Using ChIP-chip technology to reveal common principles of transcriptional repression in normal and cancer cells

Autor: Peggy J. Farnham, Luis G. Acevedo, Sharon L. Squazzo, Alina Rabinovich, Henriette O'Geen, Sushma Iyengar, Vitalina M. Komashko, Roland Green

Publikováno v: Genome Research. 18:521-532

We compared 12 different cell populations, including embryonic stem cells before and during differentiation into embryoid bodies as well as various types of normal and tumor cells to determine if pluripotent versus differentiated cell types use diffe

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1fc05662e10edfced21c2e413f13bfc9
https://doi.org/10.1101/gr.074609.107

Suz12 binds to silenced regions of the genome in a cell-type-specific manner

Autor: Peggy J. Farnham, Henriette O'Geen, Victor X. Jin, Vitalina M. Komashko, Danny Reinberg, Sung Wook Jang, Sheryl R. Krig, Roland Green, Raphaël Margueron, Sharon L. Squazzo

Publikováno v: Genome Research. 16:890-900

Suz12 is a component of the Polycomb group complexes 2, 3, and 4 (PRC 2/3/4). These complexes are critical for proper embryonic development, but very few target genes have been identified in either mouse or human cells. Using a variety of ChIP-chip a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::1d8efbd07d51d23d1e150c45e379418b
https://doi.org/10.1101/gr.5306606

Dual Roles for Spt5 in Pre-mRNA Processing and Transcription Elongation Revealed by Identification of Spt5-Associated Proteins

Autor: J. A. Mccleery, C. A. Emigh, Derek L. Lindstrom, Sharon L. Squazzo, Todd A Burckin, Nemone Muster, Grant A. Hartzog, K. C. Wachter, J. R. I. i Yates

Publikováno v: Molecular and Cellular Biology. 23:1368-1378

During transcription elongation, eukaryotic RNA polymerase II (Pol II) must contend with the barrier presented by nucleosomes. The conserved Spt4-Spt5 complex has been proposed to regulate elongation through nucleosomes by Pol II. To help define the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5950427a6a7508a64970a2d82dfc14ff
https://doi.org/10.1128/mcb.23.4.1368-1378.2003

Aggregation of Secreted Amyloid β-Protein into Sodium Dodecyl Sulfate-stable Oligomers in Cell Culture

Autor: David B. Teplow, Beth L. Ostaszewski, Sharon L. Squazzo, Edward H. Koo, Russell E. Rydell, Dennis J. Selkoe, Marcia B. Podlisny

Publikováno v: Journal of Biological Chemistry. 270:9564-9570

Filamentous aggregates of the 40-42-residue amyloid beta-protein (A beta) accumulate progressively in the limbic and cerebral cortex in Alzheimer's disease, where they are intimately associated with neuronal and glial cytopathology. Attempts to model

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d4789922da679dfbecfbf0ba54774736
https://doi.org/10.1074/jbc.270.16.9564

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

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

Publikováno v: Nature, Vol. 447, No 7146 (2007) pp. 799-816
Birney, E, Stamatoyannopoulos, J A, Dutta, A, Guigó, R, Gingeras, T R, Margulies, E H, Weng, Z, Snyder, M, Dermitzakis, E T, Thurman, R E, Kuehn, M S, Taylor, C M, Neph, S, Koch, C M, Asthana, S, Malhotra, A, Adzhubei, I, Greenbaum, J A, Andrews, R M, Flicek, P, Boyle, P J, Cao, H, Carter, N P, Clelland, G K, Davis, S, Day, N, Dhami, P, Dillon, S C, Dorschner, M O, Fiegler, H, Giresi, P G, Goldy, J, Hawrylycz, M, Haydock, A, Humbert, R, James, K D, Johnson, B E, Johnson, E M, Frum, T T, Rosenzweig, E R, Karnani, N, Lee, K, Lefebvre, G C, Navas, P A, Neri, F, Parker, S C J, Sabo, P J, Sandstrom, R, Shafer, A, Pedersen, J S & ENCODE Project Consortium 2007, ' Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project ', Nature, vol. 447, no. 7146, pp. 799-816 . https://doi.org/10.1038/nature05874

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a nu

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https://resolver.caltech.edu/CaltechAUTHORS:20170307-121815071