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Figure 1. Biased distribution of different SV classes

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1 Figure 1. Biased distribution of different SV classes
Figure 1. Biased distribution of different SV classes. (A) Clustering of SV classes based on their enrichments by ... Figure 1. Biased distribution of different SV classes. (A) Clustering of SV classes based on their enrichments by Z-score in 5 compartments, identified from Hi-C studies. Two major clusters can be observed. (B) Normalized distribution of replication timing for different Alus. Alu insertion and deletions were further classified as rare or common (minor allele frequency threshold, 1%). (C) Positive and negative Z-scores mean enrichment and depletion, respectively, of SVs across topologically associated domain (TAD) boundary or loop anchor. (D) Clustering of SV classes and functional states based on distribution of breakpoints in the states. The states were inferred from chromHMM segmentation of histone marks. Descriptions of each state are provided in Supplementary Table S1. Dashed lines show three categories of states by enrichment with SV breakpoints. * represents adjusted P-value < 0.05 (Z-test with Bonferroni correction). Abbreviations: Variable number of tandem repeats (VNTR), Tandem duplications (TDUP), Deletions with multiple transposable elements (MTE-del). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz103, The content of this slide may be subject to copyright: please see the slide notes for details.

2 Figure 4. (A) No enrichment/depletion of DNase sites is observed around retrotransposons discovered as insertions. (B) ... Figure 4. (A) No enrichment/depletion of DNase sites is observed around retrotransposons discovered as insertions. (B) Depletion of DNase sites is observed around breakpoints of deleted retrotransposons as well as non-variable Alu elements, suggesting that the effect is due to compromised read mapping around repeats. Insertion sites of processed pseudogenes are enriched with DNase sites. (C) Retrotransposon insertion sites are depleted with nucleosome signal. TEI, non-variable Alu, and processed pseudogenes also support depletion of the nucleosome signal around breakpoint. The peak at the center of the X-axis (lower panel) represents the normalized mean nucleosome signal within element boundaries. (D) DNase signal is enriched only around pseudogenes where length is away from nucleosome periodicity (∼150 bp). Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz103, The content of this slide may be subject to copyright: please see the slide notes for details.

3 Figure 3. (A) NHEJ breakpoints are enriched with DNase I hypersensitive sites, unlike NHrepl breakpoints. (B) No ... Figure 3. (A) NHEJ breakpoints are enriched with DNase I hypersensitive sites, unlike NHrepl breakpoints. (B) No enrichment/depletion of normalized nucleosome signal around 1 kb of repair related deletions. (C) Aggregations for spontaneous DSB peaks are similar to those for DNase sites. (D) Aggregation of spontaneous DSBs around regulatory elements. The largest enrichment is observed for transcription factor (TF) binding site inside DNase sites. (E) Meiotic DSBs are enriched only around NAHR breakpoints; however, the enrichment is not as high as would be expected if all NAHR events were of meiotic origin. (F) Enrichment of meiotic DSBs was observed around germline NAHR but not around somatic NAHR in cancer. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz103, The content of this slide may be subject to copyright: please see the slide notes for details.

4 Figure 2. (A) Fold enrichment (Log2 scale) of real NAHR breakpoints, simulated homologous breakpoints, ... Figure 2. (A) Fold enrichment (Log<sub>2</sub> scale) of real NAHR breakpoints, simulated homologous breakpoints, spontaneous and meiotic DSB in five compartments, relative to uniform distribution based on compartment lengths. P values were calculated using chi-square test (* indicates P < 0.05; **P < 0.005; ***P < ). (B) Differences in the number of observed and predicted NAHR events (using a multiple linear regression model) along each compartment segment. Values closer to zero imply better prediction. Dotted lines represent 3 standard deviations from the mean. Bins with values outside the dotted lines represent discordant predictions. (C) Cumulative density of Hi-C interaction observed between breakpoints of SVs in different classes, advance simulated NAHR breakpoints, and random points. Original interaction values were normalized based on a background distribution for each compartment. This eliminated the effect of overall stronger interactions in B compartments, facilitating an unbiased comparison (Supplementary Figure S7). (D) Cumulative density of normalized Hi-C interaction for NAHR breakpoints with only spontaneous DSB or only meiotic DSB within 1 kb. Unless provided in the caption above, the following copyright applies to the content of this slide: © The Author(s) Published by Oxford University Press on behalf of Nucleic Acids Research.This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. Nucleic Acids Res, gkz103, The content of this slide may be subject to copyright: please see the slide notes for details.

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