Histone chaperones play crucial roles in maintenance of stem cell niche during plant root development.

Stem cells in both plant and animal kingdoms reside in a specialized cellular context called the stem cell niche (SCN). SCN integrity is crucial for organism development. Here we show that the H3/H4 histone chaperone CHROMATIN ASSEMBLY FACTOR-1 (CAF-1) and the H2A/H2B histone chaperone NAP1-RELATED PROTEIN1/2 (NRP1/2) play synergistic roles in Arabidopsis root SCN maintenance. Compared with either the m56-1 double mutant deprived of NRP1 and NRP2 or the fas2-4 mutant deprived of CAF-1, the combined m56-1fas2-4 triple mutant displayed a much more severe short-root phenotype. The m56-1fas2-4 mutant root lost the normal organizing center Quiescent Center (QC), and some initial stem cells differentiated precociously. Microarray analysis unraveled the deregulation of 2735 genes within the Arabidopsis genome (representing >8% of all genes) in the m56-1fas2-4 mutant roots. Expression of some SCN key regulatory genes (e.g. WOX5, PLT1, SHR) was not limiting, rather the plant hormone auxin gradient maximum at QC was impaired. The mutant roots showed programmed cell death and high levels of the DNA damage marked histone H2A.X phosphorylation (γ-H2A.X). Knockout of either ATAXIA-TELANGIECTASIA MUTATED (ATM) or ATR, encoding a DNA damage response kinase, rescued in part the cell death and the short-root phenotype of the m56-1fas2-4 mutant. Collectively, our study indicated that NRP1/2 and CAF-1 act cooperatively in regulating proper genome transcription, in sustaining chromatin replication and in maintaining genome integrity, which are crucial for proper SCN function during continuous post-embryonic root development.