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Fig. 1 | Genome Biology

Fig. 1

From: Plant lamin-like proteins mediate chromatin tethering at the nuclear periphery

Fig. 1

Specific positioning of Arabidopsis chromatin at the NP. a NUP1:GFP RE-ChIP-seq signals on chromosome arms. The vertical gray bars denote pericentromeric regions (PRs). The RE-ChIP-seq results are from [27], plotted in 20-kb windows. b RE-ChIP-seq signals in chromosome arm as a function of distance to PRs. rho denotes Spearman’s rank correlation. c Comparison of LASSO (least absolute shrinkage and selection operator) regression models of predicting chromatin-NP interactions. The NUP1:GFP RE-ChIP-seq data [27] of chromosomes 1, 2, and 3 were used for generating regression models, while the data of chromosomes 4 and 5 were used for assessing the fit of the models. The input variables generating the model shown on top were from an integrated Arabidopsis epigenetic marks described previously [29], while the model shown at the bottom used genomic distances to the PRs as an additional variable. LASSO regression was performed using the R package “glmnet” with default settings [30]. The “lambda.1se” value, which was determined by tenfold cross-validation, was set as the lambda for model fitting. MSE mean squared error. d Probing chromatin localization with FISH. In each row, the plot on the left hand side shows two pools of tiling BAC probes (black segments) designed according to the NUP1:GFP RE-ChIP results [27]. Each pool of probes targets a ~ 300-kb genomic region. Boxplots show distances of the FISH signals from the NP in 2C nuclei. p values indicate the Mann-Whitney U test results

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