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

作者： Mohammad N. Qasim*1,2, Ashley Valle Arevalo*1,2, Akshay D. Paropkari*1,2, Craig L. Ennis1,2,4, Suzanne S. Sindi3, Clarissa J. Nobile1,4, Aaron D. Hernday1,4 1Department of Molecular and Cell Biology,University of California, Merced, 2Quantitative and Systems Biology Graduate Program,University of California, Merced, 3Department of Applied Mathematics,University of California, Merced, 4Health Sciences Research Institute,University of California, Merced

简介：

Overview

This protocol outlines a method for conducting cleavage under targets and release using nuclease (CUT&RUN) in the human fungal pathogen Candida albicans. The protocol includes detailed experimental procedures and computational data analysis for profiling transcription factor-DNA binding interactions.

Key Study Components

Research Area

• Microbial genetics
• Transcription factor binding analysis
• Pathogen biology

Background

• Candida albicans as a human fungal pathogen
• Importance of studying transcription factor-DNA interactions
• The advantages of CUT&RUN over traditional methods

Methods Used

• Experiments involving epitope tagging and computational analysis
• Biological system: Candida albicans
• Technologies: CUT&RUN, fluorescence microscopy

Main Results

• CUT&RUN provides more accessible, sensitive, and high-quality data than ChIP-chip and ChIP-seq
• Successful profiling of Ndt80 and Efg1 binding events
• Identification of novel binding sites not previously reported

Conclusions

• The study demonstrates the efficiency of CUT&RUN for analyzing transcription factor interactions in pathogens
• Highlights the technique's relevance and potential adaptations to other forms of Candida albicans

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