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DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide

View ORCID ProfileNicolas Altemose, View ORCID ProfileAnnie Maslan, View ORCID ProfileOwen K. Smith, View ORCID ProfileKousik Sundararajan, View ORCID ProfileRachel R. Brown, View ORCID ProfileAngela M. Detweiler, View ORCID ProfileNorma Neff, View ORCID ProfileKaren H. Miga, View ORCID ProfileAaron F. Straight, View ORCID ProfileAaron Streets
doi: https://doi.org/10.1101/2021.07.06.451383
Nicolas Altemose
1Department of Bioengineering, University of California, Berkeley, CA 94720
2UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720
*Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720
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Annie Maslan
1Department of Bioengineering, University of California, Berkeley, CA 94720
2UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720
3Center for Computational Biology, University of California, Berkeley, CA 94720
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Owen K. Smith
4Department of Biochemistry, Stanford University, Stanford, CA 94305
5Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305
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Kousik Sundararajan
4Department of Biochemistry, Stanford University, Stanford, CA 94305
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Rachel R. Brown
4Department of Biochemistry, Stanford University, Stanford, CA 94305
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Angela M. Detweiler
6Chan Zuckerberg Biohub, San Francisco, CA 94158
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Norma Neff
6Chan Zuckerberg Biohub, San Francisco, CA 94158
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Karen H. Miga
7Department of Molecular & Cell Biology, University of California, Santa Cruz, CA 95064
8UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA 95064
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Aaron F. Straight
4Department of Biochemistry, Stanford University, Stanford, CA 94305
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  • For correspondence: astreets@berkeley.edu astraigh@stanford.edu
Aaron Streets
1Department of Bioengineering, University of California, Berkeley, CA 94720
2UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, CA 94720
3Center for Computational Biology, University of California, Berkeley, CA 94720
6Chan Zuckerberg Biohub, San Francisco, CA 94158
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  • For correspondence: astreets@berkeley.edu astraigh@stanford.edu
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Abstract

Molecular studies of genome regulation often rely on the ability to map where specific proteins interact with genomic DNA. Existing techniques for mapping protein-DNA interactions genome-wide rely on DNA amplification methods followed by sequencing with short reads, which dissociates joint binding information at neighboring sites, removes endogenous DNA methylation information, and precludes the ability to reliably map interactions in repetitive regions of the genome. To address these limitations, we created a new protein-DNA mapping method, called Directed Methylation with Long-read sequencing (DiMeLo-seq), which methylates DNA near each target protein’s DNA binding site in situ, then leverages the ability to distinguish methylated and unmethylated bases on long, native DNA molecules using long-read, single-molecule sequencing technologies. We demonstrate the optimization and utility of this method by mapping the interaction sites of a variety of different proteins and histone modifications across the human genome, achieving a single-molecule binding site resolution of less than 200 bp. Furthermore, we mapped the positions of the centromeric histone H3 variant CENP-A in repetitive regions that are unmappable with short reads, while simultaneously analyzing endogenous CpG methylation and joint binding events on single molecules. DiMeLo-seq is a versatile method that can provide multimodal and truly genome-wide information for investigating protein-DNA interactions.

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-NC 4.0 International license.
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Posted July 07, 2021.
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DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide
Nicolas Altemose, Annie Maslan, Owen K. Smith, Kousik Sundararajan, Rachel R. Brown, Angela M. Detweiler, Norma Neff, Karen H. Miga, Aaron F. Straight, Aaron Streets
bioRxiv 2021.07.06.451383; doi: https://doi.org/10.1101/2021.07.06.451383
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DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome-wide
Nicolas Altemose, Annie Maslan, Owen K. Smith, Kousik Sundararajan, Rachel R. Brown, Angela M. Detweiler, Norma Neff, Karen H. Miga, Aaron F. Straight, Aaron Streets
bioRxiv 2021.07.06.451383; doi: https://doi.org/10.1101/2021.07.06.451383

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