表观遗传机制对于在哺乳动物中建立和保护细胞身份至关重要。它们动态调控基因、可移动元件和高阶染色质结构的表达。因此，这些染色质标记对于哺乳动物的发育至关重要，而其改变通常会导致疾病，如癌症。在分化和发育过程中，二项式启动子尤其重要。在这里，我们使用遗传筛选来鉴定新的二项式抑制基因调控剂。我们发现BEND3是数百个二项式启动子的调控剂，其中它一部分是抑制的，一部分是激活的。我们展示了BEND3被招募到存在于许多二项式启动子中的含CpG的共识位点。除了对其结合的启动子有直接影响外，失去BEND3会导致全基因组范围内DNA甲基化的增加，在通常由TET酶保护的区域尤为显著。Bend3突变细胞中DNA羟甲基化减少，可能是由于基因表达改变导致α-酮戊二酸产生减少，从而降低了TET酶的活性。我们的结果澄清了一个重要染色质调控因子BEND3的直接和间接作用，并且更广泛地揭示了二项式启动子的调控机制。© 2023作者。由牛津大学出版社代表核酸研究发表。

Epigenetic mechanisms are essential to establish and safeguard cellular identities in mammals. They dynamically regulate the expression of genes, transposable elements and higher-order chromatin structures. Consequently, these chromatin marks are indispensable for mammalian development and alterations often lead to disease, such as cancer. Bivalent promoters are especially important during differentiation and development. Here we used a genetic screen to identify new regulators of a bivalent repressed gene. We identify BEND3 as a regulator of hundreds of bivalent promoters, some of which it represses, and some of which it activates. We show that BEND3 is recruited to a CpG-containg consensus site that is present in multiple copies in many bivalent promoters. Besides having direct effect on the promoters it binds, the loss of BEND3 leads to genome-wide gains of DNA methylation, which are especially marked at regions normally protected by the TET enzymes. DNA hydroxymethylation is reduced in Bend3 mutant cells, possibly as consequence of altered gene expression leading to diminished alpha-ketoglutarate production, thus lowering TET activity. Our results clarify the direct and indirect roles of an important chromatin regulator, BEND3, and, more broadly, they shed light on the regulation of bivalent promoters.© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.