Fig. 1

Prosaposin (PSAP) was identified as a putative HOXC11 target gene from RNA-sequencing (RNA-seq) of endocrine-resistant breast cancer cells in which HOXC11 was knocked down. a (i) RNA-seq was performed on mRNA from endocrine-resistant breast cancer cells (LY2) in which HOXC11 had been silenced (n = 2): 1,919 hits (cutoff >= 0.95), corresponding to 1,243 Entrez gene IDs were identified. TFFind, a motif mapping programme, was used to search for the HOXC11 motif (consensus sequence: GTCGTAAA) in all annotated human genes from UCSC (26,648 sequences). The analysis of these data resulted in the identification of 711 genes putatively regulated by HOXC11. (ii) Breakdown of RNA subtype percentages identified in RNA-seq screening. b De novo motif identification was performed on sequences of HOXC11 targets that harbour hormone response elements using the MEME program resulting in the identification of a novel motif (e-value: 1.3e-1337). The novel motif has significant similarity to androgen receptor (AR) (p value: 2.26e-6) and NR3C1 (glucocorticoid receptor (GR)) (p value: 2.81e-4). c AR motif analysis of total HOXC11 target genes shows that approximately 60 % contain an androgen response element (ARE) in the proximal promoter region. d Merging RNA-sequencing and HOXC11 transcription factor motif-mapping datasets yielded a total of 29 genes, which were then ranked by magnitude of fragments per Kilobase of transcript per million. e Validation of the putative HOXC11 target gene, PSAP, was confirmed by performing chromatin immunoprecipitation to determine recruitment of HOXC11 to the PSAP promoter in LY2 (tamoxifen resistant) cells cultured in the presence of tamoxifen versus vehicle. Results are representative of three separate experiments