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

[Image: see text] 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...

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Autores principales: Nifker, Gil, Grunwald, Assaf, Margalit, Sapir, Tulpova, Zuzana, Michaeli, Yael, Har-Gil, Hagai, Maimon, Noy, Roichman, Elad, Schütz, Leonie, Weinhold, Elmar, Ebenstein, Yuval
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210529/
https://www.ncbi.nlm.nih.gov/pubmed/37154345
http://dx.doi.org/10.1021/acsnano.2c12755
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author Nifker, Gil
Grunwald, Assaf
Margalit, Sapir
Tulpova, Zuzana
Michaeli, Yael
Har-Gil, Hagai
Maimon, Noy
Roichman, Elad
Schütz, Leonie
Weinhold, Elmar
Ebenstein, Yuval
author_facet Nifker, Gil
Grunwald, Assaf
Margalit, Sapir
Tulpova, Zuzana
Michaeli, Yael
Har-Gil, Hagai
Maimon, Noy
Roichman, Elad
Schütz, Leonie
Weinhold, Elmar
Ebenstein, Yuval
author_sort Nifker, Gil
collection PubMed
description [Image: see text] 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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spelling pubmed-102105292023-05-26 Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays Nifker, Gil Grunwald, Assaf Margalit, Sapir Tulpova, Zuzana Michaeli, Yael Har-Gil, Hagai Maimon, Noy Roichman, Elad Schütz, Leonie Weinhold, Elmar Ebenstein, Yuval ACS Nano [Image: see text] 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. American Chemical Society 2023-05-08 /pmc/articles/PMC10210529/ /pubmed/37154345 http://dx.doi.org/10.1021/acsnano.2c12755 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Nifker, Gil
Grunwald, Assaf
Margalit, Sapir
Tulpova, Zuzana
Michaeli, Yael
Har-Gil, Hagai
Maimon, Noy
Roichman, Elad
Schütz, Leonie
Weinhold, Elmar
Ebenstein, Yuval
Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title_full Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title_fullStr Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title_full_unstemmed Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title_short Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays
title_sort dam assisted fluorescent tagging of chromatin accessibility (dafca) for optical genome mapping in nanochannel arrays
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10210529/
https://www.ncbi.nlm.nih.gov/pubmed/37154345
http://dx.doi.org/10.1021/acsnano.2c12755
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