Epigenetic alterations, including gain or loss of DNA methylation, are a hallmark of nearly every malignancy. Changes in DNA methylation can impact expression of cancer-related genes including apoptosis regulators and tumor suppressors. Because such epigenetic changes are reversible, they are being aggressively investigated as potential therapeutic targets. Here we use the E-TCL1 transgenic mouse model of chronic lymphocytic leukemia (CLL) to determine the timing and patterns of aberrant DNA methylation, and to investigate the mechanisms that lead to aberrant DNA methylation. We show that CLL cells from E-TCL1 mice at various stages recapitulate epigenetic alterations seen in human CLL. Aberrant methylation of promoter sequences is observed as early as 3 months of age in these animals, well before disease onset. Abnormally methylated promoter regions include binding sites for the transcription factor FOXD3. We show that loss of Foxd3 expression due to an NF-B p50/p50:HDAC1 repressor complex occurs in TCL1-positive B cells before methylation. Therefore, specific transcriptional repression is an early event leading to epigenetic silencing of target genes in murine and human CLL. These results provide strong rationale for the development of strategies to target NF-B components in CLL and potentially other B-cell malignancies.CLL ͉ DNA methylation ͉ epigenetics ͉ FOXD3 E pigenetic alterations in cancer receive great attention since their contributions to tumor development and progression have now been documented (1). Major questions in the field relate to formation of global patterns of epigenetic alterations, the mechanisms that lead to epigenetic changes and the role of target genes in healthy tissues (2). Epigenetics, or the inheritance of gene expression patterns through mechanisms that do not change the DNA sequence, were initially investigated by measurement of DNA methylation occurring at cytosine residues. However, it is also clear that additional epigenetic factors such as histone tail modifications or small RNAs cooperate in the epigenetic regulation of genes (3, 4). DNA methylation in mammals occurs predominantly at cytosine residues, creating a 5-methylcytosine. The covalent addition of a methyl group to cytosine is stable from fixation processes and therefore allows high-throughput genome-wide or gene-specific quantification of DNA methylation on archived samples (5).DNA methylation abnormalities, especially gain of methylation in normally unmethylated promoter or other regulatory regions (hypermethylation) or loss of methylation in normally methylated repetitive sequences (hypomethylation), have been described for almost all human tumor types as well as tumors from animal models, suggesting a general mechanism in cancer that leads to aberrant DNA methylation. However, there is evidence that individual patterns of aberrant methylation are tumor-type specific and non-random, thus arguing for additional tissue-specific mechanisms (6). Based on in vitro studies, several groups have put forward mechanisms o...