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Centromeres contain specialized nucleosomes at which histone H3 is partially replaced by the centromeric histone H3 variant cenH3 that is required for the assembly, maintenance, and proper function of kinetochores during mitotic and meiotic divisions. Previously, we identified a KINETOCHORE NULL 2 (KNL2) of <i>Arabidopsis thaliana</i> that is involved in the licensing of centromeres for the cenH3 recruitment. We also demonstrated that a knockout mutant for KNL2 shows mitotic and meiotic defects, slower development, reduced growth rate, and fertility. To analyze an effect of <i>KNL2</i> mutation on global gene transcription of <i>Arabidopsis,</i> we performed RNA-sequencing experiments using seedling and flower bud tissues of <i>knl2</i> and wild-type plants. The transcriptome data analysis revealed a high number of differentially expressed genes (DEGs) in <i>knl2</i> plants. The set was enriched in genes involved in the regulation of the cell cycle, transcription, development, and DNA damage repair. In addition to comprehensive information regarding the effects of <i>KNL2</i> mutation on the global gene expression, physiological changes in plants are also presented, which provides an integrated understanding of the critical role played by KNL2 in plant growth and development.