bioRxiv:
Research papers:
Kapur, I., Boulier, E., & Francis, N.J. (2022) Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding. Epigenomes 640. doi: 10.3390/epigenomes6040040
Vanzan, L., Soldati, H., Ythier, Anand, S., Braunm, S., Francis, N. J. & Murr, R. (2021) High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat Commun 12, 3337. https://doi.org/10.1038/s41467-021-23630-x
Francis, N. J. & Sihou, D. (2021) Inheritance of Histone (H3/H4): A Binary Choice? Trends in Biochemical Sciences vol. 46 5–14. https://doi.org/10.1016/j.tibs.2020.08.009
Seif, E. Kang, J.J., Sasseville, C., Senkovich, O., Kaltashov, A., Boulier, E.L., Kapur, I., Kim, C.A., & Francis, N.J. (2020) Phase separation by the Sterile Alpha Motif of Polyhomeotic compartmentalizes Polycomb Group proteins and enhances their activity. Nat Commun 11, 5609. https://doi.org/10.1038/s41467-020-19435-z
Kang, J.J., Faubert, D., Boulais, J., & Francis, N.J. (2020) DNA binding reorganizes the C-terminal region of PSC in Drosophila PRC1. J. Mol. Biol. 432(17), 4856-4871. https://doi.org/10.1016/j.jmb.2020.07.002
Alecki, C., Chiwara, V., Sanz, L. A., Grau, D., Pérez, O. A., Boulier, E. L., Armache, K.-J., Chédin, F., & Francis, N. J. (2020). RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2. Nat. Commun. , 11(1), 1–14. https://rdcu.be/b3y5P
Madamba, E.V., Berthet, E.B., and Francis, N.J. (2017) Inheritance of histones H3 and H4 during DNA replication in vitro. Cell Reports 5: 1361-1374 PMID 29091772. https://doi.org/10.1016/j.celrep.2017.10.033
Wani, A.H.*, Boettiger, A.N.*, Schorderet, P., Ergun, A., Munger, C., Sadreyev, R.I., Zhuang, X., Kingston, R.E., and Francis, N.J. (2016) Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat. Commun. 13:10291 PMID 26759081. https://doi.org/10.1038/ncomms10291
Follmer, N.E., Wani, A.H. and Francis, N.J. (2012) Polycomb Group proteins are retained at specific sites on chromatin in mitosis. PLoS Genet 8(12): e1003135. https://doi.org/10.1371/journal.pgen.1003135
Lo, S.M., McElroy, K.A. and Francis, N.J. (2012) Chromatin modification by PSC occurs at one PSC per nucleosome and does not require the acidic patch of histone H2A. PLoS ONE 7(10): e47162. PMID: 23071745. https://doi.org/10.1371/journal.pone.0047162
Lengsfeld, B.M., Berry, K.N., Ghosh, S., Takahashi, M., and Francis, N.J. (2012) A Polycomb complex remains bound through DNA replication in the absence of other eukaryotic proteins. Sci. Rep. 2: 661. PMID:22993687. https://doi.org/10.1038/srep00661
Lo, S.M.*, Follmer, N.E.*, Lengsfeld, B.M., Madamba, E.V., Seong, S., Grau, D.J., and Francis, N.J. (2012) A Bridging model for persistence of a Polycomb Group protein complex through DNA replication. Mol. Cell 46: 784-796. PMID: 22749399. https://doi.org/10.1016/j.molcel.2012.05.038
Beh, L.Y., Colwell, L.J., and Francis, N.J. (2012) A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence. PNAS, 109(18):E1063-71. PMID:22517748. https://doi.org/10.1073/pnas.1118678109
Grau, D.J., Chapman, B.A., Garlick, J.D., Borowsky, M., Francis, N.J., Kingston, R.E. (2011) Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev., 25:2210-21. PMID: 22012622. http://www.genesdev.org/cgi/doi/10.1101/gad.17288211
Lo, S.M. and Francis, N.J. (2010) Inhibition of Chromatin Remodeling by Polycomb Group Protein Posterior Sex Combs Is Mechanistically Distinct from Nucleosome Binding. Biochemistry 49:9438-9448. PMID: 20873869. https://doi.org/10.1021/bi100532a
Francis, N.J., Follmer, N.E., Simon, M.D., Aghia, G., and Butler, J.D. (2009) Polycomb proteins remain bound to chromatin and DNA during replication in vitro. Cell, 137: 110-122. PMID: 19303136. https://doi.org/10.1016/j.cell.2009.02.017
Lo, S.M., Ahuja, N.K., Francis, N.J. (2009) Polycomb group protein Suppressor 2 of zeste is a functional homolog of Posterior Sex Combs. Mol. Cell. Biol. 29: 515-525. PMID: 18981224. https://doi.org/10.1128/MCB.01044-08
Research papers before 2006:
King, I.F.G.*, Emmons, R.B.*, Francis, N.J.*, Wild, B., Mueller, J., Kingston, R.E., Wu, C.-t. (2005) Analysis of a Polycomb Group protein defines regions that link repressive activity on nucleosomal templates to in vivo function. Mol. Cell. Biol. https://doi.org/10.1128/MCB.25.15.6578-6591.2005
Francis, N.J., Kingston, R.E., and Woodcock, C.L. (2004) Chromatin compaction by a Polycomb group protein complex. Science 306:1574-1577. https://doi.org/10.1126/science.1100576
Lavigne, M., Francis, N.J., King, I.F., and Kingston, R.E. (2004) Propagation of silencing; recruitment and repression of naïve chromatin in trans by polycomb repressed chromatin. Mol. Cell 13: 415-425. https://doi.org/10.1016/S1097-2765(04)00006-1
Muller, J.*, Hart, C.M.*, Francis, N.J.*, Vargas, M.L., Sengupta, A., Wild,B., Miller, E.L., O'Connor, M.B., Kingston, R.E., and Simon, J.A. (2002) Histone methyltransferase activity of a Drosophila Polycomb Group repressor complex. Cell, 111:197-208. https://doi.org/10.1016/S0092-8674(02)00976-5
Francis. N.J., Saurin, A.J., Shao, Z. and Kingston, R.E. (2001) Reconstitution of a functional core Polycomb repressive complex. Mol. Cell, 8: 545-556. https://doi.org/10.1016/S1097-2765(01)00316-1
Reviews and commentary:
Francis, N.J. and Sihou, D. (2020) Inheritance of Histone (H3/H4): A Binary Choice? TIBS, https://www.sciencedirect.com/science/article/pii/S0968000420302061
Kim, C.A. and Francis, N.J. (2016) Chromatin: Polycomb Group SAMs unite. Current Biology, 26, R710-2 https://doi.org/10.1016/j.cub.2016.06.001
Follmer, N.E. and Francis, N.J. (2011) Speed reading for genes: bookmarks set the pace. Developmental Cell 21: 807-808. https://doi.org/10.1016/j.devcel.2011.10.020
Francis, N.J. (2011) Gene regulation: implications of histone dispersal patterns for epigenetics. Current Biology, 21: R659-661. https://doi.org/10.1016/j.cub.2011.06.062
Francis, N.J. (2009) Mechanisms of epigenetic inheritance: copying of Polycomb repressed chromatin. Cell Cycle 8: 3513-3518. https://doi.org/10.4161/cc.8.21.9876
Francis, N.J. (2009) Does maintenance of Polycomb Group proteins through DNA replication contribute to epigenetic inheritance? Epigenetics. 2009 Aug 26;4(6). https://doi.org/10.4161/epi.4.6.9374
Francis, N.J. and Kingston, R.E. (2001) Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol. 2, 409-421. https://doi.org/10.1038/35073039
Protocols:
Alecki, C. & Francis, N. J. (2021). Identification of R-loop-forming Sequences in Drosophila melanogaster Embryos and Tissue Culture Cells Using DRIP-seq. BIO-PROTOCOL 11(9): e4011.
doi: 10.21769/BioProtoc.4011
Research papers:
Kapur, I., Boulier, E., & Francis, N.J. (2022) Regulation of Polyhomeotic Condensates by Intrinsically Disordered Sequences That Affect Chromatin Binding. Epigenomes 640. doi: 10.3390/epigenomes6040040
Vanzan, L., Soldati, H., Ythier, Anand, S., Braunm, S., Francis, N. J. & Murr, R. (2021) High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites. Nat Commun 12, 3337. https://doi.org/10.1038/s41467-021-23630-x
Francis, N. J. & Sihou, D. (2021) Inheritance of Histone (H3/H4): A Binary Choice? Trends in Biochemical Sciences vol. 46 5–14. https://doi.org/10.1016/j.tibs.2020.08.009
Seif, E. Kang, J.J., Sasseville, C., Senkovich, O., Kaltashov, A., Boulier, E.L., Kapur, I., Kim, C.A., & Francis, N.J. (2020) Phase separation by the Sterile Alpha Motif of Polyhomeotic compartmentalizes Polycomb Group proteins and enhances their activity. Nat Commun 11, 5609. https://doi.org/10.1038/s41467-020-19435-z
Kang, J.J., Faubert, D., Boulais, J., & Francis, N.J. (2020) DNA binding reorganizes the C-terminal region of PSC in Drosophila PRC1. J. Mol. Biol. 432(17), 4856-4871. https://doi.org/10.1016/j.jmb.2020.07.002
Alecki, C., Chiwara, V., Sanz, L. A., Grau, D., Pérez, O. A., Boulier, E. L., Armache, K.-J., Chédin, F., & Francis, N. J. (2020). RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2. Nat. Commun. , 11(1), 1–14. https://rdcu.be/b3y5P
Madamba, E.V., Berthet, E.B., and Francis, N.J. (2017) Inheritance of histones H3 and H4 during DNA replication in vitro. Cell Reports 5: 1361-1374 PMID 29091772. https://doi.org/10.1016/j.celrep.2017.10.033
Wani, A.H.*, Boettiger, A.N.*, Schorderet, P., Ergun, A., Munger, C., Sadreyev, R.I., Zhuang, X., Kingston, R.E., and Francis, N.J. (2016) Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat. Commun. 13:10291 PMID 26759081. https://doi.org/10.1038/ncomms10291
Follmer, N.E., Wani, A.H. and Francis, N.J. (2012) Polycomb Group proteins are retained at specific sites on chromatin in mitosis. PLoS Genet 8(12): e1003135. https://doi.org/10.1371/journal.pgen.1003135
Lo, S.M., McElroy, K.A. and Francis, N.J. (2012) Chromatin modification by PSC occurs at one PSC per nucleosome and does not require the acidic patch of histone H2A. PLoS ONE 7(10): e47162. PMID: 23071745. https://doi.org/10.1371/journal.pone.0047162
Lengsfeld, B.M., Berry, K.N., Ghosh, S., Takahashi, M., and Francis, N.J. (2012) A Polycomb complex remains bound through DNA replication in the absence of other eukaryotic proteins. Sci. Rep. 2: 661. PMID:22993687. https://doi.org/10.1038/srep00661
Lo, S.M.*, Follmer, N.E.*, Lengsfeld, B.M., Madamba, E.V., Seong, S., Grau, D.J., and Francis, N.J. (2012) A Bridging model for persistence of a Polycomb Group protein complex through DNA replication. Mol. Cell 46: 784-796. PMID: 22749399. https://doi.org/10.1016/j.molcel.2012.05.038
Beh, L.Y., Colwell, L.J., and Francis, N.J. (2012) A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence. PNAS, 109(18):E1063-71. PMID:22517748. https://doi.org/10.1073/pnas.1118678109
Grau, D.J., Chapman, B.A., Garlick, J.D., Borowsky, M., Francis, N.J., Kingston, R.E. (2011) Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge. Genes Dev., 25:2210-21. PMID: 22012622. http://www.genesdev.org/cgi/doi/10.1101/gad.17288211
Lo, S.M. and Francis, N.J. (2010) Inhibition of Chromatin Remodeling by Polycomb Group Protein Posterior Sex Combs Is Mechanistically Distinct from Nucleosome Binding. Biochemistry 49:9438-9448. PMID: 20873869. https://doi.org/10.1021/bi100532a
Francis, N.J., Follmer, N.E., Simon, M.D., Aghia, G., and Butler, J.D. (2009) Polycomb proteins remain bound to chromatin and DNA during replication in vitro. Cell, 137: 110-122. PMID: 19303136. https://doi.org/10.1016/j.cell.2009.02.017
Lo, S.M., Ahuja, N.K., Francis, N.J. (2009) Polycomb group protein Suppressor 2 of zeste is a functional homolog of Posterior Sex Combs. Mol. Cell. Biol. 29: 515-525. PMID: 18981224. https://doi.org/10.1128/MCB.01044-08
Research papers before 2006:
King, I.F.G.*, Emmons, R.B.*, Francis, N.J.*, Wild, B., Mueller, J., Kingston, R.E., Wu, C.-t. (2005) Analysis of a Polycomb Group protein defines regions that link repressive activity on nucleosomal templates to in vivo function. Mol. Cell. Biol. https://doi.org/10.1128/MCB.25.15.6578-6591.2005
Francis, N.J., Kingston, R.E., and Woodcock, C.L. (2004) Chromatin compaction by a Polycomb group protein complex. Science 306:1574-1577. https://doi.org/10.1126/science.1100576
Lavigne, M., Francis, N.J., King, I.F., and Kingston, R.E. (2004) Propagation of silencing; recruitment and repression of naïve chromatin in trans by polycomb repressed chromatin. Mol. Cell 13: 415-425. https://doi.org/10.1016/S1097-2765(04)00006-1
Muller, J.*, Hart, C.M.*, Francis, N.J.*, Vargas, M.L., Sengupta, A., Wild,B., Miller, E.L., O'Connor, M.B., Kingston, R.E., and Simon, J.A. (2002) Histone methyltransferase activity of a Drosophila Polycomb Group repressor complex. Cell, 111:197-208. https://doi.org/10.1016/S0092-8674(02)00976-5
Francis. N.J., Saurin, A.J., Shao, Z. and Kingston, R.E. (2001) Reconstitution of a functional core Polycomb repressive complex. Mol. Cell, 8: 545-556. https://doi.org/10.1016/S1097-2765(01)00316-1
Reviews and commentary:
Francis, N.J. and Sihou, D. (2020) Inheritance of Histone (H3/H4): A Binary Choice? TIBS, https://www.sciencedirect.com/science/article/pii/S0968000420302061
Kim, C.A. and Francis, N.J. (2016) Chromatin: Polycomb Group SAMs unite. Current Biology, 26, R710-2 https://doi.org/10.1016/j.cub.2016.06.001
Follmer, N.E. and Francis, N.J. (2011) Speed reading for genes: bookmarks set the pace. Developmental Cell 21: 807-808. https://doi.org/10.1016/j.devcel.2011.10.020
Francis, N.J. (2011) Gene regulation: implications of histone dispersal patterns for epigenetics. Current Biology, 21: R659-661. https://doi.org/10.1016/j.cub.2011.06.062
Francis, N.J. (2009) Mechanisms of epigenetic inheritance: copying of Polycomb repressed chromatin. Cell Cycle 8: 3513-3518. https://doi.org/10.4161/cc.8.21.9876
Francis, N.J. (2009) Does maintenance of Polycomb Group proteins through DNA replication contribute to epigenetic inheritance? Epigenetics. 2009 Aug 26;4(6). https://doi.org/10.4161/epi.4.6.9374
Francis, N.J. and Kingston, R.E. (2001) Mechanisms of transcriptional memory. Nat. Rev. Mol. Cell Biol. 2, 409-421. https://doi.org/10.1038/35073039
Protocols:
Alecki, C. & Francis, N. J. (2021). Identification of R-loop-forming Sequences in Drosophila melanogaster Embryos and Tissue Culture Cells Using DRIP-seq. BIO-PROTOCOL 11(9): e4011.
doi: 10.21769/BioProtoc.4011