Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

Gil Nifker; Assaf Grunwald; Sapir Margalit; Zuzana Tulpova; Yael Michaeli; Hagai Har-Gil; Noy Maimon; Elad Roichman; Leonie Schütz; Elmar Weinhold; Yuval Ebenstein

doi:10.1021/acsnano.2c12755

Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

Gil Nifker, Assaf Grunwald, Sapir Margalit, Zuzana Tulpova, Yael Michaeli, Hagai Har-Gil, Noy Maimon, Elad Roichman, Leonie Schütz, Elmar Weinhold^*, Yuval Ebenstein^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.

Original language	English
Pages (from-to)	9178-9187
Number of pages	10
Journal	ACS Nano
Volume	17
Issue number	10
DOIs	https://doi.org/10.1021/acsnano.2c12755
State	Published - 23 May 2023

Funding

Funders	Funder number
Israel Innovation Authority and German Federal Ministry of Education and Research	NATI 61976, 13GW0282B
National Institutes of Health
National Human Genome Research Institute	R01HG009190
European Research Council	817811
Israel Science Foundation	771/21

Keywords

DNA labeling
chromatin accessibility
methyltransferase labeling
nanochannels
optical genome mapping
single-molecule

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10.1021/acsnano.2c12755

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abstract = "Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.",

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AU - Margalit, Sapir

AU - Tulpova, Zuzana

AU - Michaeli, Yael

AU - Har-Gil, Hagai

AU - Maimon, Noy

AU - Roichman, Elad

AU - Schütz, Leonie

AU - Weinhold, Elmar

AU - Ebenstein, Yuval

PY - 2023/5/23

Y1 - 2023/5/23

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AB - Proteins and enzymes in the cell nucleus require physical access to their DNA target sites in order to perform genomic tasks such as gene activation and transcription. Hence, chromatin accessibility is a central regulator of gene expression, and its genomic profile holds essential information on the cell type and state. We utilized the E. coli Dam methyltransferase in combination with a fluorescent cofactor analogue to generate fluorescent tags in accessible DNA regions within the cell nucleus. The accessible portions of the genome are then detected by single-molecule optical genome mapping in nanochannel arrays. This method allowed us to characterize long-range structural variations and their associated chromatin structure. We show the ability to create whole-genome, allele-specific chromatin accessibility maps composed of long DNA molecules extended in silicon nanochannels.

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KW - chromatin accessibility

KW - methyltransferase labeling

KW - nanochannels

KW - optical genome mapping

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Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays

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