DOCSLIB.ORG

In Response to DNA Damage and C&Sol

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
In Response to DNA Damage and C&Sol Oncogene (2009) 28, 3235–3245 & 2009 Macmillan Publishers Limited All rights reserved 0950-9232/09 $32.00 www.nature.com/onc ORIGINAL ARTICLE C/EBPa expression is partially regulated by C/EBPb in response to DNA damage and C/EBPa-deficient fibroblasts display an impaired G1 checkpoint R Ranjan1, EA Thompson1, K Yoon2 and RC Smart1 1Cell Signaling and Cancer Group, Department of Environmental and Molecular Toxicology, North Carolina State University, Raleigh, NC, USA and 2National Cancer Center, Division of Common Cancers, Lung Cancer Branch, Goyang-si, Gyeonggi-do, South Korea We observed that CCAAT/enhancer-binding protein involved in homo- or hetero-dimerization (Ramji and (C/EBP)a is highly inducible in primary fibroblasts by Foka, 2002). The N-terminal region contains transcrip- DNA-damaging agents that induce strand breaks, alky- tion activation and regulatory domains that interact late and crosslink DNA as well as those that produce with basal transcription apparatus and transcription bulky DNA lesions. Fibroblasts deficient in C/EBPa co-activators. There are six members of the C/EBP family À/À (C/EBPa ) display an impaired G1 checkpoint as and C/EBPs have important functions in fundamental evidenced by an inappropriate entry into the S-phase in cellular processes, including proliferation, apoptosis, response to DNA damage, and these cells also display an differentiation, inflammation, senescence and energy enhanced G1/S transition in response to mitogens. The metabolism (Ramji and Foka, 2002; Johnson, 2005). induction of C/EBPa by DNA damage in fibroblasts does C/EBPa mediates cell-cycle arrest associated with not require p53. Electrophoretic mobility shift assay terminal differentiation in adipocytes (Umek et al., (EMSA) analysis of nuclear extracts prepared from 1991; Lin and Lane, 1994), hepatocytes (Diehl et al., ultraviolet B (UVB)- and N-methyl-N0-nitro-N-nitroso- 1996) and myeloid cells (Radomska et al., 1998; Wang guanidine (MNNG)-treated fibroblasts showed increased et al., 1999) and it regulates the expression of genes binding of C/EBPb to a C/EBP consensus sequence associated with the differentiated phenotype in these cell and chromatin immunoprecipitation (ChIP) analysis also types. Consistent with its role in the regulation of showed increased C/EBPb binding to the C/EBPa differentiation, C/EBPa has been shown to be a tumor promoter. To determine whether C/EBPb has a function suppressor gene in acute myeloid leukemia, in which it is in the regulation of C/EBPa, we treated C/EBPbÀ/À inactivated in B9% of AML cases through specific fibroblasts with UVB or MNNG. We observed that somatic mutations (Pabst et al., 2001; Gombart et al., C/EBPa induction was impaired in both UVB- and 2002). The inactivating mutations in C/EBPa result MNNG-treated C/EBPbÀ/À fibroblasts. Our study shows in a block in granulocytic differentiation and contribute a novel function for C/EBPb in the regulation of C/EBPa to the uncontrolled proliferation of undifferentiated in response to DNA damage and provides definitive immature granulocytic blasts. Ectopic or forced expres- genetic evidence that C/EBPa has a critical role in the sion of C/EBPa inhibits cell-cycle progression in nearly DNA damage G1 checkpoint. all cell types examined (Hendricks-Taylor and Darling- Oncogene (2009) 28, 3235–3245; doi:10.1038/onc.2009.176; ton, 1995; Watkins et al., 1996; Halmos et al., 2002; published online 6 July 2009 Johnson, 2005; Shim et al., 2005); however, the intrinsic cellular signals and pathways that regulate C/EBPa Keywords: C/EBP; DNA damage response; G1/S transi- expression and its growth arrest properties are not fully tion; p53 understood. In some cases, these pathways are linked to cellular differentiation. C/EBPa expression is ablated or greatly diminished in a number of epithelial cancers, including lung (Halmos Introduction et al., 2002), skin (Oh and Smart, 1998; Shim et al., 2005), liver (Xu et al., 2001), head and neck (Bennett The CCAAT/enhancer-binding proteins (C/EBPs) are et al., 2007), endometrial (Takai et al., 2005) and breast members of the basic leucine zipper (bZIP) class of (Gery et al., 2005), suggesting a tumor suppressor transcription factors that contain a C-terminal basic function. In many cases, the C/EBPa gene is silenced DNA-binding domain and a leucine zipper domain through promoter hypermethylation (Gery et al., 2005; Tada et al., 2006; Bennett et al., 2007). Causal or genetic evidence for a suppressor role of C/EBPa in epithelial Correspondence: Dr RC Smart, Cell Signaling and Cancer Group, tumorigenesis is lacking because of the absence of Department of Environmental and Molecular Toxicology, North C/EBPa mutations in epithelial tumors. Moreover, Carolina State University, Raleigh, NC 27695-7633, USA. E-mail: [email protected] genetically engineered mouse models to document the Received 23 December 2008; revised 23 May 2009; accepted 24 May suppressor function of C/EBPa in tumorigenesis 2009; published online 6 July 2009 have been problematic as germ line or lung-specific C/EBPa is regulated by C/EBPb in response to DNA damage R Ranjan et al 3236 deletion of C/EBPa is perinatally lethal (Wang et al., 1995; types of DNA damage with the induction of C/EBPa, Basseres et al., 2006). Recently, a genetically engineered and we present genetic evidence using C/EBPaÀ/À cells to mouse model in which C/EBPa was ablated in the show a role for C/EBPa in the G1 checkpoint. epidermis was successfully developed (Loomis et al., Importantly, we have identified a novel stress pathway, 2007). These mice survived and were highly susceptible in which C/EBPb has a role in the induction of C/EBPa to carcinogen-induced skin tumorigenesis, thus provid- in response to DNA damage. ing the first genetic evidence for C/EBPa as a suppressor of epithelial tumorigenesis. Surprisingly, the epidermal- specific C/EBPa knockout mice did not show alterations Results in stratified squamous differentiation or proliferation of epidermal keratinocytes, suggesting that their enhanced UVB induces C/EBPa in fibroblasts and C/EBPaÀ/À susceptibility to tumorigenesis is not related to alterations fibroblasts display alterations in the G1/S transition in keratinocyte differentiation (Loomis et al., 2007). and G1 checkpoint To prevent or reduce stress-induced injury and Initially, we attempted cell-cycle studies in wild-type cellular damage, cells have evolved intricate pathways and C/EBPaÀ/À primary keratinocytes; however, these that permit them to respond to both intrinsic and studies were not informative because of the inherent extrinsic stressors. In terms of DNA damage, cells complexity of using primary keratinocytes for cell-cycle respond by engaging cell-cycle checkpoints and repair- regulation studies owing to the presence of mixed ing damaged DNA in order to maintain genome populations of differentiating and proliferating primary integrity and to prevent heritable mutations, which can keratinocytes. To provide direct genetic evidence for lead to genomic instability, aging and cancer (Kastan C/EBPa in the G1 checkpoint and to extend the findings and Bartek, 2004; Sancar et al., 2004; Ishikawa et al., on UVB-induced expression of C/EBPa in keratinocytes 2006). In ultraviolet B (UVB)-treated skin keratinocytes, to another cell type, mouse dermal wild-type and C/EBPa expression is highly induced through a p53- C/EBPaÀ/À primary fibroblasts were used. Wild-type dependent pathway and the partial small interfering and C/EBPaÀ/À primary fibroblasts were exposed to a RNA (siRNA) knockdown of C/EBPa in the BALB/ single dose of UVB radiation (5 mJ/cm2). UVB radiation MK2 keratinocyte cell line resulted in a diminished produced a significant increase in C/EBPa protein levels G1 checkpoint after UVB-induced DNA damage in wild-type fibroblasts (Figure 1a) and C/EBPa was (Yoon and Smart, 2004). Although C/EBPa was highly not expressed in C/EBPaÀ/À fibroblasts (Figure 1b). In induced by UVB in keratinocytes, UVB treatment wild-type fibroblasts, C/EBPa was maximally induced at of HepG2, NRK and NIH3T3 cells failed to induce 6 h post UVB treatment and returned to control levels C/EBPa. Thus, C/EBPa, at least in keratinocytes, is by 24 h post UVB treatment. Elevated levels of C/EBPa regulated by stress involving DNA damage through a were detected as early as 1 h post UVB treatment (data p53 pathway, and it appears to have a role in the not shown). UVB also induced a modest transient maintenance of genomic stability through its role in the increase in C/EBPb at 6 h post UVB treatment G1 checkpoint. However, genetic evidence supporting a (Figure 1a). role for C/EBPa in the G1 checkpoint is lacking, and as To examine the effect of the genetic ablation of mentioned above, no other cell types other than C/EBPa on cell-cycle regulation, wild-type and keratinocytes have been reported to respond to DNA C/EBPaÀ/À and primary fibroblasts were synchronized damage with the induction of C/EBPa. by serum deprivation and then released into the cell In light of C/EBPa’s role in tumorigenesis and DNA cycle by the addition of serum-containing media. damage response, it is important to understand the Fibroblasts were either left untreated or treated with a stress pathways or mechanisms through which C/EBPa single dose of UVB (5 mJ/cm2) 4 h after release. Cells is regulated in response to DNA damage and the were pulsed with 5-bromo-20-deoxyuridine (BrdU) 1 h functional importance of C/EBPa’s induction. In this before each collection time point (4, 15, 18, 21 and 24 h study, we show that fibroblasts respond to multiple post release) and fluorescence-activated cell sorting Figure 1 Ultraviolet B (UVB) radiation induces C/EBPa in primary fibroblasts and C/EBPa is involved in the G1/S transition as well as in 2 UVB-induced G1 checkpoint.
Load more

Recommended publications
  • An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum Yang Eric Li1*, Sebastian Preissl2*, Xiaomeng Hou2, Ziyang Zhang1
    bioRxiv preprint doi: https://doi.org/10.1101/2020.05.10.087585; this version posted May 11, 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 An Atlas of Gene Regulatory Elements in Adult Mouse Cerebrum 2 3 Yang Eric Li1*, Sebastian Preissl2*, Xiaomeng Hou2, Ziyang Zhang1, Kai Zhang1, Rongxin 4 Fang1, Yunjiang Qiu1, Olivier Poirion2, Bin Li1, Hanqing Liu3, Xinxin Wang2, Jee Yun Han2, 5 Jacinta Lucero4, Yiming Yan1, Samantha Kuan1, David Gorkin2, Michael Nunn3, Eran A. 6 Mukamel5, M. Margarita Behrens4, Joseph Ecker3,6 and Bing Ren1,2,7 7 8 *these authors contributed equally 9 10 1Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, CA 92093, USA 11 2Center for Epigenomics, Department of Cellular and Molecular Medicine, University of 12 California, San Diego, School of Medicine, La Jolla, CA, USA. 13 3Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 14 92037, USA. 15 4Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, 16 CA 92037, USA 17 5Department of Cognitive Science, University of California, San Diego, La Jolla, CA 18 92037, USA. 19 6Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 20 92037, USA. 21 7Institute of Genomic Medicine, Moores Cancer Center, University of California San 22 Diego, School of Medicine, La Jolla, CA, USA. 23 24 Correspondence: Bing Ren ([email protected]) 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.05.10.087585; this version posted May 11, 2020.
    [Show full text]
  • Evolution of Genomic Expression
    C H A P T E R 5 Evolution of Genomic Expression Bernardo Lemos, Christian R. Landry, Pierre Fontanillas, Susan P. Renn, Rob Kulathinal, Kyle M. Brown, and Daniel L. Hartl Introduction Genomic regulation is key to cellular differentiation, tissue morphogenesis, and development. Increasing evidence indicates that evolutionary diversity of phenotypes—from cellular to organismic—may also be, in large part, the result of variation in the regulation of genomic expression. In this chapter we explore the complexity of gene regulation from the perspective of single genes and whole genomes. The first part describes the major factors affecting gene expression levels, from rates of gene transcrip- tion—as mediated by promoter–enhancer interactions and chromatin mod- ifications—to rates of mRNA degradation. This description underscores the multiple levels at which genomic expression can be regulated as well as the complexity and variety of mechanisms used. We then briefly describe the major experimental and computational biology techniques for analyzing gene expression variation and its underlying causes. The final section reviews our understanding of the role of regulatory variation in evolution, including the molecular evolution and population genetics of noncoding DNA, as well as the inheritance and phenotypic evolution of levels of mRNA abundance. The Complex Regulation of Genomic Expression The regulation of gene expression is a complex and dynamic process. It is not a simple matter to turn a gene on and off, let alone precisely regulate its level of expression. Regulation can be accomplished through various mech- anisms at nearly every step of the process of gene expression. Furthermore, each mechanism may require a variety of elements, including DNA sequences, RNA molecules, and proteins, acting in combination to deter- 2 Chapter Five Evolution of Genomic Expression 3 mine the final amount, timing, and location of functional gene product.
    [Show full text]
  • Molecular Basis of the Function of Transcriptional Enhancers
    cells Review Molecular Basis of the Function of Transcriptional Enhancers 1,2, 1, 1,3, Airat N. Ibragimov y, Oleg V. Bylino y and Yulii V. Shidlovskii * 1 Laboratory of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia; [email protected] (A.N.I.); [email protected] (O.V.B.) 2 Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia 3 I.M. Sechenov First Moscow State Medical University, 8, bldg. 2 Trubetskaya St., 119048 Moscow, Russia * Correspondence: [email protected]; Tel.: +7-4991354096 These authors contributed equally to this study. y Received: 30 May 2020; Accepted: 3 July 2020; Published: 5 July 2020 Abstract: Transcriptional enhancers are major genomic elements that control gene activity in eukaryotes. Recent studies provided deeper insight into the temporal and spatial organization of transcription in the nucleus, the role of non-coding RNAs in the process, and the epigenetic control of gene expression. Thus, multiple molecular details of enhancer functioning were revealed. Here, we describe the recent data and models of molecular organization of enhancer-driven transcription. Keywords: enhancer; promoter; chromatin; transcriptional bursting; transcription factories; enhancer RNA; epigenetic marks 1. Introduction Gene transcription is precisely organized in time and space. The process requires the participation of hundreds of molecules, which form an extensive interaction network. Substantial progress was achieved recently in our understanding of the molecular processes that take place in the cell nucleus (e.g., see [1–9]).
    [Show full text]
  • Transcription in Eukaryotes
    Transcription in eukaryotes Chromatin structure and its effects on transcription RNA polymerases Promoters General Transcription Factors Activators and Repressors Enhancers and ( Silencers ) Order of events leading to transcription initiation in eukaryotes at a specific promoter CRC … and chemical DNA modifications The order of steps on the pathway to transcription initiation appears to be different for different promoters Acção concertada de: -Activadores/ repressores ( proteínas auxiliares acessórias) -Proteínas de remodelação da cromatina -Capacidade de ligação dos factores gerais da transcrição Chromatin Remodeling Complexes (CRC) or Nucleosome remodeling factors ATPase/Helicase activity and DNA binding protein motifs Histone acetylation is one of the Histone histone chemical modifications acetylation characteristic of actively transcribed chromatin Interaction with other histones and with DNA Lys + HAT- histone acetyltransferase HDAC- histone deacetylase DNA chemical modifications affecting transcription initiation in eukaryotes How DNA methylation may help turning off genes? The binding of gene regulatory proteins and the general transcription machinery near an active promoter may prevent DNA methylation by excluding de novo methylases . If most of these proteins dissociate from the DNA, however, as generally occurs when a cell no longer produces the required activator proteins , the DNA becomes methylated , which enables other proteins to bind, and these shut down the gene completely by further altering chromatin structure . DNA
    [Show full text]
  • Minireview Mcbindall—A Better Name for CCAAT/Enhancer Binding
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Cell, Vol. 107, 259–261, November 2, 2001, Copyright 2001 by Cell Press McBindall—A Better Name for Minireview CCAAT/Enhancer Binding Proteins? Steven L. McKnight1 code a heterodimeric transcription factor, as well as Department of Biochemistry recognition that the Myc proto-oncogene encodes a UT Southwestern Medical Center transcription factor. Such studies also provided a frame- 5323 Harry Hines Boulevard work and powerful battery of reagents useful for the Dallas, Texas 75390 biological study of C/EBP itself. Finally, biochemical studies of C/EBP helped dispel the myth, anticipated from earlier work on bacterial gene expression, that C/EBP-related transcription factors regulate the bal- eukaryotic transcription factors must have exquisite ance between cell proliferation and mitotic growth ar- binding specificity. This shift of thinking led to the under- rest during terminal differentiation. Three new studies standing that eukaryotic genes employ complex en- give evidence that this regulation is mediated by pro- hancers that integrate the instruction of multiple tran- tein:protein interactions completely distinct from the scription factors acting in a combinatorial manner role of C/EBPs in gene expression. (Thompson and McKnight, 1992). The previous issue of Cell and the most recent issue In the mid-1980s Barbara Graves and Peter Johnson of Molecular Cell present three exciting papers relevant were postdoctoral fellows in my laboratory at the Carne- to the function of various members of the C/EBP family gie Embryology Department. Barbara and Peter were of transcription factors.
    [Show full text]
  • Cross-Species Regulatory Sequence Activity Prediction
    bioRxiv preprint doi: https://doi.org/10.1101/660563; this version posted September 25, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Cross-species regulatory sequence activity prediction David R. Kelley Calico Life Sciences South San Francisco, CA [email protected] September 25, 2019 Abstract Machine learning algorithms trained to predict the regulatory activity of nucleic acid sequences have revealed principles of gene regulation and guided genetic variation analysis. While the human genome has been extensively annotated and studied, model organisms have been less explored. Model organism genomes offer both additional training sequences and unique annotations describing tissue and cell states unavailable in humans. Here, we develop a strategy to train deep convolutional neural networks simultaneously on multiple genomes and apply it to learn sequence predictors for large compendia of human and mouse data. Training on both genomes improves gene expression prediction accuracy on held out sequences. We further demonstrate a novel and powerful transfer learning approach to use mouse regulatory models to analyze human genetic variants associated with molecular phenotypes and disease. Together these techniques unleash thousands of non-human epigenetic and transcriptional profiles toward more effective investigation of how gene regulation affects human disease. Introduction Predicting the behavior of any nucleic acid sequence in any environment is a primary objective of gene regulation research. In recent years, machine learning approaches to directly tackle this problem have achieved significant accuracy gains predicting transcription factor (TF) binding, chromatin features, and gene expression from input DNA sequence (1{7).
    [Show full text]
  • Transcriptional Regulation of INSR, the Insulin Receptor Gene
    G C A T T A C G G C A T genes Review Transcriptional Regulation of INSR, the Insulin Receptor Gene Sandhya Payankaulam 1, Ana-Maria Raicu 2 and David N. Arnosti 1,2,* 1 Department of Biochemistry and Molecular Biology, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA; [email protected] 2 Cell and Molecular Biology Program, Michigan State University, 603 Wilson Rd. 413 Biochemistry, East Lansing, MI 48824, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-(517)-432-5504 Received: 28 October 2019; Accepted: 23 November 2019; Published: 29 November 2019 Abstract: The insulin receptor gene encodes an evolutionarily conserved signaling protein with a wide spectrum of functions in metazoan development. The insulin signaling pathway plays key roles in processes such as metabolic regulation, growth control, and neuronal function. Misregulation of the pathway features in diabetes, cancer, and neurodegenerative diseases, making it an important target for clinical interventions. While much attention has been focused on differential pathway activation through ligand availability, sensitization of overall signaling may also be mediated by differential expression of the insulin receptor itself. Although first characterized as a “housekeeping” gene with stable expression, comparative studies have shown that expression levels of the human INSR mRNA differ by tissue and in response to environmental signals. Our recent analysis of the transcriptional controls affecting expression of the Drosophila insulin receptor gene indicates that a remarkable amount of DNA is dedicated to encoding sophisticated feedback and feed forward signals. The human INSR gene is likely to contain a similar level of transcriptional complexity; here, we summarize over three decades of molecular biology and genetic research that points to a still incompletely understood regulatory control system.
    [Show full text]
  • Section 2: ß-Cell Genes: Functional Aspects
    Section 2: ␤-Cell Genes: Functional Aspects Regulation of pdx-1 Gene Expression Danielle Melloul, Sonya Marshak, and Erol Cerasi The homeodomain-containing transcription factor pan- tion of the endoderm, it is crucial for the development creatic duodenal homeobox 1 (PDX-1) plays a key role of endocrine and exocrine cell types (2,6). Differentiation in pancreas development and in ␤-cell function. Up- and maintenance of the ␤-cell phenotype also require stream sequences of the gene up to about ؊6 kb show PDX-1. In mice, ␤-cell–selective disruption of pdx-1 led to islet-specific activity in transgenic mice. Attempts to the development of diabetes with increasing age and was identify functional regulatory elements involved in the associated with reduced insulin and GLUT2 expression controlled expression of the pdx-1 gene led to the (7). Indeed, mice heterozygous for pdx-1 were found to be ␤ identification of distinct distal -cell–specific enhanc- glucose intolerant (7,8). In transgenic mice expressing ers in human and rat genes. Three additional sequences, ؅ an antisense ribozyme specific for mouse pdx-1 in the conserved between the mouse and the human 5 -flank- ␤ ing regions, two of which are also found in the chicken -cells, the expression of the endogenous gene was de- gene, conferred ␤-cell–specific expression on a reporter creased and followed by impaired glucose tolerance and gene, albeit to different extents. A number of transcrip- elevated glycated hemoglobin levels (9). Impaired expres- tion factors binding to and modulating the transcrip- sion of PDX-1 as a consequence of hyperglycemia or tional activity of the regulatory elements were increased lipid concentrations (10) is associated with identified, such as hepatocyte nuclear factor (HNF)-3␤, diabetes.
    [Show full text]
  • Identification of the Regulatory Sequence of Anaerobically Expressed Locus Aeg-46.5 MUHYEON Choet and WILLIAM S
    JOURNAL OF BACTERIOLOGY, Feb. 1993, p. 1165-1172 Vol. 175, No. 4 0021-9193/93/041165-08$02.00/0 Copyright X 1993, American Society for Microbiology Identification of the Regulatory Sequence of Anaerobically Expressed Locus aeg-46.5 MUHYEON CHOEt AND WILLIAM S. REZNIKOFF* Department ofBiochemistry, University of Wisconsin, 420 Henry Mall, Madison, Wisconsin 53706 Received 1 September 1992/Accepted 14 December 1992 A newly identified anaerobically expressed locus, aeg-46.5, which is located at min 46.5 on Escherichia coli linkage map, was cloned and analyzed. The phenotype of this gene was studied by using a lacZ operon fusion. aeg-46.5 is induced anaerobically in the presence of nitrate in wild-type and narL cells. It is repressed by the narL gene product, as it showed derepressed anaerobic expression in narL mutant cells. We postulate that aeg-46.5 is subject to multiple regulatory systems, activation as a result of anaerobiosis, narL-independent nitrate-dependent activation, and narL-mediated repression. The regulatory region of aeg-46.5 was identified. A 304-bp DNA sequence which includes the regulatory elements was obtained, and the 5' end of aeg-46.5 mRNA was identified. It was verified that the anaerobic regulation of aeg-46.5 expression is controlled on the transcriptional level. Computer analysis predicted possible control sites for the NarL and FNR proteins. The proposed NarL site was found in a perfect-symmetry element. The aeg-46.5 regulatory elements are adjacent to, but divergent from, those of the eco gene. Escherichia coli produces energy by breaking down a was discovered that aeg-46.5 is repressed by NarL.
    [Show full text]
  • Cis-Regulatory Code of Stress-Responsive Transcription in Arabidopsis Thaliana
    Cis-regulatory code of stress-responsive transcription in Arabidopsis thaliana Cheng Zoua, Kelian Suna, Joshua D. Mackalusoa,b,c, Alexander E. Seddona, Rong Jinb, Michael F. Thomashowd,e, and Shin-Han Shiua,1 Departments of aPlant Biology, bComputer Science and Engineering, cBiochemistry and Molecular Biology, and eCrop and Soil Sciences, and dDepartment of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 Edited by Philip Benfey, Duke University, Durham, NC, and approved July 19, 2011 (received for review March 3, 2011) Environmental stress leads to dramatic transcriptional reprogram- essential for stress-responsive transcription (e.g., refs. 3 and 4). ming, which is central to plant survival. Although substantial The importance of a few CRE combinations has also been dem- knowledge has accumulated on how a few plant cis-regulatory onstrated (17–19), indicating that stress-responsive genes are elements (CREs) function in stress regulation, many more CREs re- regulated by multiple transcription factors. In addition, the roles of main to be discovered. In addition, the plant stress cis-regulatory plant CRE copy number and location in transcriptional regulation code, i.e., how CREs work independently and/or in concert to spec- of plant stress have also been studied for a few CREs (5, 20–22). ify stress-responsive transcription, is mostly unknown. On the basis Although these pioneering studies have clearly demonstrated the of gene expression patterns under multiple stresses, we identified existence of stress cis-regulatory codes in plants, there are few a large number of putative CREs (pCREs) in Arabidopsis thaliana examples and a global description of CRE-based stress regulatory with characteristics of authentic cis-elements.
    [Show full text]
  • Epigenetics: Core Misconcept
    OPINION OPINION Epigenetics: Core misconcept Mark Ptashne1 cific genes, and encourage (activate) or dis- Ludwig Professor of Molecular Biology, Memorial Sloan–Kettering Cancer Center, New courage (repress) transcription into mRNA York, NY 10021 of those genes (2–4). The process is started by transcrip- tion factors, contributed mainly by the A recent issue of PNAS opened with an 50 years a compelling answer has emerged mother, found in the fertilized egg. In the unfortunate Core Concepts article titled from studies in a wide array of organisms. first cell division these transcription fac- “Epigenetics” (1). The author, a science Curiously, the article ignores this body of tors are distributed asymmetrically to the writer, began promisingly enough: knowledge, and substitutes for it misguided daughter cells. Then, and in subsequent musings presented as facts. cell generations, new patterns of gene ex- Despite the fact that every cell in a human body Let me begin with a very brief overview pression arise in two ways: as a matter of contains the same genetic material, not every cell of what drives development, a process that course (some transcription factors activat- looks or behaves the same….How does each cell retain its unique properties when, in its DNA- unfolds with essentially no changes in DNA ing expression of genes encoding other containing nucleus, it has the same master set of sequence. Development of an organism regulatory proteins, etc.), and in response genes as every other cell? from a fertilized egg is driven primarily by to signals sent by other cells. Signaling used the actions of regulatory proteins called in development affects expression of genes Indeed understanding this problem has transcription factors.
    [Show full text]
  • On the Concept of Cis-Regulatory Information: from Sequence Motifs to Logic Functions
    On the Concept of cis-Regulatory Information: From Sequence Motifs to Logic Functions Dedicated to Grzegorz Rozenberg's 65th Birthday Ryan Tarpine∗† Sorin Istrail∗‡ Abstract The regulatory genome is about the system level organization of the core genomic regulatory apparatus, and how this is the locus of causality underlying the twin phenomena of animal development and animal evolu- tion. [8] Information processing in the regulatory genome is done through regulatory states, dened as sets of transcription factors (sequence-specic DNA binding proteins which determine gene expression) that are ex- pressed and active at the same time. The core information processing ma- chinery consists of modular DNA sequence elements, called cis-modules, that interact with transcription factors. The cis-modules read the infor- mation contained in the regulatory state of the cell through transcription factor binding, process it, and directly or indirectly communicate with the basal transcription apparatus to determine gene expression. This en- dowment of each gene with the information-receiving capacity through their cis-regulatory modules, is essential for the response to every possi- ble regulatory state to which it might be exposed during all phases of the life cycle and in all cell types. We present here a set of challenges addressed by our CYRENE re- search project aimed at studying the cis-regulatory code of the regulatory genome. The CYRENE Project is devoted to (1) the construction of a database, the cis-Lexicon, containing comprehensive information across species about experimentally validated cis-regulatory modules; and (2) the software development of a next-generation genome browser, the cis- Browser, specialized for the regulatory genome.
    [Show full text]