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Epigenome is the set of DNA-associated proteins or chemical modifications to DNA, which regulates gene expression in processes of development and disease. While current advances have allowed researchers to routinely profile epigenomes from given samples, our understandings of the functions of epigenetic hallmarks are nonspecific at best. Applying CRISPR-screening to genome-widely interrogate the function of individual epigenetic hallmarks demands massive sgRNA libraries which are unaffordable via commercial syntheses. Our development consists of a high throughput and cost-effective controlled template-dependent elongation (CTDE) approach which converts source DNA to sgRNA templates. Affiliated screenings encompass 3.8M sgRNAs generated by CTDE targeting all major H3K4me3 and CTCF hallmarks in mESCs and HepG2 and identified 20K essential epigenetic hallmarks, which render the first batch of functional epigenome annotation of H3K4me3 and CTCF hallmarks in mammals. As an application example, we show that a H3K4me3 hallmark orchestrates CDC42 level and cell-cycle progression through promoting LINC00339 expression in HepG2.