Publications for Drosophila

Wang, S H, and Elgin, SCR (2010) “PIWI impacts transposon silencing and
heterochromatin structure in the Drosophila melanogaster female germline,”
manuscript submitted.

Mendez, DL, D Kim, M Chruszcz, GE Stephens, W Minor, S Khorasanizadeh, and SCR Elgin (2011) The HP1a disordered C-terminus and Chromo Shadow Domain
cooperate to select target peptide partners. ChemBioChem 12: 1084-96. PMCID: PMC3154745.

Abstract

The modENCODE Consortium, S Roy,…SCR Elgin...M Kellis (2010) Identification
of functional elements and regulatory circuits in Drosophila modENCODE. Science
330: 1787-97.  PMID: 21177974.

Abstract

Kharchenko, PV, AA Alekseyenko, YB Schwartz, A Minoda, NC.Riddle, J Ernst, PJ
Sabo, E Larschan, AA Gorchakov, T Gu, D Linder-Basso, A Plachetka, G Shanower,
MY Tolstorukov, LJ Luquette, R Xi, YL Jung, R Park, EP Bishop, TP Canfield, R
Sandstrom, RE Thurman, DM MacAlpine, J Stamatoyannopoulos, M Kellis, SCR
Elgin, MI Kuroda, V Pirrotta, G Karpen, PJ Park. (2011)   Comprehensive analysis of
the chromatin landscape in Drosophila melanogaster.  Nature 471: 480-5. PMID:
21179089. PMCID: PMC3109908 [Available on 2011/9/24]

Abstract

Egelhofer TA, Minoda A, Klugman S, Lee K, Kolasinska-Zwierz P, Alekseyenko AA,
Cheung MS, Day DS, Gadel S, Gorchakov AA, Gu T, Kharchenko PV, Kuan S,
Latorre I, Linder-Basso D, Luu Y, Ngo Q, Perry M, Rechtsteiner A, Riddle NC,
Schwartz YB, Shanower GA, Vielle A, Ahringer J, Elgin SCR, Kuroda MI, Pirrotta V,
Ren B, Strome S, Park PJ, Karpen GH, Hawkins RD, Lieb JD. (2011) “An assessment of histone modification antibody quality,” Nature Struct Mol Biol 18:
91-93. Epub.  PMCID: PMC3017233.

Abstract

Riddle, NC, A Minoda, PV Kharchenko, AA Alekseyenko, YB Schwartz, MY
Tolstorukov, AA Gorchakov, C Kennedy, D Linder-Basso, JD Jaffe, G Shanower, MI
Kuroda, V Pirrotta, PJ Park, SCR Elgin, GH Karpen (2010)  “Plasticity in patterns of histone modifications and chromosomal proteins in the Drosophila heterochromatin,” Genome Res. 21:147-63. PMCID: PMC3032919.

Abstract

Leung, W, CD Shaffer, T Cordonnier, J Wong, MS Itano, EE Slawson-Tempel, E  
Kellmann, DM Desruisseau, C Cain, R Carrasquillo, TM Chusak, K Falkowska, KD Grim, R Guan, J Honeybourne, S Khan, L Lo, R McGaha, J Plunkett, JM Richner, R Richt, L Sabin, A Shah, A Sharma, S Singhal, F Song, C Swope, CB  Wilen, J Buhler, ER Mardis, SCR Elgin (2010)  “A comparative study of the genomic sequences of the D. melanogaster and D virilis dot chromosomes demonstrates a distinct evolutionary domain in the Drosophila genome.” Genetics 185: 1519-1534.  PMCID: PMC2927774.

Abstract

Gracheva, E.M., and Elgin, S.C.R. (2010) “Quantitative Western Blots: simplification
leads to incorrect conclusions,” manuscript under revision.

Gracheva, E.M., Dus, M., and Elgin, S.C.R. (2009) “Drosophila RISC component VIG
and its homolog Vig2 participate in heterochromatin formation,” PLoS One. Jul
8;4(7):e6182.  PMCID: PMC2703606.

Abstract

Celniker et al….and the modENCODE Consortium  (2009) “Unlocking the secrets of the genome” Nature 459, 927-930.  (Listed as current consortium participant.) PMCID: PMC2843545.

Abstract

Brower-Toland, B., Riddle, N.C., Jiang, H., Huisinga, K.L., and Elgin, S.C.R. (2009)  “Multiple SET methyltransferases are required to maintain normal heterochromatin domains in the genome of Drosophila melanogaster,” Genetics 181: 1303-19. PMCID: PMC2666501.

Abstract

Riddle, N.C., Shaffer, C.D., and Elgin, S.C.R. (2009) “A lot about a little dot: lessons learned from Drosophila melanogaster chromosome four.”  Biochem & Cell Biol 87: 229-41. PMCID: PMC2950803.

Abstract

Huisinga, K., and Elgin, S.C.R, (2009) “Small RNA directed heterochromatin formation in the context of development:  what flies might learn from fission yeast.”  Biochem. Biophys. Acta 1789: 3-16. PMCID: PMC2633771.

Abstract

Wallrath, L.L., and Elgin, SCR (2008) “Preview: Stimulating conversations between
HP1a and histone demethylase dKDM4A.” Molec. Cell 32, 601-602. PMCID: PMC2702125.

Jones, P., Baylin, SB, Bernstein, BE, Feinberg, AP, Greally, JM, Jenuwein, T, 
Martienssen, R, Ushijima, Pirrotta, V, Allis, CD, Elgin, SC, Rine, J, and Wu, C. (European Union, Network of Excellence, Scientific Advisory Board) (2008) "Moving AHEAD with an International Human Epigenome Project” (Box 1, A European success story). Nature 454: 712. PMID: 18685699.

Yaniv, M., and Elgin, S.C.R. (2008) “Editorial overview: Chromosomes and expression mechanisms: bringing together the roles of DNA, RNA, and proteins.” Curr Opin. Genet. Develop., 18: 107-108. PMCID: PMC2710611.

Riddle, N.C., Leung, W., Haynes, K.A., Granok, H., Wuller, J, and Elgin, S.C.R. (2008) “An investigation of heterochromatin domains on the fourth chromosome of Drosophila melanogaster.”  Genetics 178: 1177-1191. PMCID: PMC2278077.

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Riddle, N.C., and Elgin, S.C.R. (2007) “A role for RNAi in heterochromatin formation in Drosophila,” in “RNA Interference” ed. P. Vogt and  P. Paddison, Curr. Topics Micro. & Immun. 320: 185-209.  PMID: 18268845.

Grewal, S.I.S., and Elgin, S.C.R. (2007) “Transcription and RNA interference in the formation of heterochromatin,” Nature 447: 399-406. PMCID: PMC2950806.

Brower-Toland, B., Findley, S.D., Jiang, L., Liu, L., Yin, H., Dus, M., Zhou, P., Elgin, S.C.R., and Lin, H. (2007) “Drosophila PIWI associates with chromatin and interacts directly with HP1a,” Genes & Develop. 21: 2300-2311. PMCID: PMC1973144.

Abstract

Haynes, K.A., Gracheva, E., and Elgin, S.C.R. (2007) “A distinct type of heterochromatin within Drosophila melanogaster chromosome four,” Genetics 175: 1539-1542. PMCID: PMC1840055.

Abstract

Haynes, K.A., Caudy, A.A., Collins, L. and Elgin S.C.R. (2006) “Element 1360 and components of the RNAi system contribute to HP1-dependent silencing of a pericentric reporter,” Current Biology 16: 2222-27. PMCID: PMC1712676.

Abstract

Stephens, G.F., Xiao, H., Lankenau, D.-H., Wu, C., and Elgin, S.C.E. (2006) “Heterochromatin Protein 2 interacts with Nap-1 and NURF: a link between heterochromatin-induced gene silencing and the chromatin remodeling machinery in Drosophila,” Biochemistry 45: 14990-9. PMCID: PMC2534143.

Abstract

Shaffer, C., Cenci, G., Thompson, B., Stephens, G.E., Slawson, E., Adu-Wusu, K., Gatti, M., and Elgin, S.C.R.  (2006) “The large isoform of Drosophila melanogaster Heterochromatin Protein 2 plays a critical role in gene silencing and chromosome structure,” Genetics 174: 1189-204. PMCID: PMC1667101.

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Elgin, S.C.R. and Reuter, G. (2006) “Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila,” in “Epigenetics,” ed. C.D. Allis, T. Jenuwein, & D. Reinberg, Cold Spring Harbor Laboratory Press, NY (pp. 81-100).

Riddle, N.C., and Elgin, S.C.R. (2006)  “The dot chromosome of Drosophila: insights into chromatin states and their change over evolutionary time,” Chromosome Research 14:405-416. PMID: 16821136.

Abstract

Eissenberg, J.C., and Elgin, S.C.R. (2006)  “Marking time” (News & Views), Nature Genet. 38: 276-277. PMID: 16501555.

Slawson, E.E., Shaffer, C.D., Malone, C.D., Leung, W., Kellmann, E., Shevchek, R.B., Craig, C.A., Bloom, S., Bogenpohl, J. II, Dee, J., Morimoto, E.T.A., Myoung, J., Nett, A.S., Ozsolak, F., Tittiger, M.E., Zeug, A., Pardue, M.L., Buhler, J., Mardis, E., and Elgin, S.C.R.  (2006) “Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains,” Genome Biology 7: R15. PMCID: PMC1431729.

Huisinga, K.L., Brower-Toland, B., and Elgin, S.C.R.  (2006)  “The contradictory definitions of heterochromatin: transcription and silencing.”  Chromosoma 115, 110-122. PMID:16506022.

Eissenberg, J.C., and Elgin, S.C.R.  (2005)  “Antagonizing the neighbors,” (News & Views), Nature 438: 1040-1041. PMID:16371991.

Stephens, G.E., Slawson, E.E., Craig, C. and Elgin, S.C.R.  (2005)  “Interaction of heterochromatin protein 2 with HP1 defines a novel HP1 binding domain,” Biochemistry 44, 13394-403. PMCID: PMC2534139.

Abstract

Schubeler, D., and Elgin, S.C.R. (2005) “Defining epigenetic states through chromatin and RNA,” a report of the Alan Wolffe EMBO Conference,” Nature Genetics 37, 917-918. PMID:16132044.

Haynes, K.A., Leibovitch, B.A., Rangwala, S.H., Craig, C., and Elgin, S.C.R. (2004) “Analyzing heterochromatin formation using chromosome four of Drosophila melanogaster,” Cold Spring Harbor Symp. Quant. Biol. 69, 267-272. PMID: 16117658.

Leibovitch, B.A., and Elgin, S.C.R. (2004)  “Heterochromatin and euchromatin – organization, packaging, and gene regulation,”  Encyclopedia of Molecular Cell Biology and Molecular Medicine, R.A. Meyers, ed., (Wiley-VCH, Germany), Vol. 6, pp. 137-154.

Gracheva, E., and Elgin, S.C.R. (2004) “Chromosome Organization and Structure, Overview,” Encyclopedia of Biological Chemistry (W. J. Lennarz & M. D. Lane, eds). Elsevier, Oxford, Vol. 1, pp. 469-474.

Sun, F.-L., Haynes, K., Simpson, C.L., Lee, S.D., Collins, L., Wuller, J., Eissenberg, J.C.,  and Elgin, S.C.R. (2004)  “Cis-acting determinants of heterochromatic formation on Drosophila melanogaster chromosome four,” Mol. Cell. Biol., 24, 8210-8220. PMCID: PMC515050.

Abstract

Dellino, G.I., Schwartz, Y.B., Farkas, G., McCabe, D., Elgin, S.C.R., Pirrotta, V.  (2004)  “Polycomb silencing blocks transcription initiation,” Mol Cell 26, 887-893. PMID: 15053881.

Abstract

Stephens, G.E., Craig, C.A., Li, Y., Wallrath, L.L., and Elgin, S.C.R. (2003)  “Immunofluorescent Staining of Polytene Chromosomes: Exploiting Genetic Tools,” Meth. Enz 376B, 372-393. PMID: 14975319.

Abstract

Pal-Bhadra, M., B. A. Leibovitch, S. G. Gandhi, M. Rao, U. Bhadra, J. A. Birchler, S. C. R. Elgin  (2004)  “Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery,” Science 303, 669-672. PMID: 14752161.

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Elgin, S.C.R., and S.I.S. Grewal (2003)  “Primer.  Heterochromatin: Silence is Golden,” Curr. Biol. 13, R895-R898. PMID: 14654010.

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Lu, Q., Teare, J.M., Granok, H., Swede, M.J., Xu, J. and Elgin, S.C.R.  (2003)  "The capacity to form H-DNA cannot substitute for GAGA factor binding to a (CT)n•(GA)n regulatory site,” Nucleic Acids Res. 31, 2483-2494. PMCID: PMC156050.

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Shaffer, C.D., Stephens, G.E., Thompson, B.A., Funches, L., Bernat, J.A., Craig, C.A., and Elgin, S.C.R. (2002) "Heterochromatin protein 2 (HP2), a partner of HP1 in Drosophila heterochromatin," Proc. Natl. Acad. Sci. USA 99, 14322-14337. PMCID: PMC137884.

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Leibovitch, B.A., Lu, Q., Benjamin, L.R., Liu, Y., Gilmour, D.S., and Elgin, S.C.R. (2002) "GAGA factor and TFIID complex collaborate in generating an open chromatin structure at the Drosophila melanogaster hsp26 gene promoter," Mol. Cell. Biol. 22, 6148-6157. PMCID: PMC134011.

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Richards, E.J., and Elgin, S.C.R. (2002)  "Epigenetic Codes for Heterochromatin Formation and Silencing: Rounding up the Usual Suspects,"  Cell 108, 489-500. PMID: 11909520.

Elgin, S.C.R. (2002)  “Report from the ASCB Education Committee” Cell Biol Educ.1, 8. PMCID: PMC118373.

Elgin, S.C.R. and Workman, J.L.  (2002)  “Chromosomes and expression mechanisms: A year dominated by histone modifications, transitory and remembered” (editorial overview), Curr. Opin. Genet. Develop. 12, 127-129.  PMID: 11893483.

Grewal, S.I.S., and Elgin, S.C.R. (2002)  "Heterochromatin: New Possibilities for the Inheritance of Structure," Curr. Opin. Genet. Develop. 12, 178-187. PMID: 11893491.

Abstract

Granok, H., Leibovitch, B.A., and Elgin, S.C.R.  (2001)  "A heat shock-activated cDNA encoding GAGA factor rescues some lethal mutations in Drosophila melanogaster Trithorax-like gene,” Genet. Res. Camb. 78, 13-21. PMID: 11556133.

Sun, F.-L., Cuaycong, M.H., and Elgin, S.C.R.  (2001)  “Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin,” Mol. Cell. Biol. 21, 2867-2879. PMCID: PMC86916.

Abstract

Eissenberg, J.C. and Elgin S.C.R.  (2001)  “Heterochromatin/euchromatin:  alternative packaging in the nucleus,” In: Encyclopedia of Life Sciences. London: Nature Publishing Group. [www.els.net]

Farkas, G., Leibovitch, B.A., Elgin, S.C.R.  (2000)  “Chromatin organization and transcriptional control of gene expression in Drosophila,” Gene 253, 117-136. PMID: 10940549.

Elgin, S.C.R. and Workman, J. J., editors  (2000)  Chromatin Structure and Gene Expression, second edition, Oxford University Press, New York.

Eissenberg, J.C., Elgin, S.C.R, and Paro, R.  (2001)  “Epigenetic regulation in Drosophila:  unraveling the conspiracy of silence,” in Chromatin Structure and Gene Expression, ed. S.C.R. Elgin and J.L. Workman (Oxford University Press, New York), pp. 228-251.

Eissenberg, J.C. and Elgin, S.C.R.  (2000)  “The HP1 protein family:  getting a grip on chromatin,” Curr Opin Genet. Develop. 10, 204-210. PMID: 10753776.

Sun, F.-L., Cuaycong, M.H., Craig, C.A., Wallrath, L.L., Locke, J., and Elgin, S.C.R.  (2000)  “The fourth chromosome of Drosophila melanogaster: interspersed euchromatic and heterochromatic domains,” Proc. Natl. Acad. Sci. USA 97, 5340-5345. PMCID: PMC25830.

Abstract