SUMMARY Human APOBEC3H and homologous single-stranded DNA cytosine deaminases are unique to mammals. These DNA editing enzymes function in innate immunity by restricting the replication of viruses and transposons. APOBEC3H also contributes to cancer mutagenesis. Here we address the fundamental nature of RNA in regulating human APOBEC3H activities. APOBEC3H co-purifies with RNA as an inactive protein, and RNase A treatment enables strong DNA deaminase activity. RNA binding-defective mutants demonstrate clear separation-of-function by becoming DNA hypermutators. Biochemical and crystallographic data demonstrate a mechanism in which double-stranded RNA mediates enzyme dimerization. Additionally, APOBEC3H separation-of-function mutants show that RNA binding is required for cytoplasmic localization, packaging into HIV-1 particles, and antiviral activity. Overall, these results support a model in which structured RNA negatively regulates the potentially harmful DNA deamination activity of APOBEC3H, while at the same time positively regulating its antiviral activity.

The APOBEC3 family of antiviral DNA cytosine deaminases is implicated as the second largest source of mutation in cancer. This mutational process may be a causal driver or inconsequential passenger to the overall tumor phenotype. We show that human APOBEC3A expression in murine colon and liver tissues increases tumorigenesis. All other APOBEC3 family members, including APOBEC3B, fail to promote liver tumor formation. Tumor DNA sequences from APOBEC3A-expressing animals display hallmark APOBEC signature mutations in TCA/T motifs. Bioinformatic comparisons of the observed APOBEC3A mutation signature in murine tumors, previously reported APOBEC3A and APOBEC3B mutation signatures in yeast, and reanalyzed APOBEC mutation signatures in human tumor datasets support cause-and-effect relationships for APOBEC3A-catalyzed deamination and mutagenesis in driving multiple human cancers.

There is ample evidence that somatic cell differentiation during development is accompanied by extensive DNA demethylation of specific sites that vary between cell types. Although the mechanism of this process has not yet been elucidated, it is likely to involve the conversion of 5mC to 5hmC by Tet enzymes. We show that a Tet2/ Tet3 conditional knockout at early stages of B-cell development largely prevents lineage-specific programmed demethylation events. This lack of demethylation affects the expression of nearby B-cell lineage genes by impairing enhancer activity, thus causing defects in B-cell differentiation and function. Thus, tissue-specific DNA demethylation appears to be necessary for proper somatic cell development in vivo.NA methylation takes place at almost all stages of development including the early embryo as well as during lineage commitment and is mediated through a combination of active and passive processes. Recent studies have raised the possibility that demethylation can occur through the involvement of the teneleven-translocation family (Tet1, Tet2, and Tet3) that catalyzes the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) as a first step in the pathway (1, 2). Removal of this unusual base may then be accomplished either by further oxidation followed by base excision repair (3) or through replication dilution (4-6). Genetic experiments have demonstrated that Tet enzymes are key players during early development, with Tet3-mediated DNA hydroxylation being involved in epigenetic programming of the zygotic paternal DNA (7, 8), whereas combinations of Tet1 and Tet2 play a role in the demethylation process that takes place during embryonic stem cell differentiation in vitro (2, 9-12).Tet enzymes also contribute to lineage development. Thus, changes in the pattern of 5hmC have been shown to accompany neurogenesis in vivo (13) (21)] appear to alter global 5hmC and 5mC distribution, perturb stem cell self-renewal, cause altered differentiation, and predispose to malignancies (refs. 19, 22, reviewed in ref. 23). None of these studies, however, has addressed the key question of whether demethylation itself is actually required for gene activation and proper lineage differentiation. To this end, we generated a Tet2/Tet3 knockout specific to B-lymphoid development, isolated cells at different stages of differentiation, and analyzed their methylation patterns. Because this approach targets the demethylation machinery in an exclusive manner, it allowed us to evaluate the role of this modification independently of the many transcription factors that drive the process of B-cell differentiation. ResultsIt has already been shown that both Tet2 and Tet3 are highly expressed in B lineage cells (24). With this in mind, we generated Tet2F mice (18, 23) and crossed them with animals expressing Cre under control of the early B-cell-specific Mb1 promoter (25) to obtain mice with a conditional knockout of these enzymes specifically in the B-cell lineage (Materials and Methods). Reduced repres...

Development in mammals is accompanied by specific de novo and demethylation events that are thought to stabilize differentiated cell phenotypes. We demonstrate that a large percentage of the tissue-specific methylation pattern is generated postnatally. Demethylation in the liver is observed in thousands of enhancer-like sequences associated with genes that undergo activation during the first few weeks of life. Using a conditional gene ablation strategy we show that the removal of these methyl groups is stable and necessary for assuring proper hepatocyte gene expression and function through its effect on chromatin accessibility. These postnatal changes in methylation come about through exposure to hormone signaling. These results define the molecular rules of 5-methyl-cytosine regulation as an epigenetic mechanism underlying cellular responses to a changing environment.