Cpg Island-Mediated Global Gene Regulatory Modes in Mouse Embryonic Stem Cells
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RNF2/Ring1b Negatively Regulates P53 Expression in Selective Cancer Cell Types to Promote Tumor Development
RNF2/Ring1b negatively regulates p53 expression in selective cancer cell types to promote tumor development Wen-jing Sua,b, Jun-shun Fanga, Feng Chenga,b, Chao Liua, Fang Zhoua, and Jian Zhanga,1 aState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology and bGraduate School, Chinese Academy of Sciences, Beijing 100101, China Edited by Carol Prives, Columbia University, New York, NY, and approved December 19, 2012 (received for review July 15, 2012) Large numbers of studies have focused on the posttranslational evolution in some invertebrates, such as Caenorhabditis elegans regulation of p53 activity. One of the best-known negative regu- and Drosophila melanogaster, suggesting that other factors (in- lators for p53 is MDM2, an E3 ubiquitin ligase that promotes p53 cluding other E3 ligases) might be involved in controlling p53 degradation through proteasome degradation pathways. Additional activities in these animals. For example, Bonus is a homolog of E3 ligases have also been reported to negatively regulate p53. How- TRIM 24, a p53 ligase in vertebrates. The results from loss-of- ever, whether these E3 ligases have distinct/overlapping roles in function studies indicated that Bonus is critical for maintaining the regulation of p53 is largely unknown. In this study, we identify p53 activity in Drosophila, suggesting that Bonus might be an RNF2 (ring finger protein 2) as an E3 ligase that targets p53 for evolutionarily conserved E3 ligase for p53 (14). The existence of multiple E3 ligases for p53 strongly suggests that specialization degradation. The E3 ligase activity of RNF2 requires Bmi1 protein, among them must be required for controlling p53 at multiple a component of the polycomb group (PcG) complex. -
Analysis of Gene Expression Data for Gene Ontology
ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION A Thesis Presented to The Graduate Faculty of The University of Akron In Partial Fulfillment of the Requirements for the Degree Master of Science Robert Daniel Macholan May 2011 ANALYSIS OF GENE EXPRESSION DATA FOR GENE ONTOLOGY BASED PROTEIN FUNCTION PREDICTION Robert Daniel Macholan Thesis Approved: Accepted: _______________________________ _______________________________ Advisor Department Chair Dr. Zhong-Hui Duan Dr. Chien-Chung Chan _______________________________ _______________________________ Committee Member Dean of the College Dr. Chien-Chung Chan Dr. Chand K. Midha _______________________________ _______________________________ Committee Member Dean of the Graduate School Dr. Yingcai Xiao Dr. George R. Newkome _______________________________ Date ii ABSTRACT A tremendous increase in genomic data has encouraged biologists to turn to bioinformatics in order to assist in its interpretation and processing. One of the present challenges that need to be overcome in order to understand this data more completely is the development of a reliable method to accurately predict the function of a protein from its genomic information. This study focuses on developing an effective algorithm for protein function prediction. The algorithm is based on proteins that have similar expression patterns. The similarity of the expression data is determined using a novel measure, the slope matrix. The slope matrix introduces a normalized method for the comparison of expression levels throughout a proteome. The algorithm is tested using real microarray gene expression data. Their functions are characterized using gene ontology annotations. The results of the case study indicate the protein function prediction algorithm developed is comparable to the prediction algorithms that are based on the annotations of homologous proteins. -
Evolution, Expression and Meiotic Behavior of Genes Involved in Chromosome Segregation of Monotremes
G C A T T A C G G C A T genes Article Evolution, Expression and Meiotic Behavior of Genes Involved in Chromosome Segregation of Monotremes Filip Pajpach , Linda Shearwin-Whyatt and Frank Grützner * School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia; fi[email protected] (F.P.); [email protected] (L.S.-W.) * Correspondence: [email protected] Abstract: Chromosome segregation at mitosis and meiosis is a highly dynamic and tightly regulated process that involves a large number of components. Due to the fundamental nature of chromosome segregation, many genes involved in this process are evolutionarily highly conserved, but duplica- tions and functional diversification has occurred in various lineages. In order to better understand the evolution of genes involved in chromosome segregation in mammals, we analyzed some of the key components in the basal mammalian lineage of egg-laying mammals. The chromosome passenger complex is a multiprotein complex central to chromosome segregation during both mitosis and meio- sis. It consists of survivin, borealin, inner centromere protein, and Aurora kinase B or C. We confirm the absence of Aurora kinase C in marsupials and show its absence in both platypus and echidna, which supports the current model of the evolution of Aurora kinases. High expression of AURKBC, an ancestor of AURKB and AURKC present in monotremes, suggests that this gene is performing all necessary meiotic functions in monotremes. Other genes of the chromosome passenger complex complex are present and conserved in monotremes, suggesting that their function has been preserved Citation: Pajpach, F.; in mammals. -
Transcriptome Analyses of Rhesus Monkey Pre-Implantation Embryos Reveal A
Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Transcriptome analyses of rhesus monkey pre-implantation embryos reveal a reduced capacity for DNA double strand break (DSB) repair in primate oocytes and early embryos Xinyi Wang 1,3,4,5*, Denghui Liu 2,4*, Dajian He 1,3,4,5, Shengbao Suo 2,4, Xian Xia 2,4, Xiechao He1,3,6, Jing-Dong J. Han2#, Ping Zheng1,3,6# Running title: reduced DNA DSB repair in monkey early embryos Affiliations: 1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 2 Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Collaborative Innovation Center for Genetics and Developmental Biology, Chinese Academy of Sciences-Max Planck Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China 3 Yunnan Key Laboratory of Animal Reproduction, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China 4 University of Chinese Academy of Sciences, Beijing, China 5 Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China 6 Primate Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China * Xinyi Wang and Denghui Liu contributed equally to this work 1 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press # Correspondence: Jing-Dong J. Han, Email: [email protected]; Ping Zheng, Email: [email protected] Key words: rhesus monkey, pre-implantation embryo, DNA damage 2 Downloaded from genome.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press ABSTRACT Pre-implantation embryogenesis encompasses several critical events including genome reprogramming, zygotic genome activation (ZGA) and cell fate commitment. -
O-Glcnacylation Regulates the Stability and Enzymatic Activity of the Histone Methyltransferase EZH2
O-GlcNAcylation regulates the stability and enzymatic activity of the histone methyltransferase EZH2 Pei-Wen Loa, Jiun-Jie Shieb, Chein-Hung Chena, Chung-Yi Wua, Tsui-Ling Hsua, and Chi-Huey Wonga,1 aGenomics Research Center, Academia Sinica, Taipei 115, Taiwan; and bInstitute of Chemistry, Academia Sinica, Taipei 115, Taiwan Contributed by Chi-Huey Wong, May 16, 2018 (sent for review February 1, 2018; reviewed by Michael D. Burkart, Benjamin G. Davis, and Gerald W. Hart) Protein O-glycosylation by attachment of β-N-acetylglucosamine maintenance and differentiation in embryonic stem cells (14, 15). (GlcNAc) to the Ser or Thr residue is a major posttranslational It was suggested that O-GlcNAcylation might play an important glycosylation event and is often associated with protein folding, role in the regulation of PRC1-mediated gene expression, and stability, and activity. The methylation of histone H3 at Lys-27 along this line the O-GlcNAcylation of EZH2 at S76 in the PRC2 catalyzed by the methyltransferase EZH2 was known to suppress complex was reported to stablize EZH2 in our previous study (16). gene expression and cancer development, and we previously The PRC2 complex is composed of Enhancer of zeste 2 (EZH2), reported that the O-GlcNAcylation of EZH2 at S76 stabilized Suppressor of Zeste 12 (Suz12), Extraembryonic endoderm (EED), EZH2 and facilitated the formation of H3K27me3 to inhibit tumor AE binding protein 2 (AEBP2), and retinoblastoma binding protein suppression. In this study, we employed a fluorescence-based method 4/7 (RBBP4/7) (17, 18). Within the PRC2 complex, EZH2 catalyzes the di- and trimethylation of histone H3 at lysine 27 (K27) to form of sugar labeling combined with mass spectrometry to investigate H3K27me2/3 to regulate embryonic and cancer development EZH2 glycosylation and identified five O-GlcNAcylation sites. -
The Mutational Landscape of Myeloid Leukaemia in Down Syndrome
cancers Review The Mutational Landscape of Myeloid Leukaemia in Down Syndrome Carini Picardi Morais de Castro 1, Maria Cadefau 1,2 and Sergi Cuartero 1,2,* 1 Josep Carreras Leukaemia Research Institute (IJC), Campus Can Ruti, 08916 Badalona, Spain; [email protected] (C.P.M.d.C); [email protected] (M.C.) 2 Germans Trias i Pujol Research Institute (IGTP), Campus Can Ruti, 08916 Badalona, Spain * Correspondence: [email protected] Simple Summary: Leukaemia occurs when specific mutations promote aberrant transcriptional and proliferation programs, which drive uncontrolled cell division and inhibit the cell’s capacity to differentiate. In this review, we summarize the most frequent genetic lesions found in myeloid leukaemia of Down syndrome, a rare paediatric leukaemia specific to individuals with trisomy 21. The evolution of this disease follows a well-defined sequence of events and represents a unique model to understand how the ordered acquisition of mutations drives malignancy. Abstract: Children with Down syndrome (DS) are particularly prone to haematopoietic disorders. Paediatric myeloid malignancies in DS occur at an unusually high frequency and generally follow a well-defined stepwise clinical evolution. First, the acquisition of mutations in the GATA1 transcription factor gives rise to a transient myeloproliferative disorder (TMD) in DS newborns. While this condition spontaneously resolves in most cases, some clones can acquire additional mutations, which trigger myeloid leukaemia of Down syndrome (ML-DS). These secondary mutations are predominantly found in chromatin and epigenetic regulators—such as cohesin, CTCF or EZH2—and Citation: de Castro, C.P.M.; Cadefau, in signalling mediators of the JAK/STAT and RAS pathways. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Redundant and Specific Roles of Cohesin STAG Subunits in Chromatin Looping and Transcriptional Control
Downloaded from genome.cshlp.org on October 10, 2021 - Published by Cold Spring Harbor Laboratory Press Research Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control Valentina Casa,1,6 Macarena Moronta Gines,1,6 Eduardo Gade Gusmao,2,3,6 Johan A. Slotman,4 Anne Zirkel,2 Natasa Josipovic,2,3 Edwin Oole,5 Wilfred F.J. van IJcken,1,5 Adriaan B. Houtsmuller,4 Argyris Papantonis,2,3 and Kerstin S. Wendt1 1Department of Cell Biology, Erasmus MC, 3015 GD Rotterdam, The Netherlands; 2Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; 3Institute of Pathology, University Medical Center, Georg-August University of Göttingen, 37075 Göttingen, Germany; 4Optical Imaging Centre, Erasmus MC, 3015 GD Rotterdam, The Netherlands; 5Center for Biomics, Erasmus MC, 3015 GD Rotterdam, The Netherlands Cohesin is a ring-shaped multiprotein complex that is crucial for 3D genome organization and transcriptional regulation during differentiation and development. It also confers sister chromatid cohesion and facilitates DNA damage repair. Besides its core subunits SMC3, SMC1A, and RAD21, cohesin in somatic cells contains one of two orthologous STAG sub- units, STAG1 or STAG2. How these variable subunits affect the function of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron (AID) tag fused to either STAG1 or STAG2. Following rapid depletion of either subunit, we perform high-resolution Hi-C, gene expression, and sequential ChIP studies to show that STAG1 and STAG2 do not co-occupy in- dividual binding sites and have distinct ways by which they affect looping and gene expression. -
Genome-Wide Analysis of Transcriptional Bursting-Induced Noise in Mammalian Cells
bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Title: Genome-wide analysis of transcriptional bursting-induced noise in mammalian cells Authors: Hiroshi Ochiai1*, Tetsutaro Hayashi2, Mana Umeda2, Mika Yoshimura2, Akihito Harada3, Yukiko Shimizu4, Kenta Nakano4, Noriko Saitoh5, Hiroshi Kimura6, Zhe Liu7, Takashi Yamamoto1, Tadashi Okamura4,8, Yasuyuki Ohkawa3, Itoshi Nikaido2,9* Affiliations: 1Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-0046, Japan 2Laboratory for Bioinformatics Research, RIKEN BDR, Wako, Saitama, 351-0198, Japan 3Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-0054, Japan 4Department of Animal Medicine, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 5Division of Cancer Biology, The Cancer Institute of JFCR, Tokyo, 135-8550, Japan 6Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan 7Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA 8Section of Animal Models, Department of Infectious Diseases, National Center for Global Health and Medicine (NCGM), Tokyo, 812-0054, Japan 9Bioinformatics Course, Master’s/Doctoral Program in Life Science Innovation (T-LSI), School of Integrative and Global Majors (SIGMA), University of Tsukuba, Wako, 351-0198, Japan *Corresponding authors Corresponding authors e-mail addresses Hiroshi Ochiai, [email protected] Itoshi Nikaido, [email protected] bioRxiv preprint doi: https://doi.org/10.1101/736207; this version posted August 15, 2019. -
A Midbody Component Homolog, Too Much Information/Prc1-Like, Is Required For
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.10.447958; this version posted June 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. A midbody component homolog, too much information/prc1-like, is required for microtubule reorganization during both cytokinesis and axis induction in the early zebrafish embryo Nair, S 1,2,*, 1Welch, E.L. 1,*, Moravec, C.E. 1, Trevena, R.L.1, Pelegri, F. 1 * shared first authorship 1. LaBoratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA 2. Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, Maharashtra, India Correspondence to: Francisco Pelegri at [email protected] 608-262-2920 Short title: zebrafish Prc-1L, cytokinesis and axis induction Key words: zebrafish, Prc-1, cytokinesis, midBody, microtuBule reorganization, axis induction bioRxiv preprint doi: https://doi.org/10.1101/2021.06.10.447958; this version posted June 11, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract We show that the zeBrafish maternal-effect mutation too much information (tmi) corresponds to zebrafish prc1-like (prc1l), which encodes a member of the MAP65/Ase1/PRC1family of microtuBule-associated proteins. Embryos from tmi/prc1l homozygous mutant mothers display cytokinesis defects in meiotic and mitotic divisions in the early embryo, indicating that tmi/prc1l has a role in midBody formation during cell division at the egg-to-embryo transition. Unexpectedly, maternal tmi/prc1l function is also essential for the reorganization of vegetal pole microtuBules required for embryonic axis induction. -
Leukemia and Lymphoma: Molecular and Therapeutic Insights
This is a free sample of content from Leukemia and Lymphoma: Molecular and Therapeutic Insights. Click here for more information on how to buy the book. Index A PRPF8, 307 AA. See Aplastic anemia SF3B1, 307 ABL1, 347, 368–369 SRSF2, 307 ABL2, 369 SUZ12, 120 ABT-199, 368 TET2, 117, 119, 121, 305 ABT-731, 181 U2AF1, 307 ACIN1, 374 U2AF2, 307 Acute lymphocytic leukemia (ALL). See also B- ZRSR2, 307 progenitor acute lymphoblastic therapeutic targeting leukemia; T-cell acute lymphoblastic combination therapy, 123–124 leukemia histone epigenetic mechanisms, 121, 123 epidemiology specific epigenetic mechanisms, 121 adult, 32–33 induced pluripotent stem cell models, 257–259 pediatric, 29–30 leukemia stem cell studies. See Leukemia stem cell Acute megakaryoblastic leukemia (AMKL) model children without Down syndrome, 326–329 mouse models. See Mouse models Down syndrome association pathophysiology, 295–296 clinical and biological features, 324–325 recurrent mutations GATA1 CEBPA, 301–302 cooperation with trisomy genes, 323–324 GATA2, 302 mutations, 323 NPM1, 300–301 genetic susceptibility, 321–322 RUNX1, 301 transforming mutation acquisition, 325–326 signal transduction mutations overview, 319–320 CBL, 303 RNA-binding proteins, 153 FLT3, 302 Acute myeloid leukemia (AML) KIT, 302–303 chromosomal abnormalities KRAS, 303 core binding factor rearrangements, 296–297 NF1, 303–304 KMT2A rearrangements, 298–299 NRAS, 303 rare translocations, 299–300 PTPN11, 303 clonal hematoipoiesis, 75 therapeutic targeting epidemiology CD123, 91–92 adult, 31–32 CD33, -
RNF2 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50Ul [email protected] 100 Ul √ √ Web
TD7403 RNF2 Antibody Order 021-34695924 [email protected] Support 400-6123-828 50ul [email protected] 100 uL √ √ Web www.ab-mart.com.cn Description: E3 ubiquitin-protein ligase that mediates monoubiquitination of 'Lys-119' of histone H2A (H2AK119Ub), thereby playing a central role in histone code and gene regulation. H2AK119Ub gives a specific tag for epigenetic transcriptional repression and participates in X chromosome inactivation of female mammals. May be involved in the initiation of both imprinted and random X inactivation (By similarity). Essential component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones, rendering chromatin heritably changed in its expressibility. E3 ubiquitin-protein ligase activity is enhanced by BMI1/PCGF4. Acts as the main E3 ubiquitin ligase on histone H2A of the PRC1 complex, while RING1 may rather act as a modulator of RNF2/RING2 activity (Probable). Association with the chromosomal DNA is cell-cycle dependent. In resting B- and T-lymphocytes, interaction with AURKB leads to block its activity, thereby maintaining transcription in resting lymphocytes (By similarity). Uniprot:Q99496 Alternative Names: BAP 1; BAP1; DING; DinG protein; E3 ubiquitin protein ligase RING 2; E3 ubiquitin protein ligase RING2; E3 ubiquitin-protein ligase RING2; HIP2 interacting protein 3; HIP2- interacting protein 3; HIPI 3; HIPI3; Huntingtin interacting protein 2 interacting protein 3; Huntingtin-interacting protein 2-interacting protein 3; OTTHUMP00000060668; Polycomb M33 interacting protein Ring 1B; Polycomb M33 interacting protein Ring1B; Protein DinG; RING 1B; RING 2; RING finger protein 1B; RING finger protein 2; RING finger protein BAP 1; RING finger protein BAP-1; RING finger protein BAP1; RING1b; RING2_HUMAN; RNF 2; Rnf2; Specificity: RNF2 Antibody detects endogenous levels of total RNF2.