Fig. 3: Genome-wide RNA-seq analysis indicates that the expression of SFTPB induced by NKX2-1 is most significantly repressed by CRISPRi targeting the first intron of SFTPB that is an ATAC-inaccessible region.
From: CRISPRi-mediated functional analysis of NKX2-1-binding sites in the lung
a Shown are pie charts that indicate the number of NKX2-1 ChIP-seq peaks and ATAC-seq peaks in A549 cells. A portion (but not all) of the NKX2-1-binding sites are located in ATAC-accessible genomic regions. b Shown is an MA plot that indicates differential gene expression regulated by CRISPRi targeting the first intron (#2) of SFTPB, which was analyzed by RNA-seq using RNA from A549 cells that express dCas9-KRAB and NKX2-1 with sgRNA #2 or the sgRNA control as described in Fig. 2b. Biologically independent triplicates were used for each group (sgRNA #2 or sgRNA control). Red points represent genes with log2 fold change ≦1 or ≧−1; padj <0.05. The expression of SFTPB was most significantly repressed (log2 fold change −5.96; p value 2.06E−257; padj 3.06E−253) while the expression of LAMP3 was weakly repressed (log2 fold change −1.85; p value 2.64E−03; padj 1.00E + 00).
