Epigenetic and transcriptional control in hematopoietic development and lineage differentiation

Hematopoiesis is a well-established model system to study molecular mechanisms of lineage-specific differentiation. Key transcription factors (TFs), such as PU.1, NF-E2 and GATA1 are implicated in crucial aspects of distinct hematopoietic lineages. How TFs collaborate with histone modificatons and how they affect the chromatin status remains to be elucidated. Chromatin-Immunoprecipitation followed by next-generation sequencing (ChIP-seq) has been proven to be an excellent tool to study chromatin modifications genome-wide. In this study, ChIP-seq was used to investigate the H3K4me2 landscape at enhancers during hematopoietic differentiation, starting from the hematopoietic stem cell (HSC) up to the fully differentiated erythrocyte, megakaryocyte or granulocyte. Although cell morphology and gene expression profiles differ extensively in committed erythrocytes, megakaryocytes and granulocytes, the genomic landscape of H3K4me2 is surprisingly alike across the three cell types. Granulocytes, in particular, seem to display an ‘erythocyte-like’ chromatin pattern. Similar results were observed for another chromatin mark, H3K27ac. Unexpectedly, the common progenitors of erythrocytes and granulocytes do not display a similar chromatin pattern, excluding the idea that the H3K4me2 mark is placed early on during differentiation. These results also suggest that the chromatin state is probably not the determining factor for lineage differentiation, but that rather lineage specific TF binding is important. In agreement with this, mature megakaryocytes loose the H3K4me2 mark surrounding erythrocyte-specific genes. This might be explained because megakaryocytes and erythrocytes both express the lineage specific TFs GATA1 and NF-E2. Altogether, we show that committed granulocytes and erythrocytes display similar H3K4me2 and H3K27ac patterns, and that those marks alone cannot predict which genes will be expressed eventually. Genomic ChIP-Seq on key transcription factors and histone modification marks in hematopoiesis

造血作用是研究谱系特异性分化分子机制的经典模型体系。关键转录因子（transcription factors, TFs）如PU.1、NF-E2及GATA1等，参与不同造血谱系的核心调控过程。转录因子如何与组蛋白修饰协同发挥作用，又如何影响染色质状态，这一问题仍有待阐明。染色质免疫共沉淀结合高通量测序（Chromatin-Immunoprecipitation followed by next-generation sequencing, ChIP-seq）已被证实是全基因组范围内研究染色质修饰的优良工具。本研究采用ChIP-seq技术，探究造血分化过程中增强子区域的H3K4me2图谱，覆盖从造血干细胞（hematopoietic stem cell, HSC）直至完全分化的红细胞、巨核细胞或粒细胞的全过程。尽管定型后的红细胞、巨核细胞与粒细胞在细胞形态与基因表达谱上差异显著，但三者的H3K4me2基因组图谱却惊人相似，其中粒细胞尤其呈现出“红细胞样”的染色质模式。针对另一染色质标记H3K27ac，也得到了类似的实验结果。出乎意料的是，红细胞与粒细胞的共同祖细胞并未展现出相似的染色质模式，这排除了“H3K4me2标记在分化早期即被建立”这一假说。本研究结果还提示，染色质状态可能并非谱系分化的决定性因素，而谱系特异性转录因子结合才是关键调控环节。与此一致，成熟巨核细胞会丢失红细胞特异性基因周围的H3K4me2标记，这或许可通过巨核细胞与红细胞共同表达谱系特异性转录因子GATA1和NF-E2来解释。综上，本研究证实定型粒细胞与红细胞具有相似的H3K4me2与H3K27ac模式，仅依靠此类标记无法预测最终哪些基因会被激活表达。本数据集包含造血过程中关键转录因子与组蛋白修饰标记的基因组ChIP-seq数据。