Papers by Ralph Samarista
ABSTRACTAcute Myeloid Leukaemia (AML) is a heterogeneous disease of dismal prognosis, with vulner... more ABSTRACTAcute Myeloid Leukaemia (AML) is a heterogeneous disease of dismal prognosis, with vulnerabilities in epigenetic and metabolic regulation. DNA demethylating agents, e.g. azacytidine (AZA), are used as first-line therapy in AML patients unable to tolerate intensive chemotherapy regimens, often in combination with BCL-2 inhibitor venetoclax. However, the impact on survival is limited, indicating the need for alternative therapeutic strategies. Methyl-group usage for epigenetic modifications depends on methionine availability and MAT2A-driven conversion to S-adenosyl-methionine. Methyl-group production is a vulnerability in multiple tumours, including AML, and has been variably linked to impairment of different histone methyl-modifications. In contrast, we herein align MAT2A effects in AML with DNA methylation and proteostasis. We show that MAT2A inhibition can be mimicked by combining AZA with unfolded protein response (UPR) activation through targeting of valosin-containing p...
Nucleic Acids Research, 2019
The CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting... more The CCCTC-binding factor (CTCF) organises the genome in 3D through DNA loops and in 1D by setting boundaries isolating different chromatin states, but these processes are not well understood. Here we investigate chromatin boundaries in mouse embryonic stem cells, defined by the regions with decreased Nucleosome Repeat Length (NRL) for ∼20 nucleosomes near CTCF sites, affecting up to 10% of the genome. We found that the nucleosome-depleted region (NDR) near CTCF is asymmetrically located >40 nucleotides 5′-upstream from the centre of CTCF motif. The strength of CTCF binding to DNA and the presence of cohesin is correlated with the decrease of NRL near CTCF, and anti-correlated with the level of asymmetry of the nucleosome array. Individual chromatin remodellers have different contributions, with Snf2h having the strongest effect on the NRL decrease near CTCF and Chd4 playing a major role in the symmetry breaking. Upon differentiation, a subset of preserved, common CTCF sites maint...
Epigenetic histone modifiers are key regulators of cell fate decisions in normal and malignant he... more Epigenetic histone modifiers are key regulators of cell fate decisions in normal and malignant hematopoiesis. Their enzymatic activities are of particular significance as putative therapeutic targets in leukemia. In contrast, less is known about the contextual role in which those enzymatic activities are exercised, and specifically, how different macromolecular complexes configure the same enzymatic activity with distinct molecular and cellular consequences. We focus on KAT2A, a lysine acetyltransferase responsible for Histone 3 Lysine 9 acetylation, which we recently identified as a dependence in Acute Myeloid Leukemia stem cells, and that participates in 2 distinct macromolecular complexes: Ada Two-A-Containing (ATAC) and Spt-Ada-Gcn5-Acetyltransferase (SAGA). Through analysis of human cord blood hematopoietic stem cells and progenitors, and of myeloid leukemia cells, we identify unique respective contributions of the ATAC complex to regulation of biosynthetic activity in undiffer...
Nucleosome repeat length (NRL) defines the average distance between adjacent nucleosomes. When ca... more Nucleosome repeat length (NRL) defines the average distance between adjacent nucleosomes. When calculated for specific genomic regions, NRL reflects the local nucleosome ordering and characterises its changes during developmental processes. The architectural protein CTCF provides one of the strongest nucleosome positioning signals, setting a decreased NRL for ~20 nucleosomes in its vicinity (thus affecting up to 10% of the mouse genome). We show that upon differentiation of mouse embryonic stem cells (ESCs) to neural progenitor cells and mouse embryonic fibroblasts, a subset of common CTCF sites preserved in all three cell types keeps small NRL despite genome-wide NRL increase. This suggests that differential CTCF binding not only affects 3D genome organisation but also defines genomic regions with conserved nucleosome arrangement. Our analysis revealed that NRL decrease near CTCF is correlated with CTCF affinity for DNA binding. Stronger CTCF binding is linked to increased probabil...
Nucleosome repeat length (NRL) defines the average distance between adjacent nucleosomes. When ca... more Nucleosome repeat length (NRL) defines the average distance between adjacent nucleosomes. When calculated for specific genomic regions, NRL reflects the local nucleosome ordering and characterises its changes during developmental processes. The architectural protein CTCF provides one of the strongest nucleosome positioning signals, setting a decreased NRL for ~20 nucleosomes in its vicinity (thus affecting up to 10% of the mouse genome). We show that upon differentiation of mouse embryonic stem cells (ESCs) to neural progenitor cells and mouse embryonic fibroblasts, a subset of common CTCF sites preserved in all three cell types keeps small NRL despite genome-wide NRL increase. This suggests that differential CTCF binding not only affects 3D genome organisation but also defines genomic regions with conserved nucleosome arrangement. Our analysis revealed that NRL decrease near CTCF is correlated with CTCF affinity for DNA binding. Stronger CTCF binding is linked to increased probabil...
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Papers by Ralph Samarista