The inconsistent impact of nanomaterials on different plant species has been reported, but little is known about this effect at the cellular and genetic levels. Here we report that single-walled carbon nanotubes (SWCNTs) accelerate maize seminal root growth, but display little effect on the primary root growth. In contrast, root hair growth inhibition by SWCNTs is observed. Further gene transcription analysis shows that SWCNTs could increase the expression of seminal root associated genes whereas decrease root hair associated gene expression. Their effect is on both tissue and gene selectiveness since both enhanced and inhibited gene expression and tissue growth are observed during root development. Microscopy images reveal the distribution of SWCNTs inside the root and mainly in the intercellular space in cortex tissues. We also find that SWCNT-treatment dynamically and selectively induces the up-regulation of epigenetic modification enzyme genes, leading to global deacetylation of histone H3, similar to the response of plants to other stress. Our results suggest that the nanoparticle-root cell interaction could cause the change in gene expression, and consequently affect relative root growth and development. (C) 2012 Elsevier B.V. All rights reserved.