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

• Published in: Nucleic acids research 2022-01, Vol.50 (2), p.e10-e10
• Main Authors: Rashid, Fatema-Zahra M, Mahlandt, Eike, van der Vaart, Michiel, Boer, Daphne E C, Varela Alvarez, Monica, Henneman, Bram, Brocken, Daan J W, Voskamp, Patrick, Blok, Anneloes J, Shimizu, Thomas S, Meijer, Annemarie H, Luijsterburg, Martijn S, Goedhart, Joachim, Crémazy, Frédéric G E, Dame, Remus T
• Format: Article
• Language: English
• Subjects: Animals; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biological Assay - methods; Cell Line; Cloning, Molecular; DNA Replication; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; DNA-Binding Proteins - genetics; DNA-Binding Proteins - metabolism; Fluorescent Dyes; Gene Expression; Genetic Vectors; Life Sciences; Methods Online; Microscopy, Fluorescence; Staining and Labeling - methods
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkab993

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.