Extended Data Fig. 7: Two distinct DNA binding motifs of KLF4.
From: Aging disrupts circadian gene regulation and function in macrophages
a, b. Circadian expression levels measured by RNA-seq of KLF family members Klf9 and Klf13. Data are mean ± s.e.m, n = 21 mice in each age group and n = 3 in each time group. p-values determined by JTK_CYCLE on normalized expression values. c, d. Depiction of the two known KLF4 binding motifs, MA0039.1 and MA0039.2. q-values from de novo motif discovery on a KLF4 ChIP-seq experiment from ENCODE (https://factorbook.org/experiment/ENCSR265WJC/motif). e. chromVAR30 deviations within all 500 bp peaks indicating KLF4 binding by estimating accessibility within peaks sharing the MA0039.2 motif or annotation. p = 0.935, two-sided Mann-Whitney U test. f. chromVAR30 deviations within peaks associated with differentially rhythmic genes indicating KLF4 binding by estimating accessibility within peaks sharing the MA0039.2 motif or annotation. p = 0.654, two-sided Mann-Whitney U test. (e, f) n = 15-16 mice in each age group and n = 2-3 mice per 4 h time interval. Boxes extend from the 25th-75th percentiles, whiskers extend to 1.5 times the IQR, and the center line is the median.
