Han, A. L. | bioRxiv Science

bioRxiv2022

Estradiol (E2) concentration shapes the chromatin binding landscape of the estrogen receptor

How transcription factors (TF) selectively occupy a minute subset of their binding sites from a sizeable pool of putative sites in large mammalian genomes remains an important unanswered question. In part, nucleosomes help by creating formidable barriers to TF binding. TF concentration itself plays a crucial role in the competition between TFs and nucleosomes. In the case of nuclear receptors, the ligand adds another layer of complexity. Estrogen receptor alpha (ER) is a classic example where its main ligand estradiol (E2) can modulate ER binding on chromatin. Here we show a complete rewiring of ER binding as a function of E2 concentration. As E2 concentration increases by two orders of magnitude, ER levels decrease, and ER binding localizes to promoter-distal sites with strong ER motifs. At low E2 levels, abundant levels of ER are present in the nucleus, and ER binding occurs mostly at sites without an identifiable ER binding motif, potentially in cooperation with other TFs like STAT1. We propose that E2s effect on ER activity plays a major role in defining genome-wide ER binding profiles. Thus, variations in E2 concentrations in ER-positive breast tumors could be a significant factor driving heterogeneity in tumor phenotype, treatment response, and potentially drug resistance.

molecular biology↗

bioRxiv2021

Mapping Transcription Factor-Nucleosome Dynamics from Plasma cfDNA

Cell-free DNA (cfDNA) contains a composite map of the epigenomes of its cells-of-origin. Tissue-specific transcription factor (TF) binding inferred from cfDNA could enable us to track disease states in humans in a minimally invasive manner. Here, by enriching for short cfDNA fragments, we directly map TF footprints at single binding sites from plasma. We show that the enrichment of TF footprints in plasma reflects the binding strength of the TF in cfDNA tissue-of-origin. Based on this principle, we were able to identify the subset of genome-wide binding sites for selected TFs that leave TF-specific footprints in plasma. These footprints enabled us to not only identify the tissue-of-origin of cfDNA but also map the chromatin structure around the factor-bound sites in their cells-of-origin. To ask if we can use these plasma TF footprints to map cancer states, we first defined pure tumor TF signatures in plasma in vivo using estrogen receptor-positive (ER+) breast cancer xenografts. We found that the tumor-specific cfDNA protections of ER- could distinguish WT, ER-amplified, and ER-mutated xenografts. Further, tumor-specific cfDNA protections of ER- and FOXA1 reflect TF-specific accessibility across human breast tumors, demonstrating our ability to capture tumor TF binding in plasma. We then scored TF binding in human plasma samples and identified specific binding sites whose plasma TF protections can identify the presence of cancer and specifically breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of cancer in humans.

genomics↗