Chromosomal translocation t(9;11)(p22;q23) in acute myeloid leukemia fuses the MLL and AF9 genes. We have inactivated the murine homologue of AF9 to elucidate its normal role. No effect on hematopoiesis was observed in mice with a null mutation of Af9. However, an Af9 null mutation caused perinatal lethality, and homozygous mice exhibited anomalies of the axial skeleton. Both the cervical and thoracic regions were affected by anterior homeotic transformation. Strikingly, mice lacking functional Af9 exhibited a grossly deformed atlas and an extra cervical vertebra. To determine the molecular mediators of this phenotype, analysis of Hox gene expression by in situ hybridization showed that Af9 null embryos have posterior changes in Hoxd4 gene expression. We conclude that the Af9 gene is required for normal embryogenesis in mice by controlling pattern formation, apparently via control of Hox gene regulation. This is analogous to the role of Mll, the murine homolog of human MLL, to which the Af9 gene fuses in acute myeloid leukemias.The consequence of chromosomal translocations in human cancer is to cause enforced expression of proto-oncogenes or the creation of tumor-specific fusion genes (reviewed in reference 52). Chromosomal translocations often involve transcription regulators (9) which function as master regulators of cell fate in their normal situations of expression (53). Human AF9 was identified as one of the most common fusion partners of the mixed-lineage leukemia protein (MLL, also called HTRX and ALL-1) (14,20,63,70) and is most usually associated with acute myeloid leukemias (AML). MLL fusion proteins are present in approximately 10% of acute lymphoid leukemias and myeloid leukemias (42) and in up to 80% of leukemias in infants (33, 51), as well as in 85% of cases of secondary leukemias developing after treatment of a primary tumor with alkylating agents or topoisomerase II inhibitors (3,8,61). In an individual leukemia, the fusion protein results from one of a variety of reciprocal chromosomal translocations, causing the association of upstream exons of the MLL gene on chromosome 11, band q23, with downstream exons of the partner gene, generally on a separate chromosome. MLL is a human homologue of Drosophila melanogaster trithorax (trx), a master homeotic gene regulator essential for normal patterning during embryo development (2, 43). Gene-targeting studies have demonstrated a similar role for MLL in mammals (17,21,67,69).More than 30 different MLL fusions have been identified (28), and these code for a structurally and functionally heterogeneous group of proteins (reviewed in references 1 and 10). However, different MLL fusion proteins are consistently associated with hematopoietic tumors of different lineages. Thus, whereas MLL-AF9 is mainly found in AML, the translocation involving the AF4 gene (16,20,47) occurs almost exclusively in tumors of the B-cell lineage. This suggests that the fusion partner plays a role in determining disease phenotype, either because it influences the site and timing of...