Publications

Featured Recent Publications


  • Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2/3 islands located in euchromatic genome

Lee, Y.C.G., Ogiyama, Y., Martins, N.M.C., Beliveau, B.J., Acevedo, D., Wu, C.T., Cavalli, G., and Karpen, G.H. (2020). PLoS Genetics 16(3): e1008673 (PMID 32203508)

  • RNA from a simple-tandem repeat is required for sperm maturation and male fertility in Drosophila melanogaster

Mills, W.K., Lee, Y.C.G., Kochendoerfer, A.M., Dunleavy, E.M., and Karpen, G.H. (2019). eLife Nov 5;8.doi: 10.7554/eLife.48940 (PMID 31687931)

  • Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA

Langley, S.A., Miga, K., Karpen, G.H. and Langley, C.H. (2019). eLife 8:e42989 (PMID 31237235)

  • Structural and enzymatic functions of the Drosophila KDM4A demethylase in heterochromatin

Colmenares, S.U., Swenson, J.M., Langley, S.A., Kennedy, C., Costes, S.V. and Karpen, G.H. (2017). Developmental Cell 42, 156 (PMID 28743002)

  • Timely double-strand break repair and pathway choice in pericentromeric heterochromatin depend on the histone demethylase dKDM4A

Janssen, A., Colmenares, S.U., Lee, T., and Karpen, G.H. (2019). Genes and Development 33, 103–115 (PMID 30578303)

  • Phase separation drives heterochromatin domain formation

Strom, A.R. Emelyanov, A.V., Mir, M., Fyodorov, D.V., Darzacq, X. and Karpen, G.H. (2017). Nature 547, 241 (PMID 28636597)

  • News & Views by Klosen, A. and Hyman, A.A. (2017) Molecular biology: A liquid reservoir for silent chromatin. Nature 547, 168

Additional Research Publications

  • Tortora, M.M., Brennan, L., Karpen, G.H., and Jost, D. (2022) Liquid-liquid phase separation recapitulates the thermodynamics and kinetics of heterochromatin formation. bioRxiv https://doi.org/10.1101/2022.07.11.499635

  • Maslan, A., Altemose, N., Mishra, R., Marcus, J., Brennan, L.D., Sundararajan, K., Karpen, G.H., Straight, A.F., and Streets, A.M. (2022) Mapping protein-DNA interactions with DiMeLo-seq. bioRxiv https://doi.org/10.1101/2022.07.03.498618

  • Cekanaviciute, E., Tran, D., Nguyen, H., Macha, A.L., Pariset, E., Langley, S., Babbi, G., Malkani, S., Penninckx, S., Schisler, J.C., Nguyen, T., Karpen, G.H. and Sylvain.V. Costes (2022) Mouse Genomic Associations with In Vitro Sensitivity to Simulated Space Radiation. Life Sci Space Res doi:10.1016/j.lssr.2022.07.006.

  • Altemose, N., Logsdon, G.A, Bzikadze, A.V., Sidhwani, P, Langley, S.A., ..., Karpen, G.H., ..., Alexandrov, I., Miga, K.H. (2022) Complete genomic and epigenetic maps of human centromeres. Science 375, eabl4178. https://doi.org/10.1126/science.abl4178

  • Kasinathan, B., Colmenares, S.U., McConnell, H., Young, J.M., Karpen, G.H. and Malik, J.S. (2020) Innovation of heterochromatin functions drives rapid evolution of essential ZAD-ZNF genes in Drosophila. eLife 2020;9:e63368 DOI: 10.7554/eLife.63368

  • Lee, Y.C.G. and Karpen, G.H. (2017) Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution. eLife 6, 2185 (PMID28695823)

  • Zhang, W., Karpen, G.H., and Zhang, Q. (2017). Exploring the role of CENP-A Ser18 phosphorylation in CIN and Tumorigenesis. Cell Cycle 16, 2323–2325 (PMID28980868)

  • Takada, M., Zhang, W., Suzuki, A., Kuroda, T., Yu, Z., Inuzuka, H., Gao, D., Wan, L., Zhuang, M., Hu, L., Zhai, B., Fry, C.J., Bloom, K., Li, G. Karpen, G.H.*, Wei, W.* and Zhang, Q.* (2017). FBW7 loss promotes chromosomal instability and tumorigenesis via Cyclin E1/CDK2-mediated phosphorylation of CENP-A. Cancer Research 77 (18), 4881-4893 (PMID 28760857)

  • Snijders, A.M., Langley, S.A., Kim, Y-M., Brislawn, C.J., Noecker, C., Zink, E.M., Fansler, S.J., Casey, C.P., Miller, D.R., Huang, Y., Karpen, G.H., Celniker, S.E., Brown, J.B., Borenstein, E., Jansson, J.K., Metz, T.O. and Mao, J-H. (2016) Relative influence of early life exposure, host genetics and diet on gut microbiome and metabolome Nature Microbiology 2, 16221 (PMID27892936).

  • Zhang, W., Mao, J-H., Zhu, W., Jain, A.K., Liu, K., Brown, J.B. and Karpen, G.H. (2016) Centromere and kinetochore gene misexpression predicts cancer patient survival and response to radiotherapy and chemotherapy. Nat Commun. 7, 12619 (PMID27577169)

  • Swenson, J.M., Colmenares, S.U., Strom, A.R., Costes, S.V. and Karpen, G.H. (2016) The composition and organization of Drosophila heterochromatin are heterogeneous and dynamic. eLife 5:e16096 (PMID27514026)

  • Janssen, A., Breuer, G.A., Brinkman, E.J., van der Meulen, A.I., Borden, S.V., van Steensel, B., Bindra, R.S., LaRocque, J.R. and. Karpen, G.H. (2016) A single double strand break system in Drosophila reveals repair dynamics and mechanisms in heterochromatin and euchromatin. Genes and Development 30, 1645–1657 (PMID27474442)

  • Mao, J.-H., S.A. Langley, Y. Huang, M. Hang, K.E. Bouchard, S.E. Celniker, J.B. Brown, J.K. Jansson, G.H. Karpen, and A.M. Snijders (2015) Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice. Scientific Reports 5:16247 (PMID26548763).

  • Ryu, T., Spatola, B., Delabaere, L., Bowlin, K., Hopp, H., Kunitake, R., Karpen, G.H. and Chiolo, I. (2015) Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nature Cell Biology 14(11):1401-1411 (PMID26502056)

  • Zhang P, Lo A, Huang Y, Huang G, Liang G, Mott J, Karpen GH, Blakely EA, Bissell MJ, Barcellos-Hoff MH, Snijders AM, and Mao JH (2015) Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment. Scientific Reports 5:8919 (PMID25747469)

  • Hoskins RA, Carlson JW, Wan KH, Park S, Mendez I, Galle SE, Booth BW, Pfeiffer BD, George RA, Svirskas R, Krzywinski M, Schein J, Accardo MC, Damia E, Messina G, Méndez-Lago M, de Pablos B, Demakova OV, Andreyeva EN, Boldyreva LV, Marra M, Carvalho AB, Dimitri P, Villasante A, Zhimulev IF, Rubin GM, Karpen GH, Celniker SE (2015) The Release 6 reference sequence of the Drosophila melanogaster genome. Genome Research 25:445-458 (PMID25589440)

  • Snijders AM, Langley S, Mao JH, Bhatnagar S, Bjornstad KA, Rosen CJ, Lo A, Huang Y, Blakely EA, Karpen G.H., Bissell MJ, Wyrobek AJ. (2014) An interferon signature identified by RNA-sequencing of mammary tissues varies across the estrous cycle and is predictive of metastasis-free survival. Oncotarget. 5(12):4011-25. (PMC4147302)

  • Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. (2014) Comparative analysis of metazoan chromatin organization. Nature 28, 449-52 (PMC4227084)

  • Langley S.A., Karpen G.H., Langley C.H. (2014) Nucleosomes shape DNA polymorphism and divergence. PLOS Genetics 10(7), e1004457 (PMC4081404)

  • Jung YL, Luquette LJ, Ho JW, Ferrari F, Tolstorukov M, Minoda A, Issner R, Epstein CB, Karpen GH, Kuroda MI, Park PJ. (2014) Impact of sequencing depth in ChIP-seq experiments. Nucleic Acids Res. 42, e74–e74. (PMC4027199)

  • Dunleavy, E.M., Beier N.L., Gorgescu, W., Tang, J., Costes, S. V., Karpen, G. H. (2012) The cell cycle timing of centromeric chromatin assembly in Drosophila meiosis Is distinct from mitosis yet requires CAL1 and CENP-C. PLoS Biology 10(12), e1001460 (PMC3531500)

  • Riddle, N.C., Jung, Y. L., Gu, T., Alekseyenko, A.A., Asker, D., Gui, H., Kharchenko, P.V., Minoda, A., Plachetka, A., Schwartz, Y.B., Tolstorukov, M.Y., Kuroda, M.I., Pirrotta, V., Karpen, G.H., Park, P.J., Elgin, S.C.R. (2012) Enrichment of HP1a on Drosophila chromosome 4 genes creates an alternate chromatin structure critical for regulation in this heterochromatic domain. PLoS Genetics 8(9), e1002954 (PMC3447959)

  • Alekseyenko, A.A., Ho, J.W.K., Peng, S., Gelbart, M., Tolstorukov, M.Y., Plachetka, A., Kharchenko, P.V., Jung, Y.L., Gorchakov, A.A., Larschan, E., Gu, T., Minoda, A., Riddle, N.C., Schwartz, Y.B., Elgin, S.C.R., Karpen, G.H., Pirrotta, V., Kuroda, M.I. and Park, P.J. (2012) Sequence-specific targeting of dosage compensation in Drosophila favors an active chromatin context. PLoS Genetics 8, e1002646 (PMC3343056)

  • Schwartz, Y.B., Linder-Basso, D., Kharchenko, P.V., Tolstorukov, M.Y., Kim, M., Li, H-B., Gorchakov, A.A., Minoda, A., Shanower, G, Alekseyenko, AA, Riddle, NC, Jung, YL, Gu, T., Plachetka, A., Elgin, S.C.R., Kuroda, M.I., Park, P.J., Savitsky, M., Karpen, G.H., Pirrotta, V. (2012) Nature and function of insulator protein binding sites in the Drosophila genome. Genome Research 22(11), 2188-98 (PMC3483548)

  • Egelhofer, T. A., Minoda, A., Klugman, S., Lee, K., Kolasinska-Zwierz, P., Alekseyenko, A. A., Cheung, M.-S., Day, D. S., Gadel, S., Gorchakov, A. A., Gu, T., Kharchenko, P. V., Kuan, S., Latorre, I., Linder-Basso, D., Luu, Y., Ngo, Q., Perry, M., Rechtsteiner, A., Riddle, N. C., Schwartz, Y. B., Shanower, G. A., Vielle, A., Ahringer, J., Elgin, S. C. R., Kuroda, M. I., Pirrotta, V., Ren, B., Strome, S., Park, P. J., Karpen, G. H., Hawkins, R. D. and Lieb, J. D. (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18(1), 91-93 (PMC3017233)

  • Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Minoda, A., Riddle, N. C., Ernst, J., Sabo, P. J., Larschan, E., Gorchakov, A. A., Gu, T., Linder-Basso, D., Plachetka, A., Shanower, G., Tolstorukov, M. Y., Luquette, L. J., Xi, R., Jung, Y. L., Park, R. W., Bishop, E. P., Canfield, T. P., Sandstrom, R., Thurman, R. E., MacAlpine, D. M., Stamatoyannopoulos, J. A., Kellis, M., Elgin, S. C. R., Kuroda, M. I., Pirrotta, V., Karpen, G. H.* and Park, P. J.* (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 471, 480-485 (*co-corr. authors (PMC3109908)

  • News & Views: Furlong, E.E.M. (2011) A fly in the face of genomics. Nature 471, 458–459

  • Riddle, N. C., Minoda, A., Kharchenko, P. V., Alekseyenko, A. A., Schwartz, Y. B., Tolstorukov, M. Y., Gorchakov, A. A., Jaffe, J. D., Kennedy, C., Linder-Basso, D., Peach, S. E., Shanower, G., Zheng, H., Kuroda, M. I., Pirrotta, V., Park, P. J., Elgin, S. C. R. and Karpen, G. H. (2011) Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Res 21(2): 147-163 (PMC3032919)

  • Chiolo, I., Minoda, A., Colmenares, S. U., Polyzos, A., Costes, S. V. and Karpen, G. H. (2011) Double-Strand Breaks in Heterochromatin Move Outside of a Dynamic HP1a Domain to Complete Recombinational Repair. Cell 144(5), 732-744 (PMC3417143)

  • Preview: Peterson, C.L. (2011) The ins and outs of heterochromatic DNA repair. Dev Cell 20, 285–287

  • Mellone, B.G., Grive, K.J., Shteyn, V., Bowers, S.R., Oderberg, I., and Karpen, G.H. (2011) Assembly of Drosophila centromeric chromatin proteins during mitosis. PLoS Genetics 7(5), e1002068 (PMC3093364)

  • Dunleavy, E.M., Almouzni, G., and Karpen, G.H. (2011) H3.3 is deposited at centromeres in S phase as a placeholder for newly assembled CENP-A in G1 phase. Nucleus 2: 146–157 (PMC3127096)

  • Zhang, W., Colmenares, S., and Karpen, G.H. (2011) Assembly of Drosophila Centromeric Nucleosomes Requires CID Dimerization. Molecular Cell 45, 263–269 (PMC3299411)

  • Consortium, ModENCODE, Roy, S., Ernst, J., Kharchenko, P. V., Kheradpour, P., Negre, N., Eaton, M. L., Landolin, J. M., Bristow, C. A., Ma, L., Lin, M. F., Washietl, S., Arshinoff, B. I., Ay, F., Meyer, P. E., Robine, N., Washington, N. L., Di Stefano, L., Berezikov, E., Brown, C. D., Candeias, R., Carlson, J. W., Carr, A., Jungreis, I., Marbach, D., Sealfon, R., Tolstorukov, M. Y., Will, S., Alekseyenko, A. A., Artieri, C., Booth, B. W., Brooks, A. N., Dai, Q., Davis, C. A., Duff, M. O., Feng, X., Gorchakov, A. A., Gu, T., Henikoff, J. G., Kapranov, P., Li, R., Macalpine, H. K., Malone, J., Minoda, A., Nordman, J., Okamura, K., Perry, M., Powell, S. K., Riddle, N. C., Sakai, A., Samsonova, A., Sandler, J. E., Schwartz, Y. B., Sher, N., Spokony, R., Sturgill, D., van Baren, M., Wan, K. H., Yang, L., Yu, C., Feingold, E., Good, P., Guyer, M., Lowdon, R., Ahmad, K., Andrews, J., Berger, B., Brenner, S. E., Brent, M. R., Cherbas, L., Elgin, S. C. R., Gingeras, T. R., Grossman, R., Hoskins, R. A., Kaufman, T. C., Kent, W., Kuroda, M. I., Orr-Weaver, T., Perrimon, N., Pirrotta, V., Posakony, J. W., Ren, B., Russell, S., Cherbas, P., Graveley, B. R., Lewis, S., Micklem, G., Oliver, B., Park, P. J., Celniker, S. E. *, Henikoff, S. *, Karpen, G. H. *, Lai, E. C. *, MacAlpine, D. M. *, Stein, L. D. *, White, K. P.* and Kellis, M. (2010) Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science 330, 1787-1797 (*senior authors contributed equally, in alphabetical order) (PMC3192495)

  • Peng, J. and Karpen, G.H. (2009) Heterochromatic genome stability requires regulators of histone H3 K9 methylation. PLoS Genet. 5(3): p. e1000435. (PMC2654965)

  • Williamson, A., Wickliffe, K.E., Mellone, Barbara G., Song, L., Karpen, G.H., Rape, M. (2009) Identification of a physiological E2 module for the human anaphase-promoting complex. PNAS 106, 18213–18218. (PMC2775311)

  • Celniker, S. E., Dillon, L. A. L., Gerstein, M. B., Gunsalus, K. C., Henikoff, S., Karpen, G. H., Kellis, M., Lai, E. C., Lieb, J. D., MacAlpine, D. M., Micklem, G., Piano, F., Snyder, M., Stein, L., White, K. P., Waterston, R. H. and Consortium, modENCODE (2009) Unlocking the secrets of the genome. Nature 459(7249): 927-930 (PMC2843545)

  • Erhardt, S.*, Mellone, B.*, Betts, C.M.*, Zhang, W., Karpen, G.H. and Straight, A.F. (2008) Genome-wide analysis reveals a cell-cycle-dependent mechanism controlling centromere propagation. J. Cell Biology 183, 805-818 (PMC2592830)

  • Smith, C.D., Edgar, R.C., Yandell, M.D., Celniker, S.E., Smith, D.R., Myers, E.W., and Karpen, G.H. (2007) Improved repeat identification and masking in Dipterans. Gene 389, 1-9 (PMC1945102)

  • Peng, J. and Karpen, G.H. (2007) H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nature Cell Biology 9(1), 25-35 (PMC2819265)

  • News & Views: Pikaard, C., and Pontes, O. (2007) Heterochromatin: condense or excise. Nat Cell Biol 9, 19–20

  • Hoskins, R.A*, Carlson, J.W.*, Kennedy, C., Acevedo, D., Evans-Holm, M., Frise, E., Wan, K.H., Park, S., Villasante, A., Mendez, M., Rossi, F., Dimitri, P., Karpen, G.H., and Celniker, S.E. (2007) Sequence finishing and mapping of Drosophila melanogaster heterochromatin. Science 316, 1625-1628 (PMC 2825053)

  • Smith, C.D., Shu, S-Q., Mungall, C.J., and Karpen, G.H. (2007) The Release 5.1 annotation of Drosophila melanogaster heterochromatin. Science 316, 1586-1591 (PMC 2819280)

  • Drosophila 12 Genomes Consortium et al. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-18 (PMC 2919768)

  • Heun , P., Erhardt, S., Blower, M.D., Weiss, S., Skora, A.D., and Karpen, G.H. (2006) Mislocalization of the Drosophila centromere-specific histone CID promotes formation of functional ectopic kinetochores. Developmental Cell 10(3), 303-15 (PMC3192491)

  • Blower, M.D., Daigle, T., Kaufman, T., and Karpen, G.H. (2006) Drosophila CENP-A mutations cause a BubR1-dependent early mitotic delay without normal localization of kinetochore components. PLoS Genetics 2(7), e110 (PMC1500813)

  • Fyodorov, D.V., Blower, M.D., Karpen, G.H., and Kadonaga, J.T. (2004) The ACF chromatin assembly factor affects transcriptional silencing and cell cycle progression. Genes and Development 18(2), 170-183 (PMC324423)

  • Le, H., Donaldson, K., Cook, K. and Karpen, G. H. (2004) A high proportion of mutations that modify position effect variegation also affect chromosome inheritance. Chromosoma 112 (6), 269-276 (PMC3116012)

  • Sullivan, B.A. and Karpen, G.H. (2004) Centromeric chromatin displays histone modification pattern that is distinct from both euchromatin and heterochromatin. Nature Struct. and Mol. Biol. 11, 1076-1083 (PMC1283111)

  • Konev, S., Yan, C., O’Hagan, E., Tickoo, S., and Karpen, G.H. (2003) Genetics of P element transposition into Drosophila centric heterochromatin. Genetics 65, 2039-2053 (PMC1462875)

  • Sun, X. Le, H, Wahlstrom, J., and Karpen, G. H. (2003) Sequence analysis of a functional Drosophila centromere. Genome Research 13, 182–194 (PMC420369)

  • Donaldson, K., Lui, A. and Karpen, G.H. (2002) Modifiers of terminal-deficiency associated position-effect variegation in Drosophila. Genetics 160, 995-1009 (PMC1462006)

  • Blower, M.D., Sullivan, B.A., and Karpen, G.H. (2002) Conserved organization of centromeric chromatin in flies and humans. Developmental Cell 2, 319-330 (PMC3192492).

  • Yan, C.M., Dobie, K., Le, H.D., Konev, A., and Karpen, G.H. (2002) Efficient recovery of centric heterochromatin P insertions in Drosophila. Genetics 161, 217-229 (PMC1462106)

  • Hoskins, R.A., Smith, C.D., Carlson, J.W., Carvalho, A.B., Halpern, A., Kaminker, J.S., Kennedy, C., Mungall, C.J., Sullivan, B.A., Sutton, G.G., Yasuhara, J.C., Wakimoto, B.T., Myers, E.W., Celniker, S.E., Rubin, G.M., and Karpen, G.H. (2002) Heterochromatic sequences in a Drosophila whole genome shotgun assembly. Genome Biology 3(12), research0085.1–0085.16. (PMC151187)

  • Dobie, K., Kennedy, C., Velasco, V. M., McGrath, T. L., Weko, J., Patterson, R.W. and Karpen, G.H. (2001) Identification of chromosome inheritance modifiers in Drosophila melanogaster. Genetics 157, 1623-37 (PMC1461595)

  • Hari, K. L., Cook, K. R., Karpen, G. H. (2001) The Drosophila Su(var)2-10 locus regulates chromosome structure and function and encodes a member of the PIAS protein family. Genes and Development 15, 1334-48 (PMC312712)

  • Maggert, K., Karpen, G. H. (2001) The activation of a neocentromere in Drosophila requires proximity to an endogenous centromere. Genetics 158, 1615-28 (PMC1461751)

  • Blower, M.D. and Karpen, G.H. (2001) The role of Drosophila CENP-A / CID in kinetochore formation, cell-cycle progression and interactions with heterochromatin. Nature Cell Biology 3, 730-9 (PMC3229202)

  • Sullivan, B.A. and Karpen, G.H. (2001) Centromere identity in Drosophila is not determined in vivo by replication timing. J. Cell Biology 154, 683-90 (PMC219645)

  • Lopez, J. M., Karpen, G. H., Orr-Weaver, T. L. (2000) Localization of MEI-S332-dependent sister-chromatid cohesion at the functional centromere. Current Biology 10, 997-1000 (PMID 10985388)

  • Adams, M.D. et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185-2195

  • News: Pennisi, E. (2000) Ideas fly at gene-finding jamboree. Science 287, 2182-2184

  • Williams, B.*, Murphy, T.M.*, Goldberg, M. and Karpen, G.H. (1998) Neocentromere activity of structurally acentric minichromosomes in Drosophila. Nature Genetics 18, 30-37

  • News & Views: Choo, K.H. (1998) Turning on the centromere. Nat Genet 18, 3–4

  • Donaldson, K.M. and Karpen, G.H. (1997) Trans-suppression of terminal deficiency-associated position effect variegation in a Drosophila minichromosome. Genetics 145, 325-337 (PMC1207798)

  • Cook, K., Murphy, T.D., Nguyen, T. and Karpen, G.H. (1997) Identification of trans-acting genes necessary for centromere function in Drosophila melanogaster using centromere-defective minichromosomes. Genetics 145, 737-747 (PMC1207858)

  • Sun, X, Wahlstrom, J. and Karpen, G.H. (1997) Molecular structure of a functional Drosophila centromere. Cell 91, 1007-1019 (PMC3209480)

  • Karpen, G.H., Le, M-H. and Le, H. (1996) Centric heterochromatin and the efficiency of achiasmate meiotic disjunction in Drosophila females. Science 273, 118-122

      • News: Marx, J. (1996) Chromosomes Yield New Clue to Pairing in Meiosis. Science 273, 35

  • Le, M.-H., Duricka, D. and Karpen, G.H. (1995) Islands of complex DNA are widespread in Drosophila melanogaster centric heterochromatin. Genetics 141, 283-303 (PMC1206727)

  • Murphy, T. and Karpen, G.H. (1995a) Interactions between the nod+ kinesin-like gene and extra-centromeric sequences are required for transmission of a Drosophila minichromosome. Cell 81, 139-148

  • Murphy, T. and Karpen, G.H. (1995b) Localization of centromere function in a Drosophila minichromosome. Cell 82, 599-609 (PMC3209481)

  • Thompson-Stewart, D., Karpen, G.H. and Spradling, A.C. (1994) A transposable element can drive the concerted evolution of tandemly repetitious DNA. Proc. Nat. Acad. Sci. 91, 9042-9046 (PMC44743)

  • Tower, J.T., Karpen, G.H., Craig, N. and Spradling, A.C. (1993) Preferential transposition of Drosophila P elements to nearby chromosomal sites. Genetics 133, 347-359

  • Glaser, B., Karpen, G.H. and Spradling, A.C. (1992) Replication forks are not found in a Drosophila minichromosome demonstrating a gradient of polytenization. Chromosoma 102, 15-19

  • Karpen, G.H. and Spradling, A.C. (1992) Analysis of subtelomeric heterochromatin in the Drosophila minichromosome Dp1187 by single P-element insertional mutagenesis. Genetics 132, 737-753

  • Karpen, G.H. and Spradling, A.C. (1990) Reduced DNA polytenization of a minichromosome region undergoing position-effect variegation in Drosophila. Cell 63, 97-107

  • McKee, B.M. and Karpen, G.H. (1990) Drosophila ribosomal RNA genes function as an X-Y pairing site during meiosis. Cell 61, 61-72

  • Karpen, G.H., Schaeffer, J. and Laird, C.D. (1988) A Drosophila rRNA gene located in euchromatin is active in transcription and nucleolus formation. Genes and Development 2, 1745-1763

  • Laird C, Jaffe E, Karpen G, Lamb M, Nelson R. (1988) Enigmatic fragile sites on human-chromosomes - Reply. Trends Genet. 4(5):121-2

  • Laird, C., Jaffe, E., Karpen, G., Lamb, M. and Nelson, R. (1987) Fragile sites in human chromosomes as regions of late-replicating DNA. Trends in Genetics 3, 274-281

  • Karpen, G.H. and Schubiger, G. (1981) Extensive Regulatory Capabilities of a Drosophila Imaginal Disk Blastema. Nature 294, 744-747

  • Abbott, L.C., Karpen, G.H. and Schubiger, G. (1981) Compartmental Restrictions and Blastema Formation during Pattern Regulation in Drosophila Imaginal Leg Discs. Developmental Biology 87, 64-75.

Reviews & Book Chapters


  • Janssen, A., Colmenares, S.U., and Karpen, G.H. (2018) Heterochromatin: Guardian of the Genome. Annu Rev Cell Dev Biol 34, 265–288 (PMID 30044650)

  • Rout, M. P. & Karpen, G. H. (2014) Editorial overview: Cell nucleus: The nucleus: a dynamic organelle. Current Opinion in Cell Biology 28, iv-vii (PMID 24908378).

  • Editor Molecular Biology of the Cell December 1, 2014 by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter

  • Dunleavy, E.M., Zhang, W., and Karpen, G.H. (2013) Solo or doppio: how many CENP-As make a centromeric nucleosome? Nature Structural & Molecular Biology 20, 648–650.

  • Earnshaw WC, Allshire RC, Black BE, Bloom K, Brinkley BR, Brown W, Cheeseman IM, Choo KH, Copenhaver GP, Deluca JG, Desai A, Diekmann S, Erhardt S, Fitzgerald-Hayes M, Foltz D, Fukagawa T, Gassmann R, Gerlich DW, Glover DM, Gorbsky GJ, Harrison SC, Heun P, Hirota T, Jansen LE, Karpen G, Kops GJ, Lampson MA, Lens SM, Losada A, Luger K, Maiato H, Maddox PS, Margolis RL, Masumoto H, McAinsh AD, Mellone BG, Meraldi P, Musacchio A, Oegema K, O'Neill RJ, Salmon ED, Scott KC, Straight AF, Stukenberg PT, Sullivan BA, Sullivan KF, Sunkel CE, Swedlow JR, Walczak CE, Warburton PE, Westermann S, Willard HF, Wordeman L, Yanagida M, Yen TJ, Yoda K, Cleveland DW. (2013) Esperanto for histones: CENP-A, not CenH3, is the centromeric histone H3 variant. Chromosome Research 21(2), 101-06 (PMC3627038)

  • Karpen, G.H. (2009) Preparation and Analysis of High-molecular-weight DNA in Drosophila. In Drosophila Protocols (Sullivan, W., Ashburner, M. and Hawley, R.S., eds.), CSH Press.

  • Mellone, B.G., W. Zhang, and Karpen, G.H. (2009) Frodos found: Behold the CENP-a "Ring" bearers. Cell 137(3): p. 409-12 (PMC3192489)

  • Peng, J. and Karpen, G.H. (2008) Epigenetic regulation of heterochromatic DNA stability. Current Opinion in Genetics & Development 18, 204-11. (PMC2814359)

  • Karpen, G.H. and Allshire, R.C. (2008) Epigenetic Regulation of Centromeric Chromatin: Old Dogs, New Tricks? Nature Reviews Genetics 9, 923-937. (PMC2586333)

  • Zhang, W., Mellone, B.G. and Karpen, G.H. (2007) A Specialized Nucleosome Has a “Point” to Make. Cell 129, 5-7 (PMC2950099)

  • Karpen, G.H. (2002). Preparation and Analysis of High-molecular-weight DNA in Drosophila. In Drosophila Protocols (Sullivan, W., Ashburner, M. and Hawley, R.S., eds.) CSH Press.

  • Sullivan, B.A, Blower, M.D. and Karpen, G.H. (2001) Determining Centromere Identity: Cyclical Stories and Forking Paths. Nature Reviews Genetics 2, 584-96

  • Dernburg, A.F. and Karpen, G.H. (2002) A Chromosome RNAissance. Cell 111, 159-162

  • Karpen, G.H. (2004) D. melanogaster genetics. Ergito Virtual Text. http://www.ergito.com

  • Karpen, G.H. and Hawley, R.S. (2006) Epigenetic Regulation of Chromosome Inheritance. In Epigenetics, CSH Press

  • Mellone, B., Erhardt, S., and Karpen, G.H. (2006) The ABCs of Centromeres. Nature Cell Biology 8(5), 427-429.

  • Maggert, K.A. and Karpen, G.H. (2000) Acquisition and metastability of centromere identity and function: sequence analysis of a human neocentromere. Genome Res. 10(6), 725-728

  • Dobie, K., Hari, K., Maggert, K. and Karpen, G. (1999) Centromere proteins and chromosome inheritance: a complex affair. Current Opinions in Genetics and Development 9, 206-217

  • Murphy, T.D. and Karpen, G.H. (1998) Centromeres Take Flight: Alpha Satellite and the Quest for the Human Centromere. Cell 93, 317-320

  • Karpen, G.H. and Endow, S.A. (1998) Meiosis: Chromosome Behaviour and Spindle Dynamics. In Frontiers in Biology (S.A. Endow and D. Glover, eds.), Oxford University Press

  • Karpen, G.H. and Allshire, R.C. (1997) The Case for Epigenetic Regulation of Centromere Function. Trends in Genetics 13 (12), 489-496

  • Karpen, G.H. (1994) Position-effect variegation and the new biology of heterochromatin. Current Opinions in Genetics and Development 4, 281-91

  • Cook KR, Karpen GH (1994) A rosy future for heterochromatin. PNAS 91, 5219-21 (PMC43965)

  • Spradling, A.C., Karpen, G.H., Glaser, R. and Zhang, P. (1992) Evolutionary conservation of developmental mechanisms: DNA elimination in Drosophila. 50th Annual Symposium, Society for Developmental Biology, Wiley-Liss, New York, pp. 39-53

  • Spradling AC, Karpen GH (1990) 60 Years of Mystery. Genetics. 126, 779-84 (PMC1204277)

  • Wakimoto, B.T. and Karpen, G.H. (1988) Transposable Elements and Germ-line Transformation in Drosophila, in Developmental Genetics of Higher Organisms (Malacinski, G.M., ed.), Macmillan Publishing Co., Inc., New York

  • Schubiger, G. and Karpen, G.H. (1983) Blastema formation in regulating imaginal disc fragments of Drosophila melanogaster. Progress in Clinical and Biological Research 110, 609-18