In Silico Insight into Nucleosome Repositioning Via Oxygen Delivery and Extracellular Movement

OBJECTIVE Histones and resulting nucleosomes occur within DNA regulating gene expression by slowing, pausing, or halting transcriptional machinery. Positions within the genome have been found with higher affinity for the histone octamer than others. Histone/nucleosome repositioning is adjusted via energy dependent remodeling complexes, and a harmonizing array of constellation proteins and molecules. The energy required to create transcriptional environments is created through oxygen intake, nutrient presence, and extracellular movement. In this paper we aim to help facilitate an in silico framework for further experimentation into how partial pressures of oxygen and other gases impact genetic transcription along with extracellular movement and nutrient delivery. RESULTS Cell and tissue culture experimentation with biomechanical strain and variable partial pressures of oxygen and other gases can be made into the expression levels of genes such as PH domain leucine-rich repeat-containing protein phosphatase 1 (PHLPP1), and Neuroligin 1 (NLGN1). These genes show in silico to have a higher affinity for a histone octamer binding motif, needing adequate cellular energy to be expressed. Extracellular movement and adequate cellular oxygenation are required to properly reposition nucleosome sequences for transcription.