Escherichia coli MG1657 Genome sequencing

The Escherichia coli chromosome is organized into a ring composed of four large structured regions called macrodomains and two less-structured regions. The organization of the Terminus region (Ter) into a macrodomain relies on the binding of the protein MatP to a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. The in vivo DNA binding pattern of MatP-SPA-tag fusion protein was analyzed by formaldehyde-mediated protein crosslinking followed by immunoprecipitation of MatP-containing complexes with anti-Flag antibodies (chromatin immunoprecipitation [ChIP] assay). To map the binding sites for MatP on a genome-wide basis, we sequenced DNA from the ChIP fraction. The amount of specific MatP binding or enrichment factor was estimated by subtraction of the abundance of a locus in the ChIP fraction of a matP-SPA-tag strain to the abundance of the same locus in the ChIP fraction of the WT strain and by normalization of the number of reads obtained in total input DNA.