Predicting Cis-Element Responses to Cell Signaling in Red Blood Cell Precursors [ER RNA-seq]

However, accurate cell type-specific prediction of functional cis-elements remains a significant computational challenge due to the lack of context regarding the role of environmental stimuli that may alter activity. Most existing datasets use static molecular and sequence features which do not evaluate cis-element responses to extracellular cues.

To investigate chromatin changes mediated by Kit/SCF, we performed ATAC-seq and RNA-seq in acutely SCF stimulated HUDEP-2 cells and mapped enhancer-promoter interactions using existing datasets. The top Kit-predictive features included Inflammatory Response (JUN, JUND, ATF2, ATF3, EGR1), blood cell maintenance (RUNX1) and chromatin remodelers/transcription factors (THAP1, MXI1, PKNOX1, CTCF). EGR1 - a transcription factor which regulates proliferation and differentiation - was 37-fold upregulated after SCF treatment.