A number of nuclear events occur during apoptosis, including DNA laddering, nuclear lamina breakdown, phosphorylation of histones H2B and histone H2AX, and the tight binding to chromatin of HMGB1 and CAD, the nuclease responsible for DNA laddering. We have performed an epistasis analysis to investigate whether these events cluster together in pathways. We find that all depend directly or indirectly on caspase-3 activation. CAD activation, H2AX phosphorylation and DNA laddering cluster together into a pathway, but all other events appear to be independent of each other downstream of caspase-3, and likely evolved subject to different functional pressures.
References
[1]
Liu X, Zou H, Slaughter C, Wang X (1997) DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell 89: 175–84.
[2]
Kawane K, Fukuyama H, Yoshida H, Nagase H, Ohsawa Y, et al. (2003) Impaired thymic development in mouse embryos deficient in apoptotic DNA degradation. Nat Immunol 4: 138–44.
[3]
Nagata S, Nagase H, Kawane K, Mukae N, Fukuyama H (2003) Degradation of chromosomal DNA during apoptosis. Cell Death Differ 10: 108–16.
[4]
Scaffidi P, Misteli T, Bianchi ME (2002) Release of chromatin protein hmgb1 by necrotic cells triggers inflammation. Nature 418: 191–5.
[5]
Lechardeur D, Xu M, Lukacs GL (2004) Contrasting nuclear dynamics of the caspase-activated DNAse (CAD) in dividing and apoptotic cells. J Cell Biol 167: 851–62.
[6]
Bianchi ME, Agresti A (2005) HMG proteins: Dynamic players in gene regulation and differentiation. Curr Opin Genet Dev 15: 496–506.
[7]
Bianchi ME, Manfredi AA (2007) High mobility group box 1 (HMGB1) protein at the crossroads between native and adaptive immunity. Immun Rev 220: 35–46.
[8]
Bianchi ME, Manfredi A (2004) Chromatin and cell death. Biochim Biophys Acta 1677: 181–6.
[9]
Ruchaud S, Korfali N, Villa P, Kottke TJ, Dingwall C, et al. (2002) Caspase-6 gene disruption reveals a requirement for lamin a cleavage in apoptotic chromatin condensation. EMBO J 21: 1967–77.
[10]
Sullivan T, Escalante-Alcalde D, Bhatt H, Anver M, Bhat N, et al. (1999) Loss of A-type lamin expression compromises nuclear envelope integrity leading to muscular dystrophy. J Cell Biol 147: 913–20.
[11]
Ahn SH, Cheung WL, Hsu JY, Diaz RL, Smith MM, et al. (2005) Sterile 20 kinase phosphorylates histone H2B at serine 10 during hydrogen peroxide-induced apoptosis in S. cerevisiae. Cell 120: 25–36.
[12]
Cheung WL, Ajiro K, Samejima K, Kloc M, Cheung P, et al. (2003) Apoptotic phosphorylation of histone H2B is mediated by Mammalian Sterile Twenty kinase. Cell 113: 507–17.
[13]
Cook PJ, Ju BG, Telese F, Wang X, Glass CK, et al. (2009) Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions. Nature 458: 591–6.
[14]
Thomas JO, Travers AA (2001) HMG1 and 2, and related 'architectural' DNA-binding proteins. Trends Biochem Sci 26: 167–74.
[15]
Hoppe G, Talcott KE, Bhattacharya SK, Crabb JW, Sears JE (2006) Molecular basis for the redox control of nuclear transport of the structural chromatin protein HMGB1. Exp Cell Res 312: 3526–38.
[16]
Agresti A, Scaffidi P, Riva A, Caiolfa VR, Bianchi ME (2005) GR and HMGB1interact only within chromatin and influence each other's residence time. Mol Cell 18: 109–21.
[17]
Roemer SC, Adelman J, Churchill ME, Edwards DP (2008) Mechanism of High-Mobility Group protein B enhancement of progesterone receptor sequence-specific DNA binding. Nucleic Acids Res 36: 3655–66.
[18]
Kazama H, Ricci JE, Herndon JM, Hoppe G, Green DR, et al. (2008) Induction of immunological tolerance by apoptotic cells requires caspase-dependent oxidation of High-Mobility Group Box-1 protein. Immunity 29: 21–32.
[19]
Janicke RU, Sprengart ML, Wati MR, Porter AG (1998) Caspase-3 is required for DNA fragmentation and morphological changes associated with apoptosis. J Biol Chem 273: 9357–60.
[20]
Yang XH, Sladek TL, Liu X, Butler BR, Froelich CJ, et al. (2001) Reconstitution of caspase 3 sensitizes MCF-7 breast cancer cells to doxorubicin- and etoposide-induced apoptosis. Cancer Res 61: 348–54.
[21]
Lu C, Zhu F, Cho YY, Tang F, Zykova T, et al. (2006) Cell apoptosis: Requirement of H2AX in DNA ladder formation, but not for the activation of caspase-3. Mol Cell 23: 121–32.
[22]
Rogakou EP, Nieves-Neira W, Boon C, Pommier Y, Bonner WM (2000) Initiation of DNA fragmentation during apoptosis induces phosphorylation of H2AX histone at serine 139. J Biol Chem 275: 9390–5.
[23]
Lakhani SA, Masud A, Kuida K, Porter GA Jr, Booth CJ, et al. (2006) Caspases 3 and 7: Key mediators of mitochondrial events of apoptosis. Science 311: 847–51.
[24]
Urbonaviciute V, Furnrohr BG, Meister S, Munoz L, Heyder P, et al. (2008) Induction of inflammatory and immune responses by HMGB1-nucleosome complexes: Implications for the pathogenesis of SLE. J Exp Med 295: 3007–18.
[25]
Kawane K, Fukuyama H, Kondoh G, Takeda J, Ohsawa Y, et al. (2001) Requirement of DNAse II for definitive erythropoiesis in the mouse fetal liver. Science 292: 1546–9.
[26]
Kawane K, Ohtani M, Miwa K, Kizawa T, Kanbara Y, et al. (2006) Chronic polyarthritis caused by mammalian DNA that escapes from degradation in macrophages. Nature 443: 998–1002.
[27]
Latorre E (2005) Multidrug resistance proteins (mrp) transport the cytokine/nuclear protein High Mobility Group Box 1 (HMGB1) across membranes. PhD thesis, Open University.
[28]
Phair RD, Gorski SA, Misteli T (2004) Measurement of dynamic protein binding to chromatin in vivo, using photobleaching microscopy. Methods Enzymol 375: 393–414.
