Considerations and caveats for analyzing chromatin compartments.
Considerations and caveats for analyzing chromatin compartments.
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DOI：
10.3389/fmolb.2023.1168562
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发表时间：
2023
影响因子：
5
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中科院分区：
文献类型：
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基因组被组织成核区室，将活性染色质与非活性染色质分开。通过绘制全基因组染色质构象的实验，染色质区室在大量物种中很容易可见。当分析这些图谱时，常见的步骤是鉴定在A（活性）和B（非活性）区室内相互作用的基因组间隔。它也变得越来越普遍，以确定和分析亚隔室。我们回顾了不同的策略，以确定A/B和子房室间隔，包括各种机器学习方法来预测这些功能的讨论。然后，我们讨论了目前的策略的优势和局限性，并研究这些方面的分析可能会影响我们对染色质区室的理解。
Genomes are organized into nuclear compartments, separating active from inactive chromatin. Chromatin compartments are readily visible in a large number of species by experiments that map chromatin conformation genome-wide. When analyzing these maps, a common step is the identification of genomic intervals that interact within A (active) and B (inactive) compartments. It has also become increasingly common to identify and analyze subcompartments. We review different strategies to identify A/B and subcompartment intervals, including a discussion of various machine-learning approaches to predict these features. We then discuss the strengths and limitations of current strategies and examine how these aspects of analysis may have impacted our understanding of chromatin compartments.