INucs: inter-nucleosome interactions.

Mehrdad Oveisi,Robin C Allshire,Stefan Dimitrov,Yuichi Taniguchi,Manu Shukla,Sunil Nahata,Ghulam J Mufti,Mohammad M Karimi,Nogayhan Seymen,Masae Ohno,Remco Loos,Pier Luigi Martelli

doi:10.1093/bioinformatics/btab698

Abstract

MotivationDeciphering nucleosome–nucleosome interactions is an important step toward mesoscale description of chromatin organization but computational tools to perform such analyses are not publicly available.ResultsWe developed iNucs, a user-friendly and efficient Python-based bioinformatics tool to compute and visualize nucleosome-resolved interactions using standard pairs format input generated from pairtools.Availabilityand implementation https://github.com/Karimi-Lab/inucs/.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

In eukaryotes, DNA is packaged in the nucleus as a nucleoprotein complex called chromatin
We describe ‘iNucs’, a user-friendly and efficient Python-based tool for computing and visualizing nucleosome-level interaction networks. iNucs is designed to receive ligation junctions in pairs format generated by pairtools and provide nucleosome resolution view consistent with pairsQC output and 4D nucleosome (4DN)-processed files
Prepare module: This module takes in nucleosome genomic coordinates, ligation junctions and chromosome names as input, and it produces a nucleosome interaction matrix (NIM) as output

Summary

Introduction

DNA is packaged in the nucleus as a nucleoprotein complex called chromatin. The packaging of chromatin in the nucleus is not linear This results in different levels of 3-D genome folding and interaction. INucs is designed to receive ligation junctions in pairs format generated by pairtools (https://pairtools.readthedocs.io/en/latest/) and provide nucleosome resolution view consistent with pairsQC (https://github.com/4dn-dcic/pairsqc) output and 4D nucleosome (4DN)-processed files. This allows iNucs to be integrated as a plugin to 4DN analysis pipeline in the future. The tool provides division and visualization of interaction pairs based on their orientation providing further spatial information about the conformation of chromatin fiber at genomic loci

Methods

Conclusion