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. 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是HOX家族转录因子，对多种组织的发育与分化至关重要。CUX1在多种癌症中频繁发生突变或缺失，尤其在髓系恶性肿瘤中更为常见。然而，CUX1调控基因表达与细胞分化的具体机制仍不甚明确，这为解析CUX1的肿瘤抑制功能带来了障碍。本研究证实，CUX1可引导BAF染色质重塑复合物结合至DNA序列，以提升造血细胞的染色质开放性。CUX1优先调控谱系特异性增强子，且CUX1的靶基因可在体内预测细胞命运。上述数据表明，CUX1作为先驱因子，在表观遗传层面调控造血谱系的定向分化与稳态维持；CUX1功能缺失会破坏干细胞与祖细胞中的上述过程，进而促进细胞转化。本研究针对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开展了染色质免疫沉淀测序（ChIP-seq）实验。针对SMARCA4与H3K27ac的ChIP-seq实验所使用的样本，包含转染CRISPR向导RNA（gRNAs）gHPRT（对照组）与gCUX1的细胞样本。