Departments of Pathology, Biochemistry and Pediatrics, University of Iowa, Iowa City, IA 52242, USA.
Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):400-406. doi: 10.1002/wsbm.36.
Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is based on locus-specific variations in the ability of protein components of chromatin to trap genomic DNA following formaldehyde treatment. This variation is mostly due to uneven nucleosome distribution since histones are the most abundant and highly crosslinkable components of chromatin. The method can identify and enrich for physically accessible DNA segments of the eukaryotic genome corresponding to known regulatory regions and regions that might have thus far unidentified structural role in the nuclear organization of chromatin. The enrichment patterns are cell type specific and thus might provide information about how transcriptional systems are organized and regulated in various tissues and how they might be disrupted in disease states. Analysis of a 268 kb region of chromosome 19 in human fibroblasts shown here demonstrates that while most DNA fragments detected by FAIRE correspond to sites of DNaseI hypersensitivity in active regions of chromatin, some are found in otherwise repressed chromatin domains and at other sites that are not found with other methods used to probe chromatin structure. Further exploration of FAIRE is warrented due to the simplicity of the protocol and recent advancements in massively parallel sequencing.
甲醛辅助分离调控元件（FAIRE）是基于染色质蛋白成分在甲醛处理后捕获基因组 DNA 的能力的局部变化。这种变化主要是由于核小体分布不均匀，因为组蛋白是染色质中最丰富和交联程度最高的成分。该方法可以鉴定和富集真核基因组中与已知调控区域和可能在核染色质组织中具有尚未确定结构作用的区域对应的物理可接近的 DNA 片段。富集模式是细胞类型特异性的，因此可能提供关于转录系统在各种组织中如何组织和调节的信息，以及它们在疾病状态下可能如何被破坏的信息。本文对人成纤维细胞 19 号染色体的 268kb 区域进行的分析表明，虽然 FAIRE 检测到的大多数 DNA 片段与染色质活跃区域的 DNaseI 超敏位点相对应，但有些则存在于其他被抑制的染色质结构域中，以及其他使用探测染色质结构的方法未发现的其他位点。由于该方法简单，并且最近在大规模平行测序方面取得了进展，因此需要进一步探索 FAIRE。
