README.md

Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organisation

Liezel Tamon, Zahra Fahmi, James Ashford, Rosana Collepardo-Guevara, and Aleksandr B. Sahakyan*

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Tamon L, Fahmi Z, Ashford J et al (2025) Analysis of long-range contacts across cell types outlines a core sequence determinant of 3D genome organisation. 2025.03.16.643527. https://www.biorxiv.org/content/10.1101/2025.03.16.643527v1 (in revision)

Each directory contains a README explaining each script. Directories relevant for each main figure:

Figure 1. Contact persistence to isolate and investigate the core genomic contacts, their determinants and implications.

• C. 11_Complementarity to generate contact maps.

Figure 2. Visualisation of persistent contacts and the chromosome organisation they mediate.

• A,C. 4_ArcPlot to generate arc plots representing contacts per chromosome.
• B,D. CoreGenomeExplorer Shiny app to generate network plots representing contacts per chromosome.

Figure 3. Persistent contacts enriched for contacts with features associated with heterochromatin and preferential AT sequence composition.

• A. 8_FeatureVsPersist/A5_metaplot.R
• B. 7_FeaturePermutation/D1_foivsij.R
• C. 23_Hub_Gene_Expression/E1_geneExprVsCp.R
• D. 16_GeneVsPersist
• E. 16_GeneVsPersist
• F. 20_ReplicationTiming
• G. 19_MutationRatesVsPersist

Figure 4. Higher sequence complementarity between persistent contacts.

• 11_Complementarity to calculate sequence complementarity and generate contact maps.
• 12_Shuffling to generate shuffled contacts.

Figure 5. Genome-wide cII values recapitulate some Hi-C features in additional human datasets of different resolutions and in another species, Drosophila.

• 11_Complementarity to calculate sequence complementarity and generate contact maps.

Figure 6. Repeat contribution to the observed sequence complementarity of contacts.

• 18_RepeatVsPersist

Others

• lib contains utility functions used in scripts across directories.