Previously, we had identified HISTONE MONOUBIQUITINATION1 (HUB1) as an unconventional ubiquitin E3 ligase that was not involved in protein degradation but in histone H2B modification implicated in transcription activation in plants. HUB1-mediated regulation of gene expression played a role in periodic and inducible processes such as cell cycle, dormancy, flowering time and defense responses. Here, we determined the effects of hub1-1 mutation on the expression of a set of diurnally induced circadian clock genes identified from a comparative microarray analysis between the hub1-1 mutant and the HUB1 overexpression line. The hub1-1 mutation reduced the amplitudes of a number of induced clock gene expression peaks as well as the HUB1-mediated histone H2BUb mark and the H3K4Me3 mark associated with the coding regions suggesting a role for HUB1 in facilitating transcription elongation in plants. Furthermore, double mutants between hub1-1 and elongator mutants showed genetic interaction as enhancement, typical for multigenic traits. The double mutant embryos arrested at the torpedo stage suggesting that both histone ubiquitination and acetylation marks are essential to activate expression of target genes in multiple pathways.