7 research outputs found
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Loci specific epigenetic drug sensitivity.
Therapeutic targeting of epigenetic modulators offers a novel approach to the treatment of multiple diseases. The cellular consequences of chemical compounds that target epigenetic regulators (epi-drugs) are complex. Epi-drugs affect global cellular phenotypes and cause local changes to gene expression due to alteration of a gene chromatin environment. Despite increasing use in the clinic, the mechanisms responsible for cellular changes are unclear. Specifically, to what degree the effects are a result of cell-wide changes or disease related locus specific effects is unknown. Here we developed a platform to systematically and simultaneously investigate the sensitivity of epi-drugs at hundreds of genomic locations by combining DNA barcoding, unique split-pool encoding, and single cell expression measurements. Internal controls are used to isolate locus specific effects separately from any global consequences these drugs have. Using this platform we discovered wide-spread loci specific sensitivities to epi-drugs for three distinct epi-drugs that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by epi-drugs. The measurements of loci specific epi-drugs sensitivities will pave the way to the development of targeted therapy for personalized medicine
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Chromosomal Position Effects on Gene Expression Variability and Epigenetic Drug Sensitivity
Chromosomal position effect, also known as position effect variegation, has been extensively studied for almost a century. A systematic approach to study positional effect is to isolate genetic from epigenetic factors specifically to measure the expression of the same gene positioned in different chromatin contexts. Current strategies to target a reporter gene at multiple genomic locations are not capable of increasing both the sensitivity and throughput of data. Here, we developed a new massively parallel method to create and identify isogenic reporter clones. This method allowed us to interrogate the effect of chromatin environment on gene expression variability and epigenetic drug sensitivity as well as identify their underlying mechanisms. In human cells, we found that the protein expression mean and noise significantly are varied by the genomic location of the gene. By mapping our measurements of reporter expression at different genomic loci with epigenetic profiles of the transcription factor enrichment and the distance to chromatin states, we identified the factors that impact gene regulation. Some factors are involved in mediating both gene expression mean and noise, while other only control one of these features. Moreover, we discovered wide-spread loci-specific sensitivities to epigenetic drugs for three distinct chemical compounds that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by these epigenetic drugs
Recommended from our members
Chromosomal Position Effects on Gene Expression Variability and Epigenetic Drug Sensitivity
Chromosomal position effect, also known as position effect variegation, has been extensively studied for almost a century. A systematic approach to study positional effect is to isolate genetic from epigenetic factors specifically to measure the expression of the same gene positioned in different chromatin contexts. Current strategies to target a reporter gene at multiple genomic locations are not capable of increasing both the sensitivity and throughput of data. Here, we developed a new massively parallel method to create and identify isogenic reporter clones. This method allowed us to interrogate the effect of chromatin environment on gene expression variability and epigenetic drug sensitivity as well as identify their underlying mechanisms. In human cells, we found that the protein expression mean and noise significantly are varied by the genomic location of the gene. By mapping our measurements of reporter expression at different genomic loci with epigenetic profiles of the transcription factor enrichment and the distance to chromatin states, we identified the factors that impact gene regulation. Some factors are involved in mediating both gene expression mean and noise, while other only control one of these features. Moreover, we discovered wide-spread loci-specific sensitivities to epigenetic drugs for three distinct chemical compounds that target histone deacetylase, DNA methylation and bromodomain proteins. By leveraging ENCODE data on chromatin modification, we identified features of chromatin environments that are most likely to be affected by these epigenetic drugs
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Identifying chromatin features that regulate gene expression distribution.
Gene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions
Recommended from our members
Identifying chromatin features that regulate gene expression distribution.
Gene expression variability, differences in the number of mRNA per cell across a population of cells, is ubiquitous across diverse organisms with broad impacts on cellular phenotypes. The role of chromatin in regulating average gene expression has been extensively studied. However, what aspects of the chromatin contribute to gene expression variability is still underexplored. Here we addressed this problem by leveraging chromatin diversity and using a systematic investigation of randomly integrated expression reporters to identify what aspects of chromatin microenvironment contribute to gene expression variability. Using DNA barcoding and split-pool decoding, we created a large library of isogenic reporter clones and identified reporter integration sites in a massive and parallel manner. By mapping our measurements of reporter expression at different genomic loci with multiple epigenetic profiles including the enrichment of transcription factors and the distance to different chromatin states, we identified new factors that impact the regulation of gene expression distributions