新兴的方法从形式素固定的抛嵌入式部分中对可访问的染色质进行剖析
Vishnu Udayakumaran Nair Sunitha Kumary1, Bryan J Venters1, Karthikeyan Raman2
1EpiCypher Inc., Durham, NC 27709, USA.
Epigenomes
|May 28, 2024
概括
绘制开放色素区域的地图对于理解基因调节和疾病至关重要. 本综述详细介绍了分析FFPE组织的方法,克服了染色质可访问性研究的固定挑战.
科学领域:
- 基因组学就是基因组学.
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
- 分子生物学分子生物学
背景情况:
- 核细胞分布决定了基因活动,开放的染色质与活跃的促进剂和增强剂联系在一起.
- 染色体可访问性模式对于理解正常发育和疾病进展至关重要.
- 像DNase-seq和ATAC-seq这样的高通量测序方法可以识别开放的染色质,但在FFPE组织中面临挑战.
研究的目的:
- 审查用于绘制开放色素区域的常用方法.
- 要突出最近对分析FPE组织的优化.
- 提供对染色质可访问性研究的数据分析管道的概述.
主要方法:
- 审查已经建立的高通量测序技术 (DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, NicE-seq).
- 讨论解决FFPE组织局限性的最新技术进步.
- 一个典型的生物信息学数据分析管道的概要.
主要成果:
- 由于交叉连接和DNA损伤,FFPE组织对染色质可访问性测定具有重大挑战.
- 优化的协议正在出现,以使FFPE样本中可靠的染色质映射成为可能.
- 标准化数据分析管道对于一致的解释至关重要.
结论:
- 通过优化方法,在FFPE组织中绘制染色质可访问性的地图正变得可行.
- 了解FFPE样本中的这些模式可以解开对疾病机制的洞察力.
- 基于FFPE的染色质可访问性研究的进一步开发和标准化是有必要的.
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