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1. Comparative analysis of metazoan chromatin organization

Author

Ho, Joshua WK, Jung, Youngsook L, Liu, Tao, Alver, Burak H, Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y, Appert, Alex, Parker, Stephen CJ, Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C, Bishop, Eric, Egelhofer, Thea A, Hu, Sheng'en Shawn, Alekseyenko, Artyom A, Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A, Bowman, Sarah K, Chen, Q Brent, Chen, Ron A-J, Day, Daniel S, Dong, Yan, Dose, Andrea C, Duan, Xikun, Epstein, Charles B, Ercan, Sevinc, Feingold, Elise A, Ferrari, Francesco, Garrigues, Jacob M, Gehlenborg, Nils, Good, Peter J, Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M, Jeffers, Tess E, Kharchenko, Peter V, Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V, Kumar, Nischay, Langley, Sasha A, Larschan, Erica N, Latorre, Isabel, Libbrecht, Maxwell W, Lin, Xueqiu, Park, Richard, Pazin, Michael J, Pham, Hoang N, Plachetka, Annette, Qin, Bo, Schwartz, Yuri B, Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M, Xue, Huiling, Kingston, Robert E, Kim, Ju Han, Bernstein, Bradley E, Dernburg, Abby F, Pirrotta, Vincenzo, Kuroda, Mitzi I, Noble, William S, Tullius, Thomas D, Kellis, Manolis, MacAlpine, David M, Strome, Susan, Elgin, Sarah CR, Liu, Xiaole Shirley, Lieb, Jason D, Ahringer, Julie, Karpen, Gary H, and Park, Peter J

Subjects
Biochemistry and Cell Biology, Biological Sciences, Immunization, Human Genome, Genetics, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Animals, Caenorhabditis elegans, Cell Line, Centromere, Chromatin, Chromatin Assembly and Disassembly, DNA Replication, Drosophila melanogaster, Enhancer Elements, Genetic, Epigenesis, Genetic, Heterochromatin, Histones, Humans, Molecular Sequence Annotation, Nuclear Lamina, Nucleosomes, Promoter Regions, Genetic, Species Specificity, General Science & Technology
Abstract

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms. Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths. To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.

Published
2014

18. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

Author

Birney, Ewan, Stamatoyannopoulos, John A., Dutta, Anindya, Guigo, Roderic, Gingeras, Thomas R., Margulies, Elliott H., Weng, Zhiping, Snyder, Michael, Dermitzakis, Emmanouil T., Thurman, Robert E., Kuehn, Michael S., Taylor, Christopher M., Neph, Shane, Koch, Christoph M., Asthana, Saurabh, Malhotra, Ankit, Adzhubei, Ivan, Greenbaum, Jason A., Andrews, Robert M., Flicek, Paul, Boyle, Patrick J., Cao, Hua, Carter, Nigel P., Clelland, Gayle K., Davis, Sean, Day, Nathan, Dhami, Pawandeep, Dillon, Shane C., Dorschner, Michael O., Fiegler, Heike, Giresi, Paul G., Goldy, Jeff, Hawrylycz, Michael, Haydock, Andrew, Humbert, Richard, James, Keith D., Johnson, Brett E., Johnson, Ericka M., Frum, Tristan T., Rosenzweig, Elizabeth R., Karnani, Neerja, Lee, Kirsten, Lefebvre, Gregory C., Navas, Patrick A., Neri, Fidencio, Parker, Stephen C. J., Sabo, Peter J., Sandstrom, Richard, Shafer, Anthony, Vetrie, David, Weaver, Molly, Wilcox, Sarah, Yu1, Man, Collins, Francis S., Dekker, Job, Lieb, Jason D., Tullius, Thomas D., Crawford, Gregory E., Sunyaev, Shamil, Noble, William S., Dunham, Ian, Denoeud, France, Reymond, Alexandre, Kapranov, Philipp, Rozowsky, Joel, Zheng, Deyou, Castelo, Robert, Frankish, Adam, Harrow, Jennifer, Ghosh, Srinka, Sandelin, Albin, Hofacker, Ivo L., Baertsch, Robert, Keefe, Damian, Dike, Sujit, Cheng, Jill, Hirsch, Heather A., Sekinger, Edward A., Lagarde, Julien, Abril, Josep F., Shahab, Atif, Flamm, Christoph, Fried, Claudia, Hackermuller, Jorg, Hertel, Jana, Lindemeyer, Manja, Missal, Kristin, Tanzer, Andrea, Washietl, Stefan, Korbel, Jan, Emanuelsson, Olof, Pedersen, Jakob S., Holroyd, Nancy, Taylor, Ruth, Swarbreck, David, Matthews, Nicholas, Dickson, Mark C., Thomas, Daryl J., Weirauch, Matthew T., Gilbert, James, Drenkow, Jorg, Bell, Ian, Zhao, XiaoDong, Srinivasan, K.G., Sung, Wing-Kin, Ooi, Hong Sain, Chiu, Kuo Ping, Foissac, Sylvain, Alioto, Tyler, Brent, Michael, Pachter, Lior, Tress, Michael L., Valencia, Alfonso, Choo, Siew Woh, Choo, Chiou Yu, Ucla, Catherine, Manzano, Caroline, Wyss, Carine, Cheung, Evelyn, Clark, Taane G., Brown, James B., Ganesh, Madhavan, Patel, Sandeep, Tammana, Hari, Chrast, Jacqueline, Henrichsen, Charlotte N., Kai, Chikatoshi, Kawai, Jun, Nagalakshmi, Ugrappa, Wu, Jiaqian, Lian, Zheng, Lian, Jin, Newburger, Peter, Zhang, Xueqing, Bickel, Peter, Mattick, John S., Carninci, Piero, Hayashizaki, Yoshihide, Weissman, Sherman, Hubbard, Tim, Myers, Richard M., Rogers, Jane, Stadler, Peter F., Lowe, Todd M., Wei, Chia-Lin, Ruan, Yijun, Struhl, Kevin, Gerstein, Mark, Antonarakis, Stylianos E., Fu, Yutao, Green, Eric D., Karaoz, Ulaş, Siepel, Adam, Taylor, James, Liefer, Laura A., Wetterstrand, Kris A., Good, Peter J., Feingold, Elise A., Guyer, Mark S., Cooper, Gregory M., Asimenos, George, Dewey, Colin N., Hou, Minmei, Nikolaev, Sergey, Montoya-Burgos, Juan I., Loytynoja, Ari, Whelan, Simon, Pardi, Fabio, Massingham, Tim, Huang, Haiyan, Zhang, Nancy R., Holmes, Ian, Mullikin, James C., Ureta-Vidal, Abel, Paten, Benedict, Seringhaus, Michael, Church, Deanna, Rosenbloom, Kate, Kent, W. James, Stone, Eric A., Batzoglou, Serafim, Goldman, Nick, Hardison, Ross C., Haussler, David, Miller, Webb, Sidow, Arend, Trinklein, Nathan D., Zhang, Zhengdong D., Barrera, Leah, Stuart, Rhona, King, David C., Ameur, Adam, Enroth, Stefan, Bieda, Mark C., Kim, Jonghwan, Bhinge, Akshay A., Jiang, Nan, Liu, Jun, Yao, Fei, Vega, Vinsensius B., Lee, Charlie W.H., Ng, Patrick, Yang, Annie, Moqtaderi, Zarmik, Zhu, Zhou, Xu, Xiaoqin, Squazzo, Sharon, Oberley, Matthew J., Inman, David, Singer, Michael A., Richmond, Todd A., Munn, Kyle J., Rada-Iglesias, Alvaro, Wallerman, Ola, Komorowski, Jan, Fowler, Joanna C., Couttet, Phillippe, Bruce, Alexander W., Dovey, Oliver M., Ellis, Peter D., Langford, Cordelia F., Nix, David A., Euskirchen, Ghia, Hartman, Stephen, Urban, Alexander E., Kraus, Peter, Van Calcar, Sara, Heintzman, Nate, Hoon Kim, Tae, Wang, Kun, Qu, Chunxu, Hon, Gary, Luna, Rosa, Glass, Christopher K., Rosenfeld, M. Geoff, Aldred, Shelley Force, Cooper, Sara J., Halees, Anason, Lin, Jane M., Shulha, Hennady P., Zhang, Xiaoling, Xu, Mousheng, Haidar, Jaafar N. S., Yu, Yong, Birney*, Ewan, Iyer, Vishwanath R., Green, Roland D., Wadelius, Claes, Farnham, Peggy J., Ren, Bing, Harte, Rachel A., Hinrichs, Angie S., Trumbower, Heather, Clawson, Hiram, Hillman-Jackson, Jennifer, Zweig, Ann S., Smith, Kayla, Thakkapallayil, Archana, Barber, Galt, Kuhn, Robert M., Karolchik, Donna, Armengol, Lluis, Bird, Christine P., de Bakker, Paul I. W., Kern, Andrew D., Lopez-Bigas, Nuria, Martin, Joel D., Stranger, Barbara E., Woodroffe, Abigail, Davydov, Eugene, Dimas, Antigone, Eyras, Eduardo, Hallgrimsdottir, Ingileif B., Huppert, Julian, Zody, Michael C., Abecasis, Goncalo R., Estivill, Xavier, Bouffard, Gerard G., Guan, Xiaobin, Hansen, Nancy F., Idol, Jacquelyn R., Maduro, Valerie V.B., Maskeri, Baishali, McDowell, Jennifer C., Park, Morgan, Thomas, Pamela J., Young, Alice C., Blakesley, Robert W., Baylor College of Medicine, Human Genome Sequencing Center, Muzny, Donna M., Sodergren, Erica, Wheeler, David A., Worley, Kim C., Jiang, Huaiyang, Weinstock, George M., Gibbs, Richard A., Graves, Tina, Fulton, Robert, Mardis, Elaine R., Wilson, Richard K., Clamp, Michele, Cuff, James, Gnerre, Sante, Jaffe, David B., Chang, Jean L., Lindblad-Toh, Kerstin, Lander, Eric S., Koriabine, Maxim, Nefedov, Mikhail, Osoegawa, Kazutoyo, Yoshinaga, Yuko, Zhu, Baoli, and de Jong, Pieter J.

Abstract

Author(s): The ENCODE Project Consortium; Analysis Coordination; Ewan Birney (corresponding author) [1]; John A. Stamatoyannopoulos (corresponding author) [2]; Anindya Dutta (corresponding author) [3]; Roderic Guigó (corresponding author) [4, 5]; Thomas [...]

Published
2007
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22. Oxidative strand scission of nucleic acids: routes initiated by hydrogen abstraction from the sugar moiety

Author

Pogozelski, Wendy Knapp and Tullius, Thomas D.

Subjects
Nucleic acids -- Research, Scission (Chemistry) -- Research, Hydrogen -- Research, Sugar -- Research, Chemistry
Abstract

Research was conducted to determine the hydrogen abstraction event that starts the cleavage process from the sugar moiety. The formation of a strand break and hydrogen atoms is considered in the elucidating mechanisms of nucleic acid degradation. A representative set of DNA-cleaving pathways that is organized by an initial hydrogen abstraction event was described. The pathways were also determined by monitoring various unique marker products.

Published
1998

23. Effect of the crystallizing agent 2-methyl-2,4-pentanediol on the structure of adenine tract DNA solution

Author

Ganunis, Ruth M., Guo, Hong, and Tullius, Thomas D.

Subjects
Nucleotide sequence -- Analysis, DNA -- Analysis, Biological sciences, Chemistry
Abstract

The effects of 2-methyl-2,4-pentanediol (MPD) precipitating agent on the crystal structure of the A-tract-containing (A5N5) deoxyribonucleic acid (DNA) was analyzed by utilizing hydroxyl radicals. MPD alters the hydroxyl radical cleavage pattern of the A5N5 DNA sequence into a mixed-sequence unbent DNA. However, the hydroxyl radical cleavage patterns of straight A-tract sequence or T4A4N2 sequence and mixed-sequence DNA was not affected by MPD.

Published
1996

25. Role of the aryl iodide in the sequence-selective cleavage of DNA by Calicheamicin. Importance of the thermodynamic binding vs kinetic activation in the cleavage process

Author

Chatterjee, Moneesh, Mah, Stanley C., Tullius, Thomas D., and Townsend, Craig A.

Subjects
Scission (Chemistry) -- Research, Calicheamicin -- Structure-activity relationships, Thermodynamics -- Research, Chemistry
Abstract

Dihydrothiophene equilibrium binding is attained before the occurrence of strand scission and the free energy differences relative to the TCCT site are calculated. To compare the amount of stabilization in the binding of CLMgama(super 1)(sub 1) and CLMepsilon at a TCCT-AGGA sequence, using isothermal titration calorimetry and quantitative hydroxyl radical footprint titration. These reaction rates are studied to get an overall estimate of the energetics involved in the calicheamicin binding to DNA and in the role played by the side-chain aryl iodide.

Published
1995

26. What species is responsible for strand scission in the reaction of (FeIIEDTA)2- and H2O2 with DNA?

Author

Pogozelski, Wendy Knapp, McNeese, Timothy J., and Tullius, Thomas D.

Subjects
Scission (Chemistry) -- Research, Radicals (Chemistry) -- Evaluation, DNA -- Analysis, Chemistry
Abstract

The hydroxyl radical is responsible for DNA strand cleavage in the reaction of (FeIIEDTA)2- and H2O2 with DNA, rather than a high-valent iron-oxo complex. DNA cleavage patterns induced by gamma radiolysis and by the reaction of (FeIIEDTA)2- and H2O2 in the presence of ascorbate are identical with the DNA cleavage pattern produced by the hydroxyl radical.

Published
1995

27. Hydroxyl radical footprinting of calicheamicin: relationship of DNA binding to cleavage

Author

Mah, Stanley C., Townsend, Craig, A., and Tullius, Thomas D.

Subjects
Calicheamicin -- Structure-activity relationships, DNA -- Analysis, Orientation -- Analysis, Biological sciences, Chemistry
Abstract

Studies on the binding of calicheamicin (CLM) epsilon with DNA reveal CLM's hydroxyl radical footprinting. A comparison of CLM epsilons binding to DNA with DNA's binding by native CLM gamma reveals that CLM epsilon molecules are oriented to the DNA strands in an extended structure. These results validate the theory that global CLM structures will have the oligosaccharide side chain of the C5' hydrogen abstraction's 3' side.

Published
1994

28. Sequence-specific cleavage of DNA via nucleophilic attack of hydrogen peroxide, assisted by Flp recombinase

Author

Kimball, Amy S., Lee, Jehee, Jayaram, Makkuni, and Tullius, Thomas D.

Subjects
Scission (Chemistry) -- Causes of, Hydrogen peroxide -- Research, Enzymes -- Research, DNA -- Research, Biological sciences, Chemistry
Abstract

A specific phosphodiester bond in DNA was cleaved using hydrogen peroxide in combination with the Flp recombinase obtained from Saccharomyces cerevisiae. In this system, cleavage resulted from peroxide's nucleophile action on a phosphorus oxygen bond rather than from oxidative damage of the DNA backbone. Under normal circumstances, the reaction would take place at a Flp binding site not damaged by the enzyme. Preoxide-mediated cleavage also occurred with an Flp mutant in which phenylalanine replaced the active site tyrosine.

Published
1993

29. Structure of DNA in a nucleosome core at high salt concentration and at high temperature

Author

Bashkin, John, Hayes, Jeffrey J., Tullius, Thomas D., and Wolffe, Alan P.

Subjects
DNA -- Research, Salt -- Physiological aspects, Temperature -- Physiological aspects, Molecular structure -- Research, Biological sciences, Chemistry
Abstract

A study was conducted on DNA structure in a nucleosome core at high salt concentration and temperature using hydroxyl radical cleavage of DNA as probe. Results reveal that a DNA fragment's rotational and translational positioning on the histone octamer is retained at NaCl concentrations of0.0-8.0 M and temperatures of 0-75 degrees centigrade. It was also found that at high salt concentrations, the helical periodicity observed in the DNA cleavage pattern in a nucleosome core at 0.0 M NaCl is retained.

Published
1993

30. How the structure of an adenine tract depends on sequence context: a new model for the structure of TnAn DNA sequence

Author

Price, Mary Ann and Tullius, Thomas D.

Subjects
DNA -- Research, Nucleotide sequence -- Research, Molecular structure -- Models, Biological sciences, Chemistry
Abstract

The cleavage patterns of several TnAn sequences was obtained to characterize the structure of such sequences in DNA. A new structural model is proposed which explains its bending and local conformational properties. It is proposed that the core of TnAn sequences are B-DNA-like with adenines and thymines localized outside the core. However, the presence of sufficient number of A and T residues induces the formation of a structure that resembles that of adenine tracts surrounded by a mixed sequence DNA.

Published
1993

34. [19] Hydroxyl radical footprinting

Author

Dixon, Wendy J., primary, Hayes, Jeffrey J., additional, Levin, Judith R., additional, Weidner, Margaret F., additional, Dombroski, Beth A., additional, and Tullius, Thomas D., additional

Published
1991
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36. Research Corporation and John Schaefer

Author

Kellman, Ray, Deardorff, Don, Dorhout, Peter, Haegel, Nancy, Iverson, Brent L., Morrison, Michael, Pladziewicz, Jack, Selen, Mats, Tullius, Thomas D., and Zwier, Timothy S.

Published
2004

42. Construction of a genome-scale structural map at single-nucleotide resolution

Author

Greenbaum, Jason A., Bo Pang, and Tullius, Thomas D.

Subjects
DNA -- Structure, Human genome -- Research, Nuclear magnetic resonance spectroscopy -- Analysis, Polymerase chain reaction -- Analysis, Health
Abstract

A relational database containing extensive hydroxyl radical cleavage data produced from two DNA libraries is used to construct genome-scale structural map.

Published
2007

43. Metal-DNA Chemistry

Author

THOMAS D. TULLIUS, Thomas D. Tullius, David S. Sigman, Chi-hong B. Chen, Ramasamy Tamilarasan, David R. McMillin, Fang Liu, Robert F. Pasternack, Esther J. Gibbs, G. Raner, J. Goodisman, J. C. Dabrowiak, Jeremy M. Berg, Betsy Frantz, Thomas V. O'Halloran, Kayoko Nakamura, Victor de Lorenzo, J. B. Neilands, Luigi G. M, Thomas D. Tullius, M. Joan Comstock

Published
1989

45. Hydroxyl Radical Footprinting: A High-Resolution Method for Mapping Protein-DNA Contacts11This research was supported by grants from the Searle Scholars Program of the Chicago Community Trust, the Research Corporation, the Biomedical Research Support Grant Program (S07 RR07041), and the National Cancer Institute (CA37444) of the National Institutes of Health.

Author

TULLIUS, THOMAS D., primary, DOMBROSKI, BETH A., additional, CHURCHILL, MAIR E.A., additional, and KAM, LAURANCE, additional

Published
1989
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50. Comparative analysis of metazoan chromatin organization

Author

Ho, Joshua W. K., June, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng'en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A., Bowmanm, Sarah K., Chens, Q. Brent, Chen, Ron A. -J., Day, Daniel S., Dong, Yan, Dose, Andrea C., Duan, Xikun, Epstein, Charles B., Ercan, Sevinc, Feingold, Elise A., Ferrari, Francesco, Garrigues, Jacob M., Gehlenborg, Nils, Good, Peter J., Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M., Jeffers, Tess E., Kharchenko, Peter V., Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V., Kumar, Nischay, Langley, Sasha A., Larschan, Erica N., Latorre, Isabel, Libbrecht, Maxwell W., Lin, Xueqiu, Park, Richard, Pazin, Michael J., Pham, Hoang N., Plachetka, Annette, Qin, Bo, Schwartz, Yuri B., Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M., Xue, Huiling, Kingstonm, Robert E., Kim, Ju Han, Bernstein, Bradley E., Dernburg, Abby F., Pirrotta, Vincenzo, Kuroda, Mitzi I., Noble, William S., Tullius, Thomas D., Kellis, Manolis, MacAlpine, David M., Strome, Susan, Elgin, Sarah C. R., Liu, Xiaole Shirley, Lieb, Jason D., Ahringer, Julie, Karpen, Gary H., Park, Peter J., Ho, Joshua W. K., June, Youngsook L., Liu, Tao, Alver, Burak H., Lee, Soohyun, Ikegami, Kohta, Sohn, Kyung-Ah, Minoda, Aki, Tolstorukov, Michael Y., Appert, Alex, Parker, Stephen C. J., Gu, Tingting, Kundaje, Anshul, Riddle, Nicole C., Bishop, Eric, Egelhofer, Thea A., Hu, Sheng'en Shawn, Alekseyenko, Artyom A., Rechtsteiner, Andreas, Asker, Dalal, Belsky, Jason A., Bowmanm, Sarah K., Chens, Q. Brent, Chen, Ron A. -J., Day, Daniel S., Dong, Yan, Dose, Andrea C., Duan, Xikun, Epstein, Charles B., Ercan, Sevinc, Feingold, Elise A., Ferrari, Francesco, Garrigues, Jacob M., Gehlenborg, Nils, Good, Peter J., Haseley, Psalm, He, Daniel, Herrmann, Moritz, Hoffman, Michael M., Jeffers, Tess E., Kharchenko, Peter V., Kolasinska-Zwierz, Paulina, Kotwaliwale, Chitra V., Kumar, Nischay, Langley, Sasha A., Larschan, Erica N., Latorre, Isabel, Libbrecht, Maxwell W., Lin, Xueqiu, Park, Richard, Pazin, Michael J., Pham, Hoang N., Plachetka, Annette, Qin, Bo, Schwartz, Yuri B., Shoresh, Noam, Stempor, Przemyslaw, Vielle, Anne, Wang, Chengyang, Whittle, Christina M., Xue, Huiling, Kingstonm, Robert E., Kim, Ju Han, Bernstein, Bradley E., Dernburg, Abby F., Pirrotta, Vincenzo, Kuroda, Mitzi I., Noble, William S., Tullius, Thomas D., Kellis, Manolis, MacAlpine, David M., Strome, Susan, Elgin, Sarah C. R., Liu, Xiaole Shirley, Lieb, Jason D., Ahringer, Julie, Karpen, Gary H., and Park, Peter J.

Abstract

Genome function is dynamically regulated in part by chromatin, which consists of the histones, non-histone proteins and RNA molecules that package DNA. Studies in Caenorhabditis elegans and Drosophila melanogaster have contributed substantially to our understanding of molecular mechanisms of genome function in humans, and have revealed conservation of chromatin components and mechanisms(1-3). Nevertheless, the three organisms have markedly different genome sizes, chromosome architecture and gene organization. On human and fly chromosomes, for example, pericentric heterochromatin flanks single centromeres, whereas worm chromosomes have dispersed heterochromatin-like regions enriched in the distal chromosomal 'arms', and centromeres distributed along their lengths(4,5). To systematically investigate chromatin organization and associated gene regulation across species, we generated and analysed a large collection of genome-wide chromatin data sets from cell lines and developmental stages in worm, fly and human. Here we present over 800 new data sets from our ENCODE and modENCODE consortia, bringing the total to over 1,400. Comparison of combinatorial patterns of histone modifications, nuclear lamina-associated domains, organization of large-scale topological domains, chromatin environment at promoters and enhancers, nucleosome positioning, and DNA replication patterns reveals many conserved features of chromatin organization among the three organisms. We also find notable differences in the composition and locations of repressive chromatin. These data sets and analyses provide a rich resource for comparative and species-specific investigations of chromatin composition, organization and function.

Published
2014
Full Text
View/download PDF

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