Topoisomerase 1, an enzyme that relieves superhelical tension when DNA strands are unwound during transcription, is implicated in transcription-associated mutagenesis, genome instability-associated neurodegenerative diseases, and activation-induced cytidine deaminase (AID)-dependent genetic alterations. To investigate the mechanisms involved in TOP1-associated genomic instability, we screened TOP1-associated proteins by co-immunoprecipitation, and identified SMARCA4, an ATP-dependent chromatin remodeler; FACT, a histone chaperone; and Histone 3 tri-methyl at Lys4 (H3K4me3), a marker of transcriptionally active chromatin. SMARCA4 knockdown (KD) in an activated B-cell line (CH12F3-2A) decreased TOP1 recruitment to chromatin, and led to dramatic increases in Igh/c-Myc chromosomal translocations, variable and switch region mutations, and negative superhelicity, all of which were also observed in response to TOP1 KD. In contrast, FACT KD inhibited association of TOP1 with H3K4me3, and severely reduced DNA cleavage and Igh/c-Myc translocation, without drastic effect on the association of TOP1 with chromatin. Although TOP1 as well as SMARCA4 deficiency reduces TOP1 binding to chromatin and enhances the formation of non-B DNA structures, the association of residual TOP1 with FACT and H3K4me3 remains intact. FACT appears to bind non-B DNA containing chromatin formed at repetitive sequences such as Igh and Myc, under the excessive negative superhelicity. We thus propose that SMARCA4 is involved in the general chromatin recruitment of TOP1, whereas FACT is required for the binding of TOP1 to H3K4m3 at non-B DNA chromatin for the site specific cleavage.