Amino Acid Regulation of Alternative Splicing

Summary

Principal Investigator: Michael S Kilberg
Abstract: DESCRIPTION (provided by applicant): Limiting dietary protein intake results in amino acid deficiency within cells and activates several signal transduction pathways collectively called the amino acid response (AAR). A number of genes have been identified that are transcriptionally-activated by the AAR, including the bZIP transcription factor ATF3, for which cellular stress induces multiple isoforms by pre-mRNA alternative splicing. Two of these isoforms, full- length ATF3 (ATF3-FL) and a form with a truncated leucine zipper, ATF3?Zip3, are induced in expression by low protein diet in vivo or by amino acid deprivation of cultured cells. These two isoforms exhibit opposing action on the AAR target gene encoding asparagine synthetase (ASNS);exogenous ATF3-FL expression causes transcriptional repression of the amino acid-dependent induction of ASNS, whereas ATF3?Zip3 further enhances the induction. How the cellular amino acid content signals to and controls pre-mRNA alternative splicing has not been investigated. In fact, the study of the regulation of alternative splicing by macro-nutrients represents an entirely new area of investigation in the splicing field. The hypothesis is that ATF3 isoforms have opposing actions within the cellular response to protein/amino acid stress and that the individual isoforms interact with activity-modifying proteins and/or transcriptional co- regulators that support these opposing activities. To address this global hypothesis, three sub- hypotheses will be tested. Hypothesis I: There are differences in the synthesis and functional activities of specific ATF3 isoforms induced by dietary low protein in mice and amino acid deprivation of cultured cells. The proposed research will investigate the kinetics of synthesis for ATF3-FL and ATF3?Zip3 and the functional consequences of each isoform will be addressed by RNA and protein microarray analysis in transgenic mice expressing either ATF3-FL or ATF3?Zip3 individually. Hypothesis II: Amino acid-dependent signaling pathways regulate the alternative splicing of ATF3 during the AAR. These studies will determine the signaling pathway responsible for sensing and transducing the amino acid deficiency signal to the proteins that regulate exon choice during alternative splicing. Hypothesis III: Protein-protein interactions of individual ATF3 isoforms modulate their action on AAR target genes. ATF3-interacting proteins will be identified and their role in the AAR determined. Collectively, the proposed studies will provide novel information and address significant gaps in our knowledge of ATF3 alternative splicing and ATF3 isoform function. The insight gained from these studies will impact the fields of: 1) macro-nutrient control of pre- mRNA alternative splicing;2) amino acid-dependent control of transcription;and 3) ATF3 function in nutrition and disease.
Funding Period: 2011-08-01 - 2015-07-31
more information: NIH RePORT

Top Publications

  1. pmc Auto-activation of c-JUN gene by amino acid deprivation of hepatocellular carcinoma cells reveals a novel c-JUN-mediated signaling pathway
    Lingchen Fu
    Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
    J Biol Chem 286:36724-38. 2011
  2. pmc The transcription factor network associated with the amino acid response in mammalian cells
    Michael S Kilberg
    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL
    Adv Nutr 3:295-306. 2012
  3. pmc ATF4-dependent regulation of the JMJD3 gene during amino acid deprivation can be rescued in Atf4-deficient cells by inhibition of deacetylation
    Jixiu Shan
    Department of Biochemistry and Molecular Biology, Genetics Institute, Shands Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
    J Biol Chem 287:36393-403. 2012
  4. pmc Dynamic changes in genomic histone association and modification during activation of the ASNS and ATF3 genes by amino acid limitation
    Mukundh N Balasubramanian
    Department of Biochemistry and Molecular Biology, Shands Cancer Center and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, FL 32610, U S A
    Biochem J 449:219-29. 2013
  5. pmc Elevated cJUN expression and an ATF/CRE site within the ATF3 promoter contribute to activation of ATF3 transcription by the amino acid response
    Lingchen Fu
    Department of Biochemistry and Molecular Biology, Genetics Institute, Shands Cancer Center, and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida, USA
    Physiol Genomics 45:127-37. 2013
  6. pmc Asparagine synthetase: regulation by cell stress and involvement in tumor biology
    Mukundh N Balasubramanian
    Department of Biochemistry and Molecular Biology, Shands Cancer Center and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, FL 32610, USA
    Am J Physiol Endocrinol Metab 304:E789-99. 2013
  7. pmc ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death
    Jaeseok Han
    Center for Neuroscience, Aging, and Stem Cell Research, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Cell Biol 15:481-90. 2013
  8. pmc Activation of the amino acid response modulates lineage specification during differentiation of murine embryonic stem cells
    Jixiu Shan
    Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Shands Cancer Center, and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida, USA
    Am J Physiol Endocrinol Metab 305:E325-35. 2013
  9. pmc CHOP induces activating transcription factor 5 (ATF5) to trigger apoptosis in response to perturbations in protein homeostasis
    Brian F Teske
    Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
    Mol Biol Cell 24:2477-90. 2013

Detail Information

Publications9

  1. pmc Auto-activation of c-JUN gene by amino acid deprivation of hepatocellular carcinoma cells reveals a novel c-JUN-mediated signaling pathway
    Lingchen Fu
    Department of Biochemistry and Molecular Biology, Shands Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
    J Biol Chem 286:36724-38. 2011
    ..The results document the novel observation that AP-1 sequences within the c-JUN gene can function as transcriptional amino acid-response elements...
  2. pmc The transcription factor network associated with the amino acid response in mammalian cells
    Michael S Kilberg
    Department of Biochemistry and Molecular Biology, University of Florida College of Medicine, Gainesville, FL
    Adv Nutr 3:295-306. 2012
    ....
  3. pmc ATF4-dependent regulation of the JMJD3 gene during amino acid deprivation can be rescued in Atf4-deficient cells by inhibition of deacetylation
    Jixiu Shan
    Department of Biochemistry and Molecular Biology, Genetics Institute, Shands Cancer Center, University of Florida College of Medicine, Gainesville, Florida 32610, USA
    J Biol Chem 287:36393-403. 2012
    ..The data are consistent with the hypothesis that ATF4 functions as a pioneer factor to alter chromatin structure and thus, enhance transcription in a gene-specific manner...
  4. pmc Dynamic changes in genomic histone association and modification during activation of the ASNS and ATF3 genes by amino acid limitation
    Mukundh N Balasubramanian
    Department of Biochemistry and Molecular Biology, Shands Cancer Center and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, FL 32610, U S A
    Biochem J 449:219-29. 2013
    ..The results of the present study document changes in gene-associated nucleosome abundance and histone modifications in response to amino-acid-dependent transcription...
  5. pmc Elevated cJUN expression and an ATF/CRE site within the ATF3 promoter contribute to activation of ATF3 transcription by the amino acid response
    Lingchen Fu
    Department of Biochemistry and Molecular Biology, Genetics Institute, Shands Cancer Center, and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida, USA
    Physiol Genomics 45:127-37. 2013
    ..The results indicate that both increased cJUN and the cis-acting ATF/CRE sequence within the ATF3 promoter contribute to the transcriptional activation of the gene during the AAR...
  6. pmc Asparagine synthetase: regulation by cell stress and involvement in tumor biology
    Mukundh N Balasubramanian
    Department of Biochemistry and Molecular Biology, Shands Cancer Center and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, FL 32610, USA
    Am J Physiol Endocrinol Metab 304:E789-99. 2013
    ..Identifying the roles of ASNS in fetal development, tissue differentiation, and tumor growth may reveal that ASNS function extends beyond asparagine biosynthesis...
  7. pmc ER-stress-induced transcriptional regulation increases protein synthesis leading to cell death
    Jaeseok Han
    Center for Neuroscience, Aging, and Stem Cell Research, Sanford Burnham Medical Research Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
    Nat Cell Biol 15:481-90. 2013
    ..The findings suggest that limiting protein synthesis will be therapeutic for diseases caused by protein misfolding in the ER...
  8. pmc Activation of the amino acid response modulates lineage specification during differentiation of murine embryonic stem cells
    Jixiu Shan
    Department of Biochemistry and Molecular Biology, McKnight Brain Institute, Shands Cancer Center, and Center for Nutritional Sciences, University of Florida College of Medicine, Gainesville, Florida, USA
    Am J Physiol Endocrinol Metab 305:E325-35. 2013
    ..Collectively, the results indicate that, during differentiation of mouse embryoid bodies in culture, the availability of nutrients, such as amino acids, can influence the formation of specific cell lineages. ..
  9. pmc CHOP induces activating transcription factor 5 (ATF5) to trigger apoptosis in response to perturbations in protein homeostasis
    Brian F Teske
    Department of Biochemistry and Molecular Biology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
    Mol Biol Cell 24:2477-90. 2013
    ..This study suggests that the ISR features a feedforward loop of stress-induced transcriptional regulators, each subject to transcriptional and translational control, which can switch cell fate toward apoptosis. ..

Research Grants30

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    Botond Banfi; Fiscal Year: 2013
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  2. ApoE Receptor Biology and Neurodegeneration
    Mary Jo Ladu; Fiscal Year: 2013
    ..This Program will thus provide new and valuable information about how apoE and apoE receptors affect the pathogenesis of Alzheimer's disease. ..
  3. Thrombus Formation and Antithrombotic Intervention
    John H Griffin; Fiscal Year: 2013
    ..New knowledge will contribute to improving prevention, diagnosis and treatment of relevant diseases related to thrombosis. ..
  4. B-cell Biology of Mucosal Immune Protection from SIV Challenge
    Eric Hunter; Fiscal Year: 2013
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  5. Model-based predictions of responses RTK Pathway therapies
    Joe W Gray; Fiscal Year: 2013
    ..abstract_text> ..
  6. GENE AND PHARMACOLOGICAL THERAPIES FOR CYSTIC FIBROSIS
    William B Guggino; Fiscal Year: 2013
    ..Project IV will focus on the Biology of AAV. Finally, there are three cores, an Expression, a Vector Core, and an Administration Core. ..
  7. Expanding the National Health Accounts
    David M Cutler; Fiscal Year: 2013
    ..Establishment of a set of national health accounts will allow us as a society to understand which medical interventions improve the health of the U.S. population most efficiently. ..
  8. Molecular Mechanisms linking Aging, Abeta Proteotoxicity and Neurodegeneration
    Jeffery W Kelly; Fiscal Year: 2013
    ..abstract_text> ..
  9. LIPID AND LIPOPROTEIN METABOLISM IN ATHEROSCLEROSIS
    Alan M Fogelman; Fiscal Year: 2013
    ..These six Projects will be supported by four cores and together will form a highly interactive and synergistic Program Project that is focused on lipid and lipoprotein metabolism in atherosclerosis. ..
  10. Arterial Dysfunction: Basic and Clinical Mechanisms
    Thomas Michel; Fiscal Year: 2013
    ..Gladyshev. P. Libby directs the Redox Biomarkers Core;metabolic characterizations of mouse models studied in this Program will take place at the Yale Mouse Metabolic Phenotyping Center, led by G. Shulman. ..
  11. IPF Fibroblast Phenotype
    Craig A Henke; Fiscal Year: 2013
    ..A major objective of this Program Project is to inform decisions of the IPF Clinical Network by providing information that can be translated into novel therapeutic strategies for IPF. ..
  12. Neurohumoral control of veins in hypertension
    Gregory D Fink; Fiscal Year: 2013
    ..This project tests the idea that altered structure or function of veins also may cause hypertension, and that it may be possible to treat hypertension using drugs that affect veins. ..
  13. Rocky Mountain Regional Center of Excellence or Biodefense and Emerging Infectiou
    John T Belisle; Fiscal Year: 2013
    ..abstract_text> ..
  14. Cell Adhesion Mechanisms in Vascular Disease &Thrombosis
    MARK HOWARD GINSBERG; Fiscal Year: 2013
    ..abstract_text> ..
  15. UNMC EPPLEY CANCER CENTER SUPPORT GRANT
    Kenneth H Cowan; Fiscal Year: 2013
    ....
  16. CENTER FOR GASTROINTESTINAL BIOLOGY AND DISEASE
    Robert S Sandler; Fiscal Year: 2013
    ..Through all of its activities, the Center improves communication, promotes collaboration, develops careers and generally enriches the intellectual climate for digestive disease research. ..