Highlights d The DHS landscape is gradually established during human embryo development d OCT4 contributes to zygotic genome activation in humans, but not in mice d Younger genes establish DHS at later stages, and older genes show the opposite trend d Human transposons SVA/HERVK harbor DHSs and are specifically expressed in embryos

BackgroundMicrobial genome editing is a powerful tool to modify chromosome in way of deletion, insertion or replacement, which is one of the most important techniques in metabolic engineering research. The emergence of CRISPR/Cas9 technique inspires various genomic editing methods.ResultsIn this research, the goal of development of a fast and easy method for Escherichia coli genome editing with high efficiency is pursued. For this purpose, we designed modular plasmid assembly strategy, compared effects of different length of homologous arms for recombination, and tested different sets of recombinases. The final technique we developed only requires one plasmid construction and one transformation of practice to edit a genomic locus with 3 days and minimal lab work. In addition, the single temperature sensitive plasmid is easy to eliminate for another round of editing. Especially, process of the modularized editing plasmid construction only takes 4 h.ConclusionIn this study, we developed a fast and easy genome editing procedure based on CRISPR/Cas9 system that only required the work of one plasmid construction and one transformation, which allowed modification of a chromosome locus within 3 days and could be performed continuously for multiple loci.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0605-5) contains supplementary material, which is available to authorized users.