The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development
Abstract
:1. Introduction
2. Low-Input Hi-C Methods and Analysis
3. Hierarchical Organization of Interphase Chromatin
4. Chromatin Remodeling in Gametogenesis and Early Embryonic Development
4.1. Chromatin Remodeling in Gametogenesis and Pre-Implantation Development in Mammals
4.2. Chromatin Organization in Non-Mammalian Vertebrates during Early Embryonic Development
4.3. Emergence of Chromatin Organization in Insect Embryos
4.4. Similarities and Differences between Species
5. Mechanisms of 3D Genome Formation in Early Embryonic Development
5.1. Architectural Proteins
5.2. Transcription and Establishment of 3D Genome
5.3. Transposable Elements (TEs) and 3D Genome Folding
5.4. Phase Separation
6. Conclusions and Perspectives
Author Contributions
Funding
Conflicts of Interest
References
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Methods | Full Name | Procedure | Characteristics |
---|---|---|---|
Hi-C [11] (in situ Hi-C) [12] | Chromosome conformation capture by high-throughput sequencing | Crosslinking, restriction enzyme digestion, end filling with biotinylated dNTP and proximity ligation (ligation performed in intact nuclei in an in situ Hi-C), reverse crosslinking, sonication and streptavidin enrichment, and sequencing. | Widely used genome-wide method |
Single-cell Hi-C [17,18] | Single-cell Hi-C | Similar to in situ Hi-C, individual nuclei selected using microscopy after proximity ligation. Remaining steps done in single cells separately. Sonication replaced with a second restriction enzyme to fragment ligation products. | The first single-cell chromatin structure method, relatively low throughput |
Sci-Hi-C [19,20] | Single-cell combinatorial indexed Hi-C | Crosslinking, restriction digestion, distributed to 96 wells and barcoded bridge-adaptor ligation, nuclei pooled and proximity ligation, redistribution to 96 wells and barcoded sequencing-adaptor ligation, sequencing. | A larger number of single cells with fewer interactions per cell |
Single-cell Hi-C [21] | Single-cell Hi-C | Crosslinking, single nuclei sorting with FACS, nuclei imaging, overlaid nuclei with low melting agarose. Remaining steps similar to in situ Hi-C but done in single cells. | Combination of imaging with determination of genome structure |
Sn Hi-C [22] | Single-nucleus Hi-C | Similar to in situ Hi-C but omitting biotin incorporation. Single nuclei sorted by FACS after proximity ligation and then whole genome amplification was done to single nuclei. | More contacts per single cell |
Improved multiplexed single-cell Hi-C [23] | Improved multiplexed single-cell Hi-C | Improved from [17], with flow cytometry sorting, Tn5 transposase library preparation, and an automation scheme. | Moderate contacts per single cell |
Dip-C [24] | Single-cell Hi-C of diploid cells | Similar to Sn Hi-C [22]. Whole-genome amplification done with multiplex end-tagging amplification. | Distinguishes two haplotypes of each chromosome |
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Li, F.; An, Z.; Zhang, Z. The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development. Cells 2019, 8, 788. https://doi.org/10.3390/cells8080788
Li F, An Z, Zhang Z. The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development. Cells. 2019; 8(8):788. https://doi.org/10.3390/cells8080788
Chicago/Turabian StyleLi, Feifei, Ziyang An, and Zhihua Zhang. 2019. "The Dynamic 3D Genome in Gametogenesis and Early Embryonic Development" Cells 8, no. 8: 788. https://doi.org/10.3390/cells8080788