@article{5cd70d9645bd4b3d84ba62780b0762f8,
title = "Changes in genome organization of parasite-specific gene families during the Plasmodium transmission stages",
abstract = "The development of malaria parasites throughout their various life cycle stages is coordinated by changes in gene expression. We previously showed that the three-dimensional organization of the Plasmodium falciparum genome is strongly associated with gene expression during its replication cycle inside red blood cells. Here, we analyze genome organization in the P. falciparum and P. vivax transmission stages. Major changes occur in the localization and interactions of genes involved in pathogenesis and immune evasion, host cell invasion, sexual differentiation, and master regulation of gene expression. Furthermore, we observe reorganization of subtelomeric heterochromatin around genes involved in host cell remodeling. Depletion of heterochromatin protein 1 (PfHP1) resulted in loss of interactions between virulence genes, confirming that PfHP1 is essential for maintenance of the repressive center. Our results suggest that the three-dimensional genome structure of human malaria parasites is strongly connected with transcriptional activity of specific gene families throughout the life cycle.",
author = "Bunnik, {Evelien M.} and Cook, {Kate B.} and Nelle Varoquaux and Gayani Batugedara and Jacques Prudhomme and Anthony Cort and Lirong Shi and Chiara Andolina and Ross, {Leila S.} and Declan Brady and Fidock, {David A.} and Francois Nosten and Rita Tewari and Photini Sinnis and Ferhat Ay and Vert, {Jean Philippe} and Noble, {William Stafford} and {Le Roch}, {Karine G.}",
note = "Funding Information: We thank Till Voss (Swiss Tropical and Public Health Institute) for preparation of the PfHP1 transgenic strain samples, Clay Clark, John Weger, and Glenn Hicks (Institute for Integrative Genome Biology, University of California Riverside) for their assistance in Illumina sequencing, Xueqing (Maggie) Lu for help with ChIP-seq analysis, and Justin Moroney and Paolo Casali for their assistance with Southern blotting. We are grateful to the Insectary and Parasitology Core Facilities at the Johns Hopkins Malaria Research Institute and in particular would like to thank Abai Tripathi, Godfree Mlambo and Chris Kizito for their outstanding work and The Bloomberg Family Foundation for supporting these facilities. SMRU is part of the Mahidol-Oxford University Research Unit, supported by the Wellcome Trust. The following reagents were obtained through the MR4 as part of the BEI Resources Repository, NIAID, NIH: NF54 (MRA-1000) deposited by Megan Dowler, Walter Reed Army Institute of Research. This study was financially supported by the National Institutes of Health (grants R01 AI85077-01A1 to K.G.L.R., R01 AI06775-01 to W.S.N. and K.G.L.R., and R01 AI056840 to P.S.), the University of California, Riverside (NIFA-Hatch-225935 to K.G.L.R.), the European Research Council (grant ERC-SMAC-280032 to N.V. and J.P.V.), the French National Research Agency (grant ABS4NGS ANR-11-BINF-0001 to N.V. and J.P.V.), the Miller Institute for Basic Research in Science (J.P.V.), the Fulbright Foundation (J.P.V.), the Bill & Melinda Gates Foundation (OPP1040938 to D.A.F.), the Medical Research Council UK (grant MR/ K011782/1 to R.T.), the Human Frontier Science Program (postdoctoral fellowship LT000507/2011-L to E.M.B.), the University of Texas Health Science Center at San Antonio (E.M.B.), the Natural Sciences and Engineering Research Council of Canada (postdoctoral fellowship to K.B.C.), the Gordon and Betty Moore Foundation (Grant GBMF3834 to UC Berkeley), the Alfred P. Sloan Foundation (Grant 2013-10-27 to UC Berkeley), Institute Leadership Funds from La Jolla Institute for Allergy and Immunology (F.A.), and used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1548562. Publisher Copyright: {\textcopyright} 2018 The Author(s).",
year = "2018",
month = dec,
day = "1",
doi = "10.1038/s41467-018-04295-5",
language = "English (US)",
volume = "9",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}