CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ChIP-seq]. CUX1 regulates human hematopoietic stem cell chromatin accessibility via the BAF complex [ChIP-seq]

CUX1 is a HOX-family transcription factor that is essential for development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor suppressive functions of CUX1. Herein, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 functions as a pioneer factor to epigenetically regulate hematopoietic lineage commitment and homeostasis, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation. Overall design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for transcription factor CUX1, BAF complex subunit SMARCA4, and histone modification H3K27ac in K562 cells. ChIP-seqs for SMARCA4 and H3K27ac include samples transfected with CRISPR gRNAs gHPRT (control) and gCUX1.

CUX1属于同源盒（HOX）家族转录因子，对多种组织的发育与分化不可或缺。CUX1在癌症中频繁发生突变或缺失，尤以髓系恶性肿瘤为显著。然而，CUX1调控基因表达与分化的具体分子机制仍不甚明晰，这成为解析其肿瘤抑制功能的一大障碍。本研究证实，CUX1可招募BAF染色质重塑复合物结合至DNA，以提升造血细胞中的染色质开放程度。CUX1优先调控谱系特异性增强子，且其靶基因可在体内预测细胞命运。上述数据表明，CUX1可作为先锋因子，表观遗传调控造血谱系的定向分化与稳态维持；CUX1缺失会破坏干细胞及祖细胞中的上述过程，进而促进细胞转化。
整体实验设计：针对K562细胞中的转录因子CUX1、BAF复合物亚基SMARCA4以及组蛋白修饰H3K27ac开展染色质免疫共沉淀测序（ChIP-seq）实验。针对SMARCA4与H3K27ac的ChIP-seq实验所用样本，分别转染了CRISPR向导RNA（gRNA）gHPRT（阴性对照）与gCUX1。