Fig. 4: NDX is preferentially associated with constitutive heterochromatin.

a Functional annotation of flag-NDX, NDX-GFP, and DRIP (R-loop) binding sites over genomic features. Cells contain observed/expected ratios for peak counts. Warmer colors represent higher enrichment. b DNA transposon and retrotransposon families associated with NDX and DRIP peaks. (Only families showing significant enrichment of ChIP or DRIP peaks are shown.) c Enrichment of NDX and DRIP peaks over the functional categories of TEs. CMT2 TEs were compared to those controlled by the RdDM pathway or both pathways (intermediate TEs). TE categories were further classified as pericentromeric and arm-associated. NA: lack of statistical power due to very low peak count in the indicated category. d The same annotation as above for histone modifications, and e chromatin states. The nine chromatin states were defined by the combinatorial pattern of epigenetic modifications and transcription⁵⁰.