DOCSLIB.ORG

Expression of EZH1-Polycomb Repressive Complex 2 and MALAT1 Lncrna and Their Combined Role in Epigenetic Adaptive Response

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Expression of EZH1-Polycomb Repressive Complex 2 and MALAT1 Lncrna and Their Combined Role in Epigenetic Adaptive Response Expression of EZH1-Polycomb Repressive Complex 2 and MALAT1 lncRNA and their Combined Role in Epigenetic Adaptive Response Thesis by Lamya Al Fuhaid In Partial Fulfillment of the Requirements For the Degree of Master of Science King Abdullah University of Science and Technology Thuwal, Kingdom of Saudi Arabia July, 2019 2 EXAMINATION COMMITTEE PAGE The thesis of Lamya Al Fuhaid is approved by the examination committee. Committee Chairperson: Prof. Valerio Orlando Committee Members: Prof. Stefan Arold, Prof. Salim Al Babili 3 COPYRIGHT © July, 2019 Lamya Al Fuhaid All Rights Reserved 4 ABSTRACT Expression of EZH1-Polycomb Repressive Complex 2 and MALAT1 lncRNA and their Combined Role in Epigenetic Adaptive Response Lamya Al Fuhaid Living cells maintain stable transcriptional programs while exhibiting plasticity that allows them to respond to environmental stimuli. The Polycomb repressive complex 2 (PRC2) is a key regulator of chromatin structure that maintains gene silencing through the methylation of histone H3 on lysine 27 (H3K27me), establishing chromatin-based memory. Two variants of PRC2 are present in mammalian cells, PRC2-EZH2 which is predominantly present in differentiating cells, and PRC2-EZH1 that predominates in post-mitotic tissues. PRC2-EZH1α/β pathway is involved in the response of muscle cells to oxidative stress. Atrophied muscle cells respond to oxidative stress by enabling the nuclear translocation of EED and its assembly with EZH1α and SUZ12. Here we prove that the metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) long noncoding RNA (lncRNA) is required for the assembly of PRC2-EZH1 components. The absence of MALAT1 significantly decreased the association between EED and EZH1α proteins. Biochemical analysis shows that the presence of MALAT1 increases the enzymatic activity of PRC2-EZH1 in vitro. In addition, we show that the simultaneous expression of PRC2 core components is necessary for their solubility. The successful expression of PRC2 proteins enables the execution of several downstream experiments, which will further explain the nature of the interplay between MALAT1 and PRC2. 5 ACKNOWLEDGEMENTS I would like to thank my supervisor, Prof. Valerio Orlando for providing me with the opportunity to explore the field of epigenetics. I would also like to show great gratitude to Dr. Peng Liu, who was generous with his time and has put immense effort into training and assisting me. I extend my thanks to my committee members, Prof. Stefan Arold and Prof. Salim Al Babili, for their time and valuable input. Acknowledgment goes to my labmate, Dr. Nadine El Said, for her insightful data, and Dr. Muhammad Tehseen from the Laboratory of DNA Replication and Recombination, for providing SF9 insect cells and pFastBac vector. Most importantly, for his guidance and patience in answering all of my questions. Special thanks to my dear friend Mohammed Alomari, for his help in the in vitro transcription. Thank you for the support, the company, and for lending me autoclaved flasks when I was too lazy to autoclave my own. My best friend, Arwa Alghuneim, you have been with me through it all, and without you, it would have been dull. Thank you for your interest in my work and for helping me whenever I asked, or did not. Last but not least, my mom, from whom I got the love of knowledge and the pursuit of perfection, epigenetics I guess, I love you. 6 TABLE OF CONTENTS EXAMINATION COMMITTEE PAGE _________________________________ 2 COPYRIGHT _______________________________________________________ 3 ABSTRACT _________________________________________________________ 4 ACKNOWLEDGEMENTS ____________________________________________ 5 TABLE OF CONTENTS ______________________________________________ 6 LIST OF ABBREVIATIONS __________________________________________ 9 LIST OF SYMBOLS ________________________________________________ 12 LIST OF ILLUSTRATIONS __________________________________________ 13 LIST OF TABLES __________________________________________________ 17 CHAPTER 1: INTRODUCTION ______________________________________ 18 1.1. Polycomb Repressive Complex ____________________________________ 20 1.1.1. Classes of Polycomb repressive complex _________________________ 20 1.1.2. PRC2 Components __________________________________________ 21 1.1.2.1. EZH protein _____________________________________________ 21 1.1.2.2. EED protein _____________________________________________ 21 1.1.2.3. SUZ12 protein ____________________________________________ 22 1.1.2.4. RbAp46 and RbAp48 proteins _______________________________ 23 1.1.2.5. AEBP2 and JARID2 proteins ________________________________ 23 1.2. PRC2 in cell development and plasticity _____________________________ 23 1.2.1. PRC2 in cellular memory _____________________________________ 23 1.2.2. The interchange between PRC2-EZH2 and PRC2-EZH1 ____________ 24 1.2.3. PRC2 and adaptive response in postmitotic cells ___________________ 26 1.3. Interplay between PRC2 and MALAT1: _____________________________ 27 1.3.1. Non-coding RNA: ___________________________________________ 27 1.3.2. lncRNA and PRC2 function: __________________________________ 28 1.3.3. Interaction between MALAT1 and PRC2 ________________________ 30 1.3.3.1. MALAT1 and PRC2-EZH2 _________________________________ 30 7 1.3.4. Investigation of the involvement of MALAT1 in PRC2-EZH1 mediated plasticity 31 1.4. Scope of the thesis: Objectives, contributions, and model system _________ 34 CHAPTER 2: MATERIALS AND METHODS __________________________ 35 2.1. Mammalian cell culture __________________________________________ 35 2.2. Stable cell lines ________________________________________________ 35 2.3. Immunofluorescence ____________________________________________ 35 2.4. Cell treatments _________________________________________________ 36 2.5. RNA isolation and RT-qPCR ______________________________________ 36 2.6. Co-immunoprecipitation _________________________________________ 37 2.7. LC-MS analysis and MS data analysis ______________________________ 37 2.8. ChIP-seq ______________________________________________________ 39 2.9. Expression plasmids _____________________________________________ 39 2.10. RNA in vitro transcription ________________________________________ 40 2.11. Protein expression and purification in bacteria ________________________ 40 2.12. Protein expression in insect cells ___________________________________ 41 2.13. Western blotting ________________________________________________ 42 2.14. Histone methyltransferase activity __________________________________ 42 2.15. Statistical analysis ______________________________________________ 43 CHAPTER 3: RESULTS _____________________________________________ 44 3.1. generation of stable C2C12 cell line expressing tagged EZH1α __________ 44 3.2. Identification of suitable antisense oligos for MALAT1 loss of function experiments _________________________________________________________ 46 3.3. MALAT1 is required for the proper association of PRC2 core components in the nucleus _________________________________________________________ 47 8 3.4. MALAT1 is necessary for the binding of EZH1α and EED to muscle-specific promoters under oxidative stress ________________________________________ 50 3.5. Expression of PRC2 core components in E. coli _______________________ 51 3.6. PRC2 proteins are insoluble in E. coli except EED _____________________ 54 3.7. Expression of PRC2 core components in insect cells ___________________ 57 3.8. Simultaneous expression of the three core components of PRC2-EZH1 is necessary for their solubility ____________________________________________ 59 3.9. In vitro transcription of MALAT1 __________________________________ 60 3.10. MALAT1 positively affects the enzymatic activity of PRC2-EZH1 in vitro _ 61 CHAPTER 4: DISCUSSION __________________________________________ 63 CHAPTER 5: CONCLUSION _________________________________________ 68 APPENDIX A: VECTOR MAPS ______________________________________ 69 1. pOZ-FH-C-Puro vector ____________________________________________ 69 2. pJET1.2 vector ___________________________________________________ 70 3. pGEX-5X-1 vector _______________________________________________ 71 4. pFastBac HT C vector _____________________________________________ 72 APPENDIX B: PRIMER SEQUENCES ________________________________ 73 1. qPCR primers ___________________________________________________ 73 2. ChIP ___________________________________________________________ 73 3. Cloning primers __________________________________________________ 74 4. Sequencing primers: ______________________________________________ 74 APPENDIX C: ANTIBODIES _________________________________________ 76 1. Western blotting _________________________________________________ 76 REFERENCES _____________________________________________________ 77 9 LIST OF ABBREVIATIONS 3D Three dimensional ASO Antisense oligos ChIP Chromatin immunoprecipitation ChIP-qPCR Chromatin immunoprecipitation followed by real-time polymerase chain reaction CRPC Castration-resistant prostate cancer Cryo-EM Cryogenic electron microscopy DMEM Dulbecco's modified Eagle's medium DNA Deoxyribonucleic acid dSfmbt Scm-related gene containing four malignant brain tumor domains EED Embryonic ectoderm development ELISA Enzyme-linked immunosorbent assay EMSA Electrophoretic mobility shift assay EMT Epithelial to mesenchymal transmission ERK Extracellular signal-regulated kinase EZH1 Enhancer of zeste homolog 1 EZH1α-FH EZH1α fused with FLAg and HA tags EZH2 Enhancer of
Load more

Recommended publications
  • A Flexible Microfluidic System for Single-Cell Transcriptome Profiling
    www.nature.com/scientificreports OPEN A fexible microfuidic system for single‑cell transcriptome profling elucidates phased transcriptional regulators of cell cycle Karen Davey1,7, Daniel Wong2,7, Filip Konopacki2, Eugene Kwa1, Tony Ly3, Heike Fiegler2 & Christopher R. Sibley 1,4,5,6* Single cell transcriptome profling has emerged as a breakthrough technology for the high‑resolution understanding of complex cellular systems. Here we report a fexible, cost‑efective and user‑ friendly droplet‑based microfuidics system, called the Nadia Instrument, that can allow 3′ mRNA capture of ~ 50,000 single cells or individual nuclei in a single run. The precise pressure‑based system demonstrates highly reproducible droplet size, low doublet rates and high mRNA capture efciencies that compare favorably in the feld. Moreover, when combined with the Nadia Innovate, the system can be transformed into an adaptable setup that enables use of diferent bufers and barcoded bead confgurations to facilitate diverse applications. Finally, by 3′ mRNA profling asynchronous human and mouse cells at diferent phases of the cell cycle, we demonstrate the system’s ability to readily distinguish distinct cell populations and infer underlying transcriptional regulatory networks. Notably this provided supportive evidence for multiple transcription factors that had little or no known link to the cell cycle (e.g. DRAP1, ZKSCAN1 and CEBPZ). In summary, the Nadia platform represents a promising and fexible technology for future transcriptomic studies, and other related applications, at cell resolution. Single cell transcriptome profling has recently emerged as a breakthrough technology for understanding how cellular heterogeneity contributes to complex biological systems. Indeed, cultured cells, microorganisms, biopsies, blood and other tissues can be rapidly profled for quantifcation of gene expression at cell resolution.
    [Show full text]
  • Role of MALAT1 in Gynecological Cancers: Pathologic and Therapeutic Aspects (Review)
    ONCOLOGY LETTERS 21: 333, 2021 Role of MALAT1 in gynecological cancers: Pathologic and therapeutic aspects (Review) FENG‑HUA QIAO1, MIN TU2 and HONG‑YAN LIU3 Departments of 1Gynecology and 2Orthopedics, Second People's Hospital of Jingmen; 3Department of Gynecology, Maternal and Child Health Hospital of Jingmen, Jingmen, Hubei 448000, P.R. China Received June 28, 2020; Accepted February 2, 2021 DOI: 10.3892/ol.2021.12594 Abstract. Gynecological cancers, including breast, ovarian, 5. Targeting MALAT1 in gynecological cancer therapeutics uterine, vaginal, cervical and vulvar cancers are among the 6. Future research major threats to modern life, particularly to female health. 7. Conclusions Long non‑coding RNAs (lncRNAs) play critical roles in normal development of organisms, as well as the tumorigenesis process, and metastasis‑associated lung adenocarcinoma tran‑ 1. Introduction script 1 (MALAT1) is a large infrequently spliced lncRNA, which have been implicated in different gynecological cancers. Gynecologic cancer is any cancer of the female reproduc‑ MALAT1 is overexpressed in breast, ovarian, cervical and tive organs, including ovarian, uterine, vaginal, cervical and endometrial cancers, which initiates cancer progression by vulvar cancers. Generally, all women are at risk of devel‑ inducing changes in the expression of several anti‑apoptotic oping gynecological cancers, and risk increases with age (1). and epithelial‑to‑mesenchymal transition‑related genes. Each gynecologic cancer is unique, with different signs and Targeting MALAT1 is an important strategy to combat symptoms, different risk factors and different therapeutic strat‑ gynecological cancers, and application of RNA‑interference egies (2,3). Gynecological cancers are associated with high technology and chemotherapeutic process are crucial to target mortality rates worldwide as it is difficult to detect the cancers and minimize MALAT1 activity.
    [Show full text]
  • Long Non-Coding RNA MALAT1 Drives Gastric Cancer Progression By
    Li et al. Cancer Cell Int (2017) 17:44 DOI 10.1186/s12935-017-0408-8 Cancer Cell International PRIMARY RESEARCH Open Access Long non‑coding RNA MALAT1 drives gastric cancer progression by regulating HMGB2 modulating the miR‑1297 Jijun Li, Jinghua Gao*, Wen Tian, Yongsheng Li and Jinghua Zhang Abstract Background: Emerging evidences have verified that long non-coding RNAs (lncRNAs) play important regulatory roles in the pathogenesis and progression of cancers. lncRNAs metastasis associated lung adenocarcinoma transcript 1 (MALAT1) have been found to be up-regulated in some human cancers. The main objective of this study was to investigate the expression level and biological function of MALAT1 in gastric cancer (GC). Methods: Quantificational real-time polymerase chain reaction (qRT-PCR) was performed to detect the mRNA levels of MALAT1 in 78 paired gastric carcinoma tissues and adjacent normal tissues, and the associations of MALAT1 expres- sion with the clinicopathological features were analyzed, and the prognosis of gastric carcinoma patients was evalu- ated. The HMGB2 mRNA and protein expressions were detected by qRT-PCR and western-blot analysis. Luciferase reporter assay was used to determine miR-1297 was a target of MALAT1. Results: In this study, we demonstrated MALAT1 was up-regulation in GC tissues compared with adjacent normal tissues and higher MALAT1 expression was correlated with local invasion, lymph node metastasis and TNM stage. Patients with higher MALAT1 expression predicted a shorter survival and poor prognosis. Functionally, we revealed that MALAT1 promoted cells proliferation and invasion in GC. Mechanistically, our results demonstrated that MALAT1 was negatively correlation with miR-1297 and functioned as a molecular sponging miR-1297, antagonizing its ability to suppress HMGB2 expression.
    [Show full text]
  • University of Florida Thesis Or Dissertation Formatting
    GENES AND GENOMES OF REPTILES By JENA LIND CHOJNOWSKI A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2010 1 © 2010 Jena Lind Chojnowski 2 To my mother and father and to all those who have overcome their own setbacks, big or small, to succeed in their happiness 3 ACKNOWLEDGMENTS I would like to thank my emotional support system, which includes my mother (my best cheerleader), my friends who had to deal with my venting, and my soccer friends who helped with my frustrations. My undergraduate assistants, especially Vipa Bernhardt, Jenessa Graham, and Rachel Seibert, were crucial in the beginning stages of my work. I would also like to thank my committee members: Mike Miyamoto, Lou Guillette, Jr., Mike Fields, Rebecca Kimball, and my advisor Ed Braun. I would like to thank Mike Miyamoto for always being positive, Lou Guillette for his invaluable technical help and pushing me to the next level, and Mike Fields for showing me there is life outside of the lab. I would like to give special thanks to Rebecca Kimball for helping me every step of the way by not only providing emotional support but also technical and psychological support. Without her expertise I would not be where I am today. Ed Braun, my advisor, is my teacher, my mentor, and my friend, all things necessary for a successful and fruitful pairing, which constitutes our union. 4 TABLE OF CONTENTS page ACKNOWLEDGMENTS .................................................................................................. 4 LIST OF TABLES ...........................................................................................................
    [Show full text]
  • MALAT1 Is Associated with Poor Response to Oxaliplatin-Based
    Published OnlineFirst January 9, 2017; DOI: 10.1158/1535-7163.MCT-16-0591 Companion Diagnostics and Cancer Biomarkers Molecular Cancer Therapeutics MALAT1 Is Associated with Poor Response to Oxaliplatin-Based Chemotherapy in Colorectal Cancer Patients and Promotes Chemoresistance through EZH2 Peilong Li1, Xin Zhang1, Haiyan Wang2, Lili Wang1, Tong Liu1, Lutao Du1, Yongmei Yang1, and Chuanxin Wang3 Abstract A major reason for oxaliplatin chemoresistance in colorectal E-cadherin expression and inhibits oxaliplatin-induced EMT in cancer is the acquisition of epithelial–mesenchymal transition colorectal cancer cells. EZH2 is highly expressed and associated (EMT) in cancer cells. The long noncoding RNA (lncRNA), with the 30 end region of lncRNA MALAT1 in colorectal cancer, MALAT1, is a highly conserved nuclear ncRNA and a key regulator and this association suppressed the expression of E-cadherin. of metastasis development in several cancers. However, its role in Furthermore, targeted inhibition of MALAT1 or EZH2 reversed oxaliplatin-induced metastasis and chemoresistance is not well EMT and chemoresistance induced by oxaliplatin. Finally, the known. In this study, we aim to investigate the prognostic and interaction between lncRNA MALAT1 and miR-218 was observed, therapeutic role of lncRNA MALAT1 in colorectal cancer patients which further indicated its prognostic value in patients who receiving oxaliplatin-based therapy and further explore the poten- received standard FOLFOX (oxaliplatin combine with 5-fluoro- tial transcriptional regulation through interaction with EZH2 uracil and leucovorin) treatment. In conclusion, this study illu- based on the established HT29 oxaliplatin-resistant cells. Our minates the prognostic role of lncRNA MALAT1 in colorectal results showed that high MALAT1 expression was associated cancer patients receiving oxaliplatin-based treatment and further with reduced patient survival and poor response to oxaliplatin- demonstrates how lncRNA MALAT1 confers a chemoresistant based chemotherapy in advanced colorectal cancer patients.
    [Show full text]
  • Rabbit Anti-Human EZH2 Monoclonal Antibody, Clone 9I43M54 (CABT-L1296) This Product Is for Research Use Only and Is Not Intended for Diagnostic Use
    Rabbit Anti-Human EZH2 monoclonal antibody, clone 9I43M54 (CABT-L1296) This product is for research use only and is not intended for diagnostic use. PRODUCT INFORMATION Specificity This antibody is predicted to react with Monkey, Rat, Horse, Mouse Target EZH2 Immunogen Protein corresponding to human EZH2 (aa156-aa265) Isotype IgG Source/Host Rabbit Species Reactivity Human Clone 9I43M54 Purification Protein A Purified Conjugate Unconjugated Applications WB Format Liquid Concentration 0.5 mg/ml Buffer PBS, pH 7.4 Preservative 0.09% Sodium Azide Storage -20°C, Avoid Freeze/Thaw Cycles Warnings For Research Use Only. Not for use in diagnostic procedures. Not for resale without express authorization. BACKGROUND Introduction EZH2 was initially identified as a homolog of the drosophila Enhancer of Zeste through exon trap screening of chromosome 21. Both EZH2 and the related protein EZH1 can form complexes with the noncanonical Polycomb repressive complex-2 (PRC2) and maintain repressive chromatin, 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 1 © Creative Diagnostics All Rights Reserved but the PRC2-EZH1 complex mediates methylation of histone H3. Both EZH1 and EZH2 are thought to function in the maintenance of embryonic stem cell pluripotency and plasticity and have been shown to be essential for hair follicle homeostasis and wound repair. Overexpression of EZH2 has been reported as a marker for advanced and metastatic cancers. Keywords EZH2;enhancer of zeste homolog 2 (Drosophila);WVS;ENX1;EZH1;KMT6;WVS2;ENX- 1;EZH2b;KMT6A;histone-lysine N-methyltransferase EZH2;lysine N-methyltransferase 6 GENE INFORMATION Entrez Gene ID 2146 UniProt ID Q15910 45-1 Ramsey Road, Shirley, NY 11967, USA Email: [email protected] Tel: 1-631-624-4882 Fax: 1-631-938-8221 2 © Creative Diagnostics All Rights Reserved.
    [Show full text]
  • Epigenetic-Mediated Apoptosis in Aggressive B-Cell Lymphomas
    Epigenetic-mediated apoptosis in aggressive B-cell lymphomas Inaugural-Dissertation to obtain the academic degree Doctor rerum naturalium (Dr. rer. nat.) submitted to the Department of Biology, Chemistry and Pharmacy of Freie Universität Berlin by Chidimma Agatha Akpa 2019 This dissertation was prepared at the Medical University, Berlin Institute of Pathology Department of Experimental Hematopathology under the supervision of Prof. Dr. Michael Hummel from January 2016 till November 2019 1st Reviewer: Prof. Dr. Michael Hummel 2nd Reviewer: Prof. Dr. Rupert Mutzel Date of defense: 16.03.2020 2 Directory Summary .................................................................................................................................... 7 Zusammenfassung ..................................................................................................................... 9 CHAPTER ONE ...................................................................................................................... 11 BACKGROUND .................................................................................................................. 11 1.1 Lymphomas .................................................................................................................... 11 1.1.1 Burkitt lymphoma (BL) ........................................................................................... 11 1.1.2 Diffuse large B-cell lymphoma (DLBCL) ............................................................... 12 1.2 Epigenetics and lymphoma ............................................................................................
    [Show full text]
  • End Processing and Maturation of MALAT1 Lncrna Xinying Zong1, Shinichi Nakagawa2, Susan M
    Nucleic Acids Research Advance Access published January 29, 2016 Nucleic Acids Research, 2016 1 doi: 10.1093/nar/gkw047 Natural antisense RNA promotes 3 end processing and maturation of MALAT1 lncRNA Xinying Zong1, Shinichi Nakagawa2, Susan M. Freier3, Jingyi Fei4, Taekjip Ha4, Supriya G. Prasanth1 and Kannanganattu V. Prasanth1,* 1Department of Cell and Developmental Biology, University of Illinois Urbana, IL 61801, USA, 2RNA Biology Laboratory, RIKEN Advanced Research Institute, Wako, Saitama 351-0198, Japan, 3Ionis Pharmaceuticals, Carlsbad, CA, USA and 4Center for Physics of living cells, Department of Physics, University of Illinois, Urbana, IL, USA Received July 09, 2015; Revised December 30, 2015; Accepted January 17, 2016 ABSTRACT is critical for the termination of RNA Pol II and also deter- Downloaded from mines the stability, subcellular localization and eventually The RNase P-mediated endonucleolytic cleavage the functionality of the mature RNA (3,4). Recent studies plays a crucial role in the 3 end processing and cellu- have reported the existence of non-canonical 3 end pro- lar accumulation of MALAT1, a nuclear-retained long cessing mechanisms at several lncRNA loci that generate noncoding RNA that promotes malignancy. The regu- non-polyadenylated RNAs (5–7). Among them, metastasis- http://nar.oxfordjournals.org/ lation of this cleavage event is largely undetermined. associated lung adenocarcinoma transcript 1 (MALAT1; Here we characterize a broadly expressed natural an- also known as NEAT2) and multiple endocrine neoplasia- tisense transcript at the MALAT1 locus, designated ␤ (MEN␤; also known as NEAT1) RNAs are unique as as TALAM1, that positively regulates MALAT1 levels they are highly abundant linear transcripts.
    [Show full text]
  • Homologs of Genes Expressed in Caenorhabditis Elegans Gabaergic
    Hammock et al. Neural Development 2010, 5:32 http://www.neuraldevelopment.com/content/5/1/32 RESEARCH ARTICLE Open Access Homologs of genes expressed in Caenorhabditis elegans GABAergic neurons are also found in the developing mouse forebrain Elizabeth AD Hammock1,2*, Kathie L Eagleson3, Susan Barlow4,6, Laurie R Earls4,7, David M Miller III2,4,5, Pat Levitt3* Abstract Background: In an effort to identify genes that specify the mammalian forebrain, we used a comparative approach to identify mouse homologs of transcription factors expressed in developing Caenorhabditis elegans GABAergic neurons. A cell-specific microarray profiling study revealed a set of transcription factors that are highly expressed in embryonic C. elegans GABAergic neurons. Results: Bioinformatic analyses identified mouse protein homologs of these selected transcripts and their expression pattern was mapped in the mouse embryonic forebrain by in situ hybridization. A review of human homologs indicates several of these genes are potential candidates in neurodevelopmental disorders. Conclusions: Our comparative approach has revealed several novel candidates that may serve as future targets for studies of mammalian forebrain development. Background As with other cell types, the diversity of GABAergic Proper forebrain patterning and cell-fate specification neurons has its basis in different developmental origins, lay the foundation for complex behaviors. These neuro- with timing and location of birth playing key roles in developmental events in large part depend on a series of cell fate [1,6-8]. gene expression refinements (reviewed in [1]) that com- Despite the phenotypic variety of GABAergic neurons, mit cells to express certain phenotypic features that all use GABA as a neurotransmitter.
    [Show full text]
  • Ezh1 Is Required for Hematopoietic Stem Cell Maintenance and Prevents Senescence-Like Cell Cycle Arrest
    Cell Stem Cell Article Ezh1 Is Required for Hematopoietic Stem Cell Maintenance and Prevents Senescence-like Cell Cycle Arrest Isabel Hidalgo,1,6 Antonio Herrera-Merchan,1,6 Jose Manuel Ligos,2 Laura Carramolino,3 Javier Nun˜ ez,4 Fernando Martinez,4 Orlando Dominguez,5 Miguel Torres,3 and Susana Gonzalez1,* 1Stem Cell Aging Group 2Cellomics Unit 3Genetic Control of Organ Development and Regeneration 4Bioinformatics Unit Centro Nacional de Investigaciones Cardiovasculares (CNIC), E-28029 Madrid, Spain 5Genomics Unit, Centro Nacional de Investigaciones Oncologicas (CNIO), E-28029 Madrid, Spain 6These authors contributed equally to this work *Correspondence: [email protected] http://dx.doi.org/10.1016/j.stem.2012.08.001 SUMMARY known about how epigenetic mechanisms dictate the activities of Polycomb factors to ensure blood homeostasis. Polycomb group (PcG) proteins are key epigenetic PcG proteins assemble in multimeric complexes and induce regulators of hematopietic stem cell (HSC) fate. The transcriptional repression of target genes through chromatin PcG members Ezh2 and Ezh1 are important determi- changes such as methylation of lysine 27 on histone 3 (H3K27). nants of embryonic stem cell identity, and the tran- Biochemical analysis revealed that PcG proteins assemble in at script levels of these histone methyltransferases least two complexes, Polycomb repressive complexes 1 and 2 are inversely correlated during development. How- (PRC1 and PRC2). Studies of mouse mutants showed that these factors are essential for normal development, with deletion of ever, the role of Ezh1 in somatic stem cells is largely Polycomb genes resulting in prenatal or early postnatal death, unknown. Here we show that Ezh1 maintains repopu- depending on inactivated gene and how the inactivation is lating HSCs in a slow-cycling, undifferentiated state, achieved (Sauvageau and Sauvageau, 2010).
    [Show full text]
  • Title Targeting Excessive EZH1 and EZH2 Activities for Abnormal Histone Methylation and Transcription Network in Malignant Lymph
    Targeting Excessive EZH1 and EZH2 Activities for Abnormal Title Histone Methylation and Transcription Network in Malignant Lymphomas Yamagishi, Makoto; Hori, Makoto; Fujikawa, Dai; Ohsugi, Takeo; Honma, Daisuke; Adachi, Nobuaki; Katano, Harutaka; Hishima, Tsunekazu; Kobayashi, Seiichiro; Nakano, Kazumi; Author(s) Nakashima, Makoto; Iwanaga, Masako; Utsunomiya, Atae; Tanaka, Yuetsu; Okada, Seiji; Tsukasaki, Kunihiro; Tobinai, Kensei; Araki, Kazushi; Watanabe, Toshiki; Uchimaru, Kaoru Citation Cell reports, 29(8): 2321-2337 Issue Date 2019-11-19 URL http://hdl.handle.net/20.500.12000/45873 Creative Commons Attribution-NonCommercial- Rights NoDerivatives 4.0 Article Targeting Excessive EZH1 and EZH2 Activities for Abnormal Histone Methylation and Transcription Network in Malignant Lymphomas Graphical Abstract Authors Makoto Yamagishi, Makoto Hori, Dai Fujikawa, ..., Kazushi Araki, Toshiki Watanabe, Kaoru Uchimaru Correspondence [email protected] (M.Y.), [email protected] (K.U.) In Brief A mechanism-based, effective strategy for controlling oncogenic H3K27me3 remains an open question. Yamagishi et al. provide the scientific rationale for dual targeting of EZH1+EZH2 in malignancies overexpressing EZH2, such as ATL, PTCL, and DLBCL, or harboring mutations in histone-modifying genes, as well as in pre-cancerous cells epigenomically perturbed by oncovirus infection. Highlights d Lymphoma transcriptome is under control of global H3K27me3 accumulation WT/WT d EZH1 and EZH2 are druggable targets in EZH2 and EZH2WT/Mu malignancies d Inactivation of chromatin-associated genes triggers EZH1/2 perturbation d Targeting epigenome for pre-cancerous states is achieved by EZH1/2 inhibition Yamagishi et al., 2019, Cell Reports 29, 2321–2337 November 19, 2019 ª 2019 The Author(s).
    [Show full text]
  • Content Based Search in Gene Expression Databases and a Meta-Analysis of Host Responses to Infection
    Content Based Search in Gene Expression Databases and a Meta-analysis of Host Responses to Infection A Thesis Submitted to the Faculty of Drexel University by Francis X. Bell in partial fulfillment of the requirements for the degree of Doctor of Philosophy November 2015 c Copyright 2015 Francis X. Bell. All Rights Reserved. ii Acknowledgments I would like to acknowledge and thank my advisor, Dr. Ahmet Sacan. Without his advice, support, and patience I would not have been able to accomplish all that I have. I would also like to thank my committee members and the Biomed Faculty that have guided me. I would like to give a special thanks for the members of the bioinformatics lab, in particular the members of the Sacan lab: Rehman Qureshi, Daisy Heng Yang, April Chunyu Zhao, and Yiqian Zhou. Thank you for creating a pleasant and friendly environment in the lab. I give the members of my family my sincerest gratitude for all that they have done for me. I cannot begin to repay my parents for their sacrifices. I am eternally grateful for everything they have done. The support of my sisters and their encouragement gave me the strength to persevere to the end. iii Table of Contents LIST OF TABLES.......................................................................... vii LIST OF FIGURES ........................................................................ xiv ABSTRACT ................................................................................ xvii 1. A BRIEF INTRODUCTION TO GENE EXPRESSION............................. 1 1.1 Central Dogma of Molecular Biology........................................... 1 1.1.1 Basic Transfers .......................................................... 1 1.1.2 Uncommon Transfers ................................................... 3 1.2 Gene Expression ................................................................. 4 1.2.1 Estimating Gene Expression ............................................ 4 1.2.2 DNA Microarrays ......................................................
    [Show full text]