Cai 蔡信平 Xinping, Zhang 张倩茹 Qianru, Liu 刘博琳 Bolin, Sun 孙露 Lu, Liu 刘宇璇 Yuxuan
State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
Tianjin Institutes of Health Science, Tianjin 301600, China.
Genomics Proteomics Bioinformatics. 2025 May 30;23(2). doi: 10.1093/gpbjnl/qzae088.
Non-coding cis-regulatory elements (CREs), such as transcriptional enhancers, are key regulators of gene expression programs. Accessible chromatin and H3K27ac are well-recognized markers for CREs associated with their biological function. Deregulation of CREs is commonly found in hematopoietic malignancies, yet the extent to which CRE dysfunction contributes to pathophysiology remains incompletely understood. Here, we developed HemaCisDB, an interactive, comprehensive, and centralized online resource for CRE characterization across hematopoietic malignancies, serving as a useful resource for investigating the pathological roles of CREs in blood disorders. Currently, we collected 922 assay of transposase accessible chromatin with sequencing (ATAC-seq), 190 DNase I hypersensitive site sequencing (DNase-seq), and 531 H3K27ac chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from patient samples and cell lines across different myeloid and lymphoid neoplasms. HemaCisDB provides comprehensive quality control metrics to assess ATAC-seq, DNase-seq, and H3K27ac ChIP-seq data quality. The analytic modules in HemaCisDB include transcription factor (TF) footprinting inference, super-enhancer identification, and core transcriptional regulatory circuitry analysis. Moreover, HemaCisDB also enables the study of TF binding dynamics by comparing TF footprints across different disease types or conditions via web-based interactive analysis. Together, HemaCisDB provides an interactive platform for CRE characterization to facilitate mechanistic studies of transcriptional regulation in hematopoietic malignancies. HemaCisDB is available at https://hemacisdb.chinablood.com.cn/.
非编码顺式调控元件（CRE），如转录增强子，是基因表达程序的关键调节因子。可及染色质和H3K27ac是与CRE生物学功能相关的公认标志物。CRE失调在造血系统恶性肿瘤中普遍存在，但CRE功能障碍对病理生理学的影响程度仍未完全了解。在此，我们开发了HemaCisDB，这是一个用于全面、集中地表征造血系统恶性肿瘤中CRE的交互式在线资源，为研究CRE在血液疾病中的病理作用提供了有用的资源。目前，我们从不同髓系和淋巴系肿瘤的患者样本和细胞系中收集了922个转座酶可及染色质测序（ATAC-seq）、190个DNase I超敏位点测序（DNase-seq）和531个H3K27ac染色质免疫沉淀测序（ChIP-seq）数据集。HemaCisDB提供了全面的质量控制指标来评估ATAC-seq、DNase-seq和H3K27ac ChIP-seq数据质量。HemaCisDB中的分析模块包括转录因子（TF）足迹推断、超级增强子识别和核心转录调控回路分析。此外，HemaCisDB还能够通过基于网络的交互式分析比较不同疾病类型或条件下的TF足迹，从而研究TF结合动力学。总之，HemaCisDB为CRE表征提供了一个交互式平台，以促进造血系统恶性肿瘤中转录调控的机制研究。可通过https://hemacisdb.chinablood.com.cn/访问HemaCisDB。
