Chromosomes Conformation Capture Coupled with Next-Generation Sequencing (Hi-C) in Plasmodium falciparum
- 28 July 2021
- book chapter
- Published by Springer Nature
- Vol. 2369, 15-25
Abstract
Over the last decades, novel methods have been developed to study the role of chromosome positioning within the nucleus may play in gene regulation. Established proximity ligation-based chromosome conformation capture (3C) techniques such as Hi-C have revealed the existence of chromosome territories, functional nuclear landmarks, and topologically associating domains (TAPs) in most eukaryotic organisms. Adaptation of these methods in apicomplexan parasites has recently uncovered new aspects of 3D genome biology in virulence factors. Here, we describe the Hi-C protocol in the human malaria parasite, Plasmodium falciparum. This method can determine the genome organization in malaria parasites and its role in gene regulation and virulence.Keywords
This publication has 16 references indexed in Scilit:
- Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer InteractionsCell, 2015
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin LoopingCell, 2014
- Three-dimensional modeling of theP. falciparumgenome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expressionGenome Research, 2014
- Genome‐wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variationMolecular Microbiology, 2013
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human GenomeScience, 2009
- Genome-wide Analysis of Heterochromatin Associates Clonally Variant Gene Regulation with Perinuclear Repressive Centers in Malaria ParasitesCell Host & Microbe, 2009
- Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture–on-chip (4C)Nature Genetics, 2006
- Chromosome Conformation Capture Carbon Copy (5C): A massively parallel solution for mapping interactions between genomic elementsGenome Research, 2006
- Capturing Chromosome ConformationScience, 2002