High-resolution mapping of genome position-dependent transcriptional propensity in Escherichia coli

To profile the gene-independent position effect on transcription in bacterial genome, we used a Tn5 transposase assay to integrate a standardized and barcoded reporter construct into the E. coli genome, generating a library of insertion locations for which transcription could be measured in parallel. The resulting map of transcriptional propensity across genome positions enables us to investigate the covariation of genomic features such as genomic sequence contexts, supercoiling, nucleoid associated protein binding, etc, to understand the contributors to transcriptional propensity. The map also allows us to identify regions of genome with particular transcriptional propensity, both for understanding the heterogeneity of gene expression levels, and for designing or choosing genomic context for expression purpose.