Choi Won-Young, Hwang Ji-Hyun, Cho Ann-Na, Lee Andrew J, Jung Inkyung, Cho Seung-Woo, Kim Lark Kyun, Kim Young-Joon
Interdisciplinary Program of Integrated OMICS for Biomedical Science, The Graduate School, Yonsei University, Seoul 03722, Korea.
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Korea.
Mol Cells. 2020 Dec 31;43(12):1011-1022. doi: 10.14348/molcells.2020.0207.
Cell type specification is a delicate biological event in which every step is under tight regulation. From a molecular point of view, cell fate commitment begins with chromatin alteration, which kickstarts lineage-determining factors to initiate a series of genes required for cell specification. Several important neuronal differentiation factors have been identified from ectopic over-expression studies. However, there is scarce information on which DNA regions are modified during induced pluripotent stem cell (iPSC) to neuronal progenitor cell (NPC) differentiation, the regulatory factors that attach to these accessible regions, or the genes that are initially expressed. In this study, we identified the DNA accessible regions of iPSCs and NPCs via the Assay for Transposase-Accessible Chromatin sequencing (ATACseq). We identified which chromatin regions were modified after neuronal differentiation and found that the enhancer regions had more active histone modification changes than the promoters. Through motif enrichment analysis, we found that NEUROD1 controls iPSC differentiation to NPC by binding to the accessible regions of enhancers in cooperation with other factors such as the Hox proteins. Finally, by using Hi-C data, we categorized the genes that directly interacted with the enhancers under the control of NEUROD1 during iPSC to NPC differentiation.
细胞类型特化是一个精细的生物学过程，其中的每一步都受到严格调控。从分子角度来看，细胞命运决定始于染色质改变，这启动了谱系决定因子，进而开启一系列细胞特化所需的基因。通过异位过表达研究已经鉴定出了几种重要的神经元分化因子。然而，关于在诱导多能干细胞（iPSC）向神经祖细胞（NPC）分化过程中哪些DNA区域被修饰、附着于这些可及区域的调控因子以及最初表达的基因，相关信息却很少。在本研究中，我们通过转座酶可及染色质测序分析（ATACseq）鉴定了iPSC和NPC的DNA可及区域。我们确定了神经元分化后哪些染色质区域被修饰，并发现增强子区域的组蛋白修饰变化比启动子区域更为活跃。通过基序富集分析，我们发现NEUROD1与Hox蛋白等其他因子协同作用，通过结合增强子的可及区域来控制iPSC向NPC的分化。最后，利用Hi-C数据，我们对在iPSC向NPC分化过程中受NEUROD1调控的与增强子直接相互作用的基因进行了分类。
