ATX1/AtCOMPASS and the H3K4me3 marks: how do they activate Arabidopsis genes?

•The Trithorax proteins as epigenetic regulators and chromatin modifiers.•The distribution of H3K4me3, ATX1, AtCOMPASS, and Pol II at transcriptionally active genes.•H3K4me3 is required for efficient transition to elongation.•How does H3K4me3 affect elongation?•Similarities and differences in the molecular machinery establishing the H3K4me3 marks in yeast, animals, and Arabidopsis.

Despite the proven correlation between gene transcriptional activity and the levels of tri-methyl marks on histone 3 lysine4 (H3K4me3) of their nucleosomes, whether H3K4me3 contributes to, or ‘registers’, activated transcription is still controversial. Other questions of broad relevance are whether histone-modifying proteins are involved in the recruitment of Pol II and the general transcription machinery and whether they have roles other than their enzyme activities. We address these questions as well as the roles of the ARABIDOPSIS HOMOLOG OF TRITHORAX1 (ATX1), of the COMPASS-related (AtCOMPASS) protein complex, and of their product, H3K4me3, at ATX1-dependent genes. We suggest that the ambiguity about the role of H3K4me3 as an activating mark is due to the unknown duality of the ATX1/AtCOMPASS to facilitate PIC assembly and to generate H3K4me3, which is essential for activating transcriptional elongation.