Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
Molecular Genetics & Epigenetics Program, University of Virginia Comprehensive Cancer Center, Charlottesville, VA, 22908, USA.
Epigenetics Chromatin. 2024 Nov 1;17(1):33. doi: 10.1186/s13072-024-00556-4.
The precise spatiotemporal expression of the hematopoietic ETS transcription factor PU.1, a key determinant of hematopoietic cell fates, is tightly regulated at the chromatin level. However, how chromatin signatures are linked to this dynamic expression pattern across different blood cell lineages remains uncharacterized. Here, we performed an in-depth analysis of the relationships between gene expression, chromatin structure, 3D architecture, and trans-acting factors at PU.1 cis-regulatory elements (PCREs). By identifying phylogenetically conserved DNA elements within chromatin-accessible regions in primary human blood lineages, we discovered multiple novel candidate PCREs within the upstream region of the human PU.1 locus. A subset of these elements localizes within an 8-kb-wide cluster exhibiting enhancer features, including open chromatin, demethylated DNA, enriched enhancer histone marks, present enhancer RNAs, and PU.1 occupation, presumably mediating PU.1 autoregulation. Importantly, we revealed the presence of a common 35-kb-wide CTCF-flanked insulated neighborhood that contains the PCRE cluster (PCREC), forming a chromatin territory for lineage-specific and PCRE-mediated chromatin interactions. These include functional PCRE-promoter interactions in myeloid and B cells that are absent in erythroid and T cells. By correlating chromatin structure and 3D architecture with PU.1 expression in various lineages, we were able to attribute enhancer versus silencer functions to individual elements. Our findings provide mechanistic insights into the interplay between dynamic chromatin structure and 3D architecture in the chromatin regulation of PU.1 expression. This study lays crucial groundwork for additional experimental studies that validate and dissect the role of PCREs in epigenetic regulation of normal and malignant hematopoiesis.
造血 ETS 转录因子 PU.1 的精确时空表达，是造血细胞命运的关键决定因素，其在染色质水平受到严格调控。然而，染色质特征如何与不同血细胞谱系的这种动态表达模式相关联仍未被描述。在这里，我们对 PU.1 顺式调控元件 (PCRE) 中的基因表达、染色质结构、3D 结构和转录因子之间的关系进行了深入分析。通过鉴定原代人血液谱系中染色质可及区域内的系统发育保守 DNA 元件，我们在人类 PU.1 基因座的上游区域发现了多个新的候选 PCRE。这些元件中的一部分位于一个 8kb 宽的簇内，表现出增强子特征，包括开放染色质、去甲基化 DNA、富集的增强子组蛋白标记、存在的增强子 RNA 和 PU.1 占据，可能介导 PU.1 自身调控。重要的是，我们揭示了存在一个常见的 35kb 宽的 CTCF 侧翼隔离邻域，其中包含 PCRE 簇 (PCREC)，形成一个染色质区域，用于谱系特异性和 PCRE 介导的染色质相互作用。这些包括髓系和 B 细胞中的功能性 PCRE-启动子相互作用，而在红系和 T 细胞中不存在。通过将染色质结构和 3D 结构与各种谱系中的 PU.1 表达相关联，我们能够将增强子与沉默子功能归因于单个元件。我们的研究结果为动态染色质结构和 3D 结构在 PU.1 表达的染色质调控中的相互作用提供了机制上的见解。这项研究为进一步的实验研究奠定了重要基础，这些研究将验证和剖析 PCRE 在正常和恶性造血的表观遗传调控中的作用。
