Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.
Centre for Computational Biology, University of Birmingham, Birmingham, UK.
Epigenetics Chromatin. 2019 Jun 4;12(1):33. doi: 10.1186/s13072-019-0282-9.
Both tissue-specific and ubiquitously expressed transcription factors, such as Sp-family members, are required for correct development. However, the molecular details of how ubiquitous factors are involved in programming tissue-specific chromatin and thus participate in developmental processes are still unclear. We previously showed that embryonic stem cells lacking Sp1 DNA-binding activity (Sp1 cells) are able to differentiate into early blood progenitors despite the inability of Sp1 to bind chromatin without its DNA-binding domain. However, gene expression during differentiation becomes progressively deregulated, and terminal differentiation is severely compromised.
Here, we studied the cooperation of Sp1 with its closest paralogue Sp3 in hematopoietic development and demonstrate that Sp1 and Sp3 binding sites largely overlap. The complete absence of either Sp1 or Sp3 or the presence of the Sp1 DNA-binding mutant has only a minor effect on the pattern of distal accessible chromatin sites and their transcription factor binding motif content, suggesting that these mutations do not affect tissue-specific chromatin programming. Sp3 cooperates with Sp1 to enable hematopoiesis, but is unable to do so in the complete absence of Sp1. Using single-cell gene expression analysis, we show that the lack of Sp1 DNA binding leads to a distortion of cell fate decision timing, indicating that stable chromatin binding of Sp1 is required to maintain robust differentiation trajectories.
Our findings highlight the essential contribution of ubiquitous factors such as Sp1 to blood cell development. In contrast to tissue-specific transcription factors which are required to direct specific cell fates, loss of Sp1 leads to a widespread deregulation in timing and coordination of differentiation trajectories during hematopoietic specification.
组织特异性和普遍表达的转录因子，如 Sp 家族成员，是正确发育所必需的。然而，普遍因子如何参与编程组织特异性染色质以及如何参与发育过程的分子细节尚不清楚。我们之前表明，缺乏 Sp1 DNA 结合活性的胚胎干细胞（Sp1 细胞）能够分化为早期血液祖细胞，尽管 Sp1 没有其 DNA 结合域就无法结合染色质。然而，分化过程中的基因表达变得逐渐失调，终末分化受到严重损害。
在这里，我们研究了 Sp1 与其最接近的同源物 Sp3 在造血发育中的合作，并证明 Sp1 和 Sp3 结合位点大部分重叠。完全缺乏 Sp1 或 Sp3 或存在 Sp1 DNA 结合突变体仅对远端可及染色质位点的模式及其转录因子结合基序含量有很小的影响，表明这些突变不会影响组织特异性染色质编程。Sp3 与 Sp1 合作以促进造血，但在完全缺乏 Sp1 的情况下无法做到这一点。使用单细胞基因表达分析，我们表明缺乏 Sp1 DNA 结合会导致细胞命运决定时间的扭曲，表明 Sp1 的稳定染色质结合对于维持强大的分化轨迹是必需的。
我们的发现强调了普遍因子（如 Sp1）对血细胞发育的重要贡献。与组织特异性转录因子需要指导特定的细胞命运不同，Sp1 的缺失会导致造血特化过程中分化轨迹的时间和协调的广泛失调。
