Genome-Wide RNA-Sequencing Analysis Identifies a Distinct
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MKL1 (C) Antibody, Rabbit Polyclonal
Order: (888)-282-5810 (Phone) (818)-707-0392 (Fax) [email protected] Web: www.Abiocode.com MKL1 (C) Antibody, Rabbit Polyclonal Cat#: R2403-2 Lot#: Refer to vial Quantity: 100 ul Application: WB Predicted I Observed M.W.: 99 I 140 kDa Uniprot ID: Q969V6 Background: MKL/myocardin-like protein 1 (MKL1) is a transcriptional coactivator of serum response factor (SRF) with the potential to modulate SRF target genes. MKL1 suppresses TNF-induced cell death by inhibiting activation of caspases; its transcriptional activity is indispensable for the antiapoptotic function. MKL1 may up-regulate antiapoptotic molecules, which in turn inhibit caspase activation. Other Names: MKL/myocardin-like protein 1, Megakaryoblastic leukemia 1 protein, Megakaryocytic acute leukemia protein, Myocardin-related transcription factor A, MRTF-A, KIAA1438, MAL Source and Purity: Rabbit polyclonal antibodies were produced by immunizing animals with a GST-fusion protein containing the C-terminal region of human MKL1. Antibodies were purified by affinity purification using immunogen. Storage Buffer and Condition: Supplied in 1 x PBS (pH 7.4), 100 ug/ml BSA, 40% Glycerol, 0.01% NaN3. Store at -20 °C. Stable for 6 months from date of receipt. Species Specificity: Human Tested Applications: WB: 1:1,000-1:3,000 (detect endogenous protein*) *: The apparent protein size on WB may be different from the calculated M.W. due to modifications. For research use only. Not for therapeutic or diagnostic purposes. Abiocode, Inc., 29397 Agoura Rd., Ste 106, Agoura Hills, CA 91301 Order: (888)-282-5810 (Phone) (818)-707-0392 (Fax) [email protected] Web: www.Abiocode.com Product Data: kDa A B 250 150 100 75 50 37 Fig 1. -
Wide-Scale Analysis of Human Functional Transcription Factor
Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site Yuval Tabach1,2, Ran Brosh2, Yossi Buganim2, Anat Reiner1, Or Zuk1, Assif Yitzhaky1, Mark Koudritsky1, Varda Rotter2 and Eytan Domany1,* 1Departments of Physics of Complex Systems and 2Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel *Corresponding author. Email: [email protected] Tel: +972-8-9343964 Fax: +972-8- 9344109 Running title: Binding Sites Location Bias Keywords: Transcription factor binding sites, location bias, cell cycle, NF-kB, promoter, Gene Ontology, TATA, myocardin 1 Summary Background: Elucidating basic principles that underlie regulation of gene expression by transcription factors (TFs) is a central challenge of the post-genomic era. Transcription factors regulate expression by binding to specific DNA sequences; such a binding event is functional when it affects gene expression. Functionality of a binding site is reflected in conservation of the binding sequence during evolution and in over represented binding in gene groups with coherent biological functions. Functionality is governed by several parameters such as the TF- DNA binding strength, distance of the binding site from the transcription start site (TSS), DNA packing, and more. Understanding how these parameters control functionality of different TFs in different biological contexts is an essential step towards identifying functional TF binding sites, a must for understanding regulation of transcription. Methodology/Principal Findings: We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. -
Co-Occupancy by Multiple Cardiac Transcription Factors Identifies
Co-occupancy by multiple cardiac transcription factors identifies transcriptional enhancers active in heart Aibin Hea,b,1, Sek Won Konga,b,c,1, Qing Maa,b, and William T. Pua,b,2 aDepartment of Cardiology and cChildren’s Hospital Informatics Program, Children’s Hospital Boston, Boston, MA 02115; and bHarvard Stem Cell Institute, Harvard University, Cambridge, MA 02138 Edited by Eric N. Olson, University of Texas Southwestern, Dallas, TX, and approved February 23, 2011 (received for review November 12, 2010) Identification of genomic regions that control tissue-specific gene study of a handful of model genes (e.g., refs. 7–10), it has not been expression is currently problematic. ChIP and high-throughput se- evaluated using unbiased, genome-wide approaches. quencing (ChIP-seq) of enhancer-associated proteins such as p300 In this study, we used a modified ChIP-seq approach to define identifies some but not all enhancers active in a tissue. Here we genome wide the binding sites of these cardiac TFs (1). We show that co-occupancy of a chromatin region by multiple tran- provide unbiased support for collaborative TF interactions in scription factors (TFs) identifies a distinct set of enhancers. GATA- driving cardiac gene expression and use this principle to show that chromatin co-occupancy by multiple TFs identifies enhancers binding protein 4 (GATA4), NK2 transcription factor-related, lo- with cardiac activity in vivo. The majority of these multiple TF- cus 5 (NKX2-5), T-box 5 (TBX5), serum response factor (SRF), and “ binding loci (MTL) enhancers were distinct from p300-bound myocyte-enhancer factor 2A (MEF2A), here referred to as cardiac enhancers in location and functional properties. -
Myocardin (MYOCD) (NM 001146312) Human Tagged ORF Clone Product Data
OriGene Technologies, Inc. 9620 Medical Center Drive, Ste 200 Rockville, MD 20850, US Phone: +1-888-267-4436 [email protected] EU: [email protected] CN: [email protected] Product datasheet for RC229055L3 Myocardin (MYOCD) (NM_001146312) Human Tagged ORF Clone Product data: Product Type: Expression Plasmids Product Name: Myocardin (MYOCD) (NM_001146312) Human Tagged ORF Clone Tag: Myc-DDK Symbol: MYOCD Synonyms: MGBL; MYCD Vector: pLenti-C-Myc-DDK-P2A-Puro (PS100092) E. coli Selection: Chloramphenicol (34 ug/mL) Cell Selection: Puromycin ORF Nucleotide The ORF insert of this clone is exactly the same as(RC229055). Sequence: Restriction Sites: SgfI-MluI Cloning Scheme: ACCN: NM_001146312 ORF Size: 2958 bp This product is to be used for laboratory only. Not for diagnostic or therapeutic use. View online » ©2021 OriGene Technologies, Inc., 9620 Medical Center Drive, Ste 200, Rockville, MD 20850, US 1 / 3 Myocardin (MYOCD) (NM_001146312) Human Tagged ORF Clone – RC229055L3 OTI Disclaimer: Due to the inherent nature of this plasmid, standard methods to replicate additional amounts of DNA in E. coli are highly likely to result in mutations and/or rearrangements. Therefore, OriGene does not guarantee the capability to replicate this plasmid DNA. Additional amounts of DNA can be purchased from OriGene with batch-specific, full-sequence verification at a reduced cost. Please contact our customer care team at [email protected] or by calling 301.340.3188 option 3 for pricing and delivery. The molecular sequence of this clone aligns with the gene accession number as a point of reference only. However, individual transcript sequences of the same gene can differ through naturally occurring variations (e.g. -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Gene Expression During Normal and FSHD Myogenesis Tsumagari Et Al
Gene expression during normal and FSHD myogenesis Tsumagari et al. Tsumagari et al. BMC Medical Genomics 2011, 4:67 http://www.biomedcentral.com/1755-8794/4/67 (27 September 2011) Tsumagari et al. BMC Medical Genomics 2011, 4:67 http://www.biomedcentral.com/1755-8794/4/67 RESEARCHARTICLE Open Access Gene expression during normal and FSHD myogenesis Koji Tsumagari1, Shao-Chi Chang1, Michelle Lacey2,3, Carl Baribault2,3, Sridar V Chittur4, Janet Sowden5, Rabi Tawil5, Gregory E Crawford6 and Melanie Ehrlich1,3* Abstract Background: Facioscapulohumeral muscular dystrophy (FSHD) is a dominant disease linked to contraction of an array of tandem 3.3-kb repeats (D4Z4) at 4q35. Within each repeat unit is a gene, DUX4, that can encode a protein containing two homeodomains. A DUX4 transcript derived from the last repeat unit in a contracted array is associated with pathogenesis but it is unclear how. Methods: Using exon-based microarrays, the expression profiles of myogenic precursor cells were determined. Both undifferentiated myoblasts and myoblasts differentiated to myotubes derived from FSHD patients and controls were studied after immunocytochemical verification of the quality of the cultures. To further our understanding of FSHD and normal myogenesis, the expression profiles obtained were compared to those of 19 non-muscle cell types analyzed by identical methods. Results: Many of the ~17,000 examined genes were differentially expressed (> 2-fold, p < 0.01) in control myoblasts or myotubes vs. non-muscle cells (2185 and 3006, respectively) or in FSHD vs. control myoblasts or myotubes (295 and 797, respectively). Surprisingly, despite the morphologically normal differentiation of FSHD myoblasts to myotubes, most of the disease-related dysregulation was seen as dampening of normal myogenesis- specific expression changes, including in genes for muscle structure, mitochondrial function, stress responses, and signal transduction. -
Viewed and Published Immediately Upon Acceptance Cited in Pubmed and Archived on Pubmed Central Yours — You Keep the Copyright
BMC Genomics BioMed Central Research article Open Access Differential gene expression in ADAM10 and mutant ADAM10 transgenic mice Claudia Prinzen1, Dietrich Trümbach2, Wolfgang Wurst2, Kristina Endres1, Rolf Postina1 and Falk Fahrenholz*1 Address: 1Johannes Gutenberg-University, Institute of Biochemistry, Mainz, Johann-Joachim-Becherweg 30, 55128 Mainz, Germany and 2Helmholtz Zentrum München – German Research Center for Environmental Health, Institute for Developmental Genetics, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany Email: Claudia Prinzen - [email protected]; Dietrich Trümbach - [email protected]; Wolfgang Wurst - [email protected]; Kristina Endres - [email protected]; Rolf Postina - [email protected]; Falk Fahrenholz* - [email protected] * Corresponding author Published: 5 February 2009 Received: 19 June 2008 Accepted: 5 February 2009 BMC Genomics 2009, 10:66 doi:10.1186/1471-2164-10-66 This article is available from: http://www.biomedcentral.com/1471-2164/10/66 © 2009 Prinzen et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: In a transgenic mouse model of Alzheimer disease (AD), cleavage of the amyloid precursor protein (APP) by the α-secretase ADAM10 prevented amyloid plaque formation, and alleviated cognitive deficits. Furthermore, ADAM10 overexpression increased the cortical synaptogenesis. These results suggest that upregulation of ADAM10 in the brain has beneficial effects on AD pathology. Results: To assess the influence of ADAM10 on the gene expression profile in the brain, we performed a microarray analysis using RNA isolated from brains of five months old mice overexpressing either the α-secretase ADAM10, or a dominant-negative mutant (dn) of this enzyme. -
Myocardin Is Sufficient and Necessary for Cardiac Gene Expression in Xenopus Eric M
Research article 987 Myocardin is sufficient and necessary for cardiac gene expression in Xenopus Eric M. Small1,*,†, Andrew S. Warkman1,*, Da-Zhi Wang2, Lillian B. Sutherland3, Eric N. Olson3 and Paul A. Krieg1,‡ 1Department of Cell Biology and Anatomy, University of Arizona Health Sciences Center, 1501 N. Campbell Avenue, PO Box 245044, Tucson, AZ, 85724, USA 2Carolina Cardiovascular Biology Center, Department of Cell and Developmental Biology, University of North Carolina, Chapel Hill, NC 27599-7126, USA 3Department of Molecular Biology, University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390-9148, USA *These authors contributed equally to this work †Present address: Cardiovascular Research, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada ‡Author for correspondence (e-mail: [email protected]) Accepted 14 December 2004 Development 132, 987-997 Published by The Company of Biologists 2005 doi:10.1242/dev.01684 Summary Myocardin is a cardiac- and smooth muscle-specific co- expression. Inhibition of myocardin activity in Xenopus factor for the ubiquitous transcription factor serum embryos using morpholino knockdown methods results in response factor (SRF). Using gain-of-function approaches inhibition of cardiac development and the absence of in the Xenopus embryo, we show that myocardin is expression of cardiac differentiation markers and severe sufficient to activate transcription of a wide range of disruption of cardiac morphological processes. We cardiac and -
Regulation of Mitochondrial Function by Myocardin During Cardiac Development and Disease
Regulation of mitochondrial function by Myocardin during cardiac development and disease By Wajihah Mughal A Thesis submitted to the Faculty of Graduate Studies University of Manitoba In partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Department of Human Anatomy and Cell Science University of Manitoba Winnipeg Copyright © by Wajihah Mughal, 2019 Abstract Metabolic specific myogenic precursors in the splanchnic, somatic mesoderm, and the neural crest give rise to specialized cell types such as cardiac, skeletal, and smooth muscle cells. This initiation of muscle cell lineage is coordinated by a reinforcing networking of transcription factors that regulate gene expression during cell proliferation and differentiation. Myocardin is a transcriptional coactivator that binds to transcription factors to regulate gene expression specific to both cardiac and smooth muscle cells. It is previously shown that Myocardin interacts with transcription factors of the MADS-Box family proteins such as myocyte enhancer factor-2 (MEF2) and serum response factor (SRF), that are known regulators of cellular differentiation and metabolism. Conversely, the role of Myocardin as well as its regulation of MADS-Box transcription factors and mitochondrial function during development and disease is not well understood. Therefore, we chose to investigate a Myocardin-regulated genetic pathway that regulates mitochondrial function in cardiac muscle that becomes dysregulated during disease. My thesis summarizes our evaluation of the hypothesis in two studies. In the first study we characterize a mechanistic pathway involving MEF2 and SRF, that regulates mitochondrial function in all three muscle lineages. This initial study demonstrates a genetic pathway in which Nix is a direct target of miR-133a, its role in regulating insulin sensitivity and metabolic dysfunction in myocytes. -
Loss-Of-Function Variants in Myocardin Cause Congenital Megabladder in Humans and Mice
Loss-of-function variants in myocardin cause congenital megabladder in humans and mice Arjan C. Houweling, … , Adrian S. Woolf, Esther E. Creemers J Clin Invest. 2019. https://doi.org/10.1172/JCI128545. Concise Communication In-Press Preview Muscle biology Myocardin (MYOCD) is the founding member of a class of transcriptional co-activators that bind serum response factor to activate gene expression programs critical in smooth muscle (SM) and cardiac muscle development. Insights into the molecular functions of MYOCD have been obtained from cell culture studies and, to date, knowledge about in vivo roles of MYOCD comes exclusively from experimental animals. Here, we defined an often lethal congenital human disease associated with inheritance of pathogenic MYOCD variants. This disease manifested as a massively dilated urinary bladder, or megabladder, with disrupted SM in its wall. We provided evidence that monoallelic loss-of-function variants in MYOCD caused congenital megabladder in males only, whereas biallelic variants were associated with disease in both sexes, with a phenotype additionally involving the cardiovascular system. These results were supported by co- segregation of MYOCD variants with the phenotype in four unrelated families, by in vitro transactivation studies where pathogenic variants resulted in abrogated SM gene expression, and finding megabladder in two distinct mouse models with reduced Myocd activity. In conclusion, we have demonstrated that variants in MYOCD result in human disease, and the collective findings highlight a vital role for MYOCD in mammalian organogenesis. Find the latest version: https://jci.me/128545/pdf Loss-of-function variants in myocardin cause congenital megabladder in humans and mice Arjan C. -
The Myocardin Family of Transcriptional Coactivators: Versatile Regulators of Cell Growth, Migration, and Myogenesis
Downloaded from genesdev.cshlp.org on October 6, 2021 - Published by Cold Spring Harbor Laboratory Press REVIEW The myocardin family of transcriptional coactivators: versatile regulators of cell growth, migration, and myogenesis G.C. Teg Pipes, Esther E. Creemers, and Eric N. Olson1 Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA The association of transcriptional coactivators with se- gene regulation and expands the regulatory potential of quence-specific DNA-binding proteins provides versatil- individual cis-regulatory elements. ity and specificity to gene regulation and expands the The regulation of serum response factor (SRF) and its regulatory potential of individual cis-regulatory DNA se- target genes provides a classic example of the diversity of quences. Members of the myocardin family of coactiva- genes controlled by a single DNA-binding protein and tors activate genes involved in cell proliferation, migra- the importance of cofactor interactions in the control of tion, and myogenesis by associating with serum re- gene expression (Shore and Sharrocks 1995). Among the sponse factor (SRF). The partnership of myocardin family many target genes of SRF are genes involved in cell pro- members and SRF also controls genes encoding compo- liferation and muscle differentiation, which represent nents of the actin cytoskeleton and confers responsive- opposing programs of gene expression: Muscle genes are ness to extracellular growth signals and intracellular repressed by growth factor signals and generally do not changes in the cytoskeleton, thereby creating a tran- become activated until myoblasts exit the cell cycle. The scriptional–cytoskeletal regulatory circuit. These func- ability of SRF to regulate different sets of downstream tions are reflected in defects in smooth muscle differen- effector genes depends on its association with positive tiation and function in mice with mutations in myocar- and negative cofactors (Treisman 1994; Shore and Shar- din family members. -
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NOTE TO USERS This reproduction is the best copy available. UMI* ACTIVE LEARNING FOR THE PREDICTION OF ASPARAGINE AND ASPARTATE HYDROXYLATION SITES ON HUMAN PROTEINS By Festus Omonigho Iyuke, B.Sc, M.Sc. ACTIVE LEARNING FOR THE PREDICTION OF ASPARAGINE AND ASPARTATE HYDROXYLATION SITES ON HUMAN PROTEINS A thesis submitted to the Faculty of Graduate Studies and Research in partial fulfillment of the requirements for the degree of Masters of Applied Science in Biomedical Engineering Ottawa-Carleton Institute for Biomedical Engineering Department of Systems and Computer Engineering Carleton University Ottawa, Ontario, Canada September 2011 Copyright © Festus Iyuke, September 2011 Library and Archives Bibliotheque et 1*1 Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington OttawaONK1A0N4 OttawaONK1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-83033-8 Our file Notre reference ISBN: 978-0-494-83033-8 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library and permettant a la Bibliotheque et Archives Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par I'lnternet, preter, telecommunication or on the Internet, distribuer et vendre des theses partout dans le loan, distribute and sell theses monde, a des fins commerciales ou autres, sur worldwide, for commercial or non support microforme, papier, electronique et/ou commercial purposes, in microform, autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in this et des droits moraux qui protege cette these.