Skip to main content
Fig. 2 | BMC Genomics

Fig. 2

From: The Krüppel-like factor 9 cistrome in mouse hippocampal neurons reveals predominant transcriptional repression via proximal promoter binding

Fig. 2

Identification of genome-wide association of Klf9 in HT22 cell chromatin using chromatin-streptavidin precipitation sequencing. a HT22 [BirA/FLBIO-Klf9] cells express biotinylated Klf9. Whole cell extracts from the HT22 parent cell line (lane 1), HT22 [BirA] cells (lane 2) or HT22 [BirA/FLBIO-Klf9] (lane 3) were fractionated on 10% SDS-PAGE and analyzed by Western blotting using streptavidin-HRP. b Chromatin-streptavidin precipitation gives ~25-fold enrichment at the Klf13 promoter in HT22 [BirA/FLBIO-Klf9] cells compared with HT22 [BirA] cells. Precipitated DNA was analyzed by qPCR at the Klf13 promoter and intron (negative control region). The asterisk indicates a statistically significant difference by Student’s two-sample t-test (p < .0005). c Genome Browser (University of California, Santa Cruz) views showing the location of Klf9 peaks at eight Klf9-repressed genes. Top track = reads from cells expressing BirA alone; bottom track = cells expressing BirA + FLBIO-Klf9. The 5′ flanking region of each locus is shown; bars below the peaks represent exons, lines represent introns. d Validation of ChSP-seq peaks (shown in C) by targeted ChSP with quantitative PCR. Chromatin isolated from HT22 [BirA] and HT22 [BirA/FLBIO-Klf9] cells is compared. The asterisks indicate statistically significant differences analyzed by Student’s two-sample t-test (p < .005). e Klf9 associates with the same genomic loci in mouse hippocampus in vivo as in HT22 cells. Targeted chromatin immunoprecipitation (ChIP) assays for Klf9 were conducted on chromatin isolated from adult mouse hippocampus. The asterisks indicate statistically significant differences from the normal goat serum (NGS) IgG control analyzed by Student’s two-sample t-test (p < .05)

Back to article page