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High similarity among ChEC-seq datasets

Chitvan Mittal, Matthew J. Rossi, View ORCID ProfileB. Franklin Pugh
doi: https://doi.org/10.1101/2021.02.04.429774
Chitvan Mittal
1Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
2Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
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Matthew J. Rossi
1Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
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B. Franklin Pugh
1Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
2Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, 14853, USA
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  • ORCID record for B. Franklin Pugh
  • For correspondence: fp265@cornell.edu
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Abstract

ChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted February 05, 2021.
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High similarity among ChEC-seq datasets
Chitvan Mittal, Matthew J. Rossi, B. Franklin Pugh
bioRxiv 2021.02.04.429774; doi: https://doi.org/10.1101/2021.02.04.429774
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High similarity among ChEC-seq datasets
Chitvan Mittal, Matthew J. Rossi, B. Franklin Pugh
bioRxiv 2021.02.04.429774; doi: https://doi.org/10.1101/2021.02.04.429774

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