PUBLICATION
Single-cell profiling of transcriptome and histone modifications with EpiDamID
- Authors
- Rang, F.J., de Luca, K.L., de Vries, S.S., Valdes-Quezada, C., Boele, E., Nguyen, P.D., Guerreiro, I., Sato, Y., Kimura, H., Bakkers, J., Kind, J.
- ID
- ZDB-PUB-220403-3
- Date
- 2022
- Source
- Molecular Cell 82(10): 1956-1970.e14 (Journal)
- Registered Authors
- Bakkers, Jeroen
- Keywords
- DamID, chromatin, embryo development, epigenetics, gene regulation, histone post-translational modifications, multi-modal omics, single-cell genomics
- Datasets
- GEO:GSE184036, GEO:GSE184035
- MeSH Terms
-
- Animals
- Chromatin/genetics
- Histone Code*
- Histones*/genetics
- Histones*/metabolism
- Mice
- Protein Processing, Post-Translational
- Transcriptome
- Zebrafish/genetics
- Zebrafish/metabolism
- PubMed
- 35366395 Full text @ Mol. Cell
Citation
Rang, F.J., de Luca, K.L., de Vries, S.S., Valdes-Quezada, C., Boele, E., Nguyen, P.D., Guerreiro, I., Sato, Y., Kimura, H., Bakkers, J., Kind, J. (2022) Single-cell profiling of transcriptome and histone modifications with EpiDamID. Molecular Cell. 82(10):1956-1970.e14.
Abstract
Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping