Fig. 5: NDX binds to heterochromatic small RNA loci (het-siRNA).
From: NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis
a Chromosomal distribution of flag-NDX binding sites (green), RNA-DNA hybrids (red), and small RNA loci. sRNA loci are classified into nine functional clusters based on their genetic and epigenetic relationships and expression profiles51. NDX-binding sites correlate with cluster 6–9 sRNA loci while R-loops are correlated with cluster 1–2 sRNA loci. b Overlap of flag-NDX, NDX-GFP, and DRIP peaks with sRNA clusters relative to random associations. Cells contain observed/expected ratios for peak counts. Warmer colors indicate higher degree of association. c Metaplot analysis of NDX ChIP signal over sRNA loci 1–5 and 6–9. sRNA loci 6–9 have been divided by chromosomal location as pericentromeric and arm associated. The NDX ChIP signal is preferentially enriched in pericentromerically located sRNA 6–9 loci, however, their binding affinity for NDX is heterogeneous. d Left: ChIP-qPCR validation of representative sRNA loci that are bound by NDX. Specific ChIP signal and background signal (“no tag”) is shown in green and grey. Error bar: SEM. Sample size n = 2 biologically independent experiments. Right: JBrowse snapshot of the test regions.
