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Genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans: a comprehensive CUT&RUN method and data analysis workflow

ABSTRACT: Genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans: a comprehensive CUT&RUN method and data analysis workflow

PROVIDER: PRJNA798025 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17644427_1.fastq.gz	Fastqsanger.gz
	SRR17644427_2.fastq.gz	Fastqsanger.gz
	SRR17644428_1.fastq.gz	Fastqsanger.gz
	SRR17644428_2.fastq.gz	Fastqsanger.gz
	SRR17644429_1.fastq.gz	Fastqsanger.gz

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Genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans: a comprehensive CUT&RUN method and data analysis workflow

Project description:Regulatory transcription factors control many important biological processes including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&RUN is amenable to a higher throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs compared to ChIP-seq. Here, we describe a comprehensive CUT&RUN protocol and accompanying data analysis workflow that is tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans. This detailed protocol describes all necessary experimental procedures, from epitope tagging of transcription factor coding genes, to library preparation for sequencing; additionally, it includes our customized computational workflow for CUT&RUN data analysis.

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Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow.

Project description:Regulatory transcription factors control many important biological processes, including cellular differentiation, responses to environmental perturbations and stresses, and host-pathogen interactions. Determining the genome-wide binding of regulatory transcription factors to DNA is essential to understanding the function of transcription factors in these often complex biological processes. Cleavage under targets and release using nuclease (CUT&RUN) is a modern method for genome-wide mapping of in vivo protein-DNA binding interactions that is an attractive alternative to the traditional and widely used chromatin immunoprecipitation followed by sequencing (ChIP-seq) method. CUT&RUN is amenable to a higher-throughput experimental setup and has a substantially higher dynamic range with lower per-sample sequencing costs than ChIP-seq. Here, a comprehensive CUT&RUN protocol and accompanying data analysis workflow tailored for genome-wide analysis of transcription factor-DNA binding interactions in the human fungal pathogen Candida albicans are described. This detailed protocol includes all necessary experimental procedures, from epitope tagging of transcription factor-coding genes to library preparation for sequencing; additionally, it includes a customized computational workflow for CUT&RUN data analysis.

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RNA-seq of intestinal epithelia of Candida albicans treated mice

Project description:Purpose: To explore the influence of Candida albicans treatment in mice intestinal epithelia. Method: 108 CFU C. albicans or PBS was gavaged to Apoe-/- mice every 3 days for 2 weeks. mRNA profiles were generated by deep sequencing.Results: Several signaling pathways were changed after C. albicans treatment, including response to hypoxia pathway.

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Candida albicans

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Global Translational Landscape of the Candida albicans Morphological Transition

Project description:Candida albicans is a major human fungal pathogen that represents the fourth leading cause of hospital-acquired bloodstream infections in the U.S. and is associated with high mortality and/or morbidity rates in a wide variety of immunocompromised individuals, including cancer and AIDS patients. While the C. albicans morphological transition from yeast to filamentous cells is required for virulence, considerably little is known about translational mechanisms important for controlling this transition as well as other virulence-related processes in C. albicans and other human fungal pathogens. Using ribosome profiling, we report the first global translational profile associated with C. albicans morphogenesis. Strikingly, many genes involved in pathogenesis, filamentation, response to stress and cell wall organization show reduced translational efficiency (TE). Several of these genes are known to be strongly induced at the transcriptional level, suggesting that a translational fine-tuning mechanism is in place. Using a recently developed ORF-calling method, we have identified a significant number of potential uORFs in genes associated with pathogenesis and at least 57 potential novel ORFs, several of which appear to show altered TE in response to filamentation. Finally, using a novel method for global analysis of ribosome pausing from Ribo-seq data, we demonstrate an enrichment of ribosome pausing sites in C. albicans genes associated with protein synthesis and cell wall functions. Altogether, our results suggest that the C. albicans morphological transition is associated with widespread global translational alterations that do not simply reflect transcriptional changes and affect the expression of many genes associated with virulence-related processes and pathogenesis.

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