Abstract
With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here, we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina towards the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100 kb resolution, which revealed radial patterns of genomic and epigenomic features, gene expression, as well as A/B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations, and found that they have distinctive radial arrangements in A/B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.
Highlights
In eukaryotic cells, the genome is spatially organized and its three-dimentional (3D) architecture is vital to the proper execution of its functions[1]
The nuclear lamina is thought to be the key organizer of the radial arrangement of chromatin in interphase nuclei[10], by creating a large nuclear compartment where the majority of inactive chromatin clusters in the form of lamina-associated domains (LADs)[11,12,13]
Specialized sub-chromosomal regions, such as centromeres and telomeres, as well as nucleolar organizing regions, are non-randomly positioned in the nucleus[14,15,16,17,18]. The latter contain ribosomal RNA gene clusters that coalesce to form the core of the largest nuclear body, the nucleolus, and organize chromatin in and around them[19]
Summary
The genome is spatially organized and its three-dimentional (3D) architecture is vital to the proper execution of its functions[1]. The role of genomic and epigenomic features in shaping radiality remains to be quantified, despite several attempts to model the contribution of various factors[35,36,37] It is unclear whether the nucleus merely consists of a peripheral transcriptionally inactive compartment as opposed to a central transcriptionally active one, or whether a finer stratification exists. 50046-250G) · Nuclease-free Phosphate-Buffered Saline (10X) pH 7.4 · YFISH hybridization buffer (YHB): 10% Dextran sulfate/25% FA/1 mg/ml E.coli tRNA /0.02 % BSA/2X SSC · Hoechst 33342 G2943CA) · Agilent RNA 6000 Pico Kit (Agilent, cat. no. 5067-1513) · Agilent High Sensitivity DNA Kit (Agilent, cat. no. 5067-4626)
Sign-in/Register to view highlights & summary 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.
