Are your single-cell chromosome conformation capture experiments looking a little flat? Is your Hi-C data missing that “pop”? Well, don´t fret; a new study serves up a refreshing twist on a popular technique – scSPRITE – that will put some fizz back into your single-cell genome organization research!
While bulk profiling provides an averaged read-out of genome organization that misses out on single-cell level information, traditional single-cell techniques (such as single-cell Hi-C) require specialized equipment and have a limited ability to capture long-range/higher-order interactions. In the hope of bypassing problems on both these scales, researchers led by Rustem F. Ismagilov and Mitchell Guttman (California Institute of Technology) added a single-cell twist to their SPRITE (split-pool recognition of interactions by tag extension) technique so that it can easily generate high-resolution, genome-wide maps of 3D genome organization in single cells without specialized equipment, techniques, or training.
So, kick off your shoes, and pour yourself a glass of something bubbly (but maybe hold off on mixing up that Radler, this gets complicated!), and let´s get a taste of this advance from Arrastia, Jachowicz, and colleagues:
- scSPRITE involves two sets of split-and-pool barcoding to:
- i) tag DNA fragments contained in the same nucleus
- ii) tag the spatial arrangement of the fragments
- Measurements of multiway DNA contacts generate higher-resolution maps than other techniques, such as proximity ligation, that use pairwise DNA contacts
- scSPRITE can detect known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) in individual mouse embryonic stem cells (mESCs)
- scSPRITE detects higher-order contacts, reflecting inter-chromosomal interactions, organized around various active (nuclear speckle) and inactive (centromeres and nucleolar contacts) nuclear bodies
- TADs represent dynamic units of genome organization in single cells, with cell-to-cell variabilities and region-to-region differences hypothesized to possess functionally relevance
- scSPRITE identifies cell-to-cell heterogeneity in mESC genome structure at different levels of resolution
- Examples include enhancer-promoter contacts related to the Nanog locus and interactions between the Tbx3 locus and a distant gene locus
The effervescent team behind this study hopes that the straightforward nature of scSPRITE (not too much “fizzical” labor then) will allow us all to conduct single-cell genome structure measurements in different cell types or homogenized tissues composed of mixed cell populations. scSPRITE may also permit the development of “sparkling” single-cell studies aiming to decipher the relationship between genome organization and nuclear function.
Obey your thirst for single-cell genome organization studies over at Nature Biotechnology, August 2021.