A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification (ATAC-seq). A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification (ATAC-seq)

Developmental control of gene expression critically depends on distal cis-regulatory elements including enhancers which interact with promoters to activate gene expression. Multiple genome-wide studies have mapped chromatin and genomic features of such elements. However, the enhancer definition is operational, and no global experiments have been conducted to date that identify their cell type and cell stage-specific transcription stimulatory activity in a chromatin context. Here, we describe a high-throughput method that identifies thousands of cis-elements capable of stimulating transcriptional activity from a minimal promoter using the blood progenitor differentiation from embryonic stem cells as model. We show that hematopoietic specification and blood cell-specific gene expression are controlled by the concerted action of thousands of differentiation stage-specific sets of cis-elements which respond to cytokine signals terminating at signalling responsive transcription factors. Our work presents a major advance in our understanding of developmental gene expression control in the hematopoietic system and beyond. Overall design: ATAC-Seq chromatin profiling from ES cells differentating to hematopoetic progenitor cells in a system using serum and a serum free system, allowing study of changes in cytokine signalling.

基因表达的发育调控关键依赖于包括增强子（enhancer）在内的远端顺式调控元件（cis-regulatory element），此类元件通过与启动子（promoter）互作以激活基因表达。
多项全基因组研究已对此类元件的染色质及基因组特征完成图谱绘制。但目前增强子的定义仍属于操作定义，迄今为止尚未有全局实验在染色质背景下，鉴定其细胞类型与细胞阶段特异性的转录激活活性。
本研究建立了一种高通量方法，以胚胎干细胞（embryonic stem cell）向造血祖细胞（hematopoietic progenitor cell）的分化过程作为模型体系，可从最小启动子（minimal promoter）处筛选出数千个具备转录激活活性的顺式调控元件。
研究发现，造血特化（hematopoietic specification）与血细胞特异性基因表达，受数千套分化阶段特异性顺式调控元件的协同作用调控；此类元件可响应终止于信号响应转录因子（signaling responsive transcription factor）的细胞因子（cytokine）信号通路。
本研究为理解造血系统乃至其他系统的发育性基因表达调控机制带来了重大进展。
实验整体设计：分别采用血清培养与无血清培养两种体系，对胚胎干细胞向造血祖细胞分化过程中的细胞进行ATAC-Seq染色质图谱分析，以此开展细胞因子信号通路变化的相关研究。