CULogo

 

 

PUBLICATIONS

Published work from the Xue Lab and collaborators

 

 

1. Ledwich, D., Wu, Y.C., Driscoll, M, and Xue, D. (2000). Methods for the study of programmed cell death in the nematode Caenorhabditis elegans. Methods in Enzymology, 322, 76-88. (Abstract and PDF)

 

2. Parrish, J., Metters, H., Chen, L., and Xue, D. (2000). Demonstration of the in vivo interaction of key cell death regulators by structure-based design of second-site suppressors. Proc. Natl. Acad. Sci. USA. 97, 11916-11921. (Abstract and PDF)

 

3. Parrish, J., Li, L., Klotz, K., Ledwich, D., Wang, X.D., and Xue, D. (2001). C. elegans mitochondrial endonuclease G is important for apoptosis. Nature 412, 90-94. (Abstract and PDF) 

 

4. Xue, D., Wu, Y.C., and Shah, M.M. (2001). Programmed cell death in C. elegans -- a genetic framework. Chapter II in "Apoptosis: The Molecular Biology of Programmed Cell Death". Page 23-55. Edited by M. Jacobson & N. McCarthy. Oxford University Press. (PDF)

 

5. Wang, X.C., Yang, C.L., Cai, J.J., Shi, Y.G., and Xue, D. (2002). Mechanisms of AIF-mediated apoptotic DNA degradation in Caenorhabditis elegans. Science 298, 1587-1592. (Abstract and PDF). Nature Reviews Molecular Cell Biology (PDF

 

6. Parrish, J. and Xue, D. (2003). Functional genomic analysis of apoptotic DNA degradation in C. elegansMol. Cell 11, 987-996. (Abstract and PDF)

 

7. Parrish, J., Yang, C.L., Shen, B.H., and Xue, D. (2003). CRN-1, a Caenorhabditis elegans FEN-1 homologue, cooperates with CPS-6/EndoG to promote apoptoticDNA degradation. EMBO. J. 22, 3451-3460. (Abstract and PDF) Science SKTE Review (PDF) 

 

8. Wu, Y.C. and Xue, D. (2003). Programmed cell death in C. elegans. Chapter IV in "Essentials of Apoptosis: A Guide for Basic and Clinical Research". Page 135-144. Edited by X.M. Yin & Z. Dong. The Humana Press Inc. (PDF)

 

9. Wang, X.C., Wu, Y.C., Fadok, V., Lee, M.C., Gengyo-Ando, K., Cheng, L.C., Ledwich, D., Hsu, P.K., Chen, J.Y., Chou, B.K., Henson, P., Mitani, S., and Xue, D. (2003). Cell Corpse Engulfment Mediated by C. elegans Phosphatidylserine Receptor Through CED-5 and CED-12. Science 302, 1563-1566.(Abstract and PDF). Science Persepectives (PDF) and Science SKTE Review (PDF)

 

10. Friedman, J. and Xue, D. (2004). To live or die by the sword: the regulation of apoptosis by the proteasome. Developmental Cell 6, 460-461. (PDF)

 

11. Yang, N, Gu, L.C., Kokel, D., Han, A.D., Chen, L., Xue, D., and Shi, Y.G. (2004). Structural, Biochemical and Functional Analyses of CED-9 Recognition by the Pro-apoptotic Proteins EGL-1 and CED-4. Mol. Cell 15, 999-1006. (Abstract and PDF)

 

12. Breckenridge, D. and Xue, D. (2004). Regulation of mitochondrial membrane permeabilization by BCL-2 family proteins and caspases. Curr. Opin. Cell Biol. 16, 647-652. (Abstract and PDF)

 

13. Conradt, B. and Xue, D. (2005). Programmed cell death. WormBook, ed. The C. elegans Research Community. (Abstract and PDF)

 

14. Yan, N., Chai, J.J., Lee, E.S., Gu, L.C., Liu, Q., He, J.Q., Wu, J.W., Li, H.L., Hao, Q., Xue, D., and Shi, Y.G. (2005). Structure of the CED-4/CED-9 complex reveals insights into programmed cell death in Caenorhabditis elegansNature 437, 831-837. (Abstract and PDF)

 

15. Fadeel, B. and Xue, D. (2005). PS externalization: from corpse clearance to drug delivery. Cell Death Differentiation 13, 360-362. (PDF)

 

16. Parrish, J., and Xue, D. (2005). Cuts can kill: the roles of apoptotic nucleases in cell death and animal development. Chromosoma 115, 89-97. (PDF)

 

17. Yang, C.L., Yan, N., Parrish, J., Wang, X.C., Shi, Y.G., and Xue, D. (2006). RNA aptamers targeting the cell death inhibitor CED-9 induce cell killing in C. elegansJournal of Biological Chemistry 281, 9137-9144. (Abstract and PDF)

 

18. Kokel, D., Li, Y.H., Qin, J., and Xue, D. (2006). The non-genotoxic carcinogens naphthalene and para-dichlorobenzene suppress apoptosis in C. elegans. Nature Chemical Biology 2, 338-345. (Abstract and PDF). News in ScienceNOWThe GuardianThe Skottish Daily RecordDenver PostSina net (新浪网)NIGMS e-newsletter Biomedical Beat

 

19. Kokel, D. and Xue, D. (2006). A class of benzenoid chemicals suppresses apoptosis in C. elegansChemBioChem 7, 2010-2015. (Abstract and PDF)

 

20. Wang, X.C., Wang, J., Gengyo-Ando, K., Gu, L.C., Sun, C.L., Yang, C.L., Shi, Y., Kobayashi, T., Shi, Y.G., Mitani, S., Xie, X.S., and Xue, D. (2007). "C. elegans mitochondrial factor WAH-1 promotes phosphatidylserine externalization in apoptotic cells through phospholipid scramblase SCRM-1". Nature Cell Biology 9, 541-549. (Abstract and PDF). Nature Reviews Molecular Cell Biology (PDF)

 

21. Peden, E., Kimberly, E.L., Gengyo-Ando, K., Mitani, S., and Xue, D. (2007). Control of sex-specific apoptosis in C. elegans by the BarH homeodomain protein CEH-30 and the transcriptional repressor UNC-37/Groucho. Genes & Development 21, 2195-3207. (Abstract and PDF).

 

22. Darland-Ransom, M., Wang, X.C., Sun, C.L., Mapes, J., Gengyo-Ando, K., Mitani, S. and Xue, D. (2008). Role of C. elegans TAT-1 protein in maintaining plasma membrane phosphatidylserine asymmetry. Science 320, 528-531. (Abstract and PDF). Science Perspectives (PDF)

 

23. Breckenridge, D., Kang, B.H., Kokel, D., Mitani, S., Staehelin, A.L., and Xue, D. (2008). Caenorhabditis elegans drp-1 and fis-2 regulate distinct cell death execution pathways downstream of ced-3 and independent of ced-9. Mol. Cell 31 586-597. (Abstract and PDFDevelopmental Cell Preview (PDF)

 

24. Peden, E., Killian, D., and Xue, D. (2008). Cell death specification in C. elegans. Cell Cycle 7, 2479-2484. (Abstract and PDF)

 

25. Killian, D., Harvey, E., Johnson, P., Otori, M., Mitani, S., and Xue, D. (2008). SKR-1, a homolog of Skp1 and a member of the SCFSEL-10 complex,regulates sex-determination and LIN-12/Notch signaling in C. elegansDevelopmental Biology 322, 322-331. (Abstract and PDF)

 

26. Geng, X., Shi, Y., Nakagawa, A., Yoshina, S., Mitani, S., Shi, Y., and Xue, D. (2008). Inhibition of CED-3 zymogen activation and apoptosis in Caenorhabditis elegans by a caspase homolog CSP-3. Nature Structural & Molecular Biology 15, 1094-1101. (Abstract and PDF). Research Focus in Trends in Biological Sciences (PDF)

 

27. Hsiao, Y.Y., Nakagawa, A., Shi, Z., Mitani, S., Xue, D. and Yuan, H. S. (2009). Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation. Mol. Cell. Biol. 29, 448-457. (Abstract and PDF)

 

28. Breckenridge, D., Kang, B.H., and Xue, D. (2009). Bcl-2 proteins EGL-1 and CED-9 do not regulate mitochondrial fission or fusion in Caenorhabditis elegansCurrent Biology 19, 768-773. (Abstract and PDF)

 

29. Geng, X., Zhou, Q.H., Kage-Nakadai, E., Shi, Y., Yan, N., Mitani, S., and Xue, D. (2009). Caenorhabditis elegans caspase homolog CSP-2 inhibits CED-3 autoactivation and apoptosis in germ cells. Cell Death & Differentiation 16, 1385-1394. (Abstract and PDF)

 

30. Fadeel, B. and Xue, D. (2009). The ins and outs of phospholipid asymmetry in the plasma membrane: roles in health and disease. Critical Reviews In Biochemistry & Molecular Biology 44: 264–277. (Abstract and PDF)

 

31. Lai, H.J., Lo, S.Z., Kage-Nakadai, E., Mitani, S., and Xue, D. (2009). The roles and acting mechanism of Caenorhabditis elegans DNase II genes in apoptotic DNA degradation and development. PLoS One 4, e7348. (Abstract and PDF)

 

32. Nakagawa, A.*, Shi, Y.*, Kage-Nakadai, E., Mitani, S., and Xue, D. (2010). Caspase-Dependent Conversion of Dicer Ribonuclease into a Death-Promoting Deoxyribonuclease. Science 328, 327-334. *Equal contributions (Abstract and PDF). Research Article featured on the cover of Science and Science PerspectivesDevelopmental Cell PreviewHighlights in Nature Structural and Molecular BiologyNature Reviews Molecular Cell Biology, Disease Models and Mechanisms, and Faculty of 1000

 

33. Wang, X.C., Li W., Zhao, D.F., Liu, B., Shi, Y., Chen, B.H., Yang, H.W., Guo, P.F., Geng, X., Shang, Z.H., Peden, E., Kage-Nakadai, E., Mitani, S., and Xue, D. (2010). C. elegans transthyretin-like protein TTR-52 mediates recognition of apoptotic cells by the CED-1 phagocyte receptor. Nature Cell Biology 12, 655-664. (Abstract and PDFNature Cell Biology News and Views

 

34. Mapes, J., Chen, J.T., Yu, J.S., and Xue, D. (2010). Somatic sex determination in C. elegans is modulated by SUP-26 repression of tra-2 translation.Proc. Natl. Acad. Sci. USA 107:18022-18027. (Abstract and PDF)

 

35. Harry, B. and Xue, D. (2010). C. elegans and apoptosis. Chapter 34 in "Apoptosis: Physiology and Pathology". In press. Edited by D.R. Green & J.C. Reed. Cambridge University Press.

 

36. Harry, B., Nakagawa, A., and Xue, D. (2010). Dicing Up Chromosomes: the Unexpected Role of Dicer in Apoptosis. Cell Cycle 9, 4772 - 4773. (PDF)

 

37. Zhou, Q.H., Li, H.M., and Xue, D. (2011). Elimination of Paternal mitochondria through the lysosomal degradation pathway in C. elegans. Cell Research 21, 1662-1669. (Abstract and PDF)

 

38. Lin, J.L., Nakagawa, A., Lin, C.L., Hsiao, Y.Y., Yang, W.Z., Wang, Y.T., Doudeva, L.G., Skeen-Gaar, R.R., Xue, D., and Yuan, H.S. (2012). Structural insights into apoptotic DNA degradation by CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegansJournal of Biological Chemistry 287:7110-7120 (Abstract and PDF).

 

39. Mapes, J., Chen, Y.Z., Kim, A., Mitani, S., Kang, B.H., and Xue, D. (2012). CED-1, CED-7, and TTR-52 act in a pathway to regulate exoplasmic phosphatidylserine expression on apoptotic and phagocytic cells. Current Biology 22, 1267-1275. (Abstract and PDF). Faculty of 1000

 

40. Geng, X., Harry, B.L., Zhou, Q.H., Skeen-Gaar, R.B., Ge, X., Lee, E.S., Mitani, S., and Xue, D. (2012). Hepatitis B Virus X protein targets the Bcl-2 protein CED-9 to induce intracellular Ca2+ increase and cell death in C. elegansProc. Natl. Acad. Sci. USA 109: 18465-18470. (Abstract and PDF)

 

41. Geng, X., Huang, C.H., Qin, Y., McComb, J., Yuan, Q., Harry, B.L., Palmer, A., Xia, N.S., and Xue, D. (2012). Hepatitis B virus X protein targets Bcl-2 proteins to increase cytosolic Ca2+, required for virus replication and cell death induction. Proc. Natl. Acad. Sci. USA 109, 18471-18476. (Abstract and PDF)

 

42. Morton, LA, Yang H, Saludes JP, Fiorini Z, Beninson L, Chapman ER, Fleshner M, Xue D, Yin H (2013). MARCKS-ED Peptide as a Curvature and Lipid Sensor. ACS Chemical Biology 8: 218-225. (Abstract and PDF)

 

43. Chen, Y.Z., Mapes, J., Lee, E.S. and Xue, D. (2013). Caspase-mediated activation of Caenorhabditis elegans CED-8 promotes apoptosis and PS externalization. Nature Communications 4:2726 doi: 10.1038/ncomms3726. (Abstract and PDF)

 

44. Ge, X., Zhao, X., Nakagawa, A., Gong, X., Skeen-Gaar, R., Shi, Y., Gong, H.P., Wang, X.Q., and Xue, D. (2013). A novel mechanism underlies caspase-dependent conversion of the dicer ribonuclease into a deoxyribonuclease during apoptosis. Cell Research 24: 218-232 (Abstract and PDF).

 

45. Zhao, P., Zhang, Z., Ke, H.M., Ye, Y.R. and Xue, D. (2014). Oligonucleotide-based targeted gene editing in C. elegans via the CRISPR/Cas9 system. Cell Research 24: 247-250 (Abstract and PDF).

 

46. Nakagawa, A., Sullivan, K., and Xue, D. (2014). Caspase-activated phosphoinositide binding by CNT-1 promotes apoptosis by inhibiting the AKT pathway. Nature Structural & Molecular Biology 21, 1082-1090 (Abstract and PDF).

 

47. Weaver, B.P., Zabinsky, R., Weaver, Y.M., Lee, E.S., Xue. D., and Han, M. (2014). CED-3 caspase acts with miRNAs to regulate non-apoptotic gene expression dynamics for robust development in C. elegans. eLife doi: 10.7554/eLife.04265 (Abstract and PDF).

 

48. Yang, H.W.*, Chen, Y.Z.*, Zhang, Y.*, Wang, X.H., Zhao, X., Godfroy, J.I., Liang, L., Zhang, M., Zhang, T.Y., Yuan, Q., Royal, M.A., Driscoll, M.D., Xia, N.S., Yin, H., and Xue, D. (2015). A lysine-rich motif in the phosphatidylserine receptor PSR-1 mediates recognition and removal of apoptotic cells. Nature Communications , 6: 5717 doi: 10.1038/ncomms6717. *Equal contribution. (Abstract and PDF). NIH Biomedical Beat

 

49. Neumann, B., Coakley, S., Giordano-Santini, R., Linton, C., Lee, E.S., Nakagawa, A., Xue, D., and Hilliard, M.A. (2015). EFF-1-mediated regenerative axonal fusion requires components of the apoptotic pathway. Nature 517, 219–222 (Abstract and PDF).

 

50. Sullivan, K.*, Nakagawa, A.*, Xue, D.#, and Espinosa, J.M.# (2015). Human ACAP2 is a homolog of C. elegans CNT-1 that promotes apoptosis in cancer cells. Cell Cycle 14, 1771-1778. *Equal contribution. #Co-corresponding authors. (Abstract and PDF).

 

51. Seervi, M. and Xue, D. (2015). Mitochondrial cell death pathways in Caenorhabiditis elegans. Current Topics in Developmental Biology 114, 43-65 (Abstract and PDF).

 

52. Nichols, A.A, Meelkop, E., Linton, C., Giordano-Santini, R., Sullivan, R., Donato, A., Nolan, C., Hall, D.H., Xue, D., Neumann, B., and Hilliard, M. (2016).  The Apoptotic Engulfment Machinery Regulates Axonal Degeneration in C. elegans Neurons. Cell Reports 14, 1673-1683 (Abstract and PDF).

 

53. Zhao, P., Zhang, Z., Lv, X.Y., Zhao, X., Suehiro, Y., Jiang, Y.N., Wang, X.Q., Mitani, S., Gong, H.P., and Xue, D. (2016). One-step homozygosity in precise gene editing by an improved CRISPR/Cas9 system. Cell Research 26, 633-636 (Abstract and PDF).

 

54. Lin, J.L.*, Nakagawa, A.*, Skeen-Gaar, R.R., Yang, W.Z., Zhao, P., Zhang, Z., Ge, X., Mitani, S., Xue, D.#, and Yuan, H.S.# (2016). Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G. Cell Reports 16, 279–287. *Equal contribution. #Co-corresponding authors. (Abstract and PDF).

 

55. Zhou, Q.H.*, Li, H.M.*, Li, H.Z.*, Nakagawa, A., Harry, B., Lee, E.S., Lin, J., William, D., Mitani, S., Yuan, H., Kang, B.H.#, and Xue, D.# (2016). Mitochondrial endonuclease G mediates breakdown of paternal mitochondria following fertilization. Science 353, 394-399 (Abstract and PDF). *Equal contribution. #Co-corresponding authors. Science PerspectivesNature Reviews Molecular Cell Biology, The New York Times, ScienceNews, TheScientist, Le Scienze, Frankfurter Allgemeine, MedicalXpress, Sciences et Avenir, DAGENS Medicin, 新华网, ScienceAlert, Bionews, THE WIRE, and THE VERGE.

 

56. Conradt, B., Wu, Y.C., and Xue, D. (2016).  Programmed Cell Death During C. elegans development.  Genetics 203, 1533-1562 (Abstract and PDF).

 

57. Wang, Y.*, Zhang, Y.*, Chen, L.W., Liang, Q., Yin, X.M., Miao, L., Kang, B.H.#, and Xue, D.# (2016). Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans. Nature Communications 7, 12569. DOI: 10.1038/ncomms12569 (Abstract and PDF). *Equal contribution. #Co-corresponding authors.

 

58. Chen, X.D.*, Wang, Y.*, Chen, Y.Z.*, Harry, Brian, L.H., Nakagawa, A., Lee, E.S., Guo, H.Y., and Xue, D. (2016). Regulation of CED-3 caspase localization and activation by C. elegans nuclear membrane protein NPP-14. Nature Structural & Molecular Biology 23, 958-964 (Abstract and PDF). *Equal contribution.

 

59. Klöditz, K., Chen, Y.Z., Xue, D., and Fadeel, B. (2017). Programmed cell clearance: From nematodes to humans. Biochemical and Biophysical Research Communications, 482: 491-497 (Abstract and PDF).

 

60. Peng, Y.*, Zhang, M.*, Zheng, L.J.*, Liang,Q.*, Li, H.Z*., Chen, J.T., Guo, H., Yoshina, S. Chen, Y.Z., Zhao, X., Wu, X.Q., Liu, B., Mitani, S., Yu, J.S., and Xue, D. (2017). Cysteine protease cathepsin B mediates radiation-induced bystander effects. Nature 547, 458-462 (Abstract and PDF). *Equal contribution