Figure 1.

Zfp281 suppresses a subset of retrotransposons in mouse ES cells. (A) Fold change (log₂) of retrotransposon expression (RPKM) after Zfp281 depletion in mouse ES cells. The consensus sequences of retrotransposons (extracted from RepBase) (54) were used to calculate their expression change. Other repeat elements, L1 and LTR sequences are color-coded. (B) Zfp281 occupies L1 and LTR repeat elements. For each repeat family, numbers of Zfp281 peaks overlapped with genomic instances of the given family were shown in x-axis. Fisher Exact Test was used to evaluate the significance of overlaps. P-values of Fisher Exact Test were calculated by FISHER in BEDTOOLS, and further adjusted for multiple testing and shown in y-axis. (C–E) Genome browser profiles showing the occupancy of Zfp281, H3K9me3 and H3K4me3 at repeat elements. Red box marks the co-occupied regions by Zfp281 and H3K9me3. Blue box marks the co-occupied regions by Zfp281 and H3K4me3.