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Reporter cell lines for epigenetic pathways
20.01.22 Tchasovnikarova lab’s TRACE method generates reporter cell lines for genetic interrogation
The Tchasovnikarova lab present TRACE (transgene reporters across chromatin environments), a high-throughput, genome-wide technique to generate fluorescent human reporter cell lines responsive to manipulation of epigenetic factors. The technique will provide mechanistic insights into the underlying biology, with strong potential for identifying novel targets for therapeutic manipulation.
Tchasovnikarova IA et al. (2022) TRACE generates fluorescent human reporter cell lines to characterize epigenetic pathways. Molecular Cell 82: 479-491.e7. DOI: 10.1016/j.molcel.2021.11.035.
Summary from the paper
Genetically encoded biosensors are powerful tools to monitor cellular behavior, but the difficulty in generating appropriate reporters for chromatin factors hampers our ability to dissect epigenetic pathways. Here, we present TRACE (transgene reporters across chromatin environments), a high-throughput, genome-wide technique to generate fluorescent human reporter cell lines responsive to manipulation of epigenetic factors.
By profiling GFP expression from a large pool of individually barcoded lentiviral integrants in the presence and absence of a perturbation, we identify reporters responsive to pharmacological inhibition of the histone lysine demethylase LSD1 and genetic ablation of the PRC2 subunit SUZ12. Furthermore, by manipulating the HIV-1 host factor LEDGF through targeted deletion or fusion to chromatin reader domains, we alter lentiviral integration site preferences, thus broadening the types of chromatin examined by TRACE.
The phenotypic reporters generated through TRACE will allow the genetic interrogation of a broad range of epigenetic pathways, furthering our mechanistic understanding of chromatin biology.
