Teloni et al.

This repository contains notebooks for the analysis and visualization of the figure panels contained in Teloni et al.

Preprocessing

Preprocessing of ChIP-seq experiments was done as follow:

Raw reads were analyzed using the nf-core ChIP-seq pipeline (v. 1.2.1), with parameters “--single_end” and “--hard_trim5 75” to maintain consistent read lengths across different sequencing runs. Reads were aligned to the human genome (hg19).
BAM files for technical and biological replicate of the same sample were merged and re-indexed with SAMtools.
Merged files were normalized to counts per million (CPM), and log₂(ChIP/input) BigWig files were created using deepTools. These normalized files were used for all ChIP-seq visualizations.

Preprocessing of sister-pore-C experiments was done by applying our sister-pore-C pipeline, adapted from the ONT pipeline to accomodate sister-chromatid-specific contacts.

Figure 1

(C) and (D)

Quantification of 53BP1 and RAD51 fluorescence intensities at a specific locus (chr19 p13.2) can be found in this notebook.

(H)

Probabilities of single- and double-cutting at sgRNA sites were computed from the 53BP1− FISH fraction using a simple stochastic model as shown in this notebook.

Figure 2

(A) and (B)

Hi-C interaction matrix around the sgRNA target locus (chr2 q14.3) in untreated G2-synchronized wildtype cells and RAD51 ChIP-seq tracks at the same locus for all conditions are shown in this notebook.

(C)

Stacked RAD51 line profiles at the 23 sgRNA loci for all conditions are shown in this notebook.

(D)

Average RAD51 profiles at the 23 sgRNA loci for all conditions are shown in this notebook.

(E) and (F)

Average Hi-C and RAD51 profiles for all conditions at TAD boundaries surrounding the induced DSBs are shown in this notebook.

(G)

γH2A.X ChIP-seq tracks at the same locus as (Fig. 2B) for all conditions are shown in this notebook.

(H)

Stacked γH2A.X line profiles at the 23 sgRNA loci for all conditions are shown in this notebook.

(I)

Average γH2A.X profiles at the 23 sgRNA loci for all conditions are shown in this notebook.

(J)

γH2A.X profiles for all conditions at TAD boundaries surrounding the induced DSBs are shown in this notebook.

Figure 3

(B)

Sister-pore-C interaction matrices for cis- and trans-sister contacts around the sgRNA target locus (chr2 q33.2) in untreated and DSB-induced cells are shown in this notebook.

(C)

Average sister-pore-C interaction matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced cells are shown in this notebook.

(D)

Average sister-pore-C log2(DSB/untreated) ratio matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced cells are shown in this notebook.

(E)

Sister-pore-C interaction matrices for cis- and trans-sister contacts around the sgRNA target locus (chr2 q33.2) in untreated and DSB-induced Sororin-depleted cells are shown in this notebook.

(F)

Average sister-pore-C interaction matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced Sororin-depleted cells are shown in this notebook.

(G)

Average sister-pore-C log2(DSB/untreated) ratio matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced Sororin-depleted cells are shown in this notebook.

Figure 4

(A) to (D)

Stacked line profiles of log2(DSB/untreated) ratio for cis- and trans-sister contacts and average pileups at all 23 sgRNA loci are shown in this notebook.

(E) and (F)

Stacked line profiles for NIPBL (E) and Sororin (F) at all 23 sgRNA loci in untreated and DSB-induced G2 cells are shown in this notebook.

(G) and (H)

Average ChIP-seq profiles for NIPBL (G) and Sororin (H) at all 23 sgRNA loci in DSB-induced G2 cells are shown in this notebook

(I) and (J)

Stacked line profiles for NIPBL (E) and Sororin (F) at all 23 sgRNA loci in untreated and DSB-induced G2 cells are shown in this notebook.

(K) and (L)

Average ChIP-seq profiles for NIPBL (G) and Sororin (H) at all 23 sgRNA loci in DSB-induced G2 cells are shown in this notebook

(M) and (N)

Box plots of NIPBL (M) and Sororin (N) ChIP-seq enrichment across baseline, repair regions and break sites are shown in this notebook

Figure S1

(G) and (J)

Genome-wide maps of predicted (G) and selected (J) sites for DSBs induction are shown in notebook

(H) and (I)

Genome-wide maps of γH2A.X enrichment in untreated (H) and DSB-induced (I) G2-synchronized cells are shown in notebook

(K) and (L)

Genome-wide maps of RAD51 enrichment in untreated (K) and DSB-induced (L) G2-synchronized cells are shown in notebook

Figure S2

(A) and (B)

Hi-C interaction matrix of 3 different sgRNA target loci in untreated G2-synchronized wildtype cells and RAD51 ChIP-seq tracks at the same loci for all conditions are shown in this notebook.

Figure S3

(A) to (D)

Box plots of γH2A.X (A, C) and RAD51 (B, D) ChIP-seq enrichment at control and sgRNA target loci in untreated and DSB-induced G1- (C, D) and G2-synchronized (A, B) cells are shown in this this notebook.

(E)

Average RAD51 profiles for all conditions at TAD boundaries, split into strong vs. weak, surrounding the induced DSBs are shown in this notebook.

Figure S4

(A)

γH2A.X ChIP-seq tracks at 3 different sgRNA target loci for all conditions are shown in this notebook.

(B)

Average γH2A.X profiles for all conditions at TAD boundaries, split into strong vs. weak, surrounding the induced DSBs are shown in this notebook.

(C) and (D)

Average RAD51 (C) and γH2A.X (D) ChIP-seq tracks at highly vs. lowly induced DSBs for all conditions in G2-synchronized cells are shown in this notebook.

Figure S5

(C) and (G)

RAD51 (C) and γH2A.X (G) ChIP-seq tracks at four different loci for G2-synchronized cells transfected with 1nM sgRNA are shown in this notebook.

(D) and (H)

Stacked line profiles of RAD51 (D) and γH2A.X (H) ChIP-seq at the 23 sgRNA loci for G2-synchronized cells transfected with 1nM sgRNA are shown in this notebook.

(E) and (I)

Average profiles of RAD51 (E) and γH2A.X (I) ChIP-seq at the 23 sgRNA loci for G2-synchronized cells transfected with 1nM sgRNA are shown in this notebook.

(F) and (J)

Average profiles of RAD51 (F) and γH2A.X (J) ChIP-seq at TAD boundaries surrounding the DSB induced at the 23 sgRNA loci for G2-synchronized cells transfected with 1nM sgRNA are shown in this notebook.

Figure S7

(B) to (E)

Yhis notebook reproduces scsHi‑C and Sister‑pore‑C contact maps at a chr2 locus in G2‑synchronized cells (20 kb bins). Plot 7B shows scsHi‑C total, cis‑sister, and trans‑sister contacts down‑sampled to 40M segments; 7C shows the same at full depth (~2B reads). Plots 7D–E show Sister‑pore‑C maps from merged replicates at the same locus (three experiments for 7D; two Sororin‑depleted for 7E), each down‑sampled to 40M segments to match the number of sister‑specific contacts.

Figure S8

(B)

Sister-pore-C interaction matrices for cis- and trans-sister contacts around three sgRNA target loci in untreated and DSB-induced cells are shown in this notebook.

(C) and (D)

Average sister-pore-C interaction matrices (C) and log2 (DSB/untreated) ratio for cis- and trans-sister contacts at TAD boundaries surrounding the DSBs at 23 sgRNA loci are shown in this notebook

(E) and (F)

Genome-wide contact probability plots for cis- (E) and trans-sister (F) contacts in untreated and DSB-induced G2-synchronized cells are shown in notebook

(G)

Box plots of log2(DSB/untreated) ratio for trans-sister contacts at the 23 sgRNA target loci in wildtype vs. Sororin-depleted G2-synchronized cells are shown in notebook

(H)

Sister-pore-C interaction matrices for cis- and trans-sister contacts around three sgRNA target loci in untreated and DSB-induced Sororin-depleted cells are shown in this notebook.

Figure S9

(A)

Average sister-pore-C interaction matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced RAD21-depleted cells are shown in this notebook.

(B)

Average sister-pore-C log2(DSB/untreated) ratio matrices for cis- and trans-sister contacts at all sgRNA loci in untreated and DSB-induced RAD21-depleted cells are shown in this notebook.

Figure S10

(A)

Stacked line profiles for RAD21 ChIP-seq at 23 sgRNA loci in untreated and DSB-induced G2 cells are shown in this notebook.

(B)

Average ChIP-seq profiles for RAD21 ChIP-seq at 23 sgRNA loci in DSB-induced G2 cells are shown in this notebook

(C)

Stacked line profiles for RAD21 ChIP-seq at 23 sgRNA loci in untreated and DSB-induced G2 cells are shown in this notebook.

(D)

Average ChIP-seq profiles for RAD21 ChIP-seq at 23 sgRNA loci in DSB-induced G2 cells are shown in this notebook

(E)

Box plots of RAD21 ChIP-seq enrichment across baseline, repair regions and break sites are shown in this notebook

(F)

Stacked line profiles for γH2A.X, NIPBL, RAD21 and Sororin ChIP-seq at 23 sgRNA loci, ordered by γH2A.X asymmetry relative to the DSB site, are shown in notebook

Homology assessment

In silico assessment of homologous sequences around each sgRNA target site was performed with this scipt.

Name		Name	Last commit message	Last commit date
Latest commit History 9 Commits
figures		figures
.DS_Store		.DS_Store
1C_D.ipynb		1C_D.ipynb
1H.ipynb		1H.ipynb
2A_B_and_S2A_B.ipynb		2A_B_and_S2A_B.ipynb
2C_H.ipynb		2C_H.ipynb
2D_I_and_S4C_D.ipynb		2D_I_and_S4C_D.ipynb
2E_F_J.ipynb		2E_F_J.ipynb
2G_S4A.ipynb		2G_S4A.ipynb
3B_S8B.ipynb		3B_S8B.ipynb
3C_F_S9A.ipynb		3C_F_S9A.ipynb
3D_G_S9B.ipynb		3D_G_S9B.ipynb
3E_S8H.ipynb		3E_S8H.ipynb
4A_to_D.ipynb		4A_to_D.ipynb
4E_F_S10A.ipynb		4E_F_S10A.ipynb
4G_H_S10B.ipynb		4G_H_S10B.ipynb
4I_J_S10C.ipynb		4I_J_S10C.ipynb
4K_L_S10D.ipynb		4K_L_S10D.ipynb
4M_N_S10E.ipynb		4M_N_S10E.ipynb
LICENSE		LICENSE
README.md		README.md
S10F.ipynb		S10F.ipynb
S1G-J.md		S1G-J.md
S1H-I.md		S1H-I.md
S1K-L.md		S1K-L.md
S3A_D.ipynb		S3A_D.ipynb
S3E_S4B.ipynb		S3E_S4B.ipynb
S5C_G.ipynb		S5C_G.ipynb
S5D_H.ipynb		S5D_H.ipynb
S5E_I.ipynb		S5E_I.ipynb
S5F_J.ipynb		S5F_J.ipynb
S7B_E.ipynb		S7B_E.ipynb
S8C_D.ipynb		S8C_D.ipynb
S8E_F.ipynb		S8E_F.ipynb
S8G.ipynb		S8G.ipynb
homology_test.sh		homology_test.sh
homology_vis.sh		homology_vis.sh

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Teloni et al.

Preprocessing

Figure 1

(C) and (D)

(H)

Figure 2

(A) and (B)

(C)

(D)

(E) and (F)

(G)

(H)

(I)

(J)

Figure 3

(B)

(C)

(D)

(E)

(F)

(G)

Figure 4

(A) to (D)

(E) and (F)

(G) and (H)

(I) and (J)

(K) and (L)

(M) and (N)

Figure S1

(G) and (J)

(H) and (I)

(K) and (L)

Figure S2

(A) and (B)

Figure S3

(A) to (D)

(E)

Figure S4

(A)

(B)

(C) and (D)

Figure S5

(C) and (G)

(D) and (H)

(E) and (I)

(F) and (J)

Figure S7

(B) to (E)

Figure S8

(B)

(C) and (D)

(E) and (F)

(G)

(H)

Figure S9

(A)

(B)

Figure S10

(A)

(B)

(C)

(D)

(E)

(F)

Homology assessment

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