The detailed locations of nucleosomes along the genomic DNA are major determinants of gene expression, in simple eukaryotes, the genomic DNA sequence explicitly encodes the majority of the in vivo nucleosome organization and thereby regulates the competition of nucleosomes and gene regulatory proteins, facilitating many specific chromosome functions. In higher organisms, however, the extent to which the genomic sequence encodes nucleosome locations has been questioned and is not known. Moreover, higher organisms have differing nucleosome concentrations in differing cell types, with unclear ramifications for nucleosome positioning and chromosome function. This project will obtain needed data and develop quantitative predictive models for nucleosome locations, chromatin superstructures, nucleosome-factor competition, and gene expression levels, in development and cancer, using mouse and human cell line systems.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Specialized Center--Cooperative Agreements (U54)
Project #
5U54CA143869-05
Application #
8549135
Study Section
Special Emphasis Panel (ZCA1-SRLB-9)
Project Start
Project End
Budget Start
2013-08-01
Budget End
2014-07-31
Support Year
5
Fiscal Year
2013
Total Cost
$208,427
Indirect Cost
Name
Northwestern University at Chicago
Department
Type
DUNS #
005436803
City
Chicago
State
IL
Country
United States
Zip Code
60611
Hill, Steven M; Heiser, Laura M; Cokelaer, Thomas et al. (2016) Inferring causal molecular networks: empirical assessment through a community-based effort. Nat Methods 13:310-8
Serebryannyy, Leonid A; Parilla, Megan; Annibale, Paolo et al. (2016) Persistent nuclear actin filaments inhibit transcription by RNA polymerase II. J Cell Sci 129:3412-25
Serebryannyy, Leonid A; Cruz, Christina M; de Lanerolle, Primal (2016) A Role for Nuclear Actin in HDAC 1 and 2 Regulation. Sci Rep 6:28460
Zhao, Baobing; Mei, Yang; Schipma, Matthew J et al. (2016) Nuclear Condensation during Mouse Erythropoiesis Requires Caspase-3-Mediated Nuclear Opening. Dev Cell 36:498-510
Voong, Lilien N; Xi, Liqun; Sebeson, Amy C et al. (2016) Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping. Cell 167:1555-1570.e15
Khalkhali-Ellis, Zhila; Kirschmann, Dawn A; Seftor, Elisabeth A et al. (2015) Divergence(s) in nodal signaling between aggressive melanoma and embryonic stem cells. Int J Cancer 136:E242-51
Hornick, Jessica E; Duncan, Francesca E; Sun, Mingxuan et al. (2015) Age-associated alterations in the micromechanical properties of chromosomes in the mammalian egg. J Assist Reprod Genet 32:765-9
Kreamer, Naomi N; Phillips, Rob; Newman, Dianne K et al. (2015) Predicting the impact of promoter variability on regulatory outputs. Sci Rep 5:18238
Wells, Daniel K; Chuang, Yishan; Knapp, Louis M et al. (2015) Spatial and functional heterogeneities shape collective behavior of tumor-immune networks. PLoS Comput Biol 11:e1004181
Imakaev, Maxim V; Fudenberg, Geoffrey; Mirny, Leonid A (2015) Modeling chromosomes: Beyond pretty pictures. FEBS Lett 589:3031-6

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