Identification and Characterization of Proteins Involved in Nuclear Organization Using Drosophila GFP Protein Trap Lines

PLoS ONE

Volumn 8, Issue 1, 2013, Pages

  Rohrbaugh, Margaret ^a   Clore, Alyssia ^b   Davis, Julia ^c   Johnson, Sharonta ^c   Jones, Brian ^c   Jones, Keith ^c   Kim, Joanne ^a   Kithuka, Bramwel ^a   Lunsford, Krystal ^c   Mitchell, Joy ^c   Mott, Brian ^a   Ramos, Edward ^a   Tchedou, Maza R ^c   Acosta, Gilbert ^a   Araujo, Mark ^a   Cushing, Stuart ^d   Duffy, Gabriel ^c   Graves, Felicia ^e   Griffin, Kyler ^f   Gurudatta, B V ^a   Jackson, Deaundra ^c   Jaimes, Denis ^g   Jamison, Kendall ^e   Jones, Khali ^c   Kelley, Dhaujee ^e   Kilgore, Marquita ^a   Laramore, Derica ^a   Le, Thuy ^g   Mazhar, Bakhtawar ^f   Mazhar, Muhammad M ^f   McCrary, Britney ^h   Miller, Teanndras ^c   Moreland, Celethia ^b   Mullins, Alex ^c   Munye, Elyas ^f   Okoorie, Sheila ^d   Pittman, Elisha ^c   Roberts, Nikkita ^c   Rose, De'Warren ^c   Rowland, Alex ^c   Shagarabi, Anwar ^f   Smith, Jamela ^b   Stallworth, Tayler ^b   Stroud, Nicole ^f   Sung, Elizabeth ^a   Sung, Kai ^a   Takenaka, Naomi ^a   Torre, Eduardo ^a   Veira, Jarvis ^f   Vu, Kim ^b   Wagstaff, William ^f   Wood, Ashley M ^a   Wu, Karen ^a   Yang, Jingping ^a   Corces, Victor G ^a   more..

^a EMORY UNIVERSITY   (United States)

^b South Atlanta High School of Health and Medical Science   (United States)

^c Carver School of Health Science and Research   (United States)

^d Baltimore Polytechnic Institute   (United States)

^e Paul Laurence Dunbar High School   (United States)

^f North Atlanta High School   (United States)

^g Cross Keys High School   (United States)

^h Frederick Douglass High School   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GREEN FLUORESCENT PROTEIN; HEAT SHOCK PROTEIN; LAMIN; NUCLEOPLASMIN; UBIQUITIN PROTEIN LIGASE E3;

ARTICLE; DROSOPHILA; NONHUMAN; NUCLEAR LAMINA; POLYTENE CHROMOSOME; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; STEM CELL; X CHROMOSOME;

ANIMALS; CELL DIFFERENTIATION; CELL NUCLEUS; DIPLOIDY; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; GERM CELLS; GREEN FLUORESCENT PROTEINS; HEAT-SHOCK RESPONSE; LAMIN TYPE A; MALE; MODELS, BIOLOGICAL; NUCLEAR LAMINA; NUCLEOPLASMINS; POLYTENE CHROMOSOMES; PROTEIN INTERACTION MAPS; UBIQUITIN-PROTEIN LIGASES;

EID: 84872463150     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0053091     Document Type: Article

References (46)

1. Bushey AM, Dorman ER, Corces VG, (2008) Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol Cell 32: 1-9.
2. Phillips JE, Corces VG, (2009) CTCF: master weaver of the genome. Cell 137: 1194-1211.
3. Negre N, Brown CD, Shah PK, Kheradpour P, Morrison CA, et al. (2010) A comprehensive map of insulator elements for the Drosophila genome. PLoS genetics 6: e1000814.
4. Bushey AM, Ramos E, Corces VG, (2009) Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev 23: 1338-1350.
5. Hoover KK, Chien AJ, Corces VG, (1993) Effects of transposable elements on the expression of the forked gene of Drosophila melanogaster. Genetics 135: 507-526.
6. Wood AM, Van Bortle K, Ramos E, Takenaka N, Rohrbaugh M, et al. (2011) Regulation of chromatin organization and inducible gene expression by a Drosophila insulator. Molecular cell 44: 29-38.
7. Gerasimova TI, Lei EP, Bushey AM, Corces VG, (2007) Coordinated control of dCTCF and gypsy chromatin insulators in Drosophila. Mol Cell 28: 761-772.
8. Capelson M, Corces VG, (2005) The ubiquitin ligase dTopors directs the nuclear organization of a chromatin insulator. Mol Cell 20: 105-116.
9. Pai CY, Lei EP, Ghosh D, Corces VG, (2004) The centrosomal protein CP190 is a component of the gypsy chromatin insulator. Mol Cell 16: 737-748.
10. Lei EP, Corces VG, (2006) RNA interference machinery influences the nuclear organization of a chromatin insulator. Nat Genet 38: 936-941.
11. Bantignies F, Cavalli G, (2011) Polycomb group proteins: repression in 3D. Trends in genetics: TIG 27: 454-464.
12. Mao YS, Zhang B, Spector DL, (2011) Biogenesis and function of nuclear bodies. Trends in genetics: TIG 27: 295-306.
13. Morin X, Daneman R, Zavortink M, Chia W, (2001) A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila. Proc Natl Acad Sci U S A 98: 15050-15055.
14. Buszczak M, Paterno S, Lighthouse D, Bachman J, Planck J, et al. (2007) The carnegie protein trap library: a versatile tool for Drosophila developmental studies. Genetics 175: 1505-1531.
15. Kelso RJ, Buszczak M, Quinones AT, Castiblanco C, Mazzalupo S, et al. (2004) Flytrap, a database documenting a GFP protein-trap insertion screen in Drosophila melanogaster. Nucleic Acids Res 32: D418-420.
16. Kimura M, (2008) IRF2-binding protein-1 is a JDP2 ubiquitin ligase and an inhibitor of ATF2-dependent transcription. Febs Letters 582: 2833-2837.
17. Drysdale R, (2008) FlyBase: a database for the Drosophila research community. Methods in molecular biology 420: 45-59.
18. Moshkovich N, Nisha P, Boyle PJ, Thompson BA, Dale RK, et al. (2011) RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function. Genes & development 25: 1686-1701.
19. Szollosi E, Bokor M, Bodor A, Perczel A, Klement E, et al. (2008) Intrinsic structural disorder of DF31, a Drosophila protein of chromatin decondensation and remodeling activities. Journal of Proteome Research 7: 2291-2299.
20. Crevel G, Cotterill S, (1995) DF 31, a sperm decondensation factor from Drosophila melanogaster: purification and characterization. EMBO J 14: 1711-1717.
21. Crevel G, Huikeshoven H, Cotterill S, (2001) Df31 is a novel nuclear protein involved in chromatin structure in Drosophila melanogaster. Journal of Cell Science 114: 37-47.
22. Guillebault D, Cotterill S, (2007) The Drosophila Df31 protein interacts with histone H3 tails and promotes chromatin bridging in vitro. Journal of Molecular Biology 373: 903-912.
23. Schubert T, Pusch MC, Diermeier S, Benes V, Kremmer E, et al. (2012) Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin. Mol Cell 48(3): 434-444.
24. Cremer T, Cremer M, Dietzel S, Muller S, Solovei I, et al. (2006) Chromosome territories-a functional nuclear landscape. Curr Opin Cell Biol 18: 307-316.
25. Misteli T, (2007) Beyond the sequence: cellular organization of genome function. Cell 128: 787-800.
26. Woodcock CL, (2006) Chromatin architecture. Curr Opin Struct Biol 16: 213-220.
27. Legube G, McWeeney SK, Lercher MJ, Akhtar A, (2006) X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev 20: 871-883.
28. Palmer MJ, Mergner VA, Richman R, Manning JE, Kuroda MI, et al. (1993) The male-specific lethal-one (msl-1) gene of Drosophila melanogaster encodes a novel protein that associates with the X chromosome in males. Genetics 134: 545-557.
29. Ito T, Tyler JK, Bulger M, Kobayashi R, Kadonaga JT, (1996) ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. Journal of Biological Chemistry 271: 25041-25048.
30. Akiyama T, (2002) Mutations of stonewall disrupt the maintenance of female germline stem cells in Drosophila melanogaster. Dev Growth Differ 44: 97-102.
31. Clark KA, McKearin DM, (1996) The Drosophila stonewall gene encodes a putative transcription factor essential for germ cell development. Development 122: 937-950.
32. Yi X, de Vries HI, Siudeja K, Rana A, Lemstra W, et al. (2009) Stwl modifies chromatin compaction and is required to maintain DNA integrity in the presence of perturbed DNA replication. Molecular Biology of the Cell 20: 983-994.
33. Maines JZ, Park JK, Williams M, McKearin DM, (2007) Stonewalling Drosophila stem cell differentiation by epigenetic controls. Development 134: 1471-1479.
34. Xie T, Spradling AC, (2000) A niche maintaining germ line stem cells in the Drosophila ovary. Science 290: 328-330.
35. Guruharsha KG, Rual JF, Zhai B, Mintseris J, Vaidya P, et al. (2011) A protein complex network of Drosophila melanogaster. Cell 147: 690-703.
36. Philpott A, Leno GH, Laskey RA, (1991) Sperm decondensation in Xenopus egg cytoplasm is mediated by nucleoplasmin. Cell 65: 569-578.
37. Philpott A, Leno GH, (1992) Nucleoplasmin remodels sperm chromatin in Xenopus egg extracts. Cell 69: 759-767.
38. Lu Z, Zhang C, Zhai Z, (2005) Nucleoplasmin regulates chromatin condensation during apoptosis. Proc Natl Acad Sci U S A 102: 2778-2783.
39. Schulze SR, Curio-Penny B, Li Y, Imani RA, Rydberg L, et al. (2005) Molecular genetic analysis of the nested Drosophila melanogaster lamin C gene. Genetics 171: 185-196.
40. Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, et al. (1999) The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics 153: 135-177.
41. Guillemin K, Williams T, Krasnow MA, (2001) A nuclear lamin is required for cytoplasmic organization and egg polarity in Drosophila. Nat Cell Biol 3: 848-851.
42. Bellen HJ, Levis RW, Liao G, He Y, Carlson JW, et al. (2004) The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 167: 761-781.
43. Ramos E, Torre EA, Bushey AM, Gurudatta BV, Corces VG, (2011) DNA Topoisomerase II Modulates Insulator Function in Drosophila. PLOS One 6: e16562.
44. Nowak SJ, Pai CY, Corces VG, (2003) Protein phosphatase 2A activity affects histone H3 phosphorylation and transcription in Drosophila melanogaster. Mol Cell Biol 23: 6129-6138.
45. Ivaldi MS, Karam CS, Corces VG, (2007) Phosphorylation of histone H3 at Ser10 facilitates RNA polymerase II release from promoter-proximal pausing in Drosophila. Genes & development 21: 2818-2831.
46. McKearin D, Ohlstein B, (1995) A role for the Drosophila bag-of-marbles protein in the differentiation of cystoblasts from germline stem cells. Development 121: 2937-2947.