Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression

• Main Authors: Narendra Pratap Singh, Bony De Kumar, Ariel Paulson, Mark E. Parrish, Carrie Scott, Ying Zhang, Laurence Florens, Robb Krumlauf
• Format: Article
• Language: English
• Published: MDPI AG 2021-02-01
• Series: Journal of Developmental Biology
• Subjects: transcription factor; mouse Hox genes; DNA binding motif; HOXB1; PBX1; REST
• Online Access: https://www.mdpi.com/2221-3759/9/1/6

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 <i>HB1RE</i> (HOXB1 response element). In vitro template binding assays showed that HOXB1, PBX1, and MEIS can bind to this motif. In vivo<i>,</i> 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 <i>HB1RE</i> motif contributes to HOXB1 function in part through a repressive role in gene expression.