SALL4 controls cell fate in response to DNA base composition

Pantier, R., Chhatbar, K., Quante, T., Skourti-Stathaki, K., Cholewa-Waclaw, J., Alston, G., Alexander-Howden, B., Lee, H.Y., Cook, A.G., Spruijt, C.G., Vermeulen, M., Selfridge, J., and Bird, A.

Molecular Cell (2021) 81,4: 845-858.e8

Pantier et al. demonstrate that the stem cell factor SALL4 regulates cell fate by reading DNA base composition. SALL4 represses the expression of early differentiation genes in proportion to their AT-content. This process is illustrated here as pendulum clock with SALL4 (blue dots) binding to short AT-rich motifs along the genome. Cover art (acrylic paint) by Deepali Vasoya.

Summary of Paper by Lori Koch

DNA sequence patterns of repeating guanosine (G) and cytosine (C) nucleotides called CpG islands are recognized and bound by specific proteins to influence expression of associated genes. It is less clear whether specific protein binding to sequence motifs containing the other two nucleotides, adenosine (A) and thymine (T), has a functional purpose or whether it is simply a by-product of passive sequence evolution. In their recent publication in Molecular Cell, scientists in the Bird group and their colleagues led by Raphael Pantier found that the protein SALL4 recognizes AT motifs and that this is required for normal cell differentiation. A screen was performed to identify proteins that bind AT-rich DNA. DNAs containing repeating motifs of five A and T nucleotides were incubated with mouse embryonic stem cell extracts. Control DNAs with G and C nucleotides interspersed were used as a negative control. Proteins which bound to the different DNAs were isolated, identified and quantified between conditions using SILAC mass spectrometry. The zinc-finger protein SALL4 was the most consistently enriched on AT-rich DNA. A HT-SELEX screen was performed to test which of the zinc-finger domains in SALL4 actually recognizes the AT motif. This revealed that the ZFC4 domain has a marked preference for AT-rich sequence. Interestingly, loss of SALL4 causes premature differentiation of stem cells but the underlying reason for this was unknown. To pursue this, the researchers performed RNA sequencing on stem cells lacking SALL4 or expressing a version of SALL4 missing the ZFC4 domain. This revealed that several thousand genes become dysregulated when SALL4 function is lost. Importantly, the ZFC4 domain, which recognizes ATs, was most important for the effect of SALL4 on gene expression while loss of other ZFC domains did not cause as many defects. In sum, the work uncovered that specific recognition of AT-rich sequence is important for regulating gene expression and cell differentiation

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