性腺类固醇激素，即睾酮、黄体酮和雌激素，通过调节基因转录影响生物体的生理状态。类固醇激素激活核激素受体 (HR) 和转录因子 (TF)，它们以组织和细胞类型特异性的方式结合 DNA，从而影响细胞功能。识别 HR 的基因组结合位点对于了解跨组织和疾病背景的激素信号传导机制至关重要。传统上，染色质免疫沉淀随后测序 (ChIP-seq) 已用于绘制癌细胞系和大组织中 HR 的基因组结合图谱。然而，ChIP-seq 缺乏检测少量细胞（例如大脑中基因定义的神经元亚型）中 TF 结合的灵敏度。低于目标的裂解

Gonadal steroid hormones, namely, testosterone, progesterone, and estrogens, influence the physiological state of an organism through the regulation of gene transcription. Steroid hormones activate nuclear hormone receptor (HR), transcription factors (TFs), which bind DNA in a tissue- and cell type-specific manner to influence cellular function. Identifying the genomic binding sites of HRs is essential to understanding mechanisms of hormone signaling across tissues and disease contexts. Traditionally, chromatin immunoprecipitation followed by sequencing (ChIP-seq) has been used to map the genomic binding of HRs in cancer cell lines and large tissues. However, ChIP-seq lacks the sensitivity to detect TF binding in small numbers of cells, such as genetically defined neuronal subtypes in the brain. Cleavage Under Targets & Release Under Nuclease (CUT&RUN) resolves most of the technical limitations of ChIP-seq, enabling the detection of protein-DNA interactions with as few as 100-1000 cells. In this chapter, we provide a stepwise CUT&RUN protocol for detecting and analyzing the genome-wide binding of estrogen receptor α (ERα) in mouse brain tissue. The steps described here can be used to identify the genomic binding sites of most TFs in the brain.© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.