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, Nuclear Matrix Constituent Proteins (NMCP, also known as CRWN in Arabidopsis, p.700

, The question 704 marks besides these chromatin contacts depict the current situation that little is known 705 about how the interactions are established. These chromatin contacts are established 706 by factor yet unknown (question marks), which we speculate to be combinatorial 707 activities of stochastic chromatin movements, specific bridging interactions of proteins 708 and RNAs, and liquid-liquid phase separation, general, chromatin regions located at the nuclear periphery (i) and at the 701 nucleolus (ii) tend to be inactive, p.710

, multiple H3K9me-marked loci can form puncta in the nucleoplasm (v), which is likely 711 driven by liquid-liquid phase separation mediated by plant-specific ADCP1 proteins 712

, LAD, lamina-associate domains; NAD, nucleolus-associated domains, p.713

, Location of LADs and NADs loci across the Arabidopsis genome

, Figure 2. Association between DNA replication timing and chromatin localization 717 in Arabidopsis

, Comparisons of Arabidopsis DNA replication activities

C. Seq-by, early and late S phase stages in LADs (a) and NADs (b), vol.63

, Note that the dataset describing nascent DNA strand 722 is from a study by Sequeira-Mendes, Distribution of leading nascent DNA strands in ORIs

, This information, in turn, can be used to infer whether ORIs occur across a given 725 genomic region evenly. For instance, the curves in (c) imply that around LAD boundary 726 regions, ORIs fire more often outside LADs than inside. Plant materials used for 727 generating

, nascent DNA strands, 4-day-old and 10-day-old seedlings; LADs, 10-day-old 729 seedlings; and NADs, 3-week-old seedlings. Datasets and scripts for reproducing plots 730 in panels (a-d) are available from figshare repository with

, Figure 3. Identification of A. thaliana proteins containing an R/G-rich and, p.735

Q. Idr, 1234 737 possess at least a GGRG motif or a stretch of Q/N (at least 12 Q or N in 30 continuous 738 amino acids). The numbers of proteins with more GGRG motifs or stronger Q/N stretch 739 are presented. The key proteins are listed, and their respective subnuclear 740 compartment is specified in brackets. (b) Venn diagram demonstrating the lack of 741 overlap between proteins, 736 (a) Among the 27416 referenced proteins in the A. thaliana genome (TAIR10)

, The 743 identification of IDR-containing proteins was based on text mining with following 744 criteria: R/G motifs were called if they exactly matched text string, GGRG

, Q/N motifs 745 were called when at least 12 Q/N residues were found in a window of 30 amino acids

, Overlapping Q/N motifs were further merged. For each IDR-containing protein, the 747 number of R/G motifs and/or the number of Q/N residues in IDR can be