Long-range Colocalizaiton (LRC) Notebooks

Long-range genomic loci stochastically assemble into combinatorial forms of chromosome skeleton Link

Highlights

1. The spatial proximity of two well-separated cis-loci (>100 Mb) is a prevalent and conserved feature of human chromosomes.
2. While most long-range localizations (LRCs) are formed transiently and present infrequently in tested chromosome copies, ~5% of them recur in 0.8% to >10% subpopulations of entire chromosomes, and are thus considered stable contacts.
3. Multivalent binding is one of the possible mechanisms that ensures a stable LRC structure.
4. A subset of genomic sites serves as nucleation centers (NCs) for clustering stable LRCs, assembling hub-like domains that may be associated with chromosome conformation and territory segregation.
5. These findings suggest a redundant, distributed component mechanism that facilitates chromosome folding into compact structures.

Hardware requirements

All codes requires a standard computer.

Software requirements

R version 4.4.1

OS requirements

These codes were supported for macOS, Linux, and Windows. The codes have been tested on the following systems:

macOS: Sonoma 14.5

Installing R version 4.4.1 on MacOS.

R Dependencies

User should install the following packages prior to run the codes, from an R terminal:

circlize, dplyr, ggExtra, ggplot2, igraph, htmlwidgets, pheatmap, plotly, viridis

Expected output

The codes are used to generate figures and results in Long-range genomic loci stochastically assemble into combinatorial forms of chromosome skeleton

Reproduction instructions

For codes to generate figures and results in Fig1 and extended Fig1-3, please download the Hi-C data as described in extended data table 1 and run the code Figure1.R. For codes to generate figures and results in Fig2-Fig5 and extended Fig4-6, please download the MERFISH data of chrosmosome 2 and chromosome 21 from https://zenodo.org/records/3928890