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Global Regulation of Gene Expression Abstracts of papers presented at the 2010 meeting on SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION March 23–March 27, 2010 View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Cold Spring Harbor Laboratory Institutional Repository Cold Spring Harbor Laboratory Cold Spring Harbor, New York Abstracts of papers presented at the 2010 meeting on SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION March 23–March 27, 2010 Arranged by Bradley Bernstein, Harvard Medical School Martha Bulyk, Harvard Medical School Harmen Bussemaker, Columbia University Marian Walhout, UMass Medical School Cold Spring Harbor Laboratory Cold Spring Harbor, New York This meeting was funded in part by the National Cancer Institute, a branch of the National Institutes of Health; and the National Science Foundation. Contributions from the following companies provide core support for the Cold Spring Harbor meetings program. Corporate Sponsors Agilent Technologies Life Technologies (Invitrogen & AstraZeneca Applied Biosystems) BioVentures, Inc. New England BioLabs, Inc. Bristol-Myers Squibb Company OSI Pharmaceuticals, Inc. Genentech, Inc. Sanofi-Aventis GlaxoSmithKline Schering-Plough Research Hoffmann-La Roche Inc. Institute Plant Corporate Associates Monsanto Company Pioneer Hi-Bred International, Inc. Foundations Hudson-Alpha Institute for Biotechnology Cover: Figure by Nynke van Berkum, Dekker Lab, University of Massachusetts Medical School. See abstract #95, van Berkum et. al. SYSTEMS BIOLOGY: GLOBAL REGULATION OF GENE EXPRESSION Tuesday, March 23 – Saturday, March 27, 2010 Tuesday 7:30 pm Keynote Speaker Tuesday 8:45 pm 1 Transcription Wednesday 9:00 am 2 Transcriptional Regulatory Networks Wednesday 2:00 pm 3 Poster Session I Wednesday 4:30pm Wine & Cheese Party Wednesday 7:30 pm Keynote Speaker Wednesday 8:45 pm 4 Chromatin Thursday 9:00 am 5 Epigenetics Thursday 2:00 pm 6 Poster Session II Thursday 7:30 pm 7 Cis-regulatory Logic Friday 9:00 am 8 Post-transcriptional Regulation Friday 2:00 pm 9 Emerging Technology Friday 6:00 pm Banquet Saturday 9:00 am 10 Variation and Evolution Mealtimes at Blackford Hall are as follows: Breakfast 7:30 am-9:00 am Lunch 11:30 am-1:30 pm Dinner 5:30 pm-7:00 pm Bar is open from 5:00 pm until late Abstracts are the responsibility of the author(s) and publication of an abstract does not imply endorsement by Cold Spring Harbor Laboratory of the studies reported in the abstract. These abstracts should not be cited in bibliographies. Material herein should be treated as personal communications and should be cited as such only with the consent of the author. Please note that recording of oral sessions by audio, video or still photography is strictly prohibited except with the advance permission of the author(s), the organizers, and Cold Spring Harbor Laboratory. Printed on 100% recycled paper. PROGRAM TUESDAY, March 23—7:30 PM KEYNOTE SPEAKER Mapping genome-wide nucleosome dynamics Steven Henikoff, Roger M. Deal, Christopher M. Weber. Presenter affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington. 1 TUESDAY, March 23—8:45 PM SESSION 1 TRANSCRIPTION Chairperson: T. Hughes, University of Toronto, Canada Variability in gene expression underlies incomplete penetrance Alexander van Oudenaarden. Presenter affiliation: Massachusetts Institute of Technology, Cambridge, Massachusetts. 2 Exploring relationships in data sets using spatial gene expression patterns for all Drosophila transcription factors Erwin Frise, Ann S. Hammonds, Susan E. Celniker. Presenter affiliation: Lawrence Berkeley National Labs, Berkeley, California. 3 A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription Michael R. Brent, Sooraj Kuttykrishnan, Jeffrey Sabina, Mark Johnston. Presenter affiliation: Washington University, Saint Louis, Missouri. 4 Genome-wide binding of MyoD in specified and differentiating muscle cells Stephen J. Tapscott, Yi Cao, Zizhen Yao, Walter L. Ruzzo, Robert C. Gentleman. Presenter affiliation: Fred Hutchinson Cancer Research Center, Seattle, Washington. 5 v WEDNESDAY, March 24—9:00 AM SESSION 2 TRANSCRIPTIONAL REGULATORY NETWORKS Chairperson: X. Shirley Liu, Dana-Farber Cancer Institute, Boston, Massachusetts Biomarkers based on networks, not individual loci Trey Ideker. Presenter affiliation: University of California, San Diego, La Jolla, California. 6 Functional modularity of nuclear hormone receptors in a C. elegans gene regulatory network H. Efsun Arda, Stefan Taubert, Colin Conine, Ben Tsuda, Marc Van Gilst, Reynaldo Sequerra, Lynn Doucette-Stamm, Keith R. Yamamoto, A.J. Marian Walhout. Presenter affiliation: University of Massachusetts Medical School, Worcester, Massachusetts 7 New insights into global transcriptional control in embryonic stem cells and tumor cells Peter B. Rahl, Charles Y. Lin, Amy C. Seila, Ryan A. Flynn, Christopher B. Burge, Phillip A. Sharp, Richard A. Young. Presenter affiliation: Whitehead Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts. 8 Unbiased reconstruction of a mammalian transcriptional network mediating the differential response to pathogens Ido Amit, Manuel Garber, Nicolas Chevrier, Ana Leite, Yoni Donner, Tom Eisenhaure, Mitchell Guttman, Jen Grenier, Lisa A. Schubert, David Root, Nir Hacohen, Aviv Regev. Presenter affiliation: Broad Institute, Cambridge, Massachusetts; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts. 9 Profiling the human protein-DNA interactome identifies unconventional DNA-binding proteins Heng Zhu. Presenter affiliation: Johns Hopkins University, Baltimore, Maryland. 10 vi From bolting to bloom—Genome-wide control of floral meristem initiation and differentiation Kerstin Kaufmann, Frank Wellmer, Jose M. Muino, Thilia Ferrier, Samuel E. Wuest, Vijaya Kumar, Pawel Krajewski, Elliot M. Meyerowitz, Gerco C. Angenent, Jose Luis Riechmann. Presenter affiliation: Wageningen University and Research Centre, Wageningen, Netherlands. 11 Elucidating the structure of the transcriptional regulatory network with genetic interactions Brenda J. Andrews, Michael Costanzo, Anastasia Barshinikova, Yungil Kim, Chad Myers. Presenter affiliation: University of Toronto, Toronto, Canada. 12 WEDNESDAY, March 24—2:00 PM SESSION 3 POSTER SESSION I Development of a genome-wide DNA damage detection assay Sheera Adar, Jason D. Lieb. Presenter affiliation: University of North Carolina at Chapel Hill, Chapel Hill, North Carolina. 13 Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites Doron Betel, Anjali Koppal, Phaedra Agius, Chris Sander, Christina Leslie. Presenter affiliation: Memorial Sloan-Kettering Cancer Center, New York, New York. 14 High resolution models of transcription factor-DNA affinities improve in vitro and in vivo binding predictions Phaedra Agius, Aaron Arvey, William Chang, William Stafford Noble, Christina Leslie. Presenter affiliation: Memorial Sloan-Kettering Cancer Center, New York, New York. 15 Inferring transcriptional and microRNA-mediated regulatory programs in glioblastoma Manu Setty, Aly A. Khan, Aaron Arvey, Frank Neezen, Phaedra Agius, Christina Leslie. Presenter affiliation: Memorial Sloan-Kettering Cancer Center, New York, New York. 16 vii A DNA-transposon based approach to functional screening in neural stem cells Ilaria Albieri, Marco Onorati, Giovanna Calabrese, Zoltan Ivics, Elena Cattaneo, Gian Giacomo Consalez. Presenter affiliation: San Raffaele Scientific Institute, Milan, Italy. 17 Small RNA regulation is dependent on target concentration Aaron Arvey, Christina Leslie, Debora S. Marks. Presenter affiliation: Memorial Sloan Kettering Cancer Center, New York, New York. 18 Fine tuning of signaling networks by microRNAs Avraham Roi, Yarden Yosef. Presenter affiliation: Weizmann Institute of Science, Rehovot, Israel. 19 Quantitative genome-wide analysis of chromatin-remodeling during 3T3-L1 adipocyte differentiation Songjoon Baek, Rasmus Siersbaek, Ronni Nielsen, Sam John, Myong- Hee Sung, Susanne Mandrup, Gordon L. Hager. Presenter affiliation: National Cancer Institute, NIH, Bethesda, Maryland. 20 Intronic antisense noncoding RNA as a candidate regulator of RASSF1 genes Felipe C. Beckedorff, Renan Crocci-Souza, Helder I. Nakaya, Daniela T. Soltys, Carlos F. Menck, Eduardo M. Reis, Sergio Verjovski- Almeida. Presenter affiliation: University of São Paulo, São Paulo, Brazil. 21 A consensus of core protein complex compositions for S. cerevisiae Joris Benschop, Nathalie Brabers, Dik van Leenen, Philip Lijnzaad, Frank Holstege, Patrick Kemmeren. Presenter affiliation: University Medical Center Utrecht, Utrecht, Netherlands. 22 Gene expression profiling of both protein-coding and non-coding RNA transcripts from small amounts of total RNA using a single microarray design Anne Bergstrom Lucas, Mitchell Guttman, Peter Tsang, Bo Curry, Vinayak Kulkarni, Stephanie Fulmer-Smentek, Anya Tsalenko, Sharoni Jacobs, John Rinn, Laurakay Bruhn. Presenter affiliation: Agilent Technologies, Santa Clara, California. 23 viii Genome-wide DNase I footprinting in a diverse set of human cell- types Alan P. Boyle, Lingyun Song, Bum-kyu Lee, Damien Keefe, Ewan Birney, Vishwanath R. Iyer, Gregory E. Crawford, Terrence S. Furey. Presenter affiliation: Duke University, Durham, North Carolina. 24 Altered genomic targeting of the oncogenic transcription factor TAL1/SCL in T-cell acute lymphoblastic leukemia Carmen
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