Review Article Grainyhead-Like 2 As a Double-Edged Sword in Development and Cancer

Total Page:16

File Type:pdf, Size:1020Kb

Review Article Grainyhead-Like 2 As a Double-Edged Sword in Development and Cancer Am J Transl Res 2020;12(2):310-331 www.ajtr.org /ISSN:1943-8141/AJTR0102841 Review Article Grainyhead-like 2 as a double-edged sword in development and cancer Jiaxing He1, Chunyang Feng1, He Zhu1, Shuying Wu1, Peng Jin2, Tianmin Xu1 1Department of Gynecology and Obstetrics, The Second Hospital of Jilin University, Changchun, Jilin, China; 2Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA Received September 26, 2019; Accepted January 4, 2020; Epub February 15, 2020; Published February 28, 2020 Abstract: Grainyhead-like 2 (GRHL2), one of the three homologs of Drosophila grainyhead, contributes to epithe- lial morphogenesis and differentiation. Dysregulation of GRHL2 has been shown to be involved in hearing loss and neural tube defects during embryogenesis. Moreover, it is well-recognized that GRHL2 suppresses epithelial- to-mesenchymal transition (EMT) that is required for migration and invasion of carcinoma, implicating, GRHL2 in carcinogenesis. Diverse mechanisms, as well as the varied roles of GRHL2 in different tumor tissues, have been elucidated. However, the functions of GRHL2 appear to be more complicated than initially thought. GRHL2, acting as either a tumor enhancer or a tumor inhibitor, depends on the type of cancer. In this review, we summarize research progress about normal physiological functions of GRHL2 including epithelial morphogenesis, neural tube closure, and hearing loss. Moreover, the mechanisms of GRHL2 in tumorigenesis, containing EMT suppression, forming a negative feedback loop with ZEB1 and miR200 family, interactions with estrogen receptor (ER)-dependent signal- ing pathway, regulation of telomerase reverse transcriptase and relationships with TGF-beta signaling pathway are discussed in this review in an effort to better understand the roles of GRHL2 in a variety of cancers toward the goal of GRHL2-targeted treatment in the near future. Keywords: Grainyhead-like 2, epithelial morphogenesis, neural tube closure, tumorigenesis, epithelial-to-mesen- chymal, estrogen receptor Introduction the cellular processes including cell cycle pro- gression and cell survival are observed as well The Grainyhead (GRH) gene, the first member [7-9]. The LSF subfamily is systematically of the Grainyhead-like (GRHL) proteins family, reviewed in the context of cancer [10]. Unlike was first reported in mutant Drosophila mela- LSF, GRHL proteins, a highly-conserved sub- nogaster embryos that showed a head defect: family, are associated with the development holes in large specific cuticular regions, abnor- and maintenance of the epithelial barrier. mal lack of cuticular structures leading to a During murine development, GRHL proteins are specific phenotype [1]. Later, more GRH family expressed in the epidermis, oral cavity, gastro- members and their specific functions were dis- intestinal tract and non-ectoderm-derived tis- covered [2-4]. According to differences of their sues including the heart, the lung and the kid- biological roles, these family members are split ney [11]. Roles of GRHL proteins have been into two different subfamilies, the LSF subfam- widely studied in the normal and abnormal ily including CP2, LBP-1a, and LBP-9 transcrip- development of the epidermis. GRHL1-null mice tion factors and the GRH subfamily, consisting show defective hair anchoring, altered keratino- of GRHL1, GRHL2, and GRHL3 transcription cyte terminal differentiation and abnormal des- factors [5, 6]. The biological roles of the LSF mosomes suggesting that GRHL1 may play a subfamily are distinguished from those of GRH key role in maturation and differentiation of epi- subfamily in that they widely regulate tissue dermis [12]. It has also been shown that the development such as liver function and neural loss of GRHL1 has an essential influence on the system development. Additionally, regulation of maintenance of the epidermal barrier [13]. The Role of GRHL2 in development and cancer GRHL3 protein is necessary for neural tube clo- transition, miR200 family as well as human sure and wound healing, knockdown of GRHL3 telomerase reverse transcriptase. Furthermo- results in spina bifida and severe barrier de- re, the role of GRHL2 appears to be more com- fects with death at birth [11, 14-16], relevant plicated than we predicted. In the present mechanisms are also explored and studied [17, review, we summarize research progress ab- 18]. out the normal physiological functions of GR- HL2 including epithelial morphogenesis, neural GRHL transcription factors are classified as tube closure, and hearing loss. Moreover, the DNA-binding nuclear proteins containing a tr- mechanisms of GRHL2 in tumorigenesis, con- ansactivation domain, a highly conserved DNA- taining EMT suppression, forming a negative binding domain (DBD), and a dimerization do- feedback loop with ZEB1 and miR200 family, main. The GRHL DBD is more structured than interactions with ER-dependent signaling path- the transactivation domains. Despite their way, regulation of telomerase reverse transcrip- importance in development and tumorigenesis, tase and relationships with the TGF-beta signal- their structure and DBD remain elusive. The ing pathway are discussed in an effort to better crystallographic analysis shows that GRHL1 understand the roles of GRHL2 in a variety of and GRHL2 share a highly conserved three- cancers toward the goal of GRHL2-targeted dimensional structure characterized by an IgG- treatment in the near future. like core. A recent report presents the first crys- tal structures study of mammalian GRHL1 DBD Physiological functions of GRHL2 in mammals and GRHL2 DBD. Their structures are closely similar and contain an Ig-like core decorated by A study by Riethdorf et al [21] revealed the ex- pression relevance of GRHL2 in a variety of nor- three α helices and a series of surface loops. mal tissues by performing a comprehensive The crystal structure of the GRHL1 DBD sh- immunohistochemical analysis. Many studies ows consensus binding sequence (AACCGGTT) show the irreplaceable role of GRHL2 in neural which is shared by all members of the GRHL tube closure during embryogenesis as well as family bound to a 12-base-pair DNA duplex. regulation of epithelial phenotype. Moreover, Lys386 benefits the overall stabilization of the hearing loss is partially regulated by GRHL2. DBD-DNA complex. Arg427, Gly387, and Arg- Thus GRHL2 may serve as an important tran- 430 are required for formation of DBD-DNA scription factor for embryo development and complex [19]. Interestingly, the protein fold of maintenance of tissues. the GRHL1 DBD resembles the tumor suppres- sor p53 and their DNA-binding modes are simi- GRHL2 influences neural development and lar suggesting cooperation of p53 and GRHL formation of the craniofacial skeleton during proteins during epidermal development and embryogenesis function [19, 20]. Neural tube closure is necessary for the devel- Recently, GRHL2 has drawn great attention for opment of the central nervous system (CNS) its physiological functions in embryogenesis during embryogenesis. If neural tube closure is and diseases including cancer. The GRHL2 defective, it will lead to neural tube defects gene is located on human chromosome 8q22. (NTDs). As the most common birth defect in GRHL2 expression is detected in epidermis tis- humans, NTDs result in malformations of the sue, lung and kidney during murine embryogen- face and brain. The most common NTDs are esis. Placenta, brain, lung, salivary gland, thy- anencephaly arising from defective closure of mus, and pancreas in human adults show rela- anterior neural tube closure, and spina bifida tive high GRHL2 expression. Therefore, once resulting from the failure of neural tube closure GRHL2 is in a disorder condition, disease may in the spinal column [22]. To date, more than follow. To date, many studies have emphasized 200 underlying genes have been associated the mechanisms and roles of GRHL2 in diseas- with NTDs [23, 24]. It has been shown that the es. It is well established that GRHL2 regulates Grainyhead family, including both GRHL2 and epithelial morphogenesis, neural tube closure, GRHL3, is involved with NTDs. The upregulation and hearing loss. In addition, GRHL2 contrib- of GRHL2 is observed in mutant NTDs murine utes to the tumorigenesis via various signaling embryos [25]. Discussed here, and summa- pathways such as epithelial-to-mesenchymal rized in Figure 1, GRHL2 deletion mice exhibit 311 Am J Transl Res 2020;12(2):310-331 Role of GRHL2 in development and cancer epithelial character in surface ectoderm, ectopic expression of N-cadherin and Sox2 indi- cates the gain of neuroepithe- lial characteristics. Mechani- stically, loss of epithelial char- acteristics in GRHL2 null em- bryos is associated with ac- tomyosin disorganization, cell shape and thickness, and ch- ange in the balance of cell-cell junctional strength in the sur- face ectoderm layer. GRHL2 overexpression embryos most likely regulate the composition of apical junction complexes and increased cell-cell stress via the actomyosin network altering the biomechanical pr- operties in the surface ecto- derm [28]. GRHL2 acts as a suppressor Figure 1. GRHL2 influences neural development and formation of the cra- of EMT and promotes neural niofacial skeleton during embryogenesis. GRHL2 dysregulation may exhibit tube closure [29]. Epithelial severe defects during development such as anencephaly, spina bifida, split- splicing regulatory protein 1 face malformation, ventricle formation and otic vesicle defects, MHB
Recommended publications
  • Characterization of Genome-Wide TFCP2 Targets In
    Xu et al. Journal of Experimental & Clinical Cancer Research (2015) 34:6 DOI 10.1186/s13046-015-0121-1 RESEARCH Open Access Characterization of genome-wide TFCP2 targets in hepatocellular carcinoma: implication of targets FN1 and TJP1 in metastasis Xiao Xu1†, Zhikun Liu1†, Lin Zhou2, Haiyang Xie2, Jun Cheng1, Qi Ling1, Jianguo Wang2, Haijun Guo1, Xuyong Wei2 and Shusen Zheng1* Abstract Background: Transcription factor CP2 (TFCP2) is overexpressed in hepatocellular carcinoma(HCC) and correlated with the progression of the disease. Here we report the use of an integrated systems biology approach to identify genome-wide scale map of TFCP2 targets as well as the molecular function and pathways regulated by TFCP2 in HCC. Methods: We combined Chromatin immunoprecipitation (ChIP) on chip along with gene expression microarrays to study global transcriptional regulation of TFCP2 in HCC. The biological functions, molecular pathways, and networks associated with TFCP2 were identified using computational approaches. Validation of selected target gene expression and direct binding of TFCP2 to promoters were performed by ChIP -PCR and promoter reporter. Results: TFCP2 fostered a highly aggressive and metastatic phenotype in different HCC cells. Transcriptome analysis showed that alteration of TFCP2 in HCC cells led to change of genes in biological functions involved in cancer, cellular growth and proliferation, angiogenesis, cell movement and attachment. Pathways related to cell movement and cancer progression were also enriched. A quest for TFCP2-regulated factors contributing to metastasis, by integration of transcriptome and ChIP on chip assay, identified fibronectin 1 (FN1) and tight junction protein 1 (TJP1) as targets of TFCP2, and as key mediators of HCC metastasis.
    [Show full text]
  • O-Glcnacylated C-Jun Antagonizes Ferroptosis Via Inhibiting GSH Synthesis in Liver Cancer T
    Cellular Signalling 63 (2019) 109384 Contents lists available at ScienceDirect Cellular Signalling journal homepage: www.elsevier.com/locate/cellsig O-GlcNAcylated c-Jun antagonizes ferroptosis via inhibiting GSH synthesis in liver cancer T Yan Chena, Guoqing Zhua, Ya Liua,QiWua, Xiao Zhangb, Zhixuan Bianc, Yue Zhangd, ⁎ ⁎ Qiuhui Panc, , Fenyong Suna, a Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, China b Shanghai Institute of Thoracic Tumors, Shanghai Chest Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200030, China c Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China d Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, China ARTICLE INFO ABSTRACT Keywords: Ferroptosis is a metabolism-related cell death. Stimulating ferroptosis in liver cancer cells is a strategy to treat Erastin liver cancer. However, how to eradicate liver cancer cells through ferroptosis and the obstacles to inducing O-GlcNAcylation ferroptosis in liver cancer remain unclear. Here, we observed that erastin suppressed the malignant phenotypes Phosphorylation of liver cancer cells by inhibiting O-GlcNAcylation of c-Jun and further inhibited protein expression, tran- Glutathione scription activity and nuclear accumulation of c-Jun. Overexpression of c-Jun-WT with simultaneous PuGNAc Transcription treatment conversely inhibited erastin-induced ferroptosis, whereas overexpression of c-Jun-WT alone or Promoter overexpression of c-Jun-S73A (a non-O-GlcNAcylated form of c-Jun) with PuGNAc treatment did not exert a similar effect. GSH downregulation induced by erastin was restored by overexpression of c-Jun-WT with si- multaneous PuGNAc treatment.
    [Show full text]
  • Organ of Corti Size Is Governed by Yap/Tead-Mediated Progenitor Self-Renewal
    Organ of Corti size is governed by Yap/Tead-mediated progenitor self-renewal Ksenia Gnedevaa,b,1, Xizi Wanga,b, Melissa M. McGovernc, Matthew Bartond,2, Litao Taoa,b, Talon Treceka,b, Tanner O. Monroee,f, Juan Llamasa,b, Welly Makmuraa,b, James F. Martinf,g,h, Andrew K. Grovesc,g,i, Mark Warchold, and Neil Segila,b,1 aDepartment of Stem Cell Biology and Regenerative Medicine, Keck Medicine of University of Southern California, Los Angeles, CA 90033; bCaruso Department of Otolaryngology–Head and Neck Surgery, Keck Medicine of University of Southern California, Los Angeles, CA 90033; cDepartment of Neuroscience, Baylor College of Medicine, Houston, TX 77030; dDepartment of Otolaryngology, Washington University in St. Louis, St. Louis, MO 63130; eAdvanced Center for Translational and Genetic Medicine, Lurie Children’s Hospital of Chicago, Chicago, IL 60611; fDepartment of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030; gProgram in Developmental Biology, Baylor College of Medicine, Houston, TX 77030; hCardiomyocyte Renewal Laboratory, Texas Heart Institute, Houston, TX 77030 and iDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030; Edited by Marianne E. Bronner, California Institute of Technology, Pasadena, CA, and approved April 21, 2020 (received for review January 6, 2020) Precise control of organ growth and patterning is executed However, what initiates this increase in Cdkn1b expression re- through a balanced regulation of progenitor self-renewal and dif- mains unclear. In addition, conditional ablation of Cdkn1b in the ferentiation. In the auditory sensory epithelium—the organ of inner ear is not sufficient to completely relieve the block on Corti—progenitor cells exit the cell cycle in a coordinated wave supporting cell proliferation (9, 10), suggesting the existence of between E12.5 and E14.5 before the initiation of sensory receptor additional repressive mechanisms.
    [Show full text]
  • MAGE-A11 Is Activated Through TFCP2/ZEB1 Binding Sites De-Methylation As Well As Histone Modification and Facilitates ESCC Tumor Growth
    www.impactjournals.com/oncotarget/ Oncotarget, 2018, Vol. 9, (No. 3), pp: 3365-3378 Research Paper MAGE-A11 is activated through TFCP2/ZEB1 binding sites de-methylation as well as histone modification and facilitates ESCC tumor growth Shina Liu1,*, Fei Liu1,*, Weina Huang1, Lina Gu1, Lingjiao Meng1, Yingchao Ju1,2, Yunyan Wu1, Juan Li1, Lihua Liu1 and Meixiang Sang1,3 1Research Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P. R. China 2Animal Center, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P. R. China 3Tumor Research Institute, the Fourth Hospital of Hebei Medical University, Shijiazhuang 050011, P. R. China *These authors contributed equally to this work Correspondence to: Meixiang Sang, email: [email protected] Keywords: MAGE-A11; ESCC; DNA methylation; histone acetylation; histone methylation Received: September 30, 2017 Accepted: November 15, 2017 Published: December 05, 2017 Copyright: Liu et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. ABSTRACT Recently, we have reported that the product of Melanoma Antigens Genes (MAGE) family member MAGE-A11 is an independent poor prognostic marker for esophageal squamous cell carcinoma (ESCC). However, the reason how MAGE-A11 is activated in ESCC progression still remains unclear. In the current study, we demonstrated that DNA methylation and the subsequent histone posttranslational modifications play crucial roles in the regulation of MAGE-A11 in ESCC progression. We found that the methylation rate of TFCP2/ZEB1 binding site on MAGE-A11 promoter in ESCC tissues and cells is higher than the normal esophageal epithelial tissues and cells.
    [Show full text]
  • Neglected Functions of TFCP2/TFCP2L1/UBP1 Transcription Factors May Offer Valuable Insights Into Their Mechanisms of Action
    International Journal of Molecular Sciences Review Neglected Functions of TFCP2/TFCP2L1/UBP1 Transcription Factors May Offer Valuable Insights into Their Mechanisms of Action Agnieszka Taracha, Grzegorz Kotarba and Tomasz Wilanowski * Laboratory of Signal Transduction, Nencki Institute of Experimental Biology of Polish Academy of Sciences, 3 Pasteur St., 02-093 Warsaw, Poland; [email protected] (A.T.); [email protected] (G.K.) * Correspondence: [email protected]; Tel.: +48-22-5892-311 Received: 21 August 2018; Accepted: 19 September 2018; Published: 20 September 2018 Abstract: In recent years, the TFCP2 (transcription factor cellular promoter 2)/TFCP2L1 (TFCP2- like 1)/UBP1 (upstream binding protein 1) subfamily of transcription factors has been attracting increasing attention in the scientific community. These factors are very important in cancer, Alzheimer’s disease, and other human conditions, and they can be attractive targets for drug development. However, the interpretation of experimental results is complicated, as in principle, any of these factors could substitute for the lack of another. Thus, studying their hitherto little known functions should enhance our understanding of mechanisms of their functioning, and analogous mechanisms might govern their functioning in medically relevant contexts. For example, there are numerous parallels between placental development and cancer growth; therefore, investigating the roles of TFCP2, TFCP2L1, and UBP1 in the placenta may help us better understand their functioning in cancer, as is evidenced by the studies of various other proteins and pathways. Our review article aims to call the attention of the scientific community to these neglected functions, and encourage further research in this field.
    [Show full text]
  • Identifying the Risky SNP of Osteoporosis with ID3-PEP Decision Tree Algorithm
    Hindawi Complexity Volume 2017, Article ID 9194801, 8 pages https://doi.org/10.1155/2017/9194801 Research Article Identifying the Risky SNP of Osteoporosis with ID3-PEP Decision Tree Algorithm Jincai Yang,1 Huichao Gu,1 Xingpeng Jiang,1 Qingyang Huang,2 Xiaohua Hu,1 and Xianjun Shen1 1 School of Computer Science, Central China Normal University, Wuhan 430079, China 2School of Life Science, Central China Normal University, Wuhan 430079, China Correspondence should be addressed to Jincai Yang; [email protected] Received 31 March 2017; Revised 26 May 2017; Accepted 8 June 2017; Published 7 August 2017 Academic Editor: Fang-Xiang Wu Copyright © 2017 Jincai Yang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. In the past 20 years, much progress has been made on the genetic analysis of osteoporosis. A number of genes and SNPs associated with osteoporosis have been found through GWAS method. In this paper, we intend to identify the suspected risky SNPs of osteoporosis with computational methods based on the known osteoporosis GWAS-associated SNPs. The process includes two steps. Firstly, we decided whether the genes associated with the suspected risky SNPs are associated with osteoporosis by using random walk algorithm on the PPI network of osteoporosis GWAS-associated genes and the genes associated with the suspected risky SNPs. In order to solve the overfitting problem in ID3 decision tree algorithm, we then classified the SNPs with positive results based on their features of position and function through a simplified classification decision tree which was constructed by ID3 decision tree algorithm with PEP (Pessimistic-Error Pruning).
    [Show full text]
  • Grimme, Acadia.Pdf
    MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme A thesis submitted to the Faculty of the University of Delaware in partial fulfillment of the requirements for the degree of Bachelors of Science in Biological Sciences with Distinction Spring 2018 © 2018 Acadia Grimme All Rights Reserved MECHANISM OF ACTION OF HISTONE DEACETYLASE INHIBITORS ON SURVIVAL MOTOR NEURON 2 PROMOTER by Acadia L. Grimme Approved: __________________________________________________________ Matthew E. R. Butchbach, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Deni S. Galileo, Ph.D. Professor in charge of thesis on behalf of the Advisory Committee Approved: __________________________________________________________ Carlton R. Cooper, Ph.D. Committee member from the Department of Biological Sciences Approved: __________________________________________________________ Gary H. Laverty, Ph.D. Committee member from the Board of Senior Thesis Readers Approved: __________________________________________________________ Michael Chajes, Ph.D. Chair of the University Committee on Student and Faculty Honors ACKNOWLEDGMENTS I would like to acknowledge my thesis director Dr. Butchbach for his wonderful guidance and patience as I worked through my project. He has been an excellent research mentor over the last two years and I am forever thankful that he welcomed me into his lab. His dedication to his work inspires me as an aspiring research scientist. His lessons will carry on with me as I pursue future research in graduate school and beyond. I would like to thank both current and former members of the Motor Neuron Disease Laboratory: Sambee Kanda, Kyle Hinkle, and Andrew Connell. Sambee and Andrew patiently taught me many of the techniques I utilized in my project, and without them it would not be what it is today.
    [Show full text]
  • Engineered Type 1 Regulatory T Cells Designed for Clinical Use Kill Primary
    ARTICLE Acute Myeloid Leukemia Engineered type 1 regulatory T cells designed Ferrata Storti Foundation for clinical use kill primary pediatric acute myeloid leukemia cells Brandon Cieniewicz,1* Molly Javier Uyeda,1,2* Ping (Pauline) Chen,1 Ece Canan Sayitoglu,1 Jeffrey Mao-Hwa Liu,1 Grazia Andolfi,3 Katharine Greenthal,1 Alice Bertaina,1,4 Silvia Gregori,3 Rosa Bacchetta,1,4 Norman James Lacayo,1 Alma-Martina Cepika1,4# and Maria Grazia Roncarolo1,2,4# Haematologica 2021 Volume 106(10):2588-2597 1Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 2Stanford Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA; 3San Raffaele Telethon Institute for Gene Therapy, Milan, Italy and 4Center for Definitive and Curative Medicine, Stanford School of Medicine, Stanford, CA, USA *BC and MJU contributed equally as co-first authors #AMC and MGR contributed equally as co-senior authors ABSTRACT ype 1 regulatory (Tr1) T cells induced by enforced expression of interleukin-10 (LV-10) are being developed as a novel treatment for Tchemotherapy-resistant myeloid leukemias. In vivo, LV-10 cells do not cause graft-versus-host disease while mediating graft-versus-leukemia effect against adult acute myeloid leukemia (AML). Since pediatric AML (pAML) and adult AML are different on a genetic and epigenetic level, we investigate herein whether LV-10 cells also efficiently kill pAML cells. We show that the majority of primary pAML are killed by LV-10 cells, with different levels of sensitivity to killing. Transcriptionally, pAML sensitive to LV-10 killing expressed a myeloid maturation signature.
    [Show full text]
  • Discovery of Biased Orientation of Human DNA Motif Sequences
    bioRxiv preprint doi: https://doi.org/10.1101/290825; this version posted January 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Discovery of biased orientation of human DNA motif sequences 2 affecting enhancer-promoter interactions and transcription of genes 3 4 Naoki Osato1* 5 6 1Department of Bioinformatic Engineering, Graduate School of Information Science 7 and Technology, Osaka University, Osaka 565-0871, Japan 8 *Corresponding author 9 E-mail address: [email protected], [email protected] 10 1 bioRxiv preprint doi: https://doi.org/10.1101/290825; this version posted January 27, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 11 Abstract 12 Chromatin interactions have important roles for enhancer-promoter interactions 13 (EPI) and regulating the transcription of genes. CTCF and cohesin proteins are located 14 at the anchors of chromatin interactions, forming their loop structures. CTCF has 15 insulator function limiting the activity of enhancers into the loops. DNA binding 16 sequences of CTCF indicate their orientation bias at chromatin interaction anchors – 17 forward-reverse (FR) orientation is frequently observed. DNA binding sequences of 18 CTCF were found in open chromatin regions at about 40% - 80% of chromatin 19 interaction anchors in Hi-C and in situ Hi-C experimental data.
    [Show full text]
  • Cyclin B1 Represses Its DNA-Binding Activity During Mitosis in Cancer Cells
    Oncogene (2012) 31, 4946–4959 & 2012 Macmillan Publishers Limited All rights reserved 0950-9232/12 www.nature.com/onc ORIGINAL ARTICLE Sp1 phosphorylation by cyclin-dependent kinase 1/cyclin B1 represses its DNA-binding activity during mitosis in cancer cells J-Y Chuang1, S-A Wang1, W-B Yang1, H-C Yang1, C-Y Hung2, T-P Su3, W-C Chang2,4,5,6 and J-J Hung1,2,4,5 1Institute of Bioinformatics and Biosignal Transduction, College of Bioscience and Biotechnology, Tainan, Taiwan; 2Institute of Medicine, College of Medicine, Tainan, Taiwan; 3National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, USA; 4Department of Pharmacology, Tainan, Taiwan; 5Center for Infectious Disease and Signal Transduction, National Cheng-Kung University, Tainan, Taiwan and 6Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei, Taiwan Sp1 is important for the transcription of many genes. Our Introduction previous studies have shown that Sp1 is degraded in normal cell, but it is preserved in cancer cells during During interphase of the cell cycle, the transcription mitosis and exists a priori in the daughter cells, ready to factor Sp1 has an important role in regulating the engage in gene transcription and thereby contributes to expression of genes involved in many cellular processes the proliferation and survival of cancer cells. The by binding to the promoter regions of its target genes. mechanism by which Sp1 is preserved in cancer cells Sp1 binds specifically to the GC-rich promoter elements during mitosis remains unknown. In this study, we via 3 C2H2-type zinc finger regions at the C-terminus of observed that Sp1 strongly colocalized with cyclin- the protein (Li and Davie, 2010) and regulates the dependent kinase 1 (CDK1)/cyclin B1 during mitosis.
    [Show full text]
  • Type of the Paper (Article
    Supplementary Methods Microarray Experiments (Single Color Mode) The Microarray utilized in this study represents a refined version of the Whole Human Genome Oligo Microarray 4 × 44K v2 (Design ID 026652, Agilent Technologies, (Santa Clara, CA, USA), called ‘054261On1M’ (Design ID 066335) developed at the Research Core Unit Transcriptomics (RCUT) of Hannover Medical School (Hannover, Germany). The microarray design was created in Agilent’s eArray portal using a 1 × 1 M design format for mRNA expression as template. All non-control probes of design ID 026652 have been printed five times within a region comprising a total of 181,560 Features (170 columns × 1068 rows). Four of such regions were placed within one 1 M region giving rise to four microarray fields per slide to be hybridized individually (Customer Specified Feature Layout). Control probes required for proper Feature Extraction software operation were determined and placed automatically by eArray using recommended default settings. An amount of 250 ng of total RNA were used for synthesis of aminoallyl-UTP-modified (aaUTP) cRNA with the ‘Quick Amp Labeling kit, no dye’ (#5190-0447, Agilent Technologies) according to the manufacturer’s recommendations, except that reaction volumes were quartered and contained NTP- mix was exchanged by NTP Set (ATP, CTP, GTP, UTP) and aminoallyl-UTP (Fermentas, Thermo Fisher Scientific; Waltham, MA, USA); order numbers R1091, R0481, respectively). Final NTP concentrations used for in-vitro transcription were 2.5 mM (ATP, CTP, GTP), 1.88 mM UTP, and 0.62 mM aaUTP. The labeling of aaUTP-cRNA was performed by use of Alexa Fluor 555 Reactive Dye (#A32756; LifeTechnologies) as described in the Amino Allyl MessageAmp™ II Kit Manual (#AM1753; Life Technologies, Carlsbad, CA, USA) except that reaction volumes were quartered.
    [Show full text]
  • A Subset of Epithelioid and Spindle Cell Rhabdomyosarcomas Is Associated with TFCP2 Fusions and Common ALK Upregulation
    Modern Pathology (2020) 33:404–419 https://doi.org/10.1038/s41379-019-0323-8 ARTICLE A subset of epithelioid and spindle cell rhabdomyosarcomas is associated with TFCP2 fusions and common ALK upregulation 1,2,3 4 5 6 7 François Le Loarer ● Arjen H. G. Cleven ● Corinne Bouvier ● Marie-Pierre Castex ● Cleofe Romagosa ● 8 9 1 10 10 Anne Moreau ● Sébastien Salas ● Benjamin Bonhomme ● Anne Gomez-Brouchet ● Camille Laurent ● 10 11 12 7 4 Sophie Le Guellec ● Virginie Audard ● Antoine Giraud ● Irma Ramos-Oliver ● Anne-Marie Cleton-Jansen ● 13 14 2,3 15,16 17 Dilara C. Savci-Heijink ● Herman M. Kroon ● Jessica Baud ● Daniel Pissaloux ● Gaëlle Pierron ● 18 1,2,3 4 11 Anand Sherwood ● Jean Michel Coindre ● Judith V. M. G. Bovée ● Frédérique Larousserie ● Franck Tirode 16 Received: 14 May 2019 / Revised: 19 June 2019 / Accepted: 19 June 2019 / Published online: 5 August 2019 © United States & Canadian Academy of Pathology 2019 Abstract Rhabdomyosarcomas with TFCP2 fusions represent an emerging subtype of tumors, initially discovered by RNA- sequencing. We report herein the clinicopathological, transcriptional, and genomic features of a series of 14 cases. Cases 1234567890();,: 1234567890();,: were retrospectively and prospectively recruited and studied by immunohistochemistry (MYF4, MYOD1, S100, AE1/E3, ALK), fluorescence in situ hybridization with TFCP2 break-apart probe (n = 10/14), array-comparative genomic hybridization (Agilent), whole RNA-sequencing (Truseq Exome, Illumina), or anchored multiplex PCR-based targeted next-generation sequencing (Archer® FusionPlex® Sarcoma kit). Patient’s age ranged between 11 and 86 years, including 5 pediatric cases. Tumors were located in the bone (n = 12/14) and soft tissue (n = 2/14).
    [Show full text]