HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

Fatema-Zahra M. Rashid; Eike Mahlandt; Michiel van der Vaart; Daphne E.C. Boer; Monica Varela Alvarez; Bram Henneman; Daan J.W. Brocken; Patrick Voskamp; Anneloes J. Blok; Thomas S. Shimizu; Annemarie H. Meijer; Martijn S. Luijsterburg; Joachim Goedhart; Frédéric G.E. Crémazy; Remus T. Dame

doi:10.1093/nar/gkab993

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

Fatema-Zahra M. Rashid
, Eike Mahlandt
, Michiel van der Vaart
, Daphne E.C. Boer
, Monica Varela Alvarez
, Bram Henneman
, Daan J.W. Brocken
, Patrick Voskamp
, Anneloes J. Blok
, Thomas S. Shimizu
, Annemarie H. Meijer
, Martijn S. Luijsterburg
, Joachim Goedhart
, Frédéric G.E. Crémazy
, Remus T. Dame

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

Original language	English
Pages (from-to)	E10
Journal	Nucleic acids research
Volume	50
Issue number	2
DOIs	https://doi.org/10.1093/nar/gkab993
Publication status	Published - 25 Jan 2022
Externally published	Yes

Funding

Netherlands Organization for Scientific Research [VICI 016.160.613 to R.T.D., ENW-M OCENW.KLEIN.090 to M.S.L., VIDI ALW.016.161.320 to M.S.L., ALWOP.306 to E.M.]; FOM Foundation for Fundamental Research on Matter program 'Crowd management: the physics of genome processing in complex environments' (to R.T.D.); Human Frontier Science Program (HFSP) [RGP0014/2014 to R.T.D.]. Funding for open access charge: Nederlandse Organisatie voor Wetenschappelijk Onderzoek VICI Grant [016.160.613].

Funders	Funder number
Human Frontier Science Program	RGP0014/2014
Stichting voor Fundamenteel Onderzoek der Materie
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	VICI 016.160.613, ENW-M OCENW.KLEIN.090, 016.160.613

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10.1093/nar/gkab993

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Rashid, F.-Z. M., Mahlandt, E., van der Vaart, M., Boer, D. E. C., Alvarez, M. V., Henneman, B., Brocken, D. J. W., Voskamp, P., Blok, A. J., Shimizu, T. S., Meijer, A. H., Luijsterburg, M. S., Goedhart, J., Crémazy, F. G. E., & Dame, R. T. (2022). HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein. Nucleic acids research, 50(2), E10. https://doi.org/10.1093/nar/gkab993

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title = "HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein",

abstract = "The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.",

author = "Rashid, \{Fatema-Zahra M.\} and Eike Mahlandt and \{van der Vaart\}, Michiel and Boer, \{Daphne E.C.\} and Alvarez, \{Monica Varela\} and Bram Henneman and Brocken, \{Daan J.W.\} and Patrick Voskamp and Blok, \{Anneloes J.\} and Shimizu, \{Thomas S.\} and Meijer, \{Annemarie H.\} and Luijsterburg, \{Martijn S.\} and Joachim Goedhart and Cr{\'e}mazy, \{Fr{\'e}d{\'e}ric G.E.\} and Dame, \{Remus T.\}",

year = "2022",

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doi = "10.1093/nar/gkab993",

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Rashid, F-ZM, Mahlandt, E, van der Vaart, M, Boer, DEC, Alvarez, MV, Henneman, B, Brocken, DJW, Voskamp, P, Blok, AJ, Shimizu, TS, Meijer, AH, Luijsterburg, MS, Goedhart, J, Crémazy, FGE & Dame, RT 2022, 'HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein', Nucleic acids research, vol. 50, no. 2, pp. E10. https://doi.org/10.1093/nar/gkab993

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AU - Rashid, Fatema-Zahra M.

AU - Mahlandt, Eike

AU - van der Vaart, Michiel

AU - Boer, Daphne E.C.

AU - Alvarez, Monica Varela

AU - Henneman, Bram

AU - Brocken, Daan J.W.

AU - Voskamp, Patrick

AU - Blok, Anneloes J.

AU - Shimizu, Thomas S.

AU - Meijer, Annemarie H.

AU - Luijsterburg, Martijn S.

AU - Goedhart, Joachim

AU - Crémazy, Frédéric G.E.

AU - Dame, Remus T.

PY - 2022/1/25

Y1 - 2022/1/25

N2 - The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

AB - The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.

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IS - 2

ER -

HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein

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