Measurement of transcription factor binding in cyanobacteria grown under simluated natural light conditions [ChIP-Seq]

We used ChIP sequencing to measure genome-wide binding of transcription factors in the cyanobacterium Synechococcus elongatus PCC 7942 grown under dynamic light regimes that mimic the rapid changes in light intensity that accompany changes in shading. Our analysis reveals that rapid changes in light intensity modulate the binding of RNA polymerase (RNAP) upstream of genes in a way that correlates with changes in downstream gene expression, suggesting that changes in transcriptional regulation control light-responsive gene expression changes. Also, binding of the circadian clock-controlled transcription factor RpaA and the light-responsive transcription factor RpaB change upstream of genes in a manner correlating with RNAP enrichment and downstream gene expression. This suggests that changes in RpaA and RpaB binding upstream of genes regulate the light-responsive expression of genes in cyanobacteria. Overall design: Cyanobacteria were grown under either a High Light pulse or Shade pulse condition and binding of RNAP, RpaA, and RpaB was measured before and after the change in light intensity using ChIP sequencing