Pioneer and nonpioneer factor cooperation drives lineage specific chromatin opening [ATAC-seq]

Pioneer transcription factors are coined as having the unique property of “opening closed chromatin sites” for implementation of cell fates. We previously showed that the pioneer Pax7 specifies melanotrope cells through deployment of an enhancer repertoire: this allows binding of Tpit, a nonpioneer factor that determines the related lineages of melanotropes and corticotropes. Here, we investigated the relation between these two factors in the pioneer mechanism. Cell-specific gene expression and chromatin landscapes were defined by scRNAseq and chromatin accessibility profiling. We found that in vivo deployment of the melanotrope enhancer repertoire and chromatin opening requires both Pax7 and Tpit. In cells, binding of heterochromatin targets by Pax7 is independent of Tpit but Pax7-dependent chromatin opening requires Tpit. The present work shows that pioneer core properties are limited to the ability to recognize heterochromatin targets and facilitate nonpioneer binding. Chromatin opening per se may be provided through cooperation with nonpioneer factors. ATACseq in pituitary cells and pituitary-derived cell lines

先驱转录因子（pioneer transcription factors）被定义为具备“开放闭合染色质位点”这一独特属性，以实现细胞命运的确立。我们此前的研究表明，先驱转录因子Pax7通过激活一套增强子谱来定向分化促黑激素细胞：这一过程使得非先驱转录因子Tpit得以结合，而Tpit可决定促黑激素细胞与促肾上腺皮质激素细胞这两个相关细胞谱系的分化。本研究旨在探究这两种因子在先驱转录因子作用机制中的相互关系。我们通过scRNAseq（单细胞RNA测序）与染色质可及性分析，明确了细胞特异性基因表达谱与染色质景观特征。研究发现，体内激活促黑激素细胞增强子谱以及开放染色质的过程，同时依赖于Pax7与Tpit。在细胞水平上，Pax7对异染色质靶点的结合不受Tpit调控，但Pax7介导的染色质开放则依赖于Tpit。本研究表明，先驱转录因子的核心属性仅局限于识别异染色质靶点并促进非先驱转录因子结合这一能力。而染色质开放本身，则可通过与非先驱转录因子的协同作用得以实现。本研究涵盖垂体细胞及垂体来源细胞系中的ATACseq（转座酶可及染色质测序）实验。