SALL4 controls cell fate in response to DNA base composition. Pantier et al.

Mammalian genomes contain long domains with distinct average compositions of A/T versus G/C base pairs. In a screen for proteins that might interpret base composition by binding to AT-rich motifs, we identified the stem cell factor SALL4 which contains multiple zinc-fingers. Mutation of the domain responsible for AT binding drastically reduced SALL4 genome occupancy and prematurely up-regulated genes in proportion to their AT content. Inactivation of this single AT-binding zinc-finger cluster mimicked defects seen in Sall4-null cells, including precocious differentiation of embryonic stem cells and embryonic lethality in mice. In contrast, deletion of two other zinc-finger clusters was phenotypically neutral. Our data indicate that loss of pluripotency is triggered by down-regulation of SALL4, leading to de-repression of a set of AT-rich genes that promotes neuronal differentiation. We conclude that base composition is not merely a passive by-product of genome evolution, but constitutes a signal that aids control of cell fate.

Python scripts and source code used for bioinformatic analyses, raw Western blot and microscopy images, as well as other types of unprocessed and processed data used to generate the figures are available here.

"Figure 1.zip", "Figure 4.zip", "Figure 5.zip", "Figure 6.zip", "Figure S1.zip", "Figure S2.zip", "Figure S3.zip", "Figure S4.zip", "Figure S5.zip" and "Figure S6.zip" contain the raw western blot, microscopy images, processed and unprocessed data associated with figure panels in respective figures.

"bioinformatics.zip" contains the respective ipynb (jupyter notebook) files for Figure 1, 2, 3, 6 and 7. Each notebook contains the source code to generate main+supplemental figure panels and the sub-folder "data" contain the processed data associated with the respective figure.

"selex_scripts.zip" contains the Python scripts and all the necessary information to reproduce the analysis of HT-SELEX data.

Raw and processed high-throughput sequencing data is deposited on Array Express, as described below.
E-MTAB-7343 RNA-seq of WT, S4KO, ZFC4mut and ZFC4Δ ESCs
E-MTAB-7655 RNA-seq of WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs
E-MTAB-9197 SALL4 ChIP-seq in WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs
E-MTAB-9198 Timecourse RNA-seq during differentiation (day 0, 2 and 5) of WT, S4KO, ZFC4mut and ZFC1-2Δ ESCs
E-MTAB-9202 RNA-seq of S4KO cells carrying Sall4 cDNA or EGFP cDNA under a doxycycline inducible promoter
E-MTAB-9236 HT-SELEX of recombinant C2H2 zinc-finger domains of SALL4
E-MTAB-9245 ATAC-seq in WT ESCs

哺乳动物基因组中存在由A/T与G/C碱基对组成差异明显的长序列区域。在一项旨在筛选可能通过结合AT富集基序来解释碱基组成的蛋白质的实验中，我们鉴定出了含有多个锌指结构的干细胞因子SALL4。负责AT结合的域突变显著降低了SALL4在基因组中的富集程度，并按AT含量比例提前上调了基因。该单个AT结合锌指簇的失活模拟了Sall4-null细胞中的缺陷，包括胚胎干细胞过早分化和小鼠胚胎致死。相比之下，删除另外两个锌指簇在表型上没有影响。我们的数据表明，多能性的丧失是由SALL4的下调触发的，导致一组AT富集基因的去抑制，这些基因促进神经元分化。我们得出结论，碱基组成不仅仅是基因组演化的被动产物，而是构成了辅助细胞命运控制的信号。所使用的生物信息学分析Python脚本和源代码、原始的Western blot和显微镜图像，以及其他用于生成图表的未处理和已处理数据均在此处提供。

“Figure 1.zip”、“Figure 4.zip”、“Figure 5.zip”、“Figure 6.zip”、“Figure S1.zip”、“Figure S2.zip”、“Figure S3.zip”、“Figure S4.zip”、“Figure S5.zip”和“Figure S6.zip”包含相应的原始Western blot、显微镜图像、处理和未处理数据。

“bioinformatics.zip”包含用于生成图1、2、3、6和7的主要和补充图表面板的相应ipynb（jupyter notebook）文件。每个notebook包含生成主要和补充图表面板的源代码，以及包含与相应图表相关的处理数据的“data”子文件夹。

“selex_scripts.zip”包含用于再现HT-SELEX数据分析的Python脚本和所有必要信息。

原始和经过处理的高通量测序数据已存放在Array Express上，具体如下：

E-MTAB-7343：WT、S4KO、ZFC4mut和ZFC4Δ ESCs的RNA-seq
E-MTAB-7655：WT、S4KO、ZFC4mut和ZFC1-2Δ ESCs的RNA-seq
E-MTAB-9197：WT、S4KO、ZFC4mut和ZFC1-2Δ ESCs的SALL4 ChIP-seq
E-MTAB-9198：WT、S4KO、ZFC4mut和ZFC1-2Δ ESCs分化过程中的时间进程RNA-seq（第0天、2天和5天）
E-MTAB-9202：携带Sall4 cDNA或EGFP cDNA的S4KO细胞在doxycycline诱导启动子下的RNA-seq
E-MTAB-9236：SALL4的重组C2H2锌指结构域的HT-SELEX
E-MTAB-9245：WT ESCs的ATAC-seq