Abstract
Although three-dimensional (3D) genome organization is central to many aspects of nuclear function, it has been difficult to measure at the single-cell level. To address this, we developed 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE). scSPRITE uses split-and-pool barcoding to tag DNA fragments in the same nucleus and their 3D spatial arrangement. Because scSPRITE measures multiway DNA contacts, it generates higher-resolution maps within an individual cell than can be achieved by proximity ligation. We applied scSPRITE to thousands of mouse embryonic stem cells and detected known genome structures, including chromosome territories, active and inactive compartments, and topologically associating domains (TADs) as well as long-range inter-chromosomal structures organized around various nuclear bodies. We observe that these structures exhibit different levels of heterogeneity across the population, with TADs representing dynamic units of genome organization across cells. We expect that scSPRITE will be a critical tool for studying genome structure within heterogeneous populations.
Highlights
In eukaryotes, linear DNA is packaged in a three-dimensional (3D) arrangement within the nucleus
In this step, ~105 nuclei are distributed across a 96-well plate, where each well contains a unique DNA barcode tag such that DNA molecules within the nuclei contained in a well are labeled with the same tag
There is no limit in the number of individual cells that can be analyzed using this approach, we focused on ~103 nuclei to ensure that we achieved high-resolution per cell at a given sequencing depth. (ii) Spatial barcoding uniquely barcodes all DNA molecules within a spatial complex in a given cell
Summary
Linear DNA is packaged in a three-dimensional (3D) arrangement within the nucleus. This includes organization of DNA regions from the same chromosome (chromosome territories)[1] which are further subdivided into megabase-sized self-associating topologically associating domains (TADs)[2,3], based on gene activity (active/inactive or A/B compartments)[1], and local interactions between regulatory elements (enhancer-promoter loops)[4,5,6]. Genome organization within a single nucleus directly impacts various nuclear functions within that cell including DNA replication[9], transcription[5,10], and RNA processing[11,12]. Gene expression levels are heterogeneous among populations of cells[18,19], suggesting that there may be differences in enhancer-promoter contacts present within each cell in the population
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
