Department of Human Genetics, University of Chicago, Howard Hughes Medical Institute, Chicago, Illinois 60637, USA;
Genome Res. 2014 Feb;24(2):267-80. doi: 10.1101/gr.143891.112. Epub 2013 Dec 5.
Both diffusible factors acting in trans and chromatin components acting in cis are implicated in gene regulation, but the extent to which either process causally determines a cell's transcriptional identity is unclear. We recently used cell fusion to define a class of silent genes termed "cis-silenced" (or "occluded") genes, which remain silent even in the presence of trans-acting transcriptional activators. We further showed that occlusion of lineage-inappropriate genes plays a critical role in maintaining the transcriptional identities of somatic cells. Here, we present, for the first time, a comprehensive map of occluded genes in somatic cells. Specifically, we mapped occluded genes in mouse fibroblasts via fusion to a dozen different rat cell types followed by whole-transcriptome profiling. We found that occluded genes are highly prevalent and stable in somatic cells, representing a sizeable fraction of silent genes. Occluded genes are also highly enriched for important developmental regulators of alternative lineages, consistent with the role of occlusion in safeguarding cell identities. Alongside this map, we also present whole-genome maps of DNA methylation and eight other chromatin marks. These maps uncover a complex relationship between chromatin state and occlusion. Furthermore, we found that DNA methylation functions as the memory of occlusion in a subset of occluded genes, while histone deacetylation contributes to the implementation but not memory of occlusion. Our data suggest that the identities of individual cell types are defined largely by the occlusion status of their genomes. The comprehensive reference maps reported here provide the foundation for future studies aimed at understanding the role of occlusion in development and disease.
无论是顺式作用的染色质成分还是反式作用的可扩散因子都参与了基因调控，但这两种过程在多大程度上能够因果确定细胞的转录特性尚不清楚。我们最近使用细胞融合来定义一类称为“顺式沉默”（或“封闭”）的沉默基因，即使存在反式作用的转录激活因子，这些基因仍然保持沉默。我们进一步表明，谱系不当基因的封闭在维持体细胞的转录特性方面起着关键作用。在这里，我们首次呈现了体细胞中封闭基因的综合图谱。具体来说，我们通过融合到十几种不同的大鼠细胞类型，然后进行全转录组谱分析，来绘制小鼠成纤维细胞中的封闭基因图谱。我们发现，封闭基因在体细胞中非常普遍且稳定，代表了很大一部分沉默基因。封闭基因也高度富集了替代谱系的重要发育调控因子，这与封闭在保护细胞特性方面的作用一致。除了这个图谱，我们还提供了 DNA 甲基化和其他八种染色质标记的全基因组图谱。这些图谱揭示了染色质状态与封闭之间的复杂关系。此外，我们发现 DNA 甲基化在一部分封闭基因中作为封闭的记忆发挥作用，而组蛋白去乙酰化作用则有助于封闭的实现，但不是记忆。我们的数据表明，单个细胞类型的特性主要由其基因组的封闭状态定义。这里报告的综合参考图谱为未来研究封闭在发育和疾病中的作用提供了基础。
