UHRF1 coordinates DNA methylation and histone post-translational modifications in colon cancer .

In Colorectal cancer (CRC) genetic and epigenetic alterations are tightly connected, although these interactions on the patient’s outcome are not clearly understood. A peculiar subclass of sporadic CRC tumors, is characterized by Microsatellite instability (MSI), due to hyper-methylated promoter of MHL1 gene and subsequent inactivation of the mismatch repair (MMR) mechanism, and the hypermethylation of CpG islands phenotype (CIMP), mediated by the hyper-methylation of promoter regions of several tumor suppressor genes (TSGs). This subclass carries a good prognosis and presents an inverse correlation with genomic and chromosome instability (CIN), together with a higher levels of DNA methylation at global level, compared to other CRCs. Among the epigenetic alterations, DNA methylation and histone modifications rearrangements are extremely important steps during tumorigenesis. UHRF1 is a key master epigenetic regulator that couples the maintenance of DNA methylation through the cell cycle with the histone-modification pattern. It monoubiquitinates H3K18/23 enabling the correct localization and activation of DNMT1 on the specific sites. UHRF1 is overexpressed in several cancer types mediating the hypermethylation of promoter regions of the TSGs and coordinating their heterochromatic silencing. Relying on the idea that UHRF1 could play a crucial role in the modulation of DNA methylation changes, the overall aim of this PhD thesis was to evaluate the role of UHRF1 in the coordination of DNA methylation and histone post-translational modifications both at genome-wide and at locus specific level in CRCs. Unexpectedly, we found that in CRC tissues UHRF1 was higher in tumors with microsatellite instability (MSI CRC), which have a better prognosis, compared to the stable ones (MSS CRC). MSI tumors were also characterized by higher levels of DNA methylation compared to the MSS. The UHRF1 knock-down in a MSI CRC cell line (RKO cells) induced an overall decrease in DNA methylation (RRB-seq analysis, pyrosequencing and MS-MLPA) both at global level and at gene promoters without affecting DNMTs levels, as observed by WB and RNA-seq analysis. ChIP experiments showed that UHRF1 depletion reduces DNMT1 binding to both repetitive elements (LINE-1) and specific gene promoters (MLH1, CDH1), decreasing H3K9me3 and increasing H3K4me3 on those hypo-methylated loci. RNA-seq data analysis showed that UHRF1 loss interferes with several important pathways, among others cell cycle, growth and proliferation. SILAC LC-MS/MS analysis showed that in RKO cells, UHRF1 loss decreases the overall presence of H3K23ub (» 30%) and H3K18ub (» 8%). These results, together with the published findings, led us to hypothesize a model in which the loss of UHRF1 directly impairs the DNA methylation maintenance by reducing H3K18/K23ub and consequently DNMT1 activity and, indirectly, impairs the binding of Suv39H1, the histone methyl transferase (HMT) responsible for H3K9me3, to both genome-wide and promoter specific loci. These changes led to a severe chromatin rearrangement of heterochromatic signatures toward a more open and transcriptionally accessible structure, probably due to the disruption of the axis UHRF1-H3ub-DNMT1-HMTs. Our molecular data, together with the analysis performed on CRC samples, led us to speculate that the better prognosis correlated with MSI-CRC model, could reside in the UHRF1-high levels that result in a sort of protective condition for the genome integrity, maintaining the global DNA methylation level closer to the normal mucosae, and probably counteracting the hyper-methylation of TSGs.