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Background  Polycomb group complexes PRC1 and PRC2 repress gene expression at the chromatin level in eukaryotes. The classic recruitment model of Polycomb group complexes in which PRC2-mediated H3K27 trimethylation recruits PRC1 for H2A monoubiquitination was recently challenged by data showing that PRC1 activity can also recruit PRC2. However, the prevalence of these two mechanisms is unknown, especially in plants as H2AK121ub marks were examined at only a handful of Polycomb group targets.    Results  By using genome-wide analyses, we show that H2AK121ub marks are surprisingly widespread in  Arabidopsis thaliana , often co-localizing with H3K27me3 but also occupying a set of transcriptionally active genes devoid of H3K27me3. Furthermore, by profiling H2AK121ub and H3K27me3 marks in  atbmi1a/b/c ,  clf/swn , and  lhp1  mutants we found that PRC2 activity is not required for H2AK121ub marking at most genes. In contrast, loss of AtBMI1 function impacts the incorporation of H3K27me3 marks at most Polycomb group targets.    Conclusions  Our findings show the relationship between H2AK121ub and H3K27me3 marks across the  A. thaliana  genome and unveil that ubiquitination by PRC1 is largely independent of PRC2 activity in plants, while the inverse is true for H3K27 trimethylation.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-017-1197-z) contains supplementary material, which is available to authorized users.

H2A monoubiquitination in Arabidopsis thaliana is generally independent of LHP1 and PRC2 activity