The soaring Eiffel Tower in Paris, the tumultuous Guggenheim in Bilbao, or the intricate genome structure of a single cell; which architectural marvel impresses you the most? For the labs of Leonid A. Mirny and Kikuë Tachibana-Konwalski, the latter looms above any such extravagant edifice, but the available analytical tools lacked the resolution required for them to appreciate every nook and cranny of every single cell.
To solve this problem and generate highly accurate single-cell structural information, researchers from the labs simplified a previously developed chromosome conformation capture (3C) methodology. This created a highly sensitive genome-wide high-throughput sequencing based technique called single nucleus high-resolution chromosome conformation capture or snHi-C. To ensure sensitivity, the authors omitted several steps from conventional Hi-C methods, including biotin incorporation and enrichment for ligated fragments, which can limit retrieval of structural data.
Now, the talented team has employed this technique to accurately depict the genome architecture changes that occur following the fertilization of the mouse oocyte, subsequent reprogramming events, and the generation of a totipotent zygote.
The zygote contains the epigenetically and spatially distinct paternal (sperm) and maternal (oocyte) genomes, although the exact three-dimensional organization of these two zygotic genomes remains unclear. The researchers hoped that understanding changes in the genome architecture of totipotent zygotes might provide them with clues on how the totipotent state arises and then apply this knowledge to shape future somatic cell reprogramming techniques.
Flyamer et al. discovered that:
- snHi-C provides higher density and higher resolution data when compared to previously reported techniques
- Zygotic genomes and normal cells during interphase display fundamental architectural differences
- Architectural reorganization represents a distinct process for paternal and maternal zygotic genomes
- Both paternal and maternal genomes contain similar levels of organizational components known as topologically associating domains (TADs) and loops
- However, segregation into active and inactive (A-B) genomic compartments only occurs in the paternal genome
- Architectural analyses provided evidence for the inheritance of paternal genome compartmentalization
- The paternal genome is compacted into protamine complexes in sperm, a packaging technique not employed for the maternal genome of the oocyte
- Paternal compartmentalization correlates to the presence of hyperacetylated histone H4, a hallmark of active chromatin, and earlier transcriptional activation, thereby also linking transcription to genome compartmentalization
- The lack of compartmentalization of the maternal zygotic genome may represent the transition towards the genome organization of a totipotent cell
- A less organized, more open genomic structure may confer the characteristics required for the acquisition of the totipotent state
With the development of a sensitive technique to assess genome architecture in single cells, the authors have provided new and exciting data on how the totipotent state may form. Can we use this information to shape reprogramming and produce totipotent stem cells in the future?
See more of the architectural masterpiece that is the mammalian zygote genome over at Nature, March 2017.