Chromatin Degradation During Apoptosis

Summary

Principal Investigator: Ding Xue
Abstract: DESCRIPTION (provided by applicant): Fragmentation of chromosomal DNA is a critical step in apoptosis that prevents a cell from transcribing and replicating its genes and thus facilitates the cell killing process. Defects in this process can cause various pathological conditions, including autoimmune disorders and cancer. We have identified ten apoptotic nucleases and several non-nuclease factors involved in regulating and executing apoptotic chromosome fragmentation in C. elegans. They act in a sequential and CED-3 caspase-dependent manner to promote stepwise fragmentation and degradation of chromosomes. The process is initiated by a novel CED-3-mediated conversion of the dicer ribonuclease (RNase) into a deoxyribonuclease (DNase), which makes the first cuts on chromosomes. In parallel, a mitochondrial nuclease CPS-6 and its activator WAH-1 are released from mitochondria and translocated to the nucleus, where they interact and cooperate with other cell death nucleases to turn the initial cuts by dicer into double-strand DNA breaks, leading to fragmentation and degradation of chromosomes. In this proposed work, we will carry out molecular genetic, biochemical, cell biological, and structural analyses to understand these two critical events of apoptotic DNA degradation. In Aim 1, we will investigate the molecular and structural basis underlying CED-3-mediated conversion of the dicer RNase into a DNase. In Aim 2, we will dissect the new signaling pathway that controls cytosolic calcium increase and release of the mitochondrial apoptogeneic factors during apoptosis. In Aim 3, we will perform molecular genetic and functional characterization of two new genes, cps-13 and cps-14, that regulate and coordinate two key cell death execution events, chromosome fragmentation and phosphatidylserine (PS) externalization. These studies should reveal the novel mechanism that controls the specificity and function switch of the dicer nuclease and new signaling mechanisms and players that control the release of the mitochondrial apoptogenic factors.
Funding Period: 2007-03-01 - 2016-02-29
more information: NIH RePORT

Top Publications

  1. pmc SKR-1, a homolog of Skp1 and a member of the SCF(SEL-10) complex, regulates sex-determination and LIN-12/Notch signaling in C. elegans
    Darrell J Killian
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Dev Biol 322:322-31. 2008
  2. pmc Somatic sex determination in Caenorhabditis elegans is modulated by SUP-26 repression of tra-2 translation
    James Mapes
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 107:18022-7. 2010
  3. ncbi Dicing up chromosomes: The unexpected role of Dicer in apoptosis 
    Brian L Harry
    University of Colorado Boulder, CO USA
    Cell Cycle 9:4772-3. 2010
  4. pmc Elimination of paternal mitochondria through the lysosomal degradation pathway in C. elegans
    Qinghua Zhou
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Cell Res 21:1662-9. 2011
  5. pmc Structural insights into apoptotic DNA degradation by CED-3 protease suppressor-6 (CPS-6) from Caenorhabditis elegans
    Jason L J Lin
    Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
    J Biol Chem 287:7110-20. 2012
  6. pmc CED-1, CED-7, and TTR-52 regulate surface phosphatidylserine expression on apoptotic and phagocytic cells
    James Mapes
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Curr Biol 22:1267-75. 2012
  7. pmc Hepatitis B virus X protein targets Bcl-2 proteins to increase intracellular calcium, required for virus replication and cell death induction
    Xin Geng
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:18471-6. 2012
  8. pmc Hepatitis B virus X protein targets the Bcl-2 protein CED-9 to induce intracellular Ca2+ increase and cell death in Caenorhabditis elegans
    Xin Geng
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:18465-70. 2012
  9. pmc Caspase-mediated activation of Caenorhabditis elegans CED-8 promotes apoptosis and phosphatidylserine externalization
    Yu Zen Chen
    1 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA 2 Division of Biochemistry and Cellular Molecular Biology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan 333, China 3
    Nat Commun 4:2726. 2013
  10. pmc A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis
    Xiao Ge
    School of Life Sciences, Tsinghua University, Beijing 100084, China
    Cell Res 24:218-32. 2014

Research Grants

  1. Molecular Mechanisms linking Aging, Abeta Proteotoxicity and Neurodegeneration
    Jeffery W Kelly; Fiscal Year: 2013
  2. piRNA biogenesis and function in germline development
    Phillip D Zamore; Fiscal Year: 2013
  3. A Genetic Model of NMDA Receptor Function in Cell Death
    Michael Lehmann; Fiscal Year: 2013
  4. HORMONAL REGULATION OF BLOOD PRESSURE
    Michal Laniado Schwartzman; Fiscal Year: 2013
  5. Progranulin, TDP-43 and Cell Death
    Leonard Petrucelli; Fiscal Year: 2013
  6. CENTER FOR GASTROINTESTINAL BIOLOGY AND DISEASE
    Robert S Sandler; Fiscal Year: 2013

Detail Information

Publications22

  1. pmc SKR-1, a homolog of Skp1 and a member of the SCF(SEL-10) complex, regulates sex-determination and LIN-12/Notch signaling in C. elegans
    Darrell J Killian
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Dev Biol 322:322-31. 2008
    ..Our results suggest that SKR-1, CUL-1 and SEL-10 constitute an SCF E3 ligase complex that plays an important role in modulating sex-determination and LIN-12/Notch signaling in C. elegans...
  2. pmc Somatic sex determination in Caenorhabditis elegans is modulated by SUP-26 repression of tra-2 translation
    James Mapes
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 107:18022-7. 2010
    ..Taken together, our results provide further insight into how mRNA-binding factors repress translation and modulate sexual development in different tissues of C. elegans...
  3. ncbi Dicing up chromosomes: The unexpected role of Dicer in apoptosis 
    Brian L Harry
    University of Colorado Boulder, CO USA
    Cell Cycle 9:4772-3. 2010
    ..Comment on: Nakagawa A, et al. Science 2010; 328:327-34...
  4. pmc Elimination of paternal mitochondria through the lysosomal degradation pathway in C. elegans
    Qinghua Zhou
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Cell Res 21:1662-9. 2011
    ..Our study indicates that C. elegans is an excellent animal model for understanding and dissecting this conserved biological process critical for animal development and reproduction...
  5. pmc Structural insights into apoptotic DNA degradation by CED-3 protease suppressor-6 (CPS-6) from Caenorhabditis elegans
    Jason L J Lin
    Institute of Molecular Biology, Academia Sinica, Taipei 11529, Taiwan
    J Biol Chem 287:7110-20. 2012
    ..elegans. Taken together, these biochemical, structural, mutagenesis, and in vivo data reveal a molecular basis of how CPS-6 binds and hydrolyzes DNA to promote cell death...
  6. pmc CED-1, CED-7, and TTR-52 regulate surface phosphatidylserine expression on apoptotic and phagocytic cells
    James Mapes
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Curr Biol 22:1267-75. 2012
    ..In addition, some living cells such as macrophages also express exPS...
  7. pmc Hepatitis B virus X protein targets Bcl-2 proteins to increase intracellular calcium, required for virus replication and cell death induction
    Xin Geng
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:18471-6. 2012
    ....
  8. pmc Hepatitis B virus X protein targets the Bcl-2 protein CED-9 to induce intracellular Ca2+ increase and cell death in Caenorhabditis elegans
    Xin Geng
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:18465-70. 2012
    ..Our results suggest that C. elegans could serve as an animal model for identifying crucial host factors and signaling pathways of HBx and aid in development of strategies to treat HBV-induced liver disorders...
  9. pmc Caspase-mediated activation of Caenorhabditis elegans CED-8 promotes apoptosis and phosphatidylserine externalization
    Yu Zen Chen
    1 Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado 80309, USA 2 Division of Biochemistry and Cellular Molecular Biology, Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan 333, China 3
    Nat Commun 4:2726. 2013
    ..elegans. Our finding identifies a crucial link between caspase activation and PS externalization, which triggers phagocytosis of apoptotic cells. ..
  10. pmc A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis
    Xiao Ge
    School of Life Sciences, Tsinghua University, Beijing 100084, China
    Cell Res 24:218-32. 2014
    ..We suggest the possibility that this phenomenon may be extrapolated to other ribonucleases. ..
  11. pmc Caenorhabditis elegans transthyretin-like protein TTR-52 mediates recognition of apoptotic cells by the CED-1 phagocyte receptor
    Xiaochen Wang
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Nat Cell Biol 12:655-64. 2010
    ..TTR-52 is therefore the first bridging molecule identified in C. elegans that mediates recognition of apoptotic cells by crosslinking the PtdSer 'eat me' signal with the phagocyte receptor CED-1...
  12. pmc Programmed cell clearance: molecular regulation of the elimination of apoptotic cell corpses and its role in the resolution of inflammation
    Bengt Fadeel
    Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
    Biochem Biophys Res Commun 396:7-10. 2010
    ..The present review will focus on the molecular regulation of programmed cell clearance, and discuss the role of cell elimination in the resolution of inflammation...
  13. pmc Cell death specification in C. elegans
    Erin Peden
    Department of Molecular, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Cell Cycle 7:2479-84. 2008
    ..However, it remains unclear if additional modes of cell death specification exist. Here we briefly summarize current findings in the field of C. elegans cell death specification and consider those questions that remain to be answered...
  14. pmc Caenorhabditis elegans drp-1 and fis-2 regulate distinct cell-death execution pathways downstream of ced-3 and independent of ced-9
    David G Breckenridge
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Mol Cell 31:586-97. 2008
    ..Our findings demonstrate that mitochondria dynamics do not regulate apoptosis activation in C. elegans and reveal distinct roles for drp-1 and fis-2 as mediators of cell-death execution downstream of caspase activation...
  15. pmc Inhibition of CED-3 zymogen activation and apoptosis in Caenorhabditis elegans by caspase homolog CSP-3
    Xin Geng
    Department of Molecular, Cellular, and Developmental Biology, Campus Box 347, University of Colorado, Boulder, Colorado 80309, USA
    Nat Struct Mol Biol 15:1094-101. 2008
    ..However, CSP-3 does not block CED-3 activation induced by CED-4, nor does it inhibit the activity of the activated CED-3 protease. Therefore CSP-3 uses a previously unreported mechanism to protect cells from apoptosis...
  16. pmc Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation
    Yu Yuan Hsiao
    Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
    Mol Cell Biol 29:448-57. 2009
    ..Combining all of the data, we suggest a structural model where chromosomal DNA is bound at the Zn-domain and cleaved at the DEDDh nuclease domain in CRN-4 when the cell is undergoing apoptosis...
  17. pmc Bcl-2 proteins EGL-1 and CED-9 do not regulate mitochondrial fission or fusion in Caenorhabditis elegans
    David G Breckenridge
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Curr Biol 19:768-73. 2009
    ..elegans. Taken together, our results argue against an evolutionarily conserved role for Bcl-2 proteins in regulating mitochondrial fission and fusion...
  18. pmc Caenorhabditis elegans caspase homolog CSP-2 inhibits CED-3 autoactivation and apoptosis in germ cells
    X Geng
    Department of Molecular, Cellular, and Developmental Biology, Campus Box 347, University of Colorado, Boulder, CO 80309, USA
    Cell Death Differ 16:1385-94. 2009
    ..elegans caspase homologs use the same mechanism to prevent caspase autoactivation and apoptosis in different tissues, suggesting that this could be a generally applicable strategy for regulating caspase activation and apoptosis...
  19. pmc The ins and outs of phospholipid asymmetry in the plasma membrane: roles in health and disease
    Bengt Fadeel
    Division of Molecular Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
    Crit Rev Biochem Mol Biol 44:264-77. 2009
    ..The functional significance of lipid asymmetry and its disruption during health and disease is also discussed...
  20. pmc The roles and acting mechanism of Caenorhabditis elegans DNase II genes in apoptotic dna degradation and development
    Huey Jen Lai
    Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    PLoS ONE 4:e7348. 2009
    ..Our study illustrates how multiple DNase II nucleases play differential roles in apoptotic DNA degradation and development and reveals an unexpected mode of DNase II action in mediating DNA degradation...
  21. ncbi Caspase-dependent conversion of Dicer ribonuclease into a death-promoting deoxyribonuclease
    Akihisa Nakagawa
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
    Science 328:327-34. 2010
    ..DCR-1 functions in fragmenting chromosomal DNA during apoptosis, in addition to processing of small RNAs, and undergoes a protease-mediated conversion from a ribonuclease to a deoxyribonuclease...

Research Grants30

  1. Molecular Mechanisms linking Aging, Abeta Proteotoxicity and Neurodegeneration
    Jeffery W Kelly; Fiscal Year: 2013
    ..abstract_text> ..
  2. piRNA biogenesis and function in germline development
    Phillip D Zamore; Fiscal Year: 2013
    ..Studies under Aim 3 will use genetic, molecular and cytological approaches to define the role of piRNA in telomere protection and chromosome segregation. ..
  3. A Genetic Model of NMDA Receptor Function in Cell Death
    Michael Lehmann; Fiscal Year: 2013
    ..Thus, the project will help understand the function of these proteins under pathological conditions and aid in the development of therapeutic measures. ..
  4. HORMONAL REGULATION OF BLOOD PRESSURE
    Michal Laniado Schwartzman; Fiscal Year: 2013
    ..ular tone, in the pathophysiology of hypertension and cardiovascular disease. ..
  5. Progranulin, TDP-43 and Cell Death
    Leonard Petrucelli; Fiscal Year: 2013
    ..Our hypothesis is that loss of functional PGRN leads to loss of functional TDP-43, which leads to cell death. ..
  6. 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. ..