Genetically encoded epigenetic sensors for visualization of H3K9me3, H3K9ac and H3K4me1 histone modifications in living cells

Afanasii I Stepanov; Lidia V Putlyaeva; Zlata Besedovskaya; Alexandra A Shuvaeva; Nikita V Karpenko; Shah Rukh; Dmitry A Gorbachev; Kseniia K Malyshevskaia; Alexey V Terskikh; Konstantin A Lukyanov; Nadya G Gurskaya

doi:10.1016/j.bbrc.2024.150715

Genetically encoded epigenetic sensors for visualization of H3K9me3, H3K9ac and H3K4me1 histone modifications in living cells

Biochem Biophys Res Commun. 2024 Nov 12:733:150715. doi: 10.1016/j.bbrc.2024.150715. Epub 2024 Sep 19.

Affiliations

¹ Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
² Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia.
³ Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
⁴ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; MIREA - Russian Technological University, Lomonosov Institute of Fine Chemical Technologies, Vernadskogo Pr. 78, 119454, Moscow, Russia.
⁵ Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
⁶ The Scintillon Research Institute, 6404 Nancy Ridge Dr., San Diego, CA, 92121, USA.
⁷ Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Bolshoi Blvd. 30, Bld. 1, 121205, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia; Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997, Moscow, Russia. Electronic address: gurskayanadya@gmail.com.

PMID: 39317113
DOI: 10.1016/j.bbrc.2024.150715

Abstract

Post-translational modifications of histones play a crucial role in chromatin structure maintenance and epigenetic regulation. The LiveMIEL (Live-cell Microscopic Imaging of Epigenetic Landscape) method represents a promising approach for tracking histone modifications. It involves visualization of epigenetic modifications using genetically encoded fluorescent sensors and further analysis of the obtained intranuclear patterns by multiparametric image analysis. In this study, we designed three new red fluorescent sensors-MPP8-Red, AF9-Red and DPF3-Red-for live-cell visualization of patterns of H3K9me3, H3K8ac and H3K4me1, respectively. The observed fluorescent patterns were visually distinguishable, and LiveMIEL analysis clearly classified them into three corresponding groups. We propose that these sensors can be used for live-cell dynamic analysis of changes in organization of three epigenetic types of chromatin.

Keywords: Epigenetics; Fluorescent proteins; Genetically encoded sensor; H3K4me1; H3K9ac; H3K9me3; Histone modification.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biosensing Techniques / methods
Chromatin / genetics
Chromatin / metabolism
Epigenesis, Genetic*
HEK293 Cells
HeLa Cells
Histones* / genetics
Histones* / metabolism
Humans
Luminescent Proteins / genetics
Luminescent Proteins / metabolism
Lysine / analogs & derivatives
Microscopy, Fluorescence / methods
Protein Processing, Post-Translational

Substances

Histones
Luminescent Proteins
Chromatin
(histone H3)-N6-methyl-L-lysine-4
Lysine