Extended Data Fig. 4: Relation between CRWN1-chroamin contacts and gene expression.
From: The plant nuclear lamina disassembles to regulate genome folding in stress conditions
a–c, Dynamic CRWN1-chromatin interactions and gene expression at selected loci. a, Schematic structures of AT3G46230, AT4G10250 and AT4G21320 showing the regions amplified by primers used for ChIP-qPCR and RT-qPCR analyses. Grey boxes represent exons. Arrows indicate transcription start sites. b, ChIP-qPCR analysis of CRWN1 enrichment at these gene loci under mock and heat conditions. The relative fold enrichment was normalized to an internal control locus TUB2, which does not interact with CRWN1 under either mock or heat conditions. The values shown are means ± SD of three independent replicates, *p < 0.05, ** p < 0.01, ‘ns’ indicates no significance (two-sided t-test). p values from left to right: 0.0184, 0.00146, and 0.092. c, RT-qPCR analysis showing the mRNA levels of these loci under mock and heat conditions. The relative expression levels were calculated by using ACTIN2 as control. The values indicate means ± SD of three independent replicates, ** p < 0.01, *** p < 0.001 (two-sided t-test). p values from left to right: 0.0014, 0.0034, and 0.00014. d, Changes in gene expression in crwn1 crwn4 mutants. The boxplots show the difference of gene expression, measured in rpkm, between WT (wild-type) and crwn14 (crwn1 crwn4). For each growth condition, genes are separated into two groups according to CRWN1 ChIP-seq data. The box plots indicate the median (line within the box), the lower and upper quartiles (box), margined by the largest and smallest data points that are still within the interval of 1.5 times the interquartile range from the box (whiskers); outliers are not shown. In the mock panel, n = 5974 for ‘enriched’; n = 21469 for ‘non-enriched’. In the heat panel, n = 5351 for ‘enriched’; n = 22092 for ‘non-enriched’. Two-sided Mann-Whitney U test results comparing the two boxplots indicated a p-value larger than 0.05.
