Singh Narendra Pratap, De Kumar Bony, Paulson Ariel, Parrish Mark E, Scott Carrie, Zhang Ying, Florens Laurence, Krumlauf Robb
Stowers Institute for Medical Research, Kansas City, MO 64110, USA.
School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND 58203, USA.
J Dev Biol. 2021 Feb 3;9(1):6. doi: 10.3390/jdb9010006.
Knowledge of the diverse DNA binding specificities of transcription factors is important for understanding their specific regulatory functions in animal development and evolution. We have examined the genome-wide binding properties of the mouse HOXB1 protein in embryonic stem cells differentiated into neural fates. Unexpectedly, only a small number of HOXB1 bound regions (7%) correlate with binding of the known HOX cofactors PBX and MEIS. In contrast, 22% of the HOXB1 binding peaks display co-occupancy with the transcriptional repressor REST. Analyses revealed that co-binding of HOXB1 with PBX correlates with active histone marks and high levels of expression, while co-occupancy with REST correlates with repressive histone marks and repression of the target genes. Analysis of HOXB1 bound regions uncovered enrichment of a novel 15 base pair HOXB1 binding motif (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo, this motif is sufficient for direct expression of a reporter gene and over-expression of HOXB1 selectively represses this activity. Our analyses suggest that HOXB1 has evolved an association with REST in gene regulation and the novel motif contributes to HOXB1 function in part through a repressive role in gene expression.
了解转录因子多样的DNA结合特异性对于理解它们在动物发育和进化中的特定调控功能至关重要。我们研究了小鼠HOXB1蛋白在分化为神经命运的胚胎干细胞中的全基因组结合特性。出乎意料的是，只有少数HOXB1结合区域（7%）与已知的HOX辅因子PBX和MEIS的结合相关。相比之下，22%的HOXB1结合峰与转录抑制因子REST共同占据。分析表明，HOXB1与PBX的共结合与活跃的组蛋白标记和高水平表达相关，而与REST的共同占据与抑制性组蛋白标记和靶基因的抑制相关。对HOXB1结合区域的分析发现了一种新的15个碱基对的HOXB1结合基序（HOXB1反应元件）的富集。体外模板结合试验表明，HOXB1、PBX1和MEIS可以结合到这个基序上。在体内，这个基序足以直接表达报告基因，而HOXB1的过表达选择性地抑制这种活性。我们的分析表明，HOXB1在基因调控中已经进化出与REST的关联，并且这个新基序部分地通过在基因表达中的抑制作用对HOXB1的功能做出贡献。
