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Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation

Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear...

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Autores principales: Lemieux, Jacob E, Kyes, Sue A, Otto, Thomas D, Feller, Avi I, Eastman, Richard T, Pinches, Robert A, Berriman, Matthew, Su, Xin-zhuan, Newbold, Chris I
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BlackWell Publishing Ltd 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894959/
https://www.ncbi.nlm.nih.gov/pubmed/23980881
http://dx.doi.org/10.1111/mmi.12381
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author Lemieux, Jacob E
Kyes, Sue A
Otto, Thomas D
Feller, Avi I
Eastman, Richard T
Pinches, Robert A
Berriman, Matthew
Su, Xin-zhuan
Newbold, Chris I
author_facet Lemieux, Jacob E
Kyes, Sue A
Otto, Thomas D
Feller, Avi I
Eastman, Richard T
Pinches, Robert A
Berriman, Matthew
Su, Xin-zhuan
Newbold, Chris I
author_sort Lemieux, Jacob E
collection PubMed
description Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear nucleolus results in the clustering of rDNA. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second-generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in var gene expression. We have generated maps of chromosomal spatial affinities within the P. falciparum nucleus at 25 Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in var gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites.
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spelling pubmed-38949592014-03-04 Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation Lemieux, Jacob E Kyes, Sue A Otto, Thomas D Feller, Avi I Eastman, Richard T Pinches, Robert A Berriman, Matthew Su, Xin-zhuan Newbold, Chris I Mol Microbiol Research Articles Spatial relationships within the eukaryotic nucleus are essential for proper nuclear function. In Plasmodium falciparum, the repositioning of chromosomes has been implicated in the regulation of the expression of genes responsible for antigenic variation, and the formation of a single, peri-nuclear nucleolus results in the clustering of rDNA. Nevertheless, the precise spatial relationships between chromosomes remain poorly understood, because, until recently, techniques with sufficient resolution have been lacking. Here we have used chromosome conformation capture and second-generation sequencing to study changes in chromosome folding and spatial positioning that occur during switches in var gene expression. We have generated maps of chromosomal spatial affinities within the P. falciparum nucleus at 25 Kb resolution, revealing a structured nucleolus, an absence of chromosome territories, and confirming previously identified clustering of heterochromatin foci. We show that switches in var gene expression do not appear to involve interaction with a distant enhancer, but do result in local changes at the active locus. These maps reveal the folding properties of malaria chromosomes, validate known physical associations, and characterize the global landscape of spatial interactions. Collectively, our data provide critical information for a better understanding of gene expression regulation and antigenic variation in malaria parasites. BlackWell Publishing Ltd 2013-11 2013-09-30 /pmc/articles/PMC3894959/ /pubmed/23980881 http://dx.doi.org/10.1111/mmi.12381 Text en © 2013 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd. http://creativecommons.org/licenses/by/3.0/ This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Articles
Lemieux, Jacob E
Kyes, Sue A
Otto, Thomas D
Feller, Avi I
Eastman, Richard T
Pinches, Robert A
Berriman, Matthew
Su, Xin-zhuan
Newbold, Chris I
Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title_full Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title_fullStr Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title_full_unstemmed Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title_short Genome-wide profiling of chromosome interactions in Plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
title_sort genome-wide profiling of chromosome interactions in plasmodium falciparum characterizes nuclear architecture and reconfigurations associated with antigenic variation
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3894959/
https://www.ncbi.nlm.nih.gov/pubmed/23980881
http://dx.doi.org/10.1111/mmi.12381
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