Supplementary Materials http://advances. phenotypes. Table S7. Seafood probes used for 3D DNA-FISH experiments. Table S8. Summary statistics for 3D DNA-FISH experiments. Table S9. Sanger sequencing validation of quiescent and senescent Hi-C libraries. Fig. S1. Hi-C interaction matrices for the q arm of chromosome 2. Fig. S2. Hi-C interaction matrices for the q arm of chromosome 3. Fig. S3. Hi-C interaction matrices for the q arm of chromosome 4. Fig. S4. Hi-C interaction matrices for the p arm of chromosome 4. Fig. S5. Indaconitin Genomic feature analysis of contact probability. Fig. S6. Comparison of first and second Hi-C experiments. Fig. S7. Characteristics of TADs and A and B compartments. Fig. S8. Representative genes that switch compartments. Fig. S9. Physical distances between individual loci within a single chromosome arm. Fig. S10. Quantification of comet assay images. Fig. S11. Measurement of chromosome arm volumes. Fig. S12. Measurement of centromere and telomere volumes in senescent cells. Fig. S13. Comparison of Hi-C data between replicative senescence and oncogene-induced senescence. Fig. S14. High-resolution comparison of Hi-C data between replicative senescence and oncogene-induced senescence. Movie S1. Rotating movie of the 3D Hi-C model for chromosome 18 in quiescent (left structure) and senescent cells (right structure). Movie S2. Rotating movie of the 3D Hi-C model for chromosome 4 quiescent (left structure) and senescent cells (right structure). Abstract Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On Indaconitin a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant Indaconitin reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells. 0.001). We also examined in senescent cells the changes in Indaconitin mean contact probability as a function of distance at specific genomic featuresgene promoters, lamin-associated domains (LADs), and regions with high GC contentusing the approach of Zuin ((fig. S8, A to D). We also observed overlap between B-to-A switching (gene set G6) and genes associated with senescence phenotypes (table S6), although to a lesser extent (1 to 4%). Two examples are the chromatin regulator and the SASP gene (fig. S8, E and F). Chromatin compaction in senescent cells Hi-C does not provide measurements of physical ranges between genomic Rabbit polyclonal to CLOCK areas nor did it address heterogeneity between cells. The preferential cis relationships between A and B domains (A having a, and B with B) should regularly position loci in various domains of the same enter closer physical closeness than indicated from the linear (genomic) range between them, and fluorescence in situ hybridization (Seafood) continues to be utilized to empirically verify the chromosome folding predictions of Indaconitin Hi-C ( 0.001). (D) Consultant 3D DNA-FISH pictures of quiescent (top -panel) and senescent (lower -panel) cells. To check this hypothesis, we investigated first.