High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq

ABSTRACT To persist in their dynamic human host environments, fungal pathogens must sense and adapt by modulating their gene expression to fulfill their cellular needs. Understanding transcriptional regulation on a global scale would uncover cellular processes linked to persistence and virulence mec...

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Autores principales:	Faiza Tebbji, Inès Khemiri, Adnane Sellam
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	Candida albicans Candida spp. ChEC-seq genome-wide occupancy transcriptional regulatory network Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/7e7012be89f2447d911ce80330d36367
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spelling	oai:doaj.org-article:7e7012be89f2447d911ce80330d363672021-11-15T15:30:58ZHigh-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq10.1128/mSphere.00646-202379-5042https://doaj.org/article/7e7012be89f2447d911ce80330d363672020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00646-20https://doaj.org/toc/2379-5042ABSTRACT To persist in their dynamic human host environments, fungal pathogens must sense and adapt by modulating their gene expression to fulfill their cellular needs. Understanding transcriptional regulation on a global scale would uncover cellular processes linked to persistence and virulence mechanisms that could be targeted for antifungal therapeutics. Infections associated with the yeast Candida albicans, a highly prevalent fungal pathogen, and the multiresistant related species Candida auris are becoming a serious public health threat. To define the set of a gene regulated by a transcriptional regulator in C. albicans, chromatin immunoprecipitation (ChIP)-based techniques, including ChIP with microarray technology (ChIP-chip) or ChIP-DNA sequencing (ChIP-seq), have been widely used. Here, we describe a new set of PCR-based micrococcal nuclease (MNase)-tagging plasmids for C. albicans and other Candida spp. to determine the genome-wide location of any transcriptional regulator of interest using chromatin endogenous cleavage (ChEC) coupled to high-throughput sequencing (ChEC-seq). The ChEC procedure does not require protein-DNA cross-linking or sonication, thus avoiding artifacts related to epitope masking or the hyper-ChIPable euchromatic phenomenon. In a proof-of-concept application of ChEC-seq, we provided a high-resolution binding map of the SWI/SNF chromatin remodeling complex, a master regulator of fungal fitness in C. albicans, in addition to the transcription factor Nsi1 that is an ortholog of the DNA-binding protein Reb1 for which genome-wide occupancy was previously established in Saccharomyces cerevisiae. The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi. IMPORTANCE Systemic fungal infections caused by Candida albicans and the “superbug” Candida auris are becoming a serious public health threat. The ability of these yeasts to cause disease is linked to their faculty to modulate the expression of genes that mediate their escape from the immune surveillance and their persistence in the different unfavorable niches within the host. Comprehensive knowledge on gene expression control of fungal fitness is consequently an interesting framework for the identification of essential infection processes that could be hindered by chemicals as potential therapeutics. Here, we expanded the use of ChEC-seq, a technique that was initially developed in the yeast model Saccharomyces cerevisiae to identify genes that are modulated by a transcriptional regulator, in pathogenic yeasts from the genus Candida. This robust technique will allow a better characterization of key gene expression regulators and their contribution to virulence and antifungal resistance in these pathogenic yeasts.Faiza TebbjiInès KhemiriAdnane SellamAmerican Society for MicrobiologyarticleCandida albicansCandida spp.ChEC-seqgenome-wide occupancytranscriptional regulatory networkMicrobiologyQR1-502ENmSphere, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Candida albicans Candida spp. ChEC-seq genome-wide occupancy transcriptional regulatory network Microbiology QR1-502
spellingShingle	Candida albicans Candida spp. ChEC-seq genome-wide occupancy transcriptional regulatory network Microbiology QR1-502 Faiza Tebbji Inès Khemiri Adnane Sellam High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
description	ABSTRACT To persist in their dynamic human host environments, fungal pathogens must sense and adapt by modulating their gene expression to fulfill their cellular needs. Understanding transcriptional regulation on a global scale would uncover cellular processes linked to persistence and virulence mechanisms that could be targeted for antifungal therapeutics. Infections associated with the yeast Candida albicans, a highly prevalent fungal pathogen, and the multiresistant related species Candida auris are becoming a serious public health threat. To define the set of a gene regulated by a transcriptional regulator in C. albicans, chromatin immunoprecipitation (ChIP)-based techniques, including ChIP with microarray technology (ChIP-chip) or ChIP-DNA sequencing (ChIP-seq), have been widely used. Here, we describe a new set of PCR-based micrococcal nuclease (MNase)-tagging plasmids for C. albicans and other Candida spp. to determine the genome-wide location of any transcriptional regulator of interest using chromatin endogenous cleavage (ChEC) coupled to high-throughput sequencing (ChEC-seq). The ChEC procedure does not require protein-DNA cross-linking or sonication, thus avoiding artifacts related to epitope masking or the hyper-ChIPable euchromatic phenomenon. In a proof-of-concept application of ChEC-seq, we provided a high-resolution binding map of the SWI/SNF chromatin remodeling complex, a master regulator of fungal fitness in C. albicans, in addition to the transcription factor Nsi1 that is an ortholog of the DNA-binding protein Reb1 for which genome-wide occupancy was previously established in Saccharomyces cerevisiae. The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi. IMPORTANCE Systemic fungal infections caused by Candida albicans and the “superbug” Candida auris are becoming a serious public health threat. The ability of these yeasts to cause disease is linked to their faculty to modulate the expression of genes that mediate their escape from the immune surveillance and their persistence in the different unfavorable niches within the host. Comprehensive knowledge on gene expression control of fungal fitness is consequently an interesting framework for the identification of essential infection processes that could be hindered by chemicals as potential therapeutics. Here, we expanded the use of ChEC-seq, a technique that was initially developed in the yeast model Saccharomyces cerevisiae to identify genes that are modulated by a transcriptional regulator, in pathogenic yeasts from the genus Candida. This robust technique will allow a better characterization of key gene expression regulators and their contribution to virulence and antifungal resistance in these pathogenic yeasts.
format	article
author	Faiza Tebbji Inès Khemiri Adnane Sellam
author_facet	Faiza Tebbji Inès Khemiri Adnane Sellam
author_sort	Faiza Tebbji
title	High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
title_short	High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
title_full	High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
title_fullStr	High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
title_full_unstemmed	High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq
title_sort	high-resolution genome-wide occupancy in <italic toggle="yes">candida</italic> spp. using chec-seq
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/7e7012be89f2447d911ce80330d36367
work_keys_str_mv	AT faizatebbji highresolutiongenomewideoccupancyinitalictoggleyescandidaitalicsppusingchecseq AT ineskhemiri highresolutiongenomewideoccupancyinitalictoggleyescandidaitalicsppusingchecseq AT adnanesellam highresolutiongenomewideoccupancyinitalictoggleyescandidaitalicsppusingchecseq
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High-Resolution Genome-Wide Occupancy in <italic toggle="yes">Candida</italic> spp. Using ChEC-seq

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