Breast cancer is a heterogeneous disease, with over 2 million new cases reported annually worldwide, yet the functional role of cis-regulatory elements including super-enhancers in different breast cancer subtypes remains poorly characterized. Basal-like, triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a poor prognosis. Through analyzing H3K27ac ChIP-seq data of 17 breast cancer cell lines and 2 immortalized breast cell lines extracted from GEO and ENCODE, we found 7333 putative TNBC unique super-enhancers in collaboration with Dr. Xin Wang. Together with TCGA breast cancer RNA-seq data analysis, 331 super-enhancers were proposed to target differentially expressed genes, including FOXC1, MET and TCOF1. These three genes are found to be overexpressed in clinical samples of TNBC as well as a panel of TNBC lines. Using Crispr/cas9 genomic editing, we deleted constituent peaks of the putative super-enhancers of FOXC1, MET and TCOF1, resulting in their reduced protein expression. Furthermore, deletion of FOXC1- and MET-associated super-enhancers led to impairment of spheroid and clonogenic growth, consistent with their oncogenic properties. Using the integrated epigenomic and transcriptomic profiling and functional studies, we thereby identified super-enhancer as a mechanism for the specific overexpression of key oncogenes in TNBC. In addition, we investigated the function of a novel gene TCOF1, which role in the pathogenesis of cancer has not been identified. RNA-seq Data from TCGA showed that TCOF1 expression is upregulated in 32% TNBC. By analyzing METABRIC data, we found that high expression of TCOF1 is corelated with shorter overall survival in breast cancer patients. Inducible knockout of TCOF1 significantly inhibited the growth of TNBC cells in vitro (2D and 3D culture) and in vivo. Our data also demonstrated that knockout of TCOF1 decreased the population of ALDH+ cells from MDA-MB-468 and HCC1806 spheroids, impaired the mammosphere formation ability and attenuated tumor-initiating ability in vivo, indicating a specific function of TCOF1 in modulating TNBC stem cell properties. Mechanistically, TCOF1 promotes the expression of KIT in TNBC. Overexpression of KIT partially rescued mammosphere formation ability impaired by TCOF1 knockout in TNBC cells, suggesting that KIT is an effector of TCOF1 in mediating TNBC stemness. These findings identified TCOF1 as a novel TNBC-specific gene regulated by super-enhancer and provide a rationale for developing therapeutics targeting TCOF1.