IntroductionBalanced translocations that lead to expression of aberrant fusion proteins are a hallmark of acute leukemias. 1 Many of these fusion proteins function as aberrant transcription factors that are an initiating event in leukemogenesis. 2 Some translocations, eg those involving the MLL gene can lead to phenotypically diverse forms of leukemia, whereas the t(15;17) uniformly leads to acute promyelocytic leukemia. The reasons why some translocations are leukemia-type specific, whereas others are not, is unknown.Histone modifications such as methylation of histone H3 at lysine 4 and 9 and acetylation of histone H3 are closely linked to the transcriptional activation status. In t(15;17), the chimeric PML-RAR␣ fusion protein has been shown to recruit corepressors such as DAXX, histone deacetylase (HDAC) activity, DNA methyltransferase activity, and the SUV39H1 histone methyltransferase to RAR2, the most extensively studied target gene. [3][4][5][6][7] PML-RAR␣ also interacts with histone deacetylase 1. 8 PML-RAR␣ homodimerization has been shown to relax the relatively stringent RAR␣ DNA binding specificity. 9,10 This gain of function is supposed to lead to many additional genomic binding sites that are not well defined. As a consequence, virtually all direct genomic targets of PML-RAR␣ are currently unknown. In addition, on a global level, the mechanistic alterations occurring at PML-RAR␣ target genes remain to be clarified.On a phenotypic level, the PML-RAR␣ fusion protein blocks differentiation and apoptosis and enhances self-renewal. 11,12 In mouse models, PML-RAR␣ induces a disease similar to acute promyelocytic leukemia (APL). 13,14 Microarray analyses elucidated several leukemogenic mechanisms and pathways. [15][16][17][18][19] For example, PML-RAR␣ induces activation of the Wnt signaling pathway. 17 Also, PML-RAR␣ alters the apoptotic response and expression of differentiation genes. 15 However, these studies do not distinguish between direct and indirect effects on gene expression. This knowledge is crucial to understand the mechanistic implications of PML-RAR␣ and to elucidate the reasons for the unique phenotype that is associated with its activities.The possibilities to understand transcription factor functions has recently been significantly improved by genome-wide approaches that identify target genes in vivo using Chromatin immunoprecipitation (ChIP)-Chip approaches. 20,21 In addition, the ability to use this method to map epigenetic modifications such as histone acetylation at promoters known to bind the transcription factor allows for the identification of the functional consequences of transcription factor binding to its genomic targets. 22,23 Using ChIP-chip analyses, we identified 372 direct PML-RAR␣ genomic targets and show that PML-RAR␣ induces heterochromatin formation on virtually all of its identified target genes. Several of the identified genes are known tumor suppressors and for one of the novel genes (S100P), we show a potential role in the PML-RAR␣-associated block in differenti...