A saturating mutagenesis CRISPR-Cas9 mediated functional genomic screen identifies cis- and trans- regulatory elements of Oct4 in embryonic stem cells (sgRNA-seq)

ABSTRACT: Regulatory elements (REs) consist of enhancers and promoters that occupy a significant portion of the non-coding genome and control gene expression programs either in –cis or in –trans. Putative REs have been identified largely based on their regulatory features (co-occupancy of ESC-specific transcription factors, enhancer histone marks and DNase hypersensitivity) in mouse embryonic stem cells (mESCs). However, less has been established regarding their regulatory functions in their native context. We deployed cis- and trans-regulatory elements scanning through saturating mutagenesis and sequencing (ctSCAN-SMS) to target elements within the ~12kb cis-region of the Oct4 gene locus, as well as genome-wide 2,613 high-confidence trans-REs (TREs), in mESCs. The ctSCAN-SMS identified 10 CREs and 12 TREs, as novel candidate REs of the Oct4 gene in mESCs. Furthermore, deletion of these REs confirmed that the majority of the CREs and TREs are functionally active, and involved in regulating Oct4 gene expression. Additionally, a subset of the functional CREs and TREs physically interact with the Oct4 promoter to varying degrees through intra- and inter-chromosomal interactions, respectively. Comparative genomics analysis reveals that functional CREs are more conserved in terms of their regulatory sequence conservation between mouse and primates (including humans) than TREs. Notably, a few active CREs are devoid of canonical regulatory features. Taken together, our work demonstrates the reliability and robustness of ctSCAN-SMS screening to identify critical REs, and probe their roles in the regulation of transcriptional output of a target gene (in this case Oct4).

ORGANISM(S): Mus musculus

PROVIDER: GSE140910 | GEO | 2020/09/28

REPOSITORIES: GEO