Mutations of leukemia-associated AF9/MLLT3 are implicated in neurodevelopmental diseases, such as epilepsy and ataxia, but little is known about how AF9 influences brain development and function. Analyses of mouse mutants revealed that during cortical development, AF9 is involved in the maintenance of TBR2-positive progenitors (intermediate precursor cells, IPCs) in the subventricular zone and prevents premature cell cycle exit of IPCs. Furthermore, in postmitotic neurons of the developing cortical plate, AF9 is implicated in the formation of the six-layered cerebral cortex by suppressing a TBR1-positive cell fate mainly in upper layer neurons. We show that the molecular mechanism of TBR1 suppression is based on the interaction of AF9 with DOT1L, a protein that mediates transcriptional control through methylation of histone H3 lysine 79 (H3K79). AF9 associates with the transcriptional start site of Tbr1, mediates H3K79 dimethylation of the Tbr1 gene, and interferes with the presence of RNA polymerase II at the Tbr1 transcriptional start site. AF9 expression favors cytoplasmic localization of TBR1 and its association with mitochondria. Increased expression of TBR1 in Af9 mutants is associated with increased levels of TBR1-regulated expression of NMDAR subunit Nr1. Thus, this study identified AF9 as a developmental active epigenetic modifier during the generation of cortical projection neurons.A F9/MLLT3 is one of multiple fusion partners of the histone methyltransferase MLL1 in acute leukemia (1, 2). However, mutations of the AF9/MLLT3 gene alone are not associated with leukemia but are implicated in anterior homeotic transformations during mouse development (3), and in neurodevelopmental diseases, such as mental retardation, epilepsy, and ataxia in human patients (4,5). Little is known about AF9 function in the CNS, although its expression pattern implies a role during development of the forebrain and cerebellum (6). In the mouse forebrain, Af9 is transcribed in the subventricular zone (SVZ), a neurogenic compartment that harbors progenitors for upper layer neurons (7,8). Af9 is also expressed in neurons dispersed over all cortical layers and diverges in this respect from other SVZ markers, such as Svet1 and Cux2 (6). On the molecular level, AF9 mediates transcriptional activation and was classified as a proto-oncogene (9). The AF9 protein interacts with many different factors and has been implicated in different cellular processes (9-11). In the extensive network of interacting proteins, AF9 associates with DOT1L (12, 13), the main enzyme responsible for histone H3 methylation at lysine 79 (14-16). Dot1 is implicated in UV damage repair (17), and affects gene expression in yeast, flies, and mammals (18, 19), whereas histone H3 lysine 79 (H3K79) methylation correlates with gene activation (20) and suppression (21). Following this line, AF9-DOT1L complexes mediate transcriptional activation through increased levels of dimethylated H3K79 (13), but are also capable of transcriptional repression through hypermethyla...