Dynamics and control of state-dependent networks for probing genomic organization

A state-dependent dynamic network is a collection of elements that interact through a network, whose geometry evolves as the state of the elements changes over time. The genome is an intriguing example of a state-dependent network, where chromosomal geometry directly relates to genomic activity, which in turn strongly correlates with geometry. Here we examine various aspects of a genomic state-dependent dynamic network. In particular, we elaborate on one of the important ramifications of viewing genomic networks as being state-dependent, namely, their controllability during processes of genomic reorganization such as in cell differentiation.

[1]  Peter R. Cook,et al.  Predicting three-dimensional genome structure from transcriptional activity , 2002, Nature Genetics.

[2]  W. L. Ruzzo,et al.  Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. , 2010, Developmental cell.

[3]  Mark Groudine,et al.  On emerging nuclear order , 2011, The Journal of cell biology.

[4]  Tom Misteli,et al.  Self-organization in the genome , 2009, Proceedings of the National Academy of Sciences.

[5]  Magnus Egerstedt,et al.  Graph Theoretic Methods in Multiagent Networks , 2010, Princeton Series in Applied Mathematics.

[6]  H. Weintraub Assembly and propagation of repressed and derepressed chromosomal states , 1985, Cell.

[7]  Albert-László Barabási,et al.  Controllability of complex networks , 2011, Nature.

[8]  Fernando Paganini,et al.  A Course in Robust Control Theory , 2000 .

[9]  Shinya Yamanaka,et al.  Pluripotency and nuclear reprogramming , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[10]  T. Tao,et al.  Additive Combinatorics: Graph-theoretic methods , 2006 .

[11]  Reinhard Diestel,et al.  Graph Theory , 1997 .

[12]  J. Leydold,et al.  Laplacian eigenvectors of graphs : Perron-Frobenius and Faber-Krahn type theorems , 2007 .

[13]  Thomas Vierbuchen,et al.  Direct conversion of fibroblasts to functional neurons by defined factors , 2010, Nature.

[14]  S. Strogatz Exploring complex networks , 2001, Nature.

[15]  Francesca Chiaromonte,et al.  Erythroid GATA 1 function revealed by genome-wide analysis of transcription factor occupancy , histone modifications , and mRNA expression , 2009 .

[16]  Charles Kooperberg,et al.  The emergence of lineage-specific chromosomal topologies from coordinate gene regulation , 2009, Proceedings of the National Academy of Sciences.

[17]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[18]  S. Tapscott,et al.  Activation of muscle-specific genes in pigment, nerve, fat, liver, and fibroblast cell lines by forced expression of MyoD. , 1989, Proceedings of the National Academy of Sciences of the United States of America.