Cooperation of a polymerizing SAM domain and an intrinsically disordered region enables full SAMD1 function on chromatin

Transcription factors orchestrate gene expression through a myriad of complex mechanisms, encompassing collaborations with other transcription factors and the formation of multimeric complexes. The chromatin-binding protein SAMD1 [sterile alpha motif (SAM) domain-containing protein 1] binds to unmethylated CpG-rich DNA utilizing its N-terminal winged-helix (WH) domain. Additionally, its C-terminal SAM domain, which mediates interactions with itself and with L3MBTL3, is crucial for chromatin binding. The precise role of the SAM domain in this process remains unclear. Using structural analyses, we elucidated the distinct homopolymerization modes within the SAM domains of L3MBTL3 and SAMD1, alongside their heterodimerization architecture. Interestingly, SAMD1 necessitates not only the WH and SAM domain but also a proline/alanine-rich intrinsically disordered region (IDR) for efficient chromatin binding. The IDR is essential for the ability of SAMD1 to form large polymers, with its functionality determined by integrity rather than the specific sequence. Mutagenesis studies underscore the critical role of arginines within the IDR for polymerization, chromatin binding, and the biological function of SAMD1. These findings propose a model in which structured and unstructured regions of SAMD1 cooperate in a coordinated fashion to facilitate chromatin binding. This work provides new insights into the diverse mechanisms transcription factors employ to interact with chromatin and regulate gene expression. ChIP-Seq of various FLAG-tagged SAMD1 versions, ectopically expressed in SAMD1 KO mouse ES cells

转录因子通过诸多复杂机制调控基因表达，涵盖与其他转录因子的协同作用以及多聚体复合物的形成。染色质结合蛋白SAMD1[含无菌α基序（SAM）结构域蛋白1]借助其N端翼螺旋（WH）结构域，结合未甲基化的富含CpG的DNA。此外，其C端SAM结构域可介导自身与L3MBTL3的相互作用，对染色质结合至关重要，但该结构域在此过程中的具体作用仍未明确。本研究通过结构解析，阐明了L3MBTL3与SAMD1的SAM结构域各自独特的均聚模式，以及二者的异二聚体构象。有趣的是，SAMD1实现高效染色质结合，不仅需要WH结构域与SAM结构域，还依赖一段富含脯氨酸/丙氨酸的内在无序区域（IDR）。该IDR是SAMD1形成大型多聚体的关键，其功能由结构完整性而非特定序列决定。诱变研究证实，IDR内的精氨酸残基在聚合过程、染色质结合以及SAMD1的生物学功能中发挥核心作用。上述研究结果提出了一个模型：SAMD1的结构化区域与非结构化区域协同配合，共同促进染色质结合。本研究为转录因子与染色质相互作用并调控基因表达的多样机制提供了全新见解。本研究包含在SAMD1基因敲除小鼠胚胎干细胞（ES细胞）中外源异位表达不同FLAG标签标记的SAMD1变体的染色质免疫共沉淀测序（ChIP-Seq）数据集。