Acute Myeloid Leukemia (AML) is a group of severe hematological malignancies with dismal outcome, as most patients relapse after initial treatment. We have shown that SUMOylation, a post-translational modification of the ubiquitin family plays an important role in AML response to both chemotherapies (Bossis et al, Cell Reports, 2014) and differentiation therapies (Baik et al, Cancer Research, 2018), through its ability to regulate the expression of specific transcriptional programs. Combining proteomic, transcriptomic and genomic studies, we now show that one of the earliest effects of daunorubicin, one of the main chemotherapeutic drug used in AMLs, is a rapid transcriptional reprogramming, which primarily affects the expression of genes involved in cell death control and inflammation. Preceding transcriptome changes, DNR induces a massive decrease in the presence of SUMOylated proteins on chromatin, in particular at gene promoters, which participates in transcriptional regulation. The most rapidly deSUMOylated proteins are primarily transcription factors, transcriptional co-regulators and chromatin organizers. These include the CCCTC-binding factor CTCF that is particularly enriched at SUMO-binding sites in the promoters of genes regulated by DNR. Importantly, DNR-induced deSUMOylation at CTCF binding sites plays an important role in the activation of DNR-responsive genes.