Jiangsu Institute of Hematology, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- National Clinical Research Center for Hematologic Diseases, Suzhou, 215006, China
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China
- MOE Engineering Center of Hematological Disease, Soochow University, Suzhou, 21513, China
| | - Haixia Zhou
- Jiangsu Institute of Hematology, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- National Clinical Research Center for Hematologic Diseases, Suzhou, 215006, China.
- MOE Engineering Center of Hematological Disease, Soochow University, Suzhou, 21513, China.
| | - Yun Zhao
- Cyrus Tang Medical Institute, Soochow University, Suzhou, 215123, China.
- National Clinical Research Center for Hematologic Diseases, Suzhou, 215006, China.
- Collaborative Innovation Center of Hematology, Soochow University, Suzhou, 215006, China.
- MOE Engineering Center of Hematological Disease, Soochow University, Suzhou, 21513, China.
| |
Collapse
|
4
|
Jin FF, Wang CJ, Cui L, Liu FF, Wang KL, Li WJ, Li ZG. Interaction of E2F3a and CASP8AP2 Regulates Histone Expression and Chemosensitivity of Leukemic Cells. J Pediatr Hematol Oncol 2023; 45:e339-e344. [PMID: 36162009 PMCID: PMC10030168 DOI: 10.1097/mph.0000000000002558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/15/2022] [Indexed: 11/27/2022]
Abstract
Low expression levels of E2F3a and caspase 8-associated protein 2 (CASP8AP2) are associated with poor outcomes in children with acute lymphoblastic leukemia. Our previous study showed that a combined assessment of E2F3a and CASP8AP2 expression was more accurate in predicting relapse in children with acute lymphoblastic leukemia. However, the underlying mechanism remains unclear. In this study, the interaction between E2F3a and CASP8AP2 and its role in the regulation of histone expression, cell proliferation, the cell cycle, and chemosensitivity were investigated. Exogenous E2F3a-GST was coprecipitated with CASP8AP2-FLAG in HEK-293T cells. E2F3a was colocalized with CASP8AP2-GFP in the nucleus. The replication-dependent histones H2A and H2B were significantly upregulated when E2F3a or CASP8AP2 was overexpressed in HEK-293T or 697 cells and downregulated by E2F3a or CASP8AP2 knockdown. E2F3a and CASP8AP2 could collaboratively enhance the transcriptional activity of HIST1H2AG and HIST1H2BK . Both CASP8AP2 and E2F3a are involved in S phase progression. E2F3a and CASP8AP2 also affected the sensitivity of leukemic cells to daunorubicin. Therefore, CASP8AP2 and E2F3a collaboratively regulated replication-dependent histone expression, cell cycle progression, and chemosensitivity of leukemic cells.
Collapse
Affiliation(s)
- Fen-fen Jin
- Beijing Key Laboratory of Pediatric Hematology-Oncology, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Diseases Laboratory, Hematology Center, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health
- Department of Hematology-Oncology, Children’s Hospital, Zhejiang University School of Medicine, The Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, Hangzhou, China
| | - Chan-juan Wang
- Beijing Key Laboratory of Pediatric Hematology-Oncology, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Diseases Laboratory, Hematology Center, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health
| | - Lei Cui
- Beijing Key Laboratory of Pediatric Hematology-Oncology, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Diseases Laboratory, Hematology Center, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health
| | - Fei-fei Liu
- Department of Pediatrics, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Kai-ling Wang
- Department of Pediatrics, Beijing Luhe Hospital, Capital Medical University, Beijing
| | - Wei-jing Li
- Beijing Key Laboratory of Pediatric Hematology-Oncology, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Diseases Laboratory, Hematology Center, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health
| | - Zhi-gang Li
- Beijing Key Laboratory of Pediatric Hematology-Oncology, National Key Discipline of Pediatrics, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematologic Diseases Laboratory, Hematology Center, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health
| |
Collapse
|
5
|
DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
Collapse
|
6
|
Zhou Y, Chai H, Guo L, Dai Z, Lai J, Duan J, Liu Y, Ding Q. Knockdown of CENPW Inhibits Hepatocellular Carcinoma Progression by Inactivating E2F Signaling. Technol Cancer Res Treat 2021; 20:15330338211007253. [PMID: 33973496 PMCID: PMC8120521 DOI: 10.1177/15330338211007253] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aim: This study aimed to evaluate the effects of centromere protein W (CENPW, also known as CUG2) in hepatocellular carcinoma (HCC). Methods: CENPW expression in HCC tissues and cells was detected by RT-qPCR assay. CCK-8 and colony formation assay were used to assess cell proliferation. Wound healing and Transwell assay was used to detect cell migration and invasion, respectively. The flow cytometry was used to analyze the cell cycle distribution and apoptosis. Results: CENPW expression was upregulated in HCC tissues and cells. Knockdown of CENPW inhibited cell proliferation, migration, and invasion and induced the G0/G1 phase arrest and cell apoptosis in HCC cells, which might involve the E2F signaling regulation. Conclusion: CENPW acted as an oncogenic role in HCC progression via activation E2F signaling. Our findings may provide new insights into the studying mechanisms of HCC.
Collapse
Affiliation(s)
- Yajing Zhou
- Department of Physical Therapy, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Hua Chai
- Department of Liver Disease, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Lei Guo
- Department of Infectious Diseases, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Zhongqiu Dai
- Department of Infectious Diseases, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Jianming Lai
- Medical College, 12593Qingdao University, Qingdao, Shandong, People's Republic of China
| | - Jianping Duan
- Department of Infectious Diseases, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Yanting Liu
- Department of Ten Areas of Liver Disease, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| | - Qian Ding
- Department of Infectious Diseases, Qingdao No.6 People's Hospital, Qingdao, Shandong, People's Republic of China
| |
Collapse
|
7
|
Ponte I, Andrés M, Jordan A, Roque A. Towards understanding the Regulation of Histone H1 Somatic Subtypes with OMICs. J Mol Biol 2020; 433:166734. [PMID: 33279581 DOI: 10.1016/j.jmb.2020.166734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
Histone H1 is involved in the regulation of chromatin higher-order structure and compaction. In humans, histone H1 is a multigene family with seven subtypes differentially expressed in somatic cells. Which are the regulatory mechanisms that determine the variability of the H1 complement is a long-standing biological question regarding histone H1. We have used a new approach based on the integration of OMICs data to address this issue. We have examined the 3D-chromatin structure, the binding of transcription factors (TFs), and the expression of somatic H1 genes in human cell lines, using data from public repositories, such as ENCODE. Analysis of Hi-C, ChIP-seq, and RNA-seq data, have revealed that transcriptional control has a greater impact on H1 regulation than previously thought. Somatic H1 genes located in topologically associated domains (TADs) show higher expression than in boundary regions. H1 genes are targeted by a variable number of transcription factors including cell cycle-related TFs, and tissue-specific TFs, suggesting a fine-tuned, subtype-specific transcriptional control. We describe, for the first time, that all H1 somatic subtypes are under transcriptional co-regulation. The replication-independent subtypes, which are encoded in different chromosomes isolated from other histone genes, are also co-regulated with the rest of the somatic H1 genes, indicating that transcriptional co-regulation extends beyond the histone cluster. Transcriptional control and transcriptional co-regulation explain, at least in part, the variability of H1 complement, the fluctuations of H1 subtypes during development, and also the compensatory effects observed, in model systems, after perturbation of one or more H1 subtypes.
Collapse
Affiliation(s)
- Inma Ponte
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Marta Andrés
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain
| | - Albert Jordan
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Alicia Roque
- Biochemistry and Molecular Biology Department, Bioscience Faculty, Autonomous University of Barcelona, Spain.
| |
Collapse
|
8
|
Abstract
Soon after fertilization the zebrafish embryo generates the pool of cells that will give rise to the germline and the three somatic germ layers of the embryo (ectoderm, mesoderm and endoderm). As the basic body plan of the vertebrate embryo emerges, evolutionarily conserved developmental signaling pathways, including Bmp, Nodal, Wnt, and Fgf, direct the nearly totipotent cells of the early embryo to adopt gene expression profiles and patterns of cell behavior specific to their eventual fates. Several decades of molecular genetics research in zebrafish has yielded significant insight into the maternal and zygotic contributions and mechanisms that pattern this vertebrate embryo. This new understanding is the product of advances in genetic manipulations and imaging technologies that have allowed the field to probe the cellular, molecular and biophysical aspects underlying early patterning. The current state of the field indicates that patterning is governed by the integration of key signaling pathways and physical interactions between cells, rather than a patterning system in which distinct pathways are deployed to specify a particular cell fate. This chapter focuses on recent advances in our understanding of the genetic and molecular control of the events that impart cell identity and initiate the patterning of tissues that are prerequisites for or concurrent with movements of gastrulation.
Collapse
Affiliation(s)
- Florence L Marlow
- Icahn School of Medicine Mount Sinai Department of Cell, Developmental and Regenerative Biology, New York, NY, United States.
| |
Collapse
|
9
|
Hsu J, Arand J, Chaikovsky A, Mooney NA, Demeter J, Brison CM, Oliverio R, Vogel H, Rubin SM, Jackson PK, Sage J. E2F4 regulates transcriptional activation in mouse embryonic stem cells independently of the RB family. Nat Commun 2019; 10:2939. [PMID: 31270324 PMCID: PMC6610666 DOI: 10.1038/s41467-019-10901-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 06/06/2019] [Indexed: 01/22/2023] Open
Abstract
E2F transcription factors are central regulators of cell division and cell fate decisions. E2F4 often represents the predominant E2F activity in cells. E2F4 is a transcriptional repressor implicated in cell cycle arrest and whose repressive activity depends on its interaction with members of the RB family. Here we show that E2F4 is important for the proliferation and the survival of mouse embryonic stem cells. In these cells, E2F4 acts in part as a transcriptional activator that promotes the expression of cell cycle genes. This role for E2F4 is independent of the RB family. Furthermore, E2F4 functionally interacts with chromatin regulators associated with gene activation and we observed decreased histone acetylation at the promoters of cell cycle genes and E2F targets upon loss of E2F4 in RB family-mutant cells. Taken together, our findings uncover a non-canonical role for E2F4 that provide insights into the biology of rapidly dividing cells. E2F transcription factors are regulators of cell division and cell fate decisions. Here the authors show that E2F4 is important for proliferation and survival of mouse ESCs, independent of the RB family, and that E2F4 interacts with chromatin regulators associated with gene activation.
Collapse
Affiliation(s)
- Jenny Hsu
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julia Arand
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Andrea Chaikovsky
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Nancie A Mooney
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Janos Demeter
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Caileen M Brison
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Romane Oliverio
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Hannes Vogel
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.,Department of Pathology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Seth M Rubin
- Department of Chemistry and Biochemistry, University of California, 1156 High Street, Santa Cruz, CA, 95064, USA
| | - Peter K Jackson
- Baxter Laboratory, Department of Microbiology & Immunology, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA
| | - Julien Sage
- Department of Pediatrics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA. .,Department of Genetics, 300 Pasteur Drive, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
10
|
Histone stress: an unexplored source of chromosomal instability in cancer? Curr Genet 2019; 65:1081-1088. [DOI: 10.1007/s00294-019-00967-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 02/27/2019] [Accepted: 04/03/2019] [Indexed: 01/24/2023]
|
11
|
Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
Collapse
Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| |
Collapse
|
12
|
Roy S, Gandra D, Seger C, Biswas A, Kushnir VA, Gleicher N, Kumar TR, Sen A. Oocyte-Derived Factors (GDF9 and BMP15) and FSH Regulate AMH Expression Via Modulation of H3K27AC in Granulosa Cells. Endocrinology 2018; 159:3433-3445. [PMID: 30060157 PMCID: PMC6112599 DOI: 10.1210/en.2018-00609] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 07/20/2018] [Indexed: 12/15/2022]
Abstract
Anti-Müllerian hormone (AMH) produced by ovarian granulosa cells (GCs) plays a crucial role in ovarian function. It is used as a diagnostic and/or prognostic marker of fertility as well as for pathophysiological conditions in women. In this study, we investigated the underlying mechanism for regulation of AMH expression in GCs using primary mouse GCs and a human GC tumor-derived KGN cell line. We find that growth differentiation factor 9 (GDF9) and bone morphogenetic factor 15 (BMP15) together (GDF9 + BMP15), but not when tested separately, significantly induce AMH expression in vitro and in vivo (serum AMH). Our results show that GDF9 + BMP15 through the PI3K/Akt and Smad2/3 pathways synergistically recruit the coactivator p300 on the AMH promoter region that promotes acetylation of histone 3 lysine 27 (H3K27ac), facilitating AMH/Amh expression. Intriguingly, we also find that FSH inhibits GDF9 + BMP15-induced increase of AMH/Amh expression. This inhibition occurs through FSH-induced protein kinase A/SF1-mediated expression of gonadotropin inducible ovarian transcription factor 1, a transcriptional repressor, that recruits histone deacetylase 2 to deacetylate H3K27ac, resulting in the suppression of AMH/Amh expression. Furthermore, we report that ovarian Amh mRNA levels are significantly higher in Fshβ-null mice (Fshβ-/-) compared with those in wild-type (WT) mice. In addition, ovarian Amh mRNA levels are restored in Fshβ-null mice expressing a human WT FSHβ transgene (FSHβ-/-hFSHβWT). Our study provides a mechanistic insight into the regulation of AMH expression that has many implications in female reproduction/fertility.
Collapse
Affiliation(s)
- Sambit Roy
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | - Divya Gandra
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | - Christina Seger
- Division of Endocrinology and Metabolism, Department of Medicine, University of Rochester Medical Center, Rochester, New York
| | - Anindita Biswas
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
| | | | - Norbert Gleicher
- Center for Human Reproduction, New York, New York
- Stem Cell Biology and Molecular Embryology Laboratory, The Rockefeller University, New York, New York
- Department of Obstetrics and Gynecology, Vienna University of Medicine, Vienna, Austria
| | - T Rajendra Kumar
- Division of Reproductive Sciences, Department of Obstetrics and Gynecology, University of Colorado Anschutz, Denver, Colorado
| | - Aritro Sen
- Reproductive and Developmental Sciences Program, Department of Animal Sciences, Michigan State University, East Lansing, Michigan
- Correspondence: Aritro Sen, PhD, Reproductive and Developmental Sciences Program, Department of Animal Sciences, 1230A Anthony Hall, Michigan State University, East Lansing, Michigan 48824. E-mail:
| |
Collapse
|
13
|
Chitwood JL, Burruel VR, Halstead MM, Meyers SA, Ross PJ. Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos. Biol Reprod 2018; 97:353-364. [PMID: 29025079 DOI: 10.1093/biolre/iox114] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 09/01/2017] [Indexed: 11/12/2022] Open
Abstract
Early mammalian embryonic transcriptomes are dynamic throughout the process of preimplantation development. Cataloging of primate transcriptomics during early development has been accomplished in humans, but global characterization of transcripts is lacking in the rhesus macaque: a key model for human reproductive processes. We report here the systematic classification of individual macaque transcriptomes using RNA-Seq technology from the germinal vesicle stage oocyte through the blastocyst stage embryo. Major differences in gene expression were found between sequential stages, with the 4- to 8-cell stages showing the highest level of differential gene expression. Analysis of putative transcription factor binding sites also revealed a striking increase in key regulatory factors in 8-cell embryos, indicating a strong likelihood of embryonic genome activation occurring at this stage. Furthermore, clustering analyses of gene co-expression throughout this period resulted in distinct groups of transcripts significantly associated to the different embryo stages assayed. The sequence data provided here along with characterizations of major regulatory transcript groups present a comprehensive atlas of polyadenylated transcripts that serves as a useful resource for comparative studies of preimplantation development in humans and other species.
Collapse
Affiliation(s)
- James L Chitwood
- Department of Animal Science, University of California, Davis, California, USA
| | - Victoria R Burruel
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, California, USA
| | - Stuart A Meyers
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, California, USA
| |
Collapse
|
14
|
Zhang X, Biagini Myers JM, Burleson JD, Ulm A, Bryan KS, Chen X, Weirauch MT, Baker TA, Butsch Kovacic MS, Ji H. Nasal DNA methylation is associated with childhood asthma. Epigenomics 2018; 10:629-641. [PMID: 29692198 DOI: 10.2217/epi-2017-0127] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
AIM We aim to study DNA methylation (DNAm) variations associated with childhood asthma. METHODS Nasal DNAm was compared between sibling pairs discordant for asthma, 29 sib pairs for genome-wide association studies and 54 sib pairs for verification by pyrosequencing. Associations of methylation with asthma symptoms, allergy and environmental exposures were evaluated. In vitro experiments and functional genomic analyses were performed to explore biologic relevance. RESULTS Three CpGs were associated with asthma. cg14830002 was associated with allergies in nonasthmatics. cg23602092 was associated with asthma symptoms. cg14830002 and cg23602092 were associated with traffic-related air pollution exposure. Nearby genes were transcriptionally regulated by diesel exhaust, house dust mite and 5-aza-2'-deoxycytidine. Active chromatin marks and transcription factor binding were found around these sites. CONCLUSION We identified novel DNAm variations associated with childhood asthma and suggested new disease-contributing epigenetic mechanisms.
Collapse
Affiliation(s)
- Xue Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jocelyn M Biagini Myers
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - J D Burleson
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Ashley Ulm
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kelly S Bryan
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Xiaoting Chen
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| | - Matthew T Weirauch
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Center for Autoimmune Genomics & Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Divisions of Biomedical Informatics & Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Theresa A Baker
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Melinda S Butsch Kovacic
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA.,Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Environmental Health, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Hong Ji
- Pyrosequencing Lab for Genomic & Epigenomic Research, Cincinnati, Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati, Cincinnati, OH 45229, USA
| |
Collapse
|
15
|
Liu FF, Wang KL, Deng LP, Liu X, Wu MY, Wang TY, Cui L, Li ZG. Transcription factor E2F3a regulates CASP8AP2 transcription and enhances sensitivity to chemotherapeutic drugs in acute lymphoblastic leukemia. Cancer Cell Int 2018; 18:40. [PMID: 29568235 PMCID: PMC5859744 DOI: 10.1186/s12935-018-0531-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 03/02/2018] [Indexed: 11/24/2022] Open
Abstract
Background Low expression of E2F3a and caspase 8 associated protein 2 (CASP8AP2) are associated with poor prognosis of childhood acute lymphoblastic leukemia (ALL). Methods Dual-luciferase reporter assay and wild type as well as four mutated types of reporter plasmids were used to demonstrate the activation of E2F3a on CASP8AP2 transcription. The direct binding of E2F3a with the promoter of CASP8AP2 was shown by Chromatin Immunoprecipitation (ChIP). Cell proliferation activity and cell cycle were determined by MTS and flow cytometry in leukemic cells after treating with common chemotherapeutic drugs vincristine and daunorubicin. Results In this study, we found that up-regulation of E2F3a in leukemic cells led to increased fraction of cells in S and G2/M phase, accelerated proliferation, and enhanced sensitivity to vincristine and daunorubicin. ChIP and luciferase assay indicated that E2F3a could directly bind to two fragments in the wild type of CASP8AP2 promotor (− 206 to − 69 and − 677 to − 507), and activate its transcription activity which was reduced in mutated promotors. The effect of E2F3a on chemotherapeutic sensitivity of leukemic cells could be reversed by down-regulating CASP8AP2. Conclusions E2F3a could promote transcription and expression of CASP8AP2. The effect of E2F3a on chemotherapeutic sensitivity of ALL cells was implemented by regulating CASP8AP2 expression to a great extent.
Collapse
Affiliation(s)
- Fei-Fei Liu
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China.,3Present Address: Department of Pediatrics, Affiliated Hospital of Binzhou Medical University, Binzhou, 256603 Shandong Province China
| | - Kai-Ling Wang
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China.,4Present Address: Department of Pediatrics, Beijing Luhe Hospital, Capital Medical University, 82 Xinhua Nan Road, Tongzhou District, Beijing, 101149 China
| | - Li-Ping Deng
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| | - Xiao Liu
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| | - Min-Yuan Wu
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| | - Tian-You Wang
- Hematology & Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| | - Lei Cui
- Hematology & Oncology Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| | - Zhi-Gang Li
- Hematology & Oncology Laboratory, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health; Beijing Key Laboratory of Pediatric Hematology Oncology; Key Laboratory of Major Diseases in Children, Ministry of Education; National Key Discipline of Pediatrics, Ministry of Education, Beijing, China
| |
Collapse
|
16
|
Castro-Mondragon JA, Jaeger S, Thieffry D, Thomas-Chollier M, van Helden J. RSAT matrix-clustering: dynamic exploration and redundancy reduction of transcription factor binding motif collections. Nucleic Acids Res 2017; 45:e119. [PMID: 28591841 PMCID: PMC5737723 DOI: 10.1093/nar/gkx314] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 06/04/2017] [Indexed: 01/08/2023] Open
Abstract
Transcription factor (TF) databases contain multitudes of binding motifs (TFBMs) from various sources, from which non-redundant collections are derived by manual curation. The advent of high-throughput methods stimulated the production of novel collections with increasing numbers of motifs. Meta-databases, built by merging these collections, contain redundant versions, because available tools are not suited to automatically identify and explore biologically relevant clusters among thousands of motifs. Motif discovery from genome-scale data sets (e.g. ChIP-seq) also produces redundant motifs, hampering the interpretation of results. We present matrix-clustering, a versatile tool that clusters similar TFBMs into multiple trees, and automatically creates non-redundant TFBM collections. A feature unique to matrix-clustering is its dynamic visualisation of aligned TFBMs, and its capability to simultaneously treat multiple collections from various sources. We demonstrate that matrix-clustering considerably simplifies the interpretation of combined results from multiple motif discovery tools, and highlights biologically relevant variations of similar motifs. We also ran a large-scale application to cluster ∼11 000 motifs from 24 entire databases, showing that matrix-clustering correctly groups motifs belonging to the same TF families, and drastically reduced motif redundancy. matrix-clustering is integrated within the RSAT suite (http://rsat.eu/), accessible through a user-friendly web interface or command-line for its integration in pipelines.
Collapse
Affiliation(s)
| | | | - Denis Thieffry
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Morgane Thomas-Chollier
- IBENS, Département de Biologie, Ecole Normale Supérieure, CNRS, Inserm, PSL Research University, F-75005 Paris, France
| | - Jacques van Helden
- Aix Marseille Univ, INSERM, TAGC, Theory and Approaches of Genomic Complexity, UMR_S 1090, Marseille, France
| |
Collapse
|
17
|
Marzluff WF, Koreski KP. Birth and Death of Histone mRNAs. Trends Genet 2017; 33:745-759. [PMID: 28867047 DOI: 10.1016/j.tig.2017.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022]
Abstract
In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73. Histone mRNAs are rapidly degraded when DNA replication is inhibited by a 3' to 5' pathway that requires extensive uridylation of mRNA decay intermediates.
Collapse
Affiliation(s)
- William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kaitlin P Koreski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| |
Collapse
|
18
|
Shen ZG, Liu XZ, Chen CX, Lu JM. Knockdown of E2F3 Inhibits Proliferation, Migration, and Invasion and Increases Apoptosis in Glioma Cells. Oncol Res 2017; 25:1555-1566. [PMID: 28337965 PMCID: PMC7841128 DOI: 10.3727/096504017x14897158009178] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
E2F3a, as a member of the E2F family, is essential for cell division associated with the progression of many cancers. However, the biological effect of E2F3a on glioma is not understood as well. To investigate the functional mechanism of E2F3a in glioma, we examined the expression of E2F3a in glioma tissue and cell lines. We found that E2F3a was upregulated in glioma tissue compared with adjacent tissue, and this was associated with a poor survival rate. E2F3a was highly expressed in glioma cell lines compared with normal HEB cell lines. Knockdown of E2F3a significantly inhibited cell proliferation, promoted G0/G1 phase arrest, elevated apoptosis rates, and suppressed cell migration and invasion. However, overexpression of E2F3a markedly promoted cell proliferation, migration, and invasion and inhibited apoptosis. Moreover, in vivo studies showed that knockdown of E2F3a expression dramatically inhibited U373 tumor growth in a nude mouse model. Results of real-time PCR and Western blot showed that the depletion of E2F3a upregulated the expression levels of cell apoptosis-related proteins and downregulated migration-related proteins. Conversely, E2F3a overexpression downregulated the expression levels of cell apoptosis-related proteins and upregulated migration-related proteins. In conclusion, our results highlight the importance of E2F3a in glioma and provide new insights into the diagnostics and therapeutics of gliomas.
Collapse
|
19
|
Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expression. Proc Natl Acad Sci U S A 2017; 114:1619-1624. [PMID: 28143937 DOI: 10.1073/pnas.1621356114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rett syndrome (RS) is a debilitating neurological disorder affecting mostly girls with heterozygous mutations in the gene encoding the methyl-CpG-binding protein MeCP2 on the X chromosome. Because restoration of MeCP2 expression in a mouse model reverses neurologic deficits in adult animals, reactivation of the wild-type copy of MeCP2 on the inactive X chromosome (Xi) presents a therapeutic opportunity in RS. To identify genes involved in MeCP2 silencing, we screened a library of 60,000 shRNAs using a cell line with a MeCP2 reporter on the Xi and found 30 genes clustered in seven functional groups. More than half encoded proteins with known enzymatic activity, and six were members of the bone morphogenetic protein (BMP)/TGF-β pathway. shRNAs directed against each of these six genes down-regulated X-inactive specific transcript (XIST), a key player in X-chromosome inactivation that encodes an RNA that coats the silent X chromosome, and modulation of regulators of this pathway both in cell culture and in mice demonstrated robust regulation of XIST. Moreover, we show that Rnf12, an X-encoded ubiquitin ligase important for initiation of X-chromosome inactivation and XIST transcription in ES cells, also plays a role in maintenance of the inactive state through regulation of BMP/TGF-β signaling. Our results identify pharmacologically suitable targets for reactivation of MeCP2 on the Xi and a genetic circuitry that maintains XIST expression and X-chromosome inactivation in differentiated cells.
Collapse
|
20
|
Sokolova M, Turunen M, Mortusewicz O, Kivioja T, Herr P, Vähärautio A, Björklund M, Taipale M, Helleday T, Taipale J. Genome-wide screen of cell-cycle regulators in normal and tumor cells identifies a differential response to nucleosome depletion. Cell Cycle 2016; 16:189-199. [PMID: 27929715 PMCID: PMC5283814 DOI: 10.1080/15384101.2016.1261765] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
To identify cell cycle regulators that enable cancer cells to replicate DNA and divide in an unrestricted manner, we performed a parallel genome-wide RNAi screen in normal and cancer cell lines. In addition to many shared regulators, we found that tumor and normal cells are differentially sensitive to loss of the histone genes transcriptional regulator CASP8AP2. In cancer cells, loss of CASP8AP2 leads to a failure to synthesize sufficient amount of histones in the S-phase of the cell cycle, resulting in slowing of individual replication forks. Despite this, DNA replication fails to arrest, and tumor cells progress in an elongated S-phase that lasts several days, finally resulting in death of most of the affected cells. In contrast, depletion of CASP8AP2 in normal cells triggers a response that arrests viable cells in S-phase. The arrest is dependent on p53, and preceded by accumulation of markers of DNA damage, indicating that nucleosome depletion is sensed in normal cells via a DNA-damage -like response that is defective in tumor cells.
Collapse
Affiliation(s)
- Maria Sokolova
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Mikko Turunen
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Oliver Mortusewicz
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Teemu Kivioja
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Patrick Herr
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Anna Vähärautio
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Mikael Björklund
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland
| | - Minna Taipale
- c Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Thomas Helleday
- b Science for Life laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| | - Jussi Taipale
- a Genome-Scale Biology Program, University of Helsinki , Helsinki , Finland.,c Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Stockholm , Sweden
| |
Collapse
|
21
|
Wu J, Xiao L, Zhou H, Liu H, Ge Y, Yang J, Li Y, Wu D, Zhao Y, Zhang X. ZFX modulates the growth of human leukemic cells via B4GALT1. Acta Biochim Biophys Sin (Shanghai) 2016; 48:1120-1127. [PMID: 27797721 DOI: 10.1093/abbs/gmw109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 09/04/2016] [Indexed: 11/14/2022] Open
Abstract
Zinc finger protein X-linked (ZFX) is a key regulator of both embryonic stem cells (ESCs) and hematopoietic stem cells (HSCs), which is required for both Notch intracellular domain (NotchIC)-induced acute T-cell leukemia and MLL-AF9-induced myeloid leukemia in mouse models. However, the role of ZFX and its underlying mechanism in human leukemic cells remain unclear yet, though accumulating data have demonstrated that ZFX is aberrantly expressed in various human tumors and plays an important role. Herein, we found that ZFX was aberrantly expressed in various human leukemic cell lines and primary cells from leukemia patients compared with control cells. The silence of ZFX led to the growth suppression through either the deregulated cell cycle or the induction of apoptosis in various cells including K562, Jurkat, Namalwa, and THP-1 cells. The gene expression analysis revealed that UDP-Gal:βGlcNAc β 1,4-galactosyltransferase, polypeptide 1 (B4GALT1) was significantly down-regulated upon ZFX silencing, which is implicated in the response of K562 cells to the treatment of imatinib mesylate (IM). In addition, lectin blot assay showed that the galactosylation of glycoproteins in K562 cells was suppressed upon ZFX silencing. Interestingly, overexpression of B4GALT1 restored the growth and conferred drug resistance to ZFX-silenced cells. Taken together, we have demonstrated that ZFX is aberrantly expressed in multiple human leukemic cells and it modulates the growth and drug response of leukemic cells partially via B4GALT1, which suggests that ZFX is a new regulator of leukemic cells and warrants intensive investigations on this 'stemness' regulator in these deadly diseases.
Collapse
Affiliation(s)
- Jie Wu
- Cyrus Tang Hematology Center , Soochow University, Suzhou 215123, China
| | - Lun Xiao
- Cyrus Tang Hematology Center , Soochow University, Suzhou 215123, China
| | - Haixia Zhou
- The First Affiliated Hospital, Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis, Soochow University, Suzhou 215006, China
| | - Hong Liu
- The First Affiliated Hospital, Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis, Soochow University, Suzhou 215006, China
| | - Yue Ge
- Cyrus Tang Hematology Center , Soochow University, Suzhou 215123, China
| | - Jing Yang
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Yuanyuan Li
- Shanghai Center for Bioinformation Technology, Shanghai 200235, China
| | - Depei Wu
- The First Affiliated Hospital, Jiangsu Institute of Hematology, Key Laboratory of Thrombosis and Hemostasis, Soochow University, Suzhou 215006, China
- The Collaborative Innovation Center of Hematology , Soochow University, Suzhou 215006, China
| | - Yun Zhao
- Cyrus Tang Hematology Center , Soochow University, Suzhou 215123, China
- The Collaborative Innovation Center of Hematology , Soochow University, Suzhou 215006, China
| | - Xiuyan Zhang
- Cyrus Tang Hematology Center , Soochow University, Suzhou 215123, China
- The Collaborative Innovation Center of Hematology , Soochow University, Suzhou 215006, China
| |
Collapse
|
22
|
Xu S, Duan P, Li J, Senkowski T, Guo F, Chen H, Romero A, Cui Y, Liu J, Jiang SW. Zinc Finger and X-Linked Factor (ZFX) Binds to Human SET Transcript 2 Promoter and Transactivates SET Expression. Int J Mol Sci 2016; 17:ijms17101737. [PMID: 27775603 PMCID: PMC5085766 DOI: 10.3390/ijms17101737] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 09/24/2016] [Accepted: 10/08/2016] [Indexed: 02/05/2023] Open
Abstract
SET (SE Translocation) protein carries out multiple functions including those for protein phosphatase 2A (PP2A) inhibition, histone modification, DNA repair, and gene regulation. SET overexpression has been detected in brain neurons of patients suffering Alzheimer's disease, follicle theca cells of Polycystic Ovary Syndrome (PCOS) patients, and ovarian cancer cells, indicating that SET may play a pathological role for these disorders. SET transcript 2, produced by a specific promoter, represents a major transcript variant in different cell types. In this study, we characterized the transcriptional activation of human SET transcript 2 promoter in HeLa cells. Promoter deletion experiments and co-transfection assays indicated that ZFX, the Zinc finger and X-linked transcription factor, was able to transactivate the SET promoter. A proximal promoter region containing four ZFX-binding sites was found to be critical for the ZFX-mediated transactivation. Mutagenesis study indicated that the ZFX-binding site located the closest to the transcription start site accounted for most of the ZFX-mediated transactivity. Manipulation of ZFX levels by overexpression or siRNA knockdown confirmed the significance and specificity of the ZFX-mediated SET promoter activation. Chromatin immunoprecipitation results verified the binding of ZFX to its cognate sites in the SET promoter. These findings have led to identification of ZFX as an upstream factor regulating SET gene expression. More studies are required to define the in vivo significance of this mechanism, and specifically, its implication for several benign and malignant diseases related to SET dysregulation.
Collapse
Affiliation(s)
- Siliang Xu
- The State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
| | - Ping Duan
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China.
| | - Jinping Li
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
| | - Tristan Senkowski
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
| | - Fengbiao Guo
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515000, China.
| | - Haibin Chen
- Department of Histology and Embryology, Shantou University Medical College, Shantou 515000, China.
| | - Alberto Romero
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
| | - Yugui Cui
- The State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.
| | - Jiayin Liu
- The State Key Laboratory of Reproductive Medicine, Clinical Center of Reproductive Medicine, First Affiliated Hospital, Nanjing Medical University, Nanjing 210029, China.
| | - Shi-Wen Jiang
- Department of Biomedical Science, Mercer University School of Medicine, Savannah, GA 31404, USA.
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, China.
| |
Collapse
|
23
|
Ding N, Xi J, Li Y, Xie X, Shi J, Zhang Z, Li Y, Fang F, Wang S, Yue W, Pei X, Fang X. Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation. Front Med 2016; 10:297-310. [PMID: 27272188 DOI: 10.1007/s11684-016-0452-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/22/2016] [Indexed: 12/26/2022]
Abstract
Studies on coding genes, miRNAs, and lncRNAs during erythroid development have been performed in recent years. However, analysis focusing on the integration of the three RNA types has yet to be done. In the present study, we compared the dynamics of coding genes, miRNA, and lncRNA expression profiles. To explore dynamic changes in erythropoiesis and potential mechanisms that control these changes in the transcriptome level, we took advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differentiation stages, as well as from mature red blood cells. Results indicated that lncRNAs were promising cell marker candidates for erythroid differentiation. Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation. Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation, and especially associated with heme metabolism and responses to oxygen species and DNA damage. These regulatory interactions were displayed in a comprehensive network, thereby inferring correlations between RNAs and their associated functions. These data provided a substantial resource for the study of normal erythropoiesis, which will permit further investigation and understanding of erythroid development and acquired erythroid disorders.
Collapse
Affiliation(s)
- Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jiafei Xi
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Yanming Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaoyan Xie
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Jian Shi
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhaojun Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yanhua Li
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Fang Fang
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Sihan Wang
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Wen Yue
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China.,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China
| | - Xuetao Pei
- Lab of Stem Cell and Regenerative Medicine, Beijing Institute of Transfusion Medicine, AMMS, Beijing, 100850, China. .,South China Research Center for Stem Cell & Regenerative Medicine, AMMS, Guangzhou, 510300, China.
| | - Xiangdong Fang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Millán-Ariño L, Izquierdo-Bouldstridge A, Jordan A. Specificities and genomic distribution of somatic mammalian histone H1 subtypes. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:510-9. [DOI: 10.1016/j.bbagrm.2015.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 11/15/2022]
|
26
|
Livyatan I, Aaronson Y, Gokhman D, Ashkenazi R, Meshorer E. BindDB: An Integrated Database and Webtool Platform for “Reverse-ChIP” Epigenomic Analysis. Cell Stem Cell 2015; 17:647-648. [DOI: 10.1016/j.stem.2015.11.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
27
|
Han T, Oh S, Kang K. ETS family protein GABP is a novel co-factor strongly associated with genomic YY1 binding sites in various cell lines. Genes Genomics 2015. [DOI: 10.1007/s13258-015-0358-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
28
|
Fang X, Huang Z, Zhou W, Wu Q, Sloan AE, Ouyang G, McLendon RE, Yu JS, Rich JN, Bao S. The zinc finger transcription factor ZFX is required for maintaining the tumorigenic potential of glioblastoma stem cells. Stem Cells 2015; 32:2033-47. [PMID: 24831540 DOI: 10.1002/stem.1730] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 03/20/2014] [Accepted: 04/04/2014] [Indexed: 12/11/2022]
Abstract
Glioblastomas are highly lethal brain tumors containing tumor-propagating glioma stem cells (GSCs). The molecular mechanisms underlying the maintenance of the GSC phenotype are not fully defined. Here we demonstrate that the zinc finger and X-linked transcription factor (ZFX) maintains GSC self-renewal and tumorigenic potential by upregulating c-Myc expression. ZFX is differentially expressed in GSCs relative to non-stem glioma cells and neural progenitor cells. Disrupting ZFX by shRNA reduced c-Myc expression and potently inhibited GSC self-renewal and tumor growth. Ectopic expression of c-Myc to its endogenous level rescued the effects caused by ZFX disruption, supporting that ZFX controls GSC properties through c-Myc. Furthermore, ZFX binds to a specific sequence (GGGCCCCG) on the human c-Myc promoter to upregulate c-Myc expression. These data demonstrate that ZFX functions as a critical upstream regulator of c-Myc and plays essential roles in the maintenance of the GSC phenotype. This study also supports that c-Myc is a dominant driver linking self-renewal to malignancy.
Collapse
Affiliation(s)
- Xiaoguang Fang
- Department of Stem Cell Biology and Regenerative Medicine, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Heterochromatin Protein 1β (HP1β) has distinct functions and distinct nuclear distribution in pluripotent versus differentiated cells. Genome Biol 2015; 16:213. [PMID: 26415775 PMCID: PMC4587738 DOI: 10.1186/s13059-015-0760-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/25/2015] [Indexed: 11/22/2022] Open
Abstract
Background Pluripotent embryonic stem cells (ESCs) have the unique ability to differentiate into every cell type and to self-renew. These characteristics correlate with a distinct nuclear architecture, epigenetic signatures enriched for active chromatin marks and hyperdynamic binding of structural chromatin proteins. Recently, several chromatin-related proteins have been shown to regulate ESC pluripotency and/or differentiation, yet the role of the major heterochromatin proteins in pluripotency is unknown. Results Here we identify Heterochromatin Protein 1β (HP1β) as an essential protein for proper differentiation, and, unexpectedly, for the maintenance of pluripotency in ESCs. In pluripotent and differentiated cells HP1β is differentially localized and differentially associated with chromatin. Deletion of HP1β, but not HP1α, in ESCs provokes a loss of the morphological and proliferative characteristics of embryonic pluripotent cells, reduces expression of pluripotency factors and causes aberrant differentiation. However, in differentiated cells, loss of HP1β has the opposite effect, perturbing maintenance of the differentiation state and facilitating reprogramming to an induced pluripotent state. Microscopy, biochemical fractionation and chromatin immunoprecipitation reveal a diffuse nucleoplasmic distribution, weak association with chromatin and high expression levels for HP1β in ESCs. The minor fraction of HP1β that is chromatin-bound in ESCs is enriched within exons, unlike the situation in differentiated cells, where it binds heterochromatic satellite repeats and chromocenters. Conclusions We demonstrate an unexpected duality in the role of HP1β: it is essential in ESCs for maintaining pluripotency, while it is required for proper differentiation in differentiated cells. Thus, HP1β function both depends on, and regulates, the pluripotent state. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0760-8) contains supplementary material, which is available to authorized users.
Collapse
|
30
|
Ramirez VP, Stamatis M, Shmukler A, Aneskievich BJ. Basal and stress-inducible expression of HSPA6 in human keratinocytes is regulated by negative and positive promoter regions. Cell Stress Chaperones 2015; 20:95-107. [PMID: 25073946 PMCID: PMC4255259 DOI: 10.1007/s12192-014-0529-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 01/08/2023] Open
Abstract
Epidermal keratinocytes serve as the primary barrier between the body and environmental stressors. They are subjected to numerous stress events and are likely to respond with a repertoire of heat shock proteins (HSPs). HSPA6 (HSP70B') is described in other cell types with characteristically low to undetectable basal expression, but is highly stress induced. Despite this response in other cells, little is known about its control in keratinocytes. We examined endogenous human keratinocyte HSPA6 expression and localized some responsible transcription factor sites in a cloned HSPA6 3 kb promoter. Using promoter 5' truncations and deletions, negative and positive regulatory regions were found throughout the 3 kb promoter. A region between -346 and -217 bp was found to be crucial to HSPA6 basal expression and stress inducibility. Site-specific mutations and DNA-binding studies show that a previously uncharacterized AP1 site contributes to the basal expression and maximal stress induction of HSPA6. Additionally, a new heat shock element (HSE) within this region was defined. While this element mediates increased transcriptional response in thermally stressed HaCaT keratinocytes, it preferentially binds a stress-inducible factor other than heat shock factor (HSF)1 or HSF2. Intriguingly, this newly characterized HSPA6 HSE competes HSF1 binding a consensus HSE and binds both HSF1 and HSF2 from other epithelial cells. Taken together, our results demonstrate that the HSPA6 promoter contains essential negative and positive promoter regions and newly identified transcription factor targets, which are key to the basal and stress-inducible expression of HSPA6. Furthermore, these results suggest that an HSF-like factor may preferentially bind this newly identified HSPA6 HSE in HaCaT cells.
Collapse
Affiliation(s)
- Vincent P. Ramirez
- />Graduate Program in Pharmacology and Toxicology, Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Michael Stamatis
- />Doctor of Pharmacy Program, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Anastasia Shmukler
- />Doctor of Pharmacy Program, School of Pharmacy, University of Connecticut, Storrs, CT 06269-3092 USA
| | - Brian J. Aneskievich
- />Department of Pharmaceutical Sciences, School of Pharmacy, University of Connecticut, U-3092, 69 North Eagleville Road, Storrs, CT 06269-3092 USA
- />University of Connecticut Stem Cell Institute, Storrs, CT 06269-3092 USA
| |
Collapse
|
31
|
Nelson AC, Cutty SJ, Niini M, Stemple DL, Flicek P, Houart C, Bruce AEE, Wardle FC. Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression. BMC Biol 2014; 12:81. [PMID: 25277163 PMCID: PMC4206766 DOI: 10.1186/s12915-014-0081-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Indexed: 12/27/2022] Open
Abstract
Background Nodal signalling is an absolute requirement for normal mesoderm and endoderm formation in vertebrate embryos, yet the transcriptional networks acting directly downstream of Nodal and the extent to which they are conserved is largely unexplored, particularly in vivo. Eomesodermin also plays a role in patterning mesoderm and endoderm in vertebrates, but its mechanisms of action and how it interacts with the Nodal signalling pathway are still unclear. Results Using a combination of expression analysis and chromatin immunoprecipitation with deep sequencing (ChIP-seq) we identify direct targets of Smad2, the effector of Nodal signalling in blastula stage zebrafish embryos, including many novel target genes. Through comparison of these data with published ChIP-seq data in human, mouse and Xenopus we show that the transcriptional network driven by Smad2 in mesoderm and endoderm is conserved in these vertebrate species. We also show that Smad2 and zebrafish Eomesodermin a (Eomesa) bind common genomic regions proximal to genes involved in mesoderm and endoderm formation, suggesting Eomesa forms a general component of the Smad2 signalling complex in zebrafish. Combinatorial perturbation of Eomesa and Smad2-interacting factor Foxh1 results in loss of both mesoderm and endoderm markers, confirming the role of Eomesa in endoderm formation and its functional interaction with Foxh1 for correct Nodal signalling. Finally, we uncover a novel role for Eomesa in repressing ectodermal genes in the early blastula. Conclusions Our data demonstrate that evolutionarily conserved developmental functions of Nodal signalling occur through maintenance of the transcriptional network directed by Smad2. This network is modulated by Eomesa in zebrafish which acts to promote mesoderm and endoderm formation in combination with Nodal signalling, whilst Eomesa also opposes ectoderm gene expression. Eomesa, therefore, regulates the formation of all three germ layers in the early zebrafish embryo. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0081-5) contains supplementary material, which is available to authorized users.
Collapse
|
32
|
Blumberg A, Sri Sailaja B, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D. Transcription factors bind negatively selected sites within human mtDNA genes. Genome Biol Evol 2014; 6:2634-46. [PMID: 25245407 PMCID: PMC4224337 DOI: 10.1093/gbe/evu210] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Transcription of mitochondrial DNA (mtDNA)-encoded genes is thought to be regulated by a handful of dedicated transcription factors (TFs), suggesting that mtDNA genes are separately regulated from the nucleus. However, several TFs, with known nuclear activities, were found to bind mtDNA and regulate mitochondrial transcription. Additionally, mtDNA transcriptional regulatory elements, which were proved important in vitro, were harbored by a deletion that normally segregated among healthy individuals. Hence, mtDNA transcriptional regulation is more complex than once thought. Here, by analyzing ENCODE chromatin immunoprecipitation sequencing (ChIP-seq) data, we identified strong binding sites of three bona fide nuclear TFs (c-Jun, Jun-D, and CEBPb) within human mtDNA protein-coding genes. We validated the binding of two TFs by ChIP-quantitative polymerase chain reaction (c-Jun and Jun-D) and showed their mitochondrial localization by electron microscopy and subcellular fractionation. As a step toward investigating the functionality of these TF-binding sites (TFBS), we assessed signatures of selection. By analyzing 9,868 human mtDNA sequences encompassing all major global populations, we recorded genetic variants in tips and nodes of mtDNA phylogeny within the TFBS. We next calculated the effects of variants on binding motif prediction scores. Finally, the mtDNA variation pattern in predicted TFBS, occurring within ChIP-seq negative-binding sites, was compared with ChIP-seq positive-TFBS (CPR). Motifs within CPRs of c-Jun, Jun-D, and CEBPb harbored either only tip variants or their nodal variants retained high motif prediction scores. This reflects negative selection within mtDNA CPRs, thus supporting their functionality. Hence, human mtDNA-coding sequences may have dual roles, namely coding for genes yet possibly also possessing regulatory potential.
Collapse
Affiliation(s)
- Amit Blumberg
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Badi Sri Sailaja
- Department of Genetics, The Institute of Life Sciences, and The Edmond Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Israel
| | - Anshul Kundaje
- Department of Genetics, Stanford University Department of Computer Science, Stanford University
| | - Liron Levin
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Sara Dadon
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Shimrit Shmorak
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Medical School, Ein Karem, Jerusalem, Israel
| | - Eitan Shaulian
- Department of Biochemistry and Molecular Biology, IMRIC, The Hebrew University Medical School, Ein Karem, Jerusalem, Israel
| | - Eran Meshorer
- Department of Genetics, The Institute of Life Sciences, and The Edmond Lily Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
| |
Collapse
|
33
|
Wang KL, Mei YY, Cui L, Zhao XX, Li WJ, Gao C, Liu SG, Jiao Y, Liu FF, Wu MY, Ding W, Li ZG. E2F3agene expression has prognostic significance in childhood acute lymphoblastic leukemia. Eur J Haematol 2014; 93:281-9. [PMID: 24758291 DOI: 10.1111/ejh.12341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2014] [Indexed: 01/27/2023]
Affiliation(s)
- Kai-Ling Wang
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Yan-Yan Mei
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Lei Cui
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Xiao-Xi Zhao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Wei-Jing Li
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Chao Gao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Shu-Guang Liu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Ying Jiao
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Fei-Fei Liu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Min-Yuan Wu
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| | - Wei Ding
- Department of Medical Genetics; School of Basic Medical Sciences; Capital Medical University; Beijing China
| | - Zhi-Gang Li
- Key Laboratory of Major Diseases in Children (Capital Medical University); Ministry of Education; National Key Discipline of Pediatrics; Ministry of Education; Hematology Center, Beijing Children's Hospital; Capital Medical University; Beijing China
| |
Collapse
|