Endocrine Abstracts (2015) 38 PL3 | DOI: 10.1530/endoabs.38.PL3

An integrated view of nuclear receptor/chromatin interactions: From genome wide to real time molecular dynamics

Gordon Hager, Ville Paakinaho, Sohyoung Kim, Stephanie Morris, Songjoon Baek, Thomas Johnson, R Louis Schiltz, David Ball, Tatiana Karpova, Erin Swinstead & Diego Presman


National Cancer Institute, Bethesda MD, USA.


Transcription factors (TFs) regulate gene expression by interacting with chromatinized DNA response elements (REs). Access to these elements is dramatically restricted by chromatin organization, and modification of the nucleoprotein structure to allow factor binding is a key feature of cell selective gene regulation (Molecular Cell 29:611, 2008; Molecular Cell 43:145, 2011). Local transitions in chromatin access (often characterized as DNaseI hypersensitive sites (DHSs)) are often associated with the action of ATP-dependent chromatin remodeling proteins (Nature Struct. Mol. Biol. 21:73, 2014; Molecular Cell 14:163, 2004); ATP-dependent remodeling may be a universal feature of these transitions. Methodologies to characterize these processes are crucially limited on two fronts. i) ChIP-seq, Dnase-Seq, FAIRE, etc. all collect signals averaged across large cell populations, and cells in these populations are highly asynchronous with respect to enhancer and promoter modification states. ii) These processes are highly dynamic, often with factor/template interactions persisting only for a few seconds (Science 287:1262, 2000; Nature Commun. 5:4456, 2014; Molecular Cell 56:275, 2014). We have integrated genome wide ChIP-seq and Dnase-Seq datasets with data from live cell imaging. We will discuss a model (Dynamic Assisted Loading) for regulatory element function that integrates critical observations from live cell imaging, genome wide characterization of binding factors, and the biochemistry of remodeling complexes.