Chromatin remodeling in silico: a stochastic model for SWI/SNF

Hierarchical approaches for systems modeling in cardiac development

Ordered cardiac morphogenesis and function are essential for all vertebrate life. The heart begins as a simple contractile tube, but quickly grows and morphs into a multichambered pumping organ complete with valves, while maintaining regulation of blood flow and nutrient distribution. Though not identical, cardiac morphogenesis shares many molecular and morphological processes across vertebrate species. Quantitative data across multiple time and length scales have been gathered through decades of reductionist single variable analyses. These range from detailed molecular signaling pathways at the cellular levels to cardiac function at the tissue/organ levels. However, none of these components act in true isolation from others, and each, in turn, exhibits short- and long-range effects in both time and space. With the absence of a gene, entire signaling cascades and genetic profiles may be shifted, resulting in complex feedback mechanisms. Also taking into account local microenvironmental changes throughout development, it is apparent that a systems level approach is an essential resource to accelerate information generation concerning the functional relationships across multiple length scales (molecular data vs physiological function) and structural development. In this review, we discuss relevant in vivo and in vitro experimental approaches, compare different computational frameworks for systems modeling, and the latest information about systems modeling of cardiac development. Finally, we conclude with some important future directions for cardiac systems modeling.

Stochastic description of single nucleosome repositioning by ACF remodelers

Chromatin remodeling plays a crucial role in the activation or repression of transcription of eukaryotic genes. The chromatin remodeler ACF acts as a dimeric, processive motor to evenly space nucleosomes, favoring repression of gene transcription. Single-molecule experiments have established that ACF moves the nucleosome more efficiently towards the longer flanking DNA than towards the shorter flanking DNA, thereby centering an initially ill-positioned nucleosome on DNA substrates. In this paper we present a one-motor model with nucleosomal repositioning rates dependent on the DNA flanking length. The corresponding master equation is solved analytically with experimentally relevant parameter values. The velocity profile and the effective diffusion constant for nucleosome sliding, computed from the probability distributions, are in accordance with available experimental data. In order to address the observed kinetic pauses in experimental Förster Resonance Energy Transfer profiles, we extend the master equation to account for transitions between explicit motor states, i.e., adenosine triphosphate (ATP) loading and ATP hydrolysis in both ACF motors. The results of this extended two-motor model are compared to the previous effective one-motor model and allow insights into the role of the synchronization of the two motors acting on the nucleosome.