Hubrecht Institute-KNAW, University Medical Center Utrecht, Utrecht 3584 CT, The Netherlands.
Genes Dev. 2011 Jul 1;25(13):1371-83. doi: 10.1101/gad.633311. Epub 2011 Jun 20.
Three-dimensional topology of DNA in the cell nucleus provides a level of transcription regulation beyond the sequence of the linear DNA. To study the relationship between the transcriptional activity and the spatial environment of a gene, we used allele-specific chromosome conformation capture-on-chip (4C) technology to produce high-resolution topology maps of the active and inactive X chromosomes in female cells. We found that loci on the active X form multiple long-range interactions, with spatial segregation of active and inactive chromatin. On the inactive X, silenced loci lack preferred interactions, suggesting a unique random organization inside the inactive territory. However, escapees, among which is Xist, are engaged in long-range contacts with each other, enabling identification of novel escapees. Deletion of Xist results in partial refolding of the inactive X into a conformation resembling the active X without affecting gene silencing or DNA methylation. Our data point to a role for Xist RNA in shaping the conformation of the inactive X chromosome at least partially independent of transcription.
细胞核内 DNA 的三维拓扑结构提供了超越线性 DNA 序列的转录调控水平。为了研究基因转录活性与空间环境之间的关系，我们使用等位基因特异性染色体构象捕获芯片（4C）技术，生成了雌性细胞中活性和非活性 X 染色体的高分辨率拓扑图谱。我们发现，活性 X 染色体上的基因座形成了多个长距离相互作用，具有活性和非活性染色质的空间分离。在非活性 X 染色体上，沉默基因座缺乏优先相互作用，这表明在非活性区域内存在独特的随机组织。然而，逃逸者，其中包括 Xist，彼此之间进行长距离接触，从而能够识别新的逃逸者。删除 Xist 会导致非活性 X 染色体部分折叠成类似于活性 X 的构象，而不影响基因沉默或 DNA 甲基化。我们的数据表明，Xist RNA 在塑造非活性 X 染色体构象方面发挥了作用，至少部分独立于转录。
