Additional file 1 of The probability of chromatin to be at the nuclear lamina has no systematic effect on its transcription level in fruit flies
Creators: name: Afanasyev, Alexander Y.
name: Kim, Yoonjin
name: Tolokh, Igor S.
name: Sharakhov, Igor V.
name: Onufriev, Alexey V.
Publisher: name: figshare
Year: 2024
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. Probabilities of TADs (LAD containing TADs (L-TADs) and TADs not containing LADs (Non-L-TADs) in control nucleus model, and all TADs in lamins-depleted nucleus model) to be in contact with the NE (to be within 0.2 μm from the NE). Null L-TAD #15 (in control and lamins-depleted nuclei), analyzed in [1] as cytological region 22A, is marked by yellow circles. Null L-TAD #120 (in control and lamins-depleted nuclei), analyzed in [1] as cytological region 36C, is marked by red triangles. PcG L-TAD #435 (in control and lamins-depleted nuclei), analyzed in [1] as cytological region 60D, is marked by orange squares. Figure S2. Left panel: Computed chromatin density averaged over the spherical layers as a function of the radial distance from the nucleus center in control nuclei (top) and in lamins-depleted nuclei (bottom). The radius of the nucleus is 2 μm. Right panel: Experimental mean chromatin radial density in the equatorial plane of the nucleus of the proventriculus. For illustration only, the azimuthal dependence of the density is averaged out to produce a schematic that shows only the radial density profile. The density is inferred from relative fluorescence intensity, as detailed in Ref. [2]. Specifically, 21 equally spaced experimental data points are taken from Fig. S3 (Group 1, bottom panel) of Ref. [2] and then interpolated using a linear interpolation process, yielding 201 equally spaced data points plotted in the figure. The radial position of the mean chromatin density is measured from the nuclear center to the periphery (0% - 100%). Table S1. A numerical simulation of gene activity with noise. Here, GC and GK are uniformly distributed random variables on the interval [0,1]. A total of 2N = 2000 random numbers were generated for each trial, and ratios of two sequential random numbers were computed and averaged over all N pairs. Each trial starts with an independent seed to initiate the random number generator Math.random() , as implemented in Java 1.16.4. Figure S3. (A) Scatter plot shows a weak negative correlation between the expression of genes in TADs (in RPKMTL) and the probability of TAD to be found in contact with the NE (i.e. to be found within 0.2 μm layer near the NE) in the control nuclei. (B) Scatter plot shows essentially no correlation between the TAD expression (in RPKMTL) and the probability of TAD being found in contact with the NE in the lamins-depleted nuclei. The Spearman, and Pearson correlation coefficients, their two-sided p-values (p), and linear regression lines (red) are shown. Figure S4. Dependencies of bin averaged TAD transcription levels (in RPKMTL) on the probability of TADs in the bin to be in contact with the NE. The binning of TADs is based on TAD-NE contact probabilities in control cells for each set (selection) of TADs. Solid bars: control cells. Empty bars: lamins-depleted cells. The same set of TADs per bin is used in the control and lamins-depleted cells. Error bars are s.e.m. (standard error of the mean). Left panels: (A) all TADs; (B) TADs not containing LADs (NonL-TADs); and (C) TADs containing LADs (L-TADs). In the left panels only, the positions of the empty bins (lamins-depleted cells) along the x-axis are deliberately kept unchanged to facilitate visual comparison with the heights of the corresponding bins for control cells. Right panels show only lamins-depleted cells: (D) all TADs; (E) TADs not containing LADs (NonL-TADs); and (F) TADs containing LADs (L-TADs). A clear shift of the average TAD positions away from the NE is evident. Figure S5. The metric of transcription activity in TADs, RPKMTL, is consistent with the epigenetic classes of TADs identified previously [3]. Median transcription level (in RPKMTL) in Active TADs (n=494) is at least 2 times greater than those of other epigenetic TAD classes, such as HP1/centromeric (n=52), Null (n=492), and PcG (n=131) (panel A, dashed lines). The medians (dashed lines) along with the means (solid boxes) demonstrate consistency with the data in Figure 3C of Ref. [3], reproduced in the panel B, which show the median gene transcription levels within each epigenetic class of TADs. The dynamic model of fruit fly nucleus employs the partitioning of the genome into TADs and their epigenetic classes, introduced in Ref. [3]. Error bars are s.e.m. (standard error of the mean). Figure S6. Distribution of TADs by types such as Active L-TADs (n=54), Active NonL-TADs (n=440), HP1/centromeric L-TADs (n=34), Null L-TADs (n=228), Null NonL-TADs (n=264), PcG L-TADs (n=50), and PcG NonL-TADs (n=81) in control (A) and lamins-depleted (B) cells. The average gene expression (black horizontal lines) in L-TADs for each type is lower than those of NonL-TADs. The red horizontal lines are the median gene expression values in TADs for each type. Figure S7. Distribution of TADs in bins by epigenetic classes (Null, Active, PcG, and HP1/centromeric). A, B, and C The red and black horizontal lines are the median and mean gene expression values (in RPKMT) in each bin, respectively. D, E, and F Comparison of the number of TADs of each epigenetic class in each bin. For NonL-TADs (control cells), the number of Active TADs is greater than those of other epigenetic classes in each bin. In contrast, for L-TADs (control cells), the number of Null TADs is greater than those of other epigenetic class in each bin. Positions of TADs along the horizontal axis in bins are not to scale.