Ezh2 Is Required for Neural Crest-Derived Cartilage and Bone
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Genome-Wide DNA Methylation Analysis of KRAS Mutant Cell Lines Ben Yi Tew1,5, Joel K
www.nature.com/scientificreports OPEN Genome-wide DNA methylation analysis of KRAS mutant cell lines Ben Yi Tew1,5, Joel K. Durand2,5, Kirsten L. Bryant2, Tikvah K. Hayes2, Sen Peng3, Nhan L. Tran4, Gerald C. Gooden1, David N. Buckley1, Channing J. Der2, Albert S. Baldwin2 ✉ & Bodour Salhia1 ✉ Oncogenic RAS mutations are associated with DNA methylation changes that alter gene expression to drive cancer. Recent studies suggest that DNA methylation changes may be stochastic in nature, while other groups propose distinct signaling pathways responsible for aberrant methylation. Better understanding of DNA methylation events associated with oncogenic KRAS expression could enhance therapeutic approaches. Here we analyzed the basal CpG methylation of 11 KRAS-mutant and dependent pancreatic cancer cell lines and observed strikingly similar methylation patterns. KRAS knockdown resulted in unique methylation changes with limited overlap between each cell line. In KRAS-mutant Pa16C pancreatic cancer cells, while KRAS knockdown resulted in over 8,000 diferentially methylated (DM) CpGs, treatment with the ERK1/2-selective inhibitor SCH772984 showed less than 40 DM CpGs, suggesting that ERK is not a broadly active driver of KRAS-associated DNA methylation. KRAS G12V overexpression in an isogenic lung model reveals >50,600 DM CpGs compared to non-transformed controls. In lung and pancreatic cells, gene ontology analyses of DM promoters show an enrichment for genes involved in diferentiation and development. Taken all together, KRAS-mediated DNA methylation are stochastic and independent of canonical downstream efector signaling. These epigenetically altered genes associated with KRAS expression could represent potential therapeutic targets in KRAS-driven cancer. Activating KRAS mutations can be found in nearly 25 percent of all cancers1. -
Accompanies CD8 T Cell Effector Function Global DNA Methylation
Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer, Benjamin G. Barwick, Benjamin A. Youngblood, Rafi Ahmed and Jeremy M. Boss This information is current as of October 1, 2021. J Immunol 2013; 191:3419-3429; Prepublished online 16 August 2013; doi: 10.4049/jimmunol.1301395 http://www.jimmunol.org/content/191/6/3419 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2013/08/20/jimmunol.130139 Material 5.DC1 References This article cites 81 articles, 25 of which you can access for free at: http://www.jimmunol.org/content/191/6/3419.full#ref-list-1 http://www.jimmunol.org/ Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! Every submission reviewed by practicing scientists by guest on October 1, 2021 • Fast Publication! 4 weeks from acceptance to publication *average Subscription Information about subscribing to The Journal of Immunology is online at: http://jimmunol.org/subscription Permissions Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Email Alerts Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts The Journal of Immunology is published twice each month by The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2013 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. The Journal of Immunology Global DNA Methylation Remodeling Accompanies CD8 T Cell Effector Function Christopher D. Scharer,* Benjamin G. Barwick,* Benjamin A. Youngblood,*,† Rafi Ahmed,*,† and Jeremy M. -
Identification of Potential Key Genes and Pathway Linked with Sporadic Creutzfeldt-Jakob Disease Based on Integrated Bioinformatics Analyses
medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Identification of potential key genes and pathway linked with sporadic Creutzfeldt-Jakob disease based on integrated bioinformatics analyses Basavaraj Vastrad1, Chanabasayya Vastrad*2 , Iranna Kotturshetti 1. Department of Biochemistry, Basaveshwar College of Pharmacy, Gadag, Karnataka 582103, India. 2. Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad 580001, Karanataka, India. 3. Department of Ayurveda, Rajiv Gandhi Education Society`s Ayurvedic Medical College, Ron, Karnataka 562209, India. * Chanabasayya Vastrad [email protected] Ph: +919480073398 Chanabasava Nilaya, Bharthinagar, Dharwad 580001 , Karanataka, India NOTE: This preprint reports new research that has not been certified by peer review and should not be used to guide clinical practice. medRxiv preprint doi: https://doi.org/10.1101/2020.12.21.20248688; this version posted December 24, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission. Abstract Sporadic Creutzfeldt-Jakob disease (sCJD) is neurodegenerative disease also called prion disease linked with poor prognosis. The aim of the current study was to illuminate the underlying molecular mechanisms of sCJD. The mRNA microarray dataset GSE124571 was downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were screened. -
Single Cell Regulatory Landscape of the Mouse Kidney Highlights Cellular Differentiation Programs and Disease Targets
ARTICLE https://doi.org/10.1038/s41467-021-22266-1 OPEN Single cell regulatory landscape of the mouse kidney highlights cellular differentiation programs and disease targets Zhen Miao 1,2,3,8, Michael S. Balzer 1,2,8, Ziyuan Ma 1,2,8, Hongbo Liu1,2, Junnan Wu 1,2, Rojesh Shrestha 1,2, Tamas Aranyi1,2, Amy Kwan4, Ayano Kondo 4, Marco Pontoglio 5, Junhyong Kim6, ✉ Mingyao Li 7, Klaus H. Kaestner2,4 & Katalin Susztak 1,2,4 1234567890():,; Determining the epigenetic program that generates unique cell types in the kidney is critical for understanding cell-type heterogeneity during tissue homeostasis and injury response. Here, we profile open chromatin and gene expression in developing and adult mouse kidneys at single cell resolution. We show critical reliance of gene expression on distal regulatory elements (enhancers). We reveal key cell type-specific transcription factors and major gene- regulatory circuits for kidney cells. Dynamic chromatin and expression changes during nephron progenitor differentiation demonstrates that podocyte commitment occurs early and is associated with sustained Foxl1 expression. Renal tubule cells follow a more complex differentiation, where Hfn4a is associated with proximal and Tfap2b with distal fate. Mapping single nucleotide variants associated with human kidney disease implicates critical cell types, developmental stages, genes, and regulatory mechanisms. The single cell multi-omics atlas reveals key chromatin remodeling events and gene expression dynamics associated with kidney development. 1 Renal, Electrolyte, and Hypertension Division, Department of Medicine, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. 2 Institute for Diabetes, Obesity, and Metabolism, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, USA. -
Solutions for Practice Problems for Molecular Biology, Session 5
Solutions to Practice Problems for Molecular Biology, Session 5: Gene Regulation and the Lac Operon Question 1 a) How does lactose (allolactose) promote transcription of LacZ? 1) Lactose binds to the polymerase and increases efficiency. 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. 3) Lactose binds to an activator protein, which can then help the RNA polymerase bind to the promoter and begin transcription. 4) Lactose prevents premature termination of transcription by directly binding to and bending the DNA. Solution: 2) Lactose binds to a repressor protein, and alters its conformation to prevent it from binding to the DNA and interfering with the binding of RNA polymerase. b) What molecule is used to signal low glucose levels to the Lac operon regulatory system? 1) Cyclic AMP 2) Calcium 3) Lactose 4) Pyruvate Solution: 1) Cyclic AMP. Question 2 You design a summer class where you recreate experiments studying the lac operon in E. coli (see schematic below). In your experiments, the activity of the enzyme b-galactosidase (β -gal) is measured by including X-gal and IPTG in the growth media. X-gal is a lactose analog that turns blue when metabolisize by b-gal, but it does not induce the lac operon. IPTG is an inducer of the lac operon but is not metabolized by b-gal. I O lacZ Plac Binding site for CAP Pi Gene encoding β-gal Promoter for activator protein Repressor (I) a) Which of the following would you expect to bind to β-galactosidase? Circle all that apply. -
Visualizing Transcription in Real-Time
Cent. Eur. J. Biol. • 3(1) • 2008 • 11-18 DOI: 10.2478/s11535-008-0001-1 Central European Journal of Biology Visualizing transcription in real-time Mini-Review Yehuda Brody, Yaron Shav-Tal* The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 52900, Israel Received 31 October 2007; Accepted 10 December 2007 Abstract: The transcriptional process is at the center of the gene expression pathway. In eukaryotes, the transcription of protein-coding genes into messenger RNAs is performed by RNA polymerase II. This enzyme is directed to bind at upstream gene sequences by the aid of transcription factors that assemble transcription-competent complexes. A series of biochemical and structural modifications render the polymerase transcriptionally active so that it can proceed from an initiation state into a functional elongating phase. Recent experi- mental efforts have attempted to visualize these processes as they take place on genes in living cells and to quantify the kinetics of in vivo transcription. Keywords: mRNA transcription • Nucleus • Live-cell imaging • Cellular dynamics © Versita Warsaw and Springer-Verlag Berlin Heidelberg. 1. Introduction review will describe the developments in the field of live-cell imaging that have allowed the analysis of mammalian RNA polymerase II transcription kinetics as The central dogma of molecular biology describes the they unfold in real-time. flow of information in the living cell from DNA to RNA to protein [1]. Information can also flow back from protein to nucleic acids. The fundamental process within this pathway that enables the mobility of genetic information 2. Lighting-up the nucleus from the stagnant DNA molecules contained within the cell nucleus to the ribosomal centers of protein Fluorescence microscopy provides the capability of translation and production in the cytoplasm is the following specific molecules as they are produced and process of messenger RNA (mRNA) transcription. -
Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the Tna Operon of Escherichia Coli
JOURNAL OF BACTERIOLOGY, Aug. 1995, p. 4451–4456 Vol. 177, No. 15 0021-9193/95/$04.0010 Copyright 1995, American Society for Microbiology Bicyclomycin Sensitivity and Resistance Affect Rho Factor-Mediated Transcription Termination in the tna Operon of Escherichia coli CHARLES YANOFSKY* AND VIRGINIA HORN Department of Biological Sciences, Stanford University, Stanford, California 94305-5020 Received 13 March 1995/Accepted 27 May 1995 The growth-inhibiting drug bicyclomycin, known to be an inhibitor of Rho factor activity in Escherichia coli, was shown to increase basal level expression of the tryptophanase (tna) operon and to allow growth of a tryptophan auxotroph on indole. The drug also relieved polarity in the trp operon and permitted growth of a trp double nonsense mutant on indole. Nine bicyclomycin-resistant mutants were isolated and partially characterized. Recombination data and genetic and biochemical complementation analyses suggest that five have mutations that affect rho, three have mutations that affect rpoB, and one has a mutation that affects a third locus, near rpoB. Individual mutants showed decreased, normal, or increased basal-level expression of the tna operon. All but one of the resistant mutants displayed greatly increased tna operon expression when grown in the presence of bicyclomycin. The tna operon of the wild-type drug-sensitive parent was also shown to be highly expressed during growth with noninhibitory concentrations of bicyclomycin. These findings demonstrate that resistance to this drug may be acquired by mutations at any one of three loci, two of which appear to be rho and rpoB. Zwiefka et al. (24) found that the antibiotic bicyclomycin segment and interacts with the transcribing RNA polymerase (bicozamycin), an inhibitor of the growth of several gram- molecule, causing it to terminate transcription (7, 9). -
Evidence for a Role of Developmental Genes in the Origin of Obesity and Body Fat Distribution
Evidence for a role of developmental genes in the origin of obesity and body fat distribution Stephane Gesta*, Matthias Blu¨ her†, Yuji Yamamoto*, Andrew W. Norris*, Janin Berndt†, Susan Kralisch†, Jeremie Boucher*, Choy Lewis*, and C. Ronald Kahn*‡ *Joslin Diabetes Center and Harvard Medical School, Boston, MA 02215; and †Department of Internal Medicine III, University of Leipzig, 04103 Leipzig, Germany Contributed by C. Ronald Kahn, March 9, 2006 Obesity, especially central obesity, is a hereditable trait associated In the present study, we have explored the hypothesis that with a high risk for development of diabetes and metabolic patterns of fat distribution and, perhaps, to some degree, obesity disorders. Combined gene expression analysis of adipocyte- and itself may have a developmental genetic origin. Indeed, we find preadipocyte-containing fractions from intraabdominal and sub- major differences in expression of multiple genes involved in cutaneous adipose tissue of mice revealed coordinated depot- embryonic development and pattern specification between adipo- specific differences in expression of multiple genes involved in cytes taken from intraabdominal and s.c. depots in rodents and embryonic development and pattern specification. These differ- humans. We also demonstrate similar differences in the stromo- ences were intrinsic and persisted during in vitro culture and vascular fraction (SVF)-containing preadipocytes and that these differentiation. Similar depot-specific differences in expression of differences persist in culture. Most importantly, we demonstrate developmental genes were observed in human subcutaneous ver- that some of these developmental genes exhibit changes in expres- sus visceral adipose tissue. Furthermore, in humans, several genes sion that are closely correlated with the level of obesity and the exhibited changes in expression that correlated closely with body pattern of fat distribution. -
Supplementary Material Sumoylation Regulates the Chromatin
Supplementary material SUMOylation Regulates the Chromatin Occupancy and Anti-Proliferative Gene Programs of Glucocorticoid Receptor Ville Paakinaho, Sanna Kaikkonen, Harri Makkonen, Vladimir Benes, and Jorma J. Palvimo A FRT wtGR GR3KR clone wt-1 wt-2 wt-3 3KR-1 3KR-2 3KR-3 - - - - - - - dex + + + + + + + kDa a-GR - 100 a-GAPDH - 35 A549 + - - HEK293-wtGR - + - - - HEK293-GR3KR + kDa a-GR - 100 a-GAPDH - 35 B wtGR GR3KR 43°C - - + + - - + + dex - + - + - + - + kDa - 170 a-GR - 130 - 100 a-GAPDH - 35 - 170 a-SUMO-1 - 130 R - 100 G - a : P I a-SUMO-2/3 - 170 - 130 - 100 Figure S1. Expression and SUMOylation of GR in stable isogenic HEK293 cells. (A) Upper panel, immunoblot analysis of three HEK293 cell clones expressing either wtGR (wt-1-3) or GR3KR (3KR-1-3). The clones and background HEK293 (FRT) cells were exposed to vehicle or dex for 17 h, and cell samples were immunoblotting with anti-GR (Santa Cruz, sc-1003) and anti- GAPDH (Santa Cruz, sc-25778) antibodies. Lower panel, comparison of the GR level in A549 cells (from ATCC) with that of the selected clones from isogenic HEK293 cells (wt-3 and 3KR-3) by immunoblotting. (B) To analyse GR SUMOylation, wtGR- and GR3KR-expressing cells were grown with of without dex for 2 h and exposed for 30 min to 43°C. Immunoprecipitation (IP) with anti- GR antibody and immunoblotting with anti-SUMO-1 (Invitrogen, 33-2400) or anti-SUMO-2/3 (MBL M114-3) antibody were performed essentially as described (Rytinki et al. 2011, Methods Mol. Biol.). A total dex- sensitivity induced for dex expression ADARB1 -
I = Chpt 15. Positive and Negative Transcriptional Control at Lac BMB
BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac B M B 400 Part Four: Gene Regulation Section I = Chapter 15 POSITIVE AND NEGATIVE CONTROL SHOWN BY THE lac OPERON OF E. COLI A. Definitions and general comments 1. Operons An operon is a cluster of coordinately regulated genes. It includes structural genes (generally encoding enzymes), regulatory genes (encoding, e.g. activators or repressors) and regulatory sites (such as promoters and operators). 2. Negative versus positive control a. The type of control is defined by the response of the operon when no regulatory protein is present. b. In the case of negative control, the genes in the operon are expressed unless they are switched off by a repressor protein. Thus the operon will be turned on constitutively (the genes will be expressed) when the repressor in inactivated. c. In the case of positive control, the genes are expressed only when an active regulator protein, e.g. an activator, is present. Thus the operon will be turned off when the positive regulatory protein is absent or inactivated. Table 4.1.1. Positive vs. negative control BMB 400 Part Four - I = Chpt 15. Positive and Negative Transcriptional Control at lac 3. Catabolic versus biosynthetic operons a. Catabolic pathways catalyze the breakdown of nutrients (the substrate for the pathway) to generate energy, or more precisely ATP, the energy currency of the cell. In the absence of the substrate, there is no reason for the catabolic enzymes to be present, and the operon encoding them is repressed. In the presence of the substrate, when the enzymes are needed, the operon is induced or de-repressed. -
Aberrant HOXC Expression Accompanies the Malignant Phenotype in Human Prostate1
[CANCER RESEARCH 63, 5879–5888, September 15, 2003] Aberrant HOXC Expression Accompanies the Malignant Phenotype in Human Prostate1 Gary J. Miller,2 Heidi L. Miller, Adrie van Bokhoven, James R. Lambert, Priya N. Werahera, Osvaldo Schirripa,3 M. Scott Lucia, and Steven K. Nordeen4 Department of Pathology, University of Colorado Health Sciences Center, Denver, Colorado 80262 ABSTRACT breast (13, 14), and renal (15) carcinomas; melanomas (16); and squamous carcinomas of the skin (17). Because the genes implicated Dysregulation of HOX gene expression has been implicated as a factor show little consensus, the dysregulation may be a tissue-specific in malignancies for a number of years. However, no consensus has perturbation of the existing HOX expression pattern rather than a emerged regarding specific causative genes. Using a degenerate reverse transcription-PCR technique, we show up-regulation of genes from the single causative gene. Tissue-specific expression patterns have been HOXC cluster in malignant prostate cell lines and lymph node metastases. reported in kidney and colon, by Northern blot analysis (12, 15). When relative expression levels of the four HOX clusters were examined, Primary tumors in both kidney and colon showed variations in spe- lymph node metastases and cell lines derived from lymph node metastases cific HOX gene expression from the corresponding normal tissue, but exhibited very similar patterns, patterns distinct from those in benign cells overall expression patterns for individual tumors were not reported. or malignant cell lines derived from other tumor sites. Specific reverse Only primary kidney tumors were examined (15), but liver metastases transcription-PCR for HOXC4, HOXC5, HOXC6, and HOXC8 confirmed from colon tumors reportedly displayed expression of specific HOX overexpression of these genes in malignant cell lines and lymph node genes similar to that seen in either primary colon tumors or normal metastases. -
Fgf/Ets Signalling in Xenopus Ectoderm Initiates Neural Induction and Patterning in An
bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.191288; this version posted July 7, 2020. 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. 1 Fgf/Ets signalling in Xenopus ectoderm initiates neural induction and patterning in an 2 autonomous and paracrine manners 3 4 Ikuko Hongo* and Harumasa Okamoto*+ 5 6 Department of Life Science, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, 7 Toshima-ku, Tokyo 171-8588, Japan 8 9 *Present address: Institute for Biomolecular Science, Gakushuin University, 1-5-1 Mejiro, 10 Toshima-ku, Tokyo 171-8588, Japan 11 12 +Author for correspondence ([email protected]) 13 14 15 Running title 16 Fgf/Ets in neural development 17 18 Keywords 19 Fgf, Ets, signalling, neural induction, AP patterning, morphogen 20 21 Summary statement 22 Fgf/Ets signalling in ectodermal cells is required to initiate the expression of both anterior and 23 posterior neural genes from the late blastula to gastrula stages, independent of anti-Bmp 24 signalling. 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.07.07.191288; this version posted July 7, 2020. 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. 25 ABSTRACT 26 Fibroblast growth factor (Fgf) and anti-bone morphogenetic protein (Bmp) signals are derived 27 from the organiser of mesoderm origin and cooperate to promote Xenopus neural development 28 from the gastrula ectoderm.