TY - JOUR AU - Boyle, A. P. AU - Davis, S. AU - Shulha, H. P. AU - Meltzer, P. AU - Margulies, E. H. AU - Weng, Z. AU - Furey, T. S. AU - Crawford, G. E. PY - 2008 DA - 2008// TI - High-resolution mapping and characterization of open chromatin across the genome JO - Cell VL - 132 UR - https://doi.org/10.1016/j.cell.2007.12.014 DO - 10.1016/j.cell.2007.12.014 ID - Boyle2008 ER - TY - JOUR AU - Crawford, G. E. AU - Holt, I. E. AU - Whittle, J. AU - Webb, B. D. AU - Tai, D. AU - Davis, S. AU - Margulies, E. H. AU - Chen, Y. AU - Bernat, J. A. AU - Ginsburg, D. PY - 2006 DA - 2006// TI - Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS) JO - Genome Res VL - 16 UR - https://doi.org/10.1101/gr.4074106 DO - 10.1101/gr.4074106 ID - Crawford2006 ER - TY - JOUR AU - Jessen, W. J. AU - Dhasarathy, A. AU - Hoose, S. A. AU - Carvin, C. D. AU - Risinger, A. L. AU - Kladde, M. P. PY - 2004 DA - 2004// TI - Mapping chromatin structure in vivo using DNA methyltransferases JO - Methods VL - 33 UR - https://doi.org/10.1016/j.ymeth.2003.10.025 DO - 10.1016/j.ymeth.2003.10.025 ID - Jessen2004 ER - TY - JOUR AU - Kladde, M. P. AU - Simpson, R. T. PY - 1994 DA - 1994// TI - Positioned nucleosomes inhibit Dam methylation in vivo JO - Proc Natl Acad Sci USA VL - 91 UR - https://doi.org/10.1073/pnas.91.4.1361 DO - 10.1073/pnas.91.4.1361 ID - Kladde1994 ER - TY - JOUR AU - Wines, D. R. AU - Talbert, P. B. AU - Clark, D. V. AU - Henikoff, S. PY - 1996 DA - 1996// TI - Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo JO - Chromosoma VL - 104 UR - https://doi.org/10.1007/BF00337221 DO - 10.1007/BF00337221 ID - Wines1996 ER - TY - JOUR AU - Flick, J. T. AU - Eissenberg, J. C. AU - Elgin, S. C. R. PY - 1986 DA - 1986// TI - Micrococcal nuclease as a DNA structural probe: Its recognition sequences, their genomic distribution and correlation with DNA structure determinants JO - Journal of Molecular Biology VL - 190 UR - https://doi.org/10.1016/0022-2836(86)90247-0 DO - 10.1016/0022-2836(86)90247-0 ID - Flick1986 ER - TY - JOUR AU - Yuan, G. AU - Liu, Y. AU - Dion, M. F. AU - Slack, M. D. AU - Wu, L. F. AU - Altschuler, S. J. AU - Rando, O. J. PY - 2005 DA - 2005// TI - Genome-scale identification of nucleosome positions in S. cerevisiae JO - Science VL - 309 UR - https://doi.org/10.1126/science.1112178 DO - 10.1126/science.1112178 ID - Yuan2005 ER - TY - JOUR AU - Wingert, L. AU - Von Hippel, P. H. PY - 1968 DA - 1968// TI - The conformation dependent hydrolysis of DNA by micrococcal nuclease JO - Biochim Biophys Acta VL - 157 UR - https://doi.org/10.1016/0005-2787(68)90270-0 DO - 10.1016/0005-2787(68)90270-0 ID - Wingert1968 ER - TY - JOUR AU - Horz, W. AU - Altenburger, W. PY - 1981 DA - 1981// TI - Sequence specific cleavage of DNA by micrococcal nuclease JO - Nucleic Acids Res VL - 9 UR - https://doi.org/10.1093/nar/9.12.2643 DO - 10.1093/nar/9.12.2643 ID - Horz1981 ER - TY - JOUR AU - McGhee, J. D. AU - Felsenfeld, G. PY - 1983 DA - 1983// TI - Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease JO - Cell VL - 32 UR - https://doi.org/10.1016/0092-8674(83)90303-3 DO - 10.1016/0092-8674(83)90303-3 ID - McGhee1983 ER - TY - JOUR AU - Shi, B. AU - Guo, X. AU - Wu, T. AU - Sheng, S. AU - Wang, J. AU - Skogerbo, G. AU - Zhu, X. AU - Chen, R. PY - 2009 DA - 2009// TI - Genome-scale identification of Caenorhabditis elegans regulatory elements by tiling-array mapping of DNase I hypersensitive sites JO - BMC Genomics VL - 10 UR - https://doi.org/10.1186/1471-2164-10-92 DO - 10.1186/1471-2164-10-92 ID - Shi2009 ER - TY - JOUR AU - Parker, S. C. AU - Hansen, L. AU - Abaan, H. O. AU - Tullius, T. D. AU - Margulies, E. H. PY - 2009 DA - 2009// TI - Local DNA topography correlates with functional noncoding regions of the human genome JO - Science VL - 324 UR - https://doi.org/10.1126/science.1169050 DO - 10.1126/science.1169050 ID - Parker2009 ER - TY - JOUR AU - Widlak, P. AU - Garrard, W. T. PY - 2006 DA - 2006// TI - Unique features of the apoptotic endonuclease DFF40/CAD relative to micrococcal nuclease as a structural probe for chromatin JO - Biochem Cell Biol VL - 84 UR - https://doi.org/10.1139/o06-063 DO - 10.1139/o06-063 ID - Widlak2006 ER - TY - JOUR AU - Cartwright, I. L. AU - Hertzberg, R. P. AU - Dervan, P. B. AU - Elgin, S. C. PY - 1983 DA - 1983// TI - Cleavage of chromatin with methidiumpropyl-EDTA. iron(II) JO - Proc Natl Acad Sci USA VL - 80 UR - https://doi.org/10.1073/pnas.80.11.3213 DO - 10.1073/pnas.80.11.3213 ID - Cartwright1983 ER - TY - JOUR AU - Gargiulo, G. AU - Levy, S. AU - Bucci, G. AU - Romanenghi, M. AU - Fornasari, L. AU - Beeson, K. Y. AU - Goldberg, S. M. AU - Cesaroni, M. AU - Ballarini, M. AU - Santoro, F. PY - 2009 DA - 2009// TI - NA-Seq: a discovery tool for the analysis of chromatin structure and dynamics during differentiation JO - Dev Cell VL - 16 UR - https://doi.org/10.1016/j.devcel.2009.02.002 DO - 10.1016/j.devcel.2009.02.002 ID - Gargiulo2009 ER - TY - JOUR AU - Barras, F. AU - Marinus, M. G. PY - 1989 DA - 1989// TI - The great GATC: DNA methylation in E. coli JO - Trends Genet VL - 5 UR - https://doi.org/10.1016/0168-9525(89)90054-1 DO - 10.1016/0168-9525(89)90054-1 ID - Barras1989 ER - TY - JOUR AU - Lobner-Olesen, A. AU - Skovgaard, O. AU - Marinus, M. G. PY - 2005 DA - 2005// TI - Dam methylation: coordinating cellular processes JO - Curr Opin Microbiol VL - 8 UR - https://doi.org/10.1016/j.mib.2005.02.009 DO - 10.1016/j.mib.2005.02.009 ID - Lobner-Olesen2005 ER - TY - JOUR AU - Palmer, B. R. AU - Marinus, M. G. PY - 1994 DA - 1994// TI - The dam and dcm strains of Escherichia coli--a review JO - Gene VL - 143 UR - https://doi.org/10.1016/0378-1119(94)90597-5 DO - 10.1016/0378-1119(94)90597-5 ID - Palmer1994 ER - TY - JOUR AU - Buryanov, Y. AU - Shevchuk, T. PY - 2005 DA - 2005// TI - The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology JO - Anal Biochem VL - 338 UR - https://doi.org/10.1016/j.ab.2004.02.048 DO - 10.1016/j.ab.2004.02.048 ID - Buryanov2005 ER - TY - JOUR AU - van Steensel, B. AU - Delrow, J. AU - Henikoff, S. PY - 2001 DA - 2001// TI - Chromatin profiling using targeted DNA adenine methyltransferase JO - Nat Genet VL - 27 UR - https://doi.org/10.1038/85871 DO - 10.1038/85871 ID - van Steensel2001 ER - TY - JOUR AU - van Steensel, B. AU - Henikoff, S. PY - 2000 DA - 2000// TI - Identification of in vivo DNA targets of chromatin proteins using tethered dam methyltransferase JO - Nat Biotechnol VL - 18 UR - https://doi.org/10.1038/74487 DO - 10.1038/74487 ID - van Steensel2000 ER - TY - JOUR AU - Bulanenkova, S. AU - Snezhkov, E. AU - Nikolaev, L. AU - Sverdlov, E. PY - 2007 DA - 2007// TI - Identification and mapping of open chromatin regions within a 140 kb polygenic locus of human chromosome 19 using E. coli Dam methylase JO - Genetica VL - 130 UR - https://doi.org/10.1007/s10709-006-0026-1 DO - 10.1007/s10709-006-0026-1 ID - Bulanenkova2007 ER - TY - JOUR AU - Boivin, A. AU - Dura, J. M. PY - 1998 DA - 1998// TI - In vivo chromatin accessibility correlates with gene silencing in Drosophila JO - Genetics VL - 150 ID - Boivin1998 ER - TY - JOUR AU - Kyrion, G. AU - Liu, K. AU - Liu, C. AU - Lustig, A. J. PY - 1993 DA - 1993// TI - RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae JO - Genes Dev VL - 7 UR - https://doi.org/10.1101/gad.7.7a.1146 DO - 10.1101/gad.7.7a.1146 ID - Kyrion1993 ER - TY - JOUR AU - Naumova, N. M. AU - Olenkina, O. M. AU - Gvozdev, V. A. PY - 2003 DA - 2003// TI - [Inactivation of reporter genes by cloned heterochromatic repeats of Drosophila melanogaster is accompanied by chromatin compaction] JO - Genetika VL - 39 ID - Naumova2003 ER - TY - JOUR AU - Hoekstra, M. F. AU - Malone, R. E. PY - 1985 DA - 1985// TI - Expression of the Escherichia coli dam methylase in Saccharomyces cerevisiae: effect of in vivo adenine methylation on genetic recombination and mutation JO - Mol Cell Biol VL - 5 UR - https://doi.org/10.1128/MCB.5.4.610 DO - 10.1128/MCB.5.4.610 ID - Hoekstra1985 ER - TY - JOUR AU - Nakai, H. AU - Storm, T. A. AU - Kay, M. A. PY - 2000 DA - 2000// TI - Recruitment of single-stranded recombinant adeno-associated virus vector genomes and intermolecular recombination are responsible for stable transduction of liver in vivo JO - J Virol VL - 74 UR - https://doi.org/10.1128/JVI.74.20.9451-9463.2000 DO - 10.1128/JVI.74.20.9451-9463.2000 ID - Nakai2000 ER - TY - JOUR AU - Okkema, P. G. AU - Harrison, S. W. AU - Plunger, V. AU - Aryana, A. AU - Fire, A. PY - 1993 DA - 1993// TI - Sequence requirements for myosin gene expression and regulation in Caenorhabditis elegans JO - Genetics VL - 135 ID - Okkema1993 ER - TY - JOUR AU - Granato, M. AU - Schnabel, H. AU - Schnabel, R. PY - 1994 DA - 1994// TI - pha-1, a selectable marker for gene transfer in C. elegans JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.9.1762 DO - 10.1093/nar/22.9.1762 ID - Granato1994 ER - TY - JOUR AU - Ardizzi, J. P. AU - Epstein, H. F. PY - 1987 DA - 1987// TI - Immunochemical localization of myosin heavy chain isoforms and paramyosin in developmentally and structurally diverse muscle cell types of the nematode Caenorhabditis elegans JO - J Cell Biol VL - 105 UR - https://doi.org/10.1083/jcb.105.6.2763 DO - 10.1083/jcb.105.6.2763 ID - Ardizzi1987 ER - TY - JOUR AU - Fire, A. AU - Xu, S. AU - Montgomery, M. K. AU - Kostas, S. A. AU - Driver, S. E. AU - Mello, C. C. PY - 1998 DA - 1998// TI - Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans JO - Nature VL - 391 UR - https://doi.org/10.1038/35888 DO - 10.1038/35888 ID - Fire1998 ER - TY - JOUR AU - Krause, M. AU - Hirsh, D. PY - 1987 DA - 1987// TI - A trans-spliced leader sequence on actin mRNA in C. elegans JO - Cell VL - 49 UR - https://doi.org/10.1016/0092-8674(87)90613-1 DO - 10.1016/0092-8674(87)90613-1 ID - Krause1987 ER - TY - JOUR AU - Nelson, D. W. AU - Honda, B. M. PY - 1989 DA - 1989// TI - Two highly conserved transcribed regions in the 5S DNA repeats of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae JO - Nucleic Acids Res VL - 17 UR - https://doi.org/10.1093/nar/17.21.8657 DO - 10.1093/nar/17.21.8657 ID - Nelson1989 ER - TY - JOUR AU - Hunt-Newbury, R. AU - Viveiros, R. AU - Johnsen, R. AU - Mah, A. AU - Anastas, D. AU - Fang, L. AU - Halfnight, E. AU - Lee, D. AU - Lin, J. AU - Lorch, A. PY - 2007 DA - 2007// TI - High-throughput in vivo analysis of gene expression in Caenorhabditis elegans JO - PLoS Biol VL - 5 UR - https://doi.org/10.1371/journal.pbio.0050237 DO - 10.1371/journal.pbio.0050237 ID - Hunt-Newbury2007 ER - TY - JOUR AU - Valouev, A. AU - Ichikawa, J. AU - Tonthat, T. AU - Stuart, J. AU - Ranade, S. AU - Peckham, H. AU - Zeng, K. AU - Malek, J. A. AU - Costa, G. AU - McKernan, K. PY - 2008 DA - 2008// TI - A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning JO - Genome Res VL - 18 UR - https://doi.org/10.1101/gr.076463.108 DO - 10.1101/gr.076463.108 ID - Valouev2008 ER - TY - JOUR AU - Gu, S. G. AU - Fire, A. PY - 2009 DA - 2009// TI - Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning JO - Chromosoma VL - 119 UR - https://doi.org/10.1007/s00412-009-0235-3 DO - 10.1007/s00412-009-0235-3 ID - Gu2009 ER - TY - JOUR AU - Grewal, S. I. AU - Moazed, D. PY - 2003 DA - 2003// TI - Heterochromatin and epigenetic control of gene expression JO - Science VL - 301 UR - https://doi.org/10.1126/science.1086887 DO - 10.1126/science.1086887 ID - Grewal2003 ER - TY - JOUR AU - Barski, A. AU - Cuddapah, S. AU - Cui, K. AU - Roh, T. Y. AU - Schones, D. E. AU - Wang, Z. AU - Wei, G. AU - Chepelev, I. AU - Zhao, K. PY - 2007 DA - 2007// TI - High-resolution profiling of histone methylations in the human genome JO - Cell VL - 129 UR - https://doi.org/10.1016/j.cell.2007.05.009 DO - 10.1016/j.cell.2007.05.009 ID - Barski2007 ER - TY - JOUR AU - Brenner, S. PY - 1974 DA - 1974// TI - The genetics of Caenorhabditis elegans JO - Genetics VL - 77 ID - Brenner1974 ER - TY - CHAP AU - Fire, A. AU - Ahnn, J. AU - Kelly, W. AU - Harfe, B. AU - Kostas, S. AU - Hsieh, J. AU - Hsu, M. AU - Xu, S. ED - M Chalfie, S. K. PY - 1998 DA - 1998// TI - GFP applications in C. elegans BT - GFP Strategies and Applications PB - John Wiley and Sons CY - NY ID - Fire1998 ER - TY - JOUR AU - Mello, C. C. AU - Kramer, J. M. AU - Stinchcomb, D. AU - Ambros, V. PY - 1991 DA - 1991// TI - Efficient gene transfer in C.elegans: extrachromosomal maintenance and integration of transforming sequences JO - EMBO J VL - 10 ID - Mello1991 ER - TY - JOUR AU - Hoppe, P. E. AU - Waterston, R. H. PY - 2000 DA - 2000// TI - A region of the myosin rod important for interaction with paramyosin in Caenorhabditis elegans striated muscle JO - Genetics VL - 156 ID - Hoppe2000 ER - TY - JOUR AU - McKay, S. J. AU - Johnsen, R. AU - Khattra, J. AU - Asano, J. AU - Baillie, D. L. AU - Chan, S. AU - Dube, N. AU - Fang, L. AU - Goszczynski, B. AU - Ha, E. PY - 2003 DA - 2003// TI - Gene expression profiling of cells, tissues, and developmental stages of the nematode C. elegans JO - Cold Spring Harb Symp Quant Biol VL - 68 UR - https://doi.org/10.1101/sqb.2003.68.159 DO - 10.1101/sqb.2003.68.159 ID - McKay2003 ER -