Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.
Identification of chromatin states during zebrafish gastrulation using CUT&RUN and CUT&Tag.
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DOI：
10.1002/dvdy.430
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发表时间：
2022-04
期刊：
影响因子：
--
通讯作者：
Goll MG
中科院分区：
文献类型：
--
作者：
Akdogan-Ozdilek B;Duval KL;Meng FW;Murphy PJ;Goll MG
细胞命运的决定是由序列特异性转录因子和动态染色质景观之间的相互作用。斑马鱼提供了一个强大的系统来探索驱动这些细胞命运选择的机制，特别是在早期胚胎发生的背景下。然而，与传统的染色质分析方法相关的技术挑战已经减缓了理解斑马鱼胚胎发生过程中染色质变化，转录因子结合和细胞分化之间确切关系的进展。为了克服这些挑战，我们采用了染色质分析方法CUT&RUN和CUT&Tag用于斑马鱼，并应用这些方法来生成H3K4me3，H3K27me3，H3K9me3，RNA聚合酶II和组蛋白变体H2A.Z的高分辨率富集图，使用从完整的中期原肠胚阶段胚胎分离的组织。使用这些数据，我们确定了一个基因的子集，可能是生物素调节在斑马鱼和小鼠原肠胚形成，提供证据的一个不断发展的H2A.Z景观在胚胎发育过程中，并证明了CUT&RUN检测H3K9me3富集在重复序列的有效性。我们的研究结果表明，CUT&RUN和CUT&Tag方法与斑马鱼系统的优势相结合，可以在脊椎动物胚胎发生的背景下定义新兴的染色质景观。
Cell fate decisions are governed by interactions between sequence-specific transcription factors and a dynamic chromatin landscape. Zebrafish offer a powerful system for probing the mechanisms that drive these cell fate choices, especially in the context of early embryogenesis. However, technical challenges associated with conventional methods for chromatin profiling have slowed progress toward understanding the exact relationships between chromatin changes, transcription factor binding, and cellular differentiation during zebrafish embryogenesis. To overcome these challenges, we adapted the chromatin profiling methods CUT&RUN and CUT&Tag for use in zebrafish, and applied these methods to generate high resolution enrichment maps for H3K4me3, H3K27me3, H3K9me3, RNA polymerase II, and the histone variant H2A.Z using tissue isolated from whole, mid-gastrula stage embryos. Using this data, we identify a subset of genes that may be bivalently regulated during both zebrafish and mouse gastrulation, provide evidence for an evolving H2A.Z landscape during embryo development, and demonstrate the effectiveness of CUT&RUN for detecting H3K9me3 enrichment at repetitive sequences. Our results demonstrate the power of combining CUT&RUN and CUT&Tag methods with the strengths of the zebrafish system to define emerging chromatin landscapes in the context of vertebrate embryogenesis.
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