Downstream-analysis-3D-chromatin-loops

Additional analysis to understand chromatin loop impact in cells

A short tutorial on R to integrate loops from HiC/ HiChIP for further downstream analysis.

Example analysis

Use the requiredPackages.R to install the packages we shall use in the analysis. The entire tutorial with output is depicted in an HTML file called loop-additional-analysis.html in the PALS2024 folder.

Download the tutorial with git

git clone https://github.com/remeseirogrp/Downstream-analysis-3D-chromatin-loops.git

Toy Data

The data_chr15.2_studentsdataframe.txt is a dummy data created from the super H3K4me3-HiChIP loops dataset from ChakrabortyC et al., 2023.

The additional_files folder

This folder has the script and the subsetted data that was used to build the tutorial. Example output for UPSET plot, loop length and other output files are located in this folder.

Web resources for publicly available 3D data and tools

4D Nucleome

3D Genome Browser

Hemtools for HiC and capture C

3D-genome

HiC-analysis with HiCExplorer with GalaxyTools

HiC-Pro

HiC tools: Aiden Lab

HiC/ HiChIP tools: Ferhat Ay lab

HiC/ HiChIP tools: Aryee lab

Articles

Methods for mapping 3D chromosome architecture

Kempfer, R., Pombo, A. Methods for mapping 3D chromosome architecture. Nat Rev Genet 21, 207–226 (2020). https://doi.org/10.1038/s41576-019-0195-2

Understanding 3D genome organization by multidisciplinary methods

https://www.nature.com/articles/s41580-021-00362-w

The era of 3D and spatial genomics

Bouwman BAM, Crosetto N, Bienko M. The era of 3D and spatial genomics. Trends Genet. 2022 Oct;38(10):1062-1075. doi: 10.1016/j.tig.2022.05.010. Epub 2022 Jun 6. PMID: 35680466.

Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency

Hörnblad A, Remeseiro S. Epigenetics, Enhancer Function and 3D Chromatin Organization in Reprogramming to Pluripotency. Cells. 2022; 11(9):1404. https://doi.org/10.3390/cells11091404

Computational methods for analyzing multiscale 3D genome organization

Zhang, Y., Boninsegna, L., Yang, M. et al. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet 25, 123–141 (2024). https://doi.org/10.1038/s41576-023-00638-1

Comparison of computational methods for 3D genome analysis at single-cell Hi-C level

Li X, An Z, Zhang Z. Comparison of computational methods for 3D genome analysis at single-cell Hi-C level. Methods. 2020 Oct 1;181-182:52-61. doi: 10.1016/j.ymeth.2019.08.005. Epub 2019 Aug 21. PMID: 31445093.

Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data

Kimberly MacKay, Anthony Kusalik, Computational methods for predicting 3D genomic organization from high-resolution chromosome conformation capture data, Briefings in Functional Genomics, Volume 19, Issue 4, July 2020, Pages 292–308, https://doi.org/10.1093/bfgp/elaa004