Loss of TET is associated with global DNA hypomethylation and regional DNA hypermethylation

Paradoxical association of TET loss of function with genome-wide DNA hypomethylation

Isaac F López-Moyado  1   2   3 Ageliki Tsagaratou  1 Hiroshi Yuita  1 Hyungseok Seo  1 Benjamin Delatte  1 Sven Heinz  4 Christopher Benner  4 Anjana Rao  5   3   6   7 Affiliations

Significance

Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. We show that TET deficiency in diverse cell types (ESCs, NPCs, HSCs, pro-B cells, and T cells) results in a similar methylation landscape, with the expected localized increases in DNA methylation in active euchromatic regions, concurrently with unexpected losses of DNA methylation, reactivation of repeat elements, and enrichment for single-nucleotide alterations primarily in heterochromatic compartments. Thus, TET loss of function may be a primary mechanism underlying the characteristic pattern of global hypomethylation coupled to regional hypermethylation observed in diverse cancer genomes. Our data potentially explain the synergy between DNMT3A and TET2 mutations in hematopoietic malignancies, as well as the recurrent association of TET loss of function with cancer.

Abstract

Cancer genomes are characterized by focal increases in DNA methylation, co-occurring with widespread hypomethylation. Here, we show that TET loss of function results in a similar genomic footprint. Both 5hmC in wild-type (WT) genomes and DNA hypermethylation in TET-deficient genomes are largely confined to the active euchromatic compartment, consistent with the known functions of TET proteins in DNA demethylation and the known distribution of 5hmC at transcribed genes and active enhancers. In contrast, an unexpected DNA hypomethylation noted in multiple TET-deficient genomes is primarily observed in the heterochromatin compartment. In a mouse model of T cell lymphoma driven by TET deficiency (Tet2/3 DKO T cells), genomic analysis of malignant T cells revealed DNA hypomethylation in the heterochromatic genomic compartment, as well as reactivation of repeat elements and enrichment for single-nucleotide alterations, primarily in heterochromatic regions of the genome. Moreover, hematopoietic stem/precursor cells (HSPCs) doubly deficient for Tet2 and Dnmt3a displayed greater losses of DNA methylation than HSPCs singly deficient for Tet2 or Dnmt3a alone, potentially explaining the unexpected synergy between DNMT3A and TET2 mutations in myeloid and lymphoid malignancies. Tet1-deficient cells showed decreased localization of DNMT3A in the heterochromatin compartment compared with WT cells, pointing to a functional interaction between TET and DNMT proteins and providing a potential explanation for the hypomethylation observed in TET-deficient genomes. Our data suggest that TET loss of function may at least partially underlie the characteristic pattern of global hypomethylation coupled to regional hypermethylation observed in diverse cancer genomes, and highlight the potential contribution of heterochromatin hypomethylation to oncogenesis.

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