Name: genome-wide profiling of transcription factor-dna binding interactions in candida albicans: a comprehensive cut&amp;run method and data analysis workflow
Uploaded: 2022-04-01T14:45:00
Description: Watch this Scientific Journal Video about Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow at JoVE.

We thank all past and present members of the Nobile and Hernday laboratories for feedback on the manuscript.&#160;This work was supported by the National Institutes of Health (NIH) National Institute of General Medical Sciences (NIGMS) award number R35GM124594 and by the Kamangar family in the form of an endowed chair to C.J.N. This work was also supported by the NIH National Institute of Allergy and Infectious Diseases (NIAID) award number R15AI137975 to A.D.H. C.L.E. was supported by the NIH National Institute of Dental and Craniofacial Research (NIDCR) fellowship number F31DE028488. The content is the sole responsibility of the authors and does not represent the views of the funders. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript; or in the decision to publish the results.

1. Epitope Tagging of C. albicans strains
<ol>
	<li>Upload the gene of interest, along with its 1 kb upstream and downstream flanking sequences, from the Candida Genome Database to the primer design tool (see the Table of Materials). Design a guide RNA (gRNA) by highlighting 50 bp upstream and downstream from the stop codon, and click the gRNA selection tool on the right. Select Design and Analyze Guides. Use the Ca22 (Candida alb...

<ol>
	<li>Gulati, M., Nobile, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Candida+albicans+biofilms:+development,+regulation,+and+molecular+mechanisms.">Candida albicans biofilms: development, regulation, and molecular mechanisms.</a> Microbes and Infection. 18 (5), 310-321 (2016).</li><li>Lohse, M. B., Gulati, M., Johnson, A. D., Nobile, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+and+regulation+of+single-and+multi-species+Candida+albicans+biofilms.">Development and regulation of single-and multi-species Candida albicans biofilms.</a> Nature Reviews Microbiology. 16 (1), 19-31 (2018).</li><li>Nobile, C. J., Johnson, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Candida+albicans+biofilms+and+human+disease.">Candida albicans biofilms and human disease.</a> Annual Review of Microbiology. 69 (1), 71-92 (2015).</li><li>Nobile, C. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+recently+evolved+transcriptional+network+controls+biofilm+development+in+Candida+albicans.">A recently evolved transcriptional network controls biofilm development in Candida albicans.</a> Cell. 148 (1-2), 126-138 (2012).</li><li>Iracane, E., Vega-Est&#233;vez, S., Buscaino, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+and+off:+epigenetic+regulation+of+C.+albicans+morphological+switches.">On and off: epigenetic regulation of C. albicans morphological switches.</a> Pathogens. 10 (11), 1463 (2021).</li><li>Qasim, M. N., Valle Arevalo, A., Nobile, C. J., Hernday, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+roles+of+chromatin+accessibility+in+regulating+the+Candida+albicans+white-opaque+phenotypic+switch.">The roles of chromatin accessibility in regulating the Candida albicans white-opaque phenotypic switch.</a> Journal of Fungi. 7 (1), 37 (2021).</li><li>Mancera, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evolution+of+the+complex+transcription+network+controlling+biofilm+formation+in+candida+species.">Evolution of the complex transcription network controlling biofilm formation in candida species.</a> eLife. 10, 64682 (2021).</li><li>Lohse, M. B., Johnson, A. 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A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chromatin+immunoprecipitation+and+microarray-based+analysis+of+protein+location.">Chromatin immunoprecipitation and microarray-based analysis of protein location.</a> Nature Protocols. 1 (2), 729-748 (2006).</li><li>Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R., Henikoff, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChEC-seq+kinetics+discriminates+transcription+factor+binding+sites+by+DNA+sequence+and+shape+in+vivo.">ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.</a> Nature Communications. 6, 8733 (2015).</li><li>Schmid, M., Durussel, T., Laemmli, U. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChIC+and+ChEC:+Genomic+mapping+of+chromatin+proteins.">ChIC and ChEC: Genomic mapping of chromatin proteins.</a> Molecular Cell. 16 (1), 147-157 (2004).</li><li>Skene, P. J., Henikoff, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+efficient+targeted+nuclease+strategy+for+high-resolution+mapping+of+DNA+binding+sites.">An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites.</a> eLife. 6, 21856 (2017).</li><li>Skene, P. J., Henikoff, J. G., Henikoff, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Targeted+in+situ+genome-wide+profiling+with+high+efficiency+for+low+cell+numbers.">Targeted in situ genome-wide profiling with high efficiency for low cell numbers.</a> Nature Protocols. 13 (5), 1006-1019 (2018).</li><li>Nguyen, N., Quail, M. M. F., Hernday, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+efficient,+rapid,+and+recyclable+system+for+CRISPR-mediated+genome+editing+in+Candida+albicans.">An efficient, rapid, and recyclable system for CRISPR-mediated genome editing in Candida albicans.</a> American Society For Microbiology. 2 (2), 00149 (2017).</li><li>Ennis, C. L., Hernday, A. D., Nobile, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+markerless+CRISPR-mediated+system+for+genome+editing+in+Candida+auris+reveals+a+conserved+role+for+Cas5+in+the+caspofungin+response.">A markerless CRISPR-mediated system for genome editing in Candida auris reveals a conserved role for Cas5 in the caspofungin response.</a> Microbiology Spectrum. 9 (3), 0182021 (2021).</li><li>Meers, M. P., Bryson, T. D., Henikoff, J. G., Henikoff, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+CUT&amp;RUN+chromatin+profiling+tools.">Improved CUT&amp;RUN chromatin profiling tools.</a> eLife. 8, 46314 (2019).</li><li>Skrzypek, M. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Candida+Genome+Database+(CGD):+Incorporation+of+Assembly+22,+systematic+identifiers+and+visualization+of+high+throughput+sequencing+data.">The Candida Genome Database (CGD): Incorporation of Assembly 22, systematic identifiers and visualization of high throughput sequencing data.</a> Nucleic Acids Research. 45, 592-596 (2017).</li><li>Quinlan, A. R., Hall, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BEDTools:+a+flexible+suite+of+utilities+for+comparing+genomic+features.">BEDTools: a flexible suite of utilities for comparing genomic features.</a> Bioinformatics. 26 (6), 841-842 (2010).</li><li>Landt, S. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ChIP-seq+guidelines+and+practices+of+the+ENCODE+and+modENCODE+consortia.">ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.</a> Genome Research. 22 (9), 1813-1831 (2012).</li><li>Boyd, J., Rodriguez, P., Schjerven, H., Frietze, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ssvQC:+an+integrated+CUT&amp;RUN+quality+control+workflow+for+histone+modifications+and+transcription+factors.">ssvQC: an integrated CUT&amp;RUN quality control workflow for histone modifications and transcription factors.</a> BMC Research Notes. 14 (1), 366 (2021).</li><li>Kent, W. J., Zweig, A. S., Barber, G., Hinrichs, A. S., Karolchik, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BigWig+and+BigBed:+enabling+browsing+of+large+distributed+datasets.">BigWig and BigBed: enabling browsing of large distributed datasets.</a> Bioinformatics. 26 (17), 2204-2207 (2010).</li><li>Homann, O. R., Johnson, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=MochiView:+Versatile+software+for+genome+browsing+and+DNA+motif+analysis.">MochiView: Versatile software for genome browsing and DNA motif analysis.</a> BMC Biology. 8, 49 (2010).</li><li>Hainer, S. J., Fazzio, T. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-resolution+chromatin+profiling+using+CUT&amp;RUN.">High-resolution chromatin profiling using CUT&amp;RUN.</a> Current Protocols in Molecular Biology. 126 (1), 85 (2019).</li><li>Kaya-Okur, H. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CUT&amp;Tag+for+efficient+epigenomic+profiling+of+small+samples+and+single+cells.">CUT&amp;Tag for efficient epigenomic profiling of small samples and single cells.</a> Nature Communications. 10 (1), 1930 (2019).</li><li>Rodriguez, D. L., Quail, M. M., Hernday, A. D., Nobile, C. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcriptional+circuits+regulating+developmental+processes+in+Candida+albicans.">Transcriptional circuits regulating developmental processes in Candida albicans.</a> Frontiers in Cellular and Infection Microbiology. 10, 605711 (2020).</li><li>Zhu, Q., Liu, N., Orkin, S. H., Yuan, G. -. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=CUT&amp;amp;RUNTools:+a+flexible+pipeline+for+CUT&amp;amp;RUN+processing+and+footprint+analysis.">CUT&amp;amp;RUNTools: a flexible pipeline for CUT&amp;amp;RUN processing and footprint analysis.</a> Genome Biology. 20 (1), 192 (2019).</li><li>Teytelman, L., Thurtle, D. M., Rine, J., Van Oudenaarden, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+expressed+loci+are+vulnerable+to+misleading+ChIP+localization+of+multiple+unrelated+proteins.">Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.</a> Proceedings of the National Academy of Sciences of the United States of America. 110 (46), 18602-18607 (2013).</li></ol>

This protocol presents a comprehensive experimental and computational pipeline for genome-wide localization of regulatory TFs in C. albicans. It is designed to be highly accessible to anyone with standard microbiology and molecular biology training. By leveraging the high dynamic range and low sample input requirements of the CUT&amp;RUN assay and including optimizations for the localization of TF-DNA binding interactions in C. albicans biofilm and planktonic cultures, this protocol presents a powerful ...

Candida albicans is a clinically relevant, polymorphic human fungal pathogen that exists in a variety of different modes of growth, such as the planktonic (free-floating) mode of growth and as communities of tightly adhered cells protected by an extracellular matrix, known as the biofilm mode of growth1,2,3. Similar to other developmental and cellular processes, biofilm development is an important C. albicans virulence trait that is known to be controlled at the transcriptional level by regulatory transcription factors (TFs) that bind to DNA in a sequence-specific manner4. Recently, chromatin regulators and histone modifiers have also emerged as important regulators of C. albicans biofilm formation5 and morphogenesis6 by mediating DNA accessibility. To understand the complex biology of this important fungal pathogen, effective methods to determine the genome-wide localization of specific TFs during distinct developmental and cellular processes is valuable.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a widely used method to investigate protein-DNA interactions in C. albicans5,6 and has largely replaced the more classical chromatin immunoprecipitation followed by microarray (ChIP-chip)9 method. Both ChIP-seq and ChIP-chip methods, however, require a large number of input cells10, which can be a complicating factor when investigating TFs in the context of specific samples and modes of growth, such as biofilms collected from patients or animal models of infection. In addition, the chromatin immunoprecipitation (ChIP) assay often yields a significant amount of background signal throughout the genome, requiring a high level of enrichment for the target of interest to sufficiently separate signal from noise. While the ChIP-chip assay is largely outdated today, the sequencing depths necessary for ChIP-seq make this assay prohibitively expensive for many researchers, particularly those studying multiple TFs and/or chromatin-associated proteins.

Cleavage under targets and release using nuclease (CUT&#38;RUN) is an attractive alternative to ChIP-seq. It was developed by the Henikoff lab in 2017 to circumvent the limitations of ChIP-seq and chromatin endogenous cleavage followed by sequencing ChEC-seq11,12, another method to identify protein-DNA interactions on a genome-wide level, while providing high-resolution, genome-wide mapping of TFs and chromatin-associated proteins13. CUT&#38;RUN relies on the targeted digestion of chromatin within permeabilized nuclei using tethered micrococcal nucleases, followed by sequencing of the digested DNA fragments9,10. As DNA fragments are specifically generated at the loci that are bound by a protein of interest, rather than being generated throughout the genome via random fragmentation as in ChIP assays, the CUT&#38;RUN approach results in greatly reduced background signals and, thus, requires 1/10th&#160;of the sequencing depth compared to ChIP-seq11,13,14. These improvements ultimately lead to significant reductions in sequencing costs and reductions in the total number of input cells needed as starting material for each sample.
Here, a robust CUT&#38;RUN protocol is described that has been adapted and optimized for determining the genome-wide localization of TFs in C. albicans cells isolated from biofilms and planktonic cultures. A thorough data analysis pipeline is also presented, which enables the processing and analysis of the resulting sequence data and requires users to have minimal expertise in coding or bioinformatics. Briefly, this protocol describes epitope tagging of TF-coding genes, harvesting of biofilm and planktonic cells, isolation of intact permeabilized nuclei, incubation with primary antibodies against the specific protein or epitope-tagged protein of interest, tethering of the chimeric A/G-micrococcal nuclease (pAG-MNase) fusion proteins to the primary antibodies, genomic DNA recovery after chromatin digestion, and preparation of genomic DNA libraries for sequencing.
The experimental CUT&#38;RUN protocol is followed by a purpose-built data analysis pipeline, which takes raw DNA sequencing reads in FASTQ format and implements all required processing steps to provide a complete list of significantly enriched loci bound by the TF of interest (targeted by the primary antibody). Note that multiple steps of the described library preparation protocol have been specifically adapted and optimized for CUT&#38;RUN analysis of TFs (as opposed to nucleosomes). While the data presented in this manuscript were generated using TF-specific adaptations of a commercial CUT&#38;RUN kit, these protocols have also been validated using individually sourced components (i.e., pAG-MNase enzyme and magnetic DNA purification beads) and in-house-prepared buffers, which can significantly reduce experimental cost. The comprehensive experimental and data analysis protocols are described in detail below in a step-by-step format. All reagents and critical equipment, as well as buffer and media recipes, are listed in the Table of Materials and Supplementary File 1, respectively.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.22 &#956;m filter</td>
			<td>Millipore Sigma</td>
			<td>SLGPM33RS</td>
			<td></td>
		</tr>
		<tr>
			<td>0.65 mL low-adhesion tubes</td>
			<td>VWR</td>
			<td>490003-190</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M CaCl2</td>
			<td>Fisher Scientific</td>
			<td>50-152-341</td>
			<td></td>
		</tr>
		<tr>
			<td>1 M PIPES</td>
			<td>Fisher Scientific</td>
			<td>AAJ61224AK</td>
			<td></td>
		</tr>
		<tr>
			<td>12-well untreated cell culture plates</td>
			<td>Corning</td>
			<td>351143</td>
			<td></td>
		</tr>
		<tr>
			<td>2-mercaptoethanol</td>
			<td>Sigma-Aldrich</td>
			<td>60-24-2</td>
			<td></td>
		</tr>
		<tr>
			<td>2% Digitonin</td>
			<td>Fisher Scientific</td>
			<td>CHR103MI</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL conical tubes</td>
			<td>VWR</td>
			<td>89039-658</td>
			<td></td>
		</tr>
		<tr>
			<td>5x phusion HF buffer</td>
			<td>Fisher Scientific</td>
			<td>F530S</td>
			<td>Item part of the Phusion high fidelity DNA polymerase; referred to in text as &#34;DNA polymerase buffer&#34;</td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Criterion</td>
			<td>C5001</td>
			<td></td>
		</tr>
		<tr>
			<td>Agencourt AMPure XP magnetic beads</td>
			<td>Beckman Coulter</td>
			<td>A63880</td>
			<td></td>
		</tr>
		<tr>
			<td>Agilent Bioanalyzer</td>
			<td>Agilent</td>
			<td>G2939BA</td>
			<td>Referred to in the text as &#34;capillary electrophoresis instrument&#34;; user-dependepent</td>
		</tr>
		<tr>
			<td>Amplitube PCR reaction strips with attached caps, Simport Scientific</td>
			<td>VWR</td>
			<td>89133-910</td>
			<td></td>
		</tr>
		<tr>
			<td>Bacto peptone</td>
			<td>BD Biosciences</td>
			<td>211677</td>
			<td></td>
		</tr>
		<tr>
			<td>Benchling primer design tool</td>
			<td>Benchling</td>
			<td></td>
			<td>https://www.benchling.com/molecular-biology/; Referred to in the text as &#34;the primer design tool&#34;</td>
		</tr>
		<tr>
			<td>Betaine</td>
			<td>Fisher Scientific</td>
			<td>AAJ77507AB</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcofluor white stain</td>
			<td>Sigma-Aldrich</td>
			<td>18909-100ML-F</td>
			<td></td>
		</tr>
		<tr>
			<td>Candida Genome Database</td>
			<td></td>
			<td></td>
			<td>http://www.candidagenome.org/</td>
		</tr>
		<tr>
			<td>Concanavalin A (ConA) conjugated paramagnetic beads</td>
			<td>Polysciences</td>
			<td>&#160;86057-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Conda software</td>
			<td></td>
			<td></td>
			<td>https://docs.conda.io/en/latest/miniconda.html</td>
		</tr>
		<tr>
			<td>curl tool</td>
			<td></td>
			<td></td>
			<td>http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/C_albicans_SC5314_A21_current_ 
			chromosomes.fasta.gz</td>
		</tr>
		<tr>
			<td>CUTANA ChIC/CUT&#38;RUN kit</td>
			<td>Epicypher</td>
			<td>14-1048</td>
			<td>Referred to in the text as &#34;the CUT&#38;RUN kit&#34;</td>
		</tr>
		<tr>
			<td>Deoxynucleotide (dNTP) solution mix (10 mM)</td>
			<td>New England Biolabs</td>
			<td>N0447S</td>
			<td></td>
		</tr>
		<tr>
			<td>Dextrose (D-glucose)</td>
			<td>Fisher Scientific</td>
			<td>D163</td>
			<td></td>
		</tr>
		<tr>
			<td>Difco D-mannitol</td>
			<td>&#160;BD Biosciences</td>
			<td>217020</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable cuvettes</td>
			<td>Fisher Scientific</td>
			<td>14-955-127</td>
			<td></td>
		</tr>
		<tr>
			<td>Disposable transfer pipets</td>
			<td>Fisher Scientific</td>
			<td>13-711-20</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA Gel Loading Dye (6x)</td>
			<td>Fisher Scientific</td>
			<td>R0611</td>
			<td></td>
		</tr>
		<tr>
			<td>DreamTaq green DNA polymerase</td>
			<td>Fisher Scientific</td>
			<td>EP0713</td>
			<td>Referred to in the text as &#34;cPCR DNA polymerase&#34;</td>
		</tr>
		<tr>
			<td>DreamTaq green DNA polymerase buffer</td>
			<td>Fisher Scientific</td>
			<td>EP0713</td>
			<td>Item part of the DreamTaq green DNA polymerase; referred to in the text as &#34;cPCR DNA polymerase buffer&#34;</td>
		</tr>
		<tr>
			<td>E. coli spike-in DNA</td>
			<td>Epicypher</td>
			<td>18-1401</td>
			<td></td>
		</tr>
		<tr>
			<td>ELMI Microplate incubator</td>
			<td>ELMI</td>
			<td>TRMS-04</td>
			<td>Referred to in the text as &#34;microplate incubator&#34;</td>
		</tr>
		<tr>
			<td>End Prep Enzyme Mix</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit</td>
		</tr>
		<tr>
			<td>End Prep Reaction Buffer</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit</td>
		</tr>
		<tr>
			<td>Ethanol 200 proof</td>
			<td>VWR</td>
			<td>89125-170</td>
			<td></td>
		</tr>
		<tr>
			<td>FastDigest MssI</td>
			<td>Fisher Scientific</td>
			<td>FD1344</td>
			<td>Referred to in the text as &#34;restriction enzyme&#34;</td>
		</tr>
		<tr>
			<td>FastDigest MssI Buffer</td>
			<td>Fisher Scientific</td>
			<td>FD1344</td>
			<td>Item part of the FastDigest MssI kit; referred to in the text as &#34;restriction enzyme buffer&#34;</td>
		</tr>
		<tr>
			<td>Ficoll 400</td>
			<td>Fisher BioReagents</td>
			<td>BP525-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorescence microscope</td>
			<td></td>
			<td></td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>Gel electrophoresis apparatus</td>
			<td></td>
			<td></td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>GeneRuler low range DNA ladder</td>
			<td>Fisher Scientific</td>
			<td>FERSM1192</td>
			<td></td>
		</tr>
		<tr>
			<td>GitBash workflow</td>
			<td></td>
			<td></td>
			<td>https://gitforwindows.org/</td>
		</tr>
		<tr>
			<td>GitHub source code</td>
			<td></td>
			<td></td>
			<td>https://github.com/akshayparopkari/cut_run_analysis</td>
		</tr>
		<tr>
			<td>HEPES-KOH pH 7.5</td>
			<td>Boston BioProducts</td>
			<td>BBH-75-K</td>
			<td></td>
		</tr>
		<tr>
			<td>High-speed centrifuge</td>
			<td></td>
			<td></td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>Isopropanol</td>
			<td>Sigma-Aldrich</td>
			<td>PX1830-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Lens paper</td>
			<td>VWR</td>
			<td>52846-001</td>
			<td></td>
		</tr>
		<tr>
			<td>Ligation Enhancer</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit</td>
		</tr>
		<tr>
			<td>Lithium acetate dihydrate</td>
			<td>MP Biomedicals</td>
			<td>215525683</td>
			<td></td>
		</tr>
		<tr>
			<td>Living Colors Full-Length GFP polyclonal antibody</td>
			<td>Takara</td>
			<td>632592</td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>MACS2</td>
			<td></td>
			<td></td>
			<td>https://pypi.org/project/MACS2/</td>
		</tr>
		<tr>
			<td>Magnetic separation rack, 0.2 mL tubes</td>
			<td>Epicypher</td>
			<td>10-0008</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic separation rack, 1.5 mL tubes</td>
			<td>Fisher Scientific</td>
			<td>MR02</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma-Aldrich</td>
			<td>M8266</td>
			<td></td>
		</tr>
		<tr>
			<td>Microcentrifuge tubes 1.5 mL</td>
			<td>Fisher Scientific</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr>
			<td>Microplate and cuvette spectrophotometer</td>
			<td>BioTek</td>
			<td>EPOCH2TC</td>
			<td>Referred to in the text as &#34;spectrophotometer&#34;; user-dependent</td>
		</tr>
		<tr>
			<td>MochiView</td>
			<td></td>
			<td></td>
			<td>http://www.johnsonlab.ucsf.edu/mochiview-downloads</td>
		</tr>
		<tr>
			<td>MOPS</td>
			<td>Sigma-Aldrich</td>
			<td>M3183</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>VWR</td>
			<td>470302-522</td>
			<td></td>
		</tr>
		<tr>
			<td>NaOH</td>
			<td>Fisher Scientific</td>
			<td>S318-500</td>
			<td></td>
		</tr>
		<tr>
			<td>NCBI GEO</td>
			<td></td>
			<td></td>
			<td>https://www.ncbi.nlm.nih.gov/geo/</td>
		</tr>
		<tr>
			<td>NEBNext Adaptor for Illumina</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1); referred to in the text as &#34;Adapter&#34;</td>
		</tr>
		<tr>
			<td>NEBNext Index X Primer for Illumina</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1); referred to in the text as &#34;Reverse Uniquely Indexed Library Amplification Primer&#34;</td>
		</tr>
		<tr>
			<td>NEBNext Multiplex Oligos for Illumina (Index Primers Set 1)</td>
			<td>New England Biolabs</td>
			<td>E7335S</td>
			<td></td>
		</tr>
		<tr>
			<td>NEBNext Ultra II DNA Library Prep kit</td>
			<td>New England Biolabs</td>
			<td>E7645S</td>
			<td>Referred to in the text as &#34;library prep kit&#34;</td>
		</tr>
		<tr>
			<td>NEBNext Universal PCR Primer for Illumina</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1); referred to in the text as &#34;Universal Forward Library Amplification Primer&#34;</td>
		</tr>
		<tr>
			<td>Nourseothricin sulfate (NAT)</td>
			<td>Goldbio</td>
			<td>N-500-2</td>
			<td></td>
		</tr>
		<tr>
			<td>Novex TBE Gels, 10%, 15 well</td>
			<td>Fisher Scientific</td>
			<td>EC62755BOX</td>
			<td></td>
		</tr>
		<tr>
			<td>Nutating mixer</td>
			<td>VWR</td>
			<td>82007-202</td>
			<td></td>
		</tr>
		<tr>
			<td>Nutrient broth</td>
			<td>Criterion</td>
			<td>C6471</td>
			<td></td>
		</tr>
		<tr>
			<td>pADH110</td>
			<td>Addgene</td>
			<td>90982</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 90982&#34;</td>
		</tr>
		<tr>
			<td>pADH119</td>
			<td>Addgene</td>
			<td>90985</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 90985&#34;</td>
		</tr>
		<tr>
			<td>pADH137</td>
			<td>Addgene</td>
			<td>90986</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 90986&#34;</td>
		</tr>
		<tr>
			<td>pADH139</td>
			<td>Addgene</td>
			<td>90987</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 90987&#34;</td>
		</tr>
		<tr>
			<td>pADH140</td>
			<td>Addgene</td>
			<td>90988</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 90988&#34;</td>
		</tr>
		<tr>
			<td>pAG-MNase</td>
			<td>Epicypher</td>
			<td>15-1016 or 15-1116</td>
			<td>50 rxn or 250 rxn</td>
		</tr>
		<tr>
			<td>pCE1</td>
			<td>Addgene</td>
			<td>174434</td>
			<td>Referred to in the text as &#34;plasmid repository ID# 174434&#34;</td>
		</tr>
		<tr>
			<td>Petri dishes with clear lid</td>
			<td>Fisher Scientific</td>
			<td>FB0875712</td>
			<td></td>
		</tr>
		<tr>
			<td>Phusion high fidelity DNA polymerase</td>
			<td>Fisher Scientific</td>
			<td>F530S</td>
			<td>Referred to in the text as &#34;DNA polymerase&#34;</td>
		</tr>
		<tr>
			<td>Polyethylene glycol (PEG) 3350</td>
			<td>VWR</td>
			<td>10791-816</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium phosphate monobasic</td>
			<td>Fisher Scientific</td>
			<td>P285-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit 1x dsDNA HS assay kit</td>
			<td>Invitrogen</td>
			<td>Q33230</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit fluorometer</td>
			<td>Life Technologies</td>
			<td>Q33216</td>
			<td>Referred to in the text as &#34;fluorometer&#34;; user-dependent</td>
		</tr>
		<tr>
			<td>Rabbit IgG negative control antibody</td>
			<td>Epicypher</td>
			<td>13-0042</td>
			<td></td>
		</tr>
		<tr>
			<td>RNase A</td>
			<td>Sigma-Aldrich</td>
			<td>10109169001</td>
			<td></td>
		</tr>
		<tr>
			<td>Roche Complete protease inhibitor (EDTA-free) tablets</td>
			<td>Sigma-Aldrich</td>
			<td>5056489001</td>
			<td></td>
		</tr>
		<tr>
			<td>RPMI-1640</td>
			<td>Sigma-Aldrich</td>
			<td>R6504</td>
			<td></td>
		</tr>
		<tr>
			<td>Shaking incubator</td>
			<td>Eppendorf</td>
			<td>M12820004</td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>Sorbitol</td>
			<td>Sigma-Aldrich</td>
			<td>S1876-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Spin-X centrifuge tube filters</td>
			<td>Fisher Scientific</td>
			<td>07-200-385</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile inoculating loops</td>
			<td>VWR</td>
			<td>30002-094</td>
			<td></td>
		</tr>
		<tr>
			<td>SYBR Gold nucleic acid gel stain</td>
			<td>Fisher Scientific</td>
			<td>S11494</td>
			<td></td>
		</tr>
		<tr>
			<td>SYTO 13 nucleic acid stain</td>
			<td>Fisher Scientific</td>
			<td>S7575</td>
			<td>Referred to in the text as &#34;nucleic acid gel stain&#34;</td>
		</tr>
		<tr>
			<td>Thermocycler</td>
			<td></td>
			<td></td>
			<td>User-dependent</td>
		</tr>
		<tr>
			<td>ThermoMixer C</td>
			<td>Eppendorf</td>
			<td>5382000023</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris (hydroxymethyl) aminomethane</td>
			<td>Sigma-Aldrich</td>
			<td>252859-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Ultra II Ligation Master Mix</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit; referred to in the text as &#34;Ligation Master Mix&#34;</td>
		</tr>
		<tr>
			<td>Ultra II Q5 Master Mix</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit; referred to in the text as &#34;High Fidelity DNA Polymerase Master Mix &#34;</td>
		</tr>
		<tr>
			<td>UltraPure salmon sperm DNA solution</td>
			<td>Invitrogen</td>
			<td>15632011</td>
			<td></td>
		</tr>
		<tr>
			<td>USER Enzyme</td>
			<td></td>
			<td></td>
			<td>Item part of the NEBNext Ultra II DNA Library Prep kit; referred to in the text as &#34;Uracil Excision Enzyme&#34;</td>
		</tr>
		<tr>
			<td>Vortex mixer</td>
			<td>VWR</td>
			<td>10153-834</td>
			<td></td>
		</tr>
		<tr>
			<td>wget tool</td>
			<td></td>
			<td></td>
			<td>http://www.candidagenome.org/download/sequence/C_albicans_SC5314/Assembly21/current/C_albicans_SC5314_A21_current_ 
			chromosomes.fasta.gz</td>
		</tr>
		<tr>
			<td>Yeast extract</td>
			<td>Criterion</td>
			<td>C7341</td>
			<td></td>
		</tr>
		<tr>
			<td>Zymolyase 100T (lyticase, yeast lytic enzyme)</td>
			<td>Fisher Scientific</td>
			<td>NC0439194</td>
			<td></td>
		</tr>
	</tbody>
</table>

genome-wide profiling of transcription factor-dna binding interactions in candida albicans: a comprehensive cut&amp;run method and data analysis workflow

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&amp;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&amp;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&amp;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&amp;RUN data analysis.

This robust CUT&#38;RUN protocol was adapted and optimized for investigating the genome-wide localization of specific TFs in C. albicans biofilms and planktonic cultures (see Figure 2 for an overview of the experimental approach). A thorough data analysis pipeline is also included to facilitate analysis of the resulting CUT&#38;RUN sequencing data and requires users to have minimal expertise in coding or bioinformatics (see Figure 3 for an overview of t...

Watch this Scientific Journal Video about Genome-wide Profiling of Transcription Factor-DNA Binding Interactions in Candida albicans: A Comprehensive CUT&RUN Method and Data Analysis Workflow at JoVE.

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

This protocol describes an experimental method and data analysis workflow for cleavage under targets and release using nuclease (CUT&amp;RUN) in the human fungal pathogen Candida albicans.

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

Regulatory transcription factors control many important biological processes, including cellular differentiation, responses to environmental perturbations ...

This protocol details all experimental procedures, from epitope tagging of transcription factor coding genes through computational data analysis, to perform genome-wide profiling of transcription factor-DNA binding interactions in Candida albicans via CUT&RUN. This is a more accessible, faster, more sensitive, less expensive technique, and provides higher quality data than traditional ChIP-chip and ChIP-seq approaches. Although our protocol is developed for Candida albicans cells isolated from biofilms or planktonic cultures, it should be practical to adapt it to virtually any good form of Candida albicans cells.After incubating the cell suspension, transfer a five-microliter aliquot into a new PCR tube. To five microliters of isolated nuclei and a five-microliter aliquot of intact cells previously stored at four degree Celsius, add one microliter each of calcofluor-white and SYTO 13. Incubate at 30 degrees Celsius in the dark for 30 minutes.Visually inspect the integrity and purity of the isolated nuclei using a fluorescence microscope. Look for isolated nuclei showing prominent SYTO 13 staining and ensure no cell wall staining by the calcofluor-white dye. Repeat the inspection with intact cells as a control for cell wall staining with calcofluor-white dye.Place the tubes on a magnetic rack and wait until the slurry is completely clear. Discard the supernatant using a pipette. Add 50 microliters of the antibody buffer and gently mix by pipetting.Add three microliters of the anti-GFP polyclonal antibody to the tubes and incubate the tubes on a nutating mixer at 4 degrees Celsius for two hours. Briefly centrifuge the tubes at 100 times g at room temperature for five seconds and place the tubes on a magnetic rack. Once the slurry is clear, discard the supernatant using a pipette.While the tubes with the beads are still on the magnetic rack, add 200 microliters of ice-cold cell permeabilization buffer directly onto the beads. Discard the supernatant using a pipette. Repeat two washes with the ice-cold cell permeabilization buffer.Add 50 microliters of ice-cold cell permeabilization buffer to each tube and gently mix by pipetting. Add 2.5 microliters of the protein AG-MNase to each sample and mix by pipetting. Place the samples on a nutating mixer at 4 degrees Celsius and incubate the samples for one hour.Briefly centrifuge the strip tubes at 100 times g at room temperature for five seconds, then place the tubes on a magnetic rack. Once the slurry is clear, discard the supernatant using a pipette. While the tubes with the beads are still on the magnetic rack, add 200 microliters of ice-cold cell permeabilization buffer directly onto the beads.Discard the supernatant using a pipette. Repeat two washes with the ice-cold cell permeabilization buffer. Add 100 microliters of the ice-cold cell permeabilization buffer to the samples and gently pipette up and down five times.Remove the gel cast from the gel box and open the gel cast per the manufacturer's instructions. Gently remove the gel from the gel cast and place it inside a gel-holding tray containing 100 milliliters of single-strength TBE. Add 10 microliters of the nucleic acid gel stain to the tray and gently swirl.Cover with foil to protect from light and incubate statically at room temperature for 10 minutes. Then rinse the gel twice with 100 milliliters of deionized tap water. Image the gel under blue light illumination using an amber filter cover.For each library, cut the gel slightly above the approximately 125 base pair prominent adapter dimer band and below the 400 base pair ladder mark. Puncture the bottom of a 0.65-milliliter tube using a 22-gauge needle and place the punctured tube inside a sterile two-milliliter microfuge tube. Transfer the gel slice to the punctured tube inside the two-milliliter microfuge tube.Centrifuge the two-milliliter microfuge tube containing the 0.65-milliliter punctured tube and sample at 10, 000 times g at room temperature for two minutes to collect the gel slurry inside the two-milliliter microfuge tube. Add 300 microliters of ice-cold gel elution buffer to the gel slurry. Mix on a nutator at room temperature for a minimum of three hours or overnight.Transfer all liquid and gel slurry to a 0.22 micrometer filter column and centrifuge at 10, 000 times g at room temperature for one minute. Download the source code for the CUT&RUN analysis from the GitHub page by clicking on the green Code button, followed by Download ZIP option. Unzip the folder to a relevant location on the local machine.Install Conda Environment and run only once. Once Conda is installed, create a virtual environment provided with the relevant command. Activate the virtual environment every time this workflow is executed.Cell wall digestion and nuclear integrity were assessed by visualizing both control intact cells and isolated nuclei stained with fluorescent cell wall and nucleic acid stains. In contrast to the isolated intact nuclei where cell wall staining is not observed, both the nuclei and the cell walls are fluorescently labeled in the intact control cells. The figure shows CUT&RUN TF libraries analyzed using a capillary electrophoresis instrument.Successful CUT&RUN TF libraries are enriched for short fragments smaller than 200 base pairs. Suboptimal CUT&RUN TF libraries show enrichment for large DNA fragments. The figure herein shows that Ndt80 DNA-binding motifs are enriched across all the Ndt80-bound loci identified by CUT&RUN, indicating that the additional peaks identified by this methodology are likely bonafide Ndt80-bound sites.Comparative analysis indicated that the CUT&RUN protocol identified most of the previously known binding events for Ndt80 and Efg1 during biofilm formation. Overall, both Ndt80 and Efg1 bound to loci overlap with previously published chromatin immune precipitation ChIP data and are identified only using the CUT&RUN. It enables us to significantly increase the scope and pace of our research focused on transcriptional regulatory networks and Candida albicans.

Research

JoVE Journal

Biology

Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays

Genome-wide Analysis of Aminoacylation Charging Levels of tRNA Using Microarrays

tRNA aminoacylation, or charging, levels can rapidly change within a cell in response to the environment[1]. Changes in tRNA charging levels in both ...

Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the ...

A Quantitative Fitness Analysis Workflow

Quantitative Fitness Analysis (QFA) is an experimental and computational workflow for comparing fitnesses of microbial cultures grown in parallel1,2,3,4. ...

A Novel Bayesian Change-point Algorithm for Genome-wide Analysis of Diverse ChIPseq Data Types

ChIPseq is a widely used technique for investigating protein-DNA interactions. Read density profiles are generated by using next-sequencing of ...

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Genome-wide Gene Deletions in Streptococcus sanguinis by High Throughput PCR

Transposon  mutagenesis and single-gene deletion are two methods applied in genome-wide  gene knockout in bacteria 1,2. Although transposon mutagenesis is ...

Polysome Fractionation and Analysis of Mammalian Translatomes on a Genome-wide Scale

mRNA translation plays a central role in the regulation of gene expression and represents the most energy consuming process in mammalian cells. ...

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC (Crosslinking of Small Molecules to Isolate Chromatin)

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin

The genome is the target of some of the most effective chemotherapeutics, but most of these drugs lack DNA sequence specificity, which leads to ...

Complete Workflow for Analysis of Histone Post-translational Modifications Using Bottom-up Mass Spectrometry: From Histone Extraction to Data Analysis

Nucleosomes are the smallest structural unit of chromatin, composed of 147 base pairs of DNA wrapped around an octamer of histone proteins. Histone ...

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the ...