Chromosomes Conformation Capture Coupled with Next-Generation Sequencing (Hi-C) in Plasmodium falciparum

Mohit Kumar Gupta; Todd Lenz; Karine G Le Roch

doi:10.1007/978-1-0716-1681-9_2

Chromosomes Conformation Capture Coupled with Next-Generation Sequencing (Hi-C) in Plasmodium falciparum

Methods Mol Biol. 2021:2369:15-25. doi: 10.1007/978-1-0716-1681-9_2.

Authors

Mohit Kumar Gupta¹, Todd Lenz¹, Karine G Le Roch²

Affiliations

¹ Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA.
² Department of Molecular, Cell and Systems Biology, University of California, Riverside, CA, USA. karine.leroch@ucr.edu.

PMID: 34313981
DOI: 10.1007/978-1-0716-1681-9_2

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: Genome organization; Hi-C; Plasmodium falciparum; Virulence.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Chromosomes / genetics
Genome, Protozoan
High-Throughput Nucleotide Sequencing
Humans
Malaria
Plasmodium falciparum* / genetics

Abstract

Publication types

MeSH terms

Grants and funding