SALL4 recruits BAF to activate enhancers required for cranial neural crest cell specification
SALL4 is a critical transcription factor involved in early embryonic development. While its role in pluripotency remains debated, SALL4 has been implicated in various lineage specification processes. The neural crest-derived anomalies observed in individuals with SALL4 haploinsufficiency, combined with high SALL4 expression observed in mouse cranial neural crest cells (CNCCs), suggest a role for this transcription factor in CNCC specification and craniofacial development, however, this has not yet been investigated. Moreover, while SALL4 is an established interactor of the NuRD chromatin remodeling complex, recent mass-spectrometry studies from our group have suggested a novel interaction between SALL4 and the BAF complex during human CNCC specification. Here, we investigate the functional significance of this interaction and the broader role of SALL4 in CNCC development. We generated a human iPSC line with SALL4 heterozygous knock-out to model the haploinsufficient variants observed in SALL4-associated human developmental syndromes. Our findings reveal that the SALL4A isoform directly interacts with the BAF subunit DPF2 via its zinc-finger-cluster-3 and -4 domain. During early CNCC specification, SALL4A is required for BAF-mediated chromatin remodeling at enhancers essential for CNCC fate. In the absence of SALL4A, cells progress normally through the neuroectodermal stage but fail to specify into CNCCs, as CNCC lineage-specific enhancers remain repressed. Moreover, we demonstrate that the SALL4B isoform cannot compensate for SALL4A loss, as it lacks the zinc-finger-3 domain necessary for BAF interaction. These findings establish a novel role for SALL4A in CNCC specification by regulating BAF-mediated enhancer activation, shedding light on the molecular mechanisms underlying SALL4-associated craniofacial anomalies. Overall design: RNA-seq of SV20 WT and SV20 SALL4-het-KO iPSC lines  (2 replicates per line) RNA-seq of SV20 WT and SV20 SALL4-het-KO at day 5 of in vitro cranial neural crest cell specification (3 replicates per line) RNA-seq of SV20 WT and SV20 SALL4-het-KO at day 14 of in vitro cranial neural crest cell specification (2 replicates per line) CUT&RUN of SALL4 in SV20 WT iPSC lines (1 replicate per line) CUT&RUN of SALL4 in SV20 WT cell line at day 5 of in vitro cranial neural crest cell specification (2 replicates per line) ChIP-seq of BRG1 in SV20 WT and SV20 SALL4-het-KO cell lines at day 5 of in vitro cranial neural crest cell specification (at least 1 replicate per line) ATAC-seq of SV20 WT iPSC lines  (2 replicates per line) ATAC-seq of SV20 WT and SV20 SALL4-het-KO at day 5 of in vitro cranial neural crest cell specification (2 replicates per line)