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Constitutive and Inducible Systems for Genetic In Vivo Modification of Mouse Hepatocytes Using Hydrodynamic Tail Vein Injection
Published on: February 2, 2018
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HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo
Ting-Ya Chang1, David J Waxman2
1Departments of Biology and Biomedical Engineering, and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
BMC Genomics
|December 23, 2024
Summary
Hydrodynamic injection STARR-seq (HDI-STARR-seq) enables functional enhancer profiling in mouse liver tissue. This method overcomes limitations of cell models, revealing condition-dependent enhancers in vivo with reduced immune responses.
Area of Science:
- Genomics and Molecular Biology
- Epigenetics and Gene Regulation
- Mammalian Systems Biology
Background:
- Massively-parallel reporter assays like STARR-seq are used to find functional enhancers in cell models.
- Cell-based assays can be confounded by immune responses and do not reflect the in vivo chromatin state or multicellular environment.
- Existing methods lack the ability to profile enhancers in their native tissue context, limiting understanding of complex gene regulation.
Purpose of the Study:
- To develop and validate a novel method, HDI-STARR-seq, for large-scale functional enhancer profiling directly in mouse liver tissue.
- To overcome limitations of cell-based assays by assessing enhancers in an endogenous chromatin state and multicellular environment.
- To identify condition-dependent enhancers and characterize their regulatory roles in vivo.
Main Methods:
- Hydrodynamic tail vein injection (HDI) was used to deliver STARR-seq plasmid libraries to mouse livers.
- A minimal Albumin promoter was employed to drive reporter RNA transcriptional initiation, essential for liver enhancer activity.
- High-complexity libraries of DNase I-digested genomic regions were used to identify thousands of active liver enhancers.
Main Results:
- HDI-STARR-seq demonstrated minimal vector-induced type-I interferon responses, unlike traditional cell-based methods.
- The method identified numerous condition-dependent enhancers, correlating with specific gene expression patterns in response to stimuli (e.g., CAR ligand treatment).
- Active enhancers identified were enriched for open chromatin and activating histone marks (H3K27ac, H3K4me1, H3K4me3) and depleted of repressive marks.
Conclusions:
- HDI-STARR-seq provides a robust platform for in vivo functional enhancer profiling in liver tissue, improving upon existing methodologies.
- The technique facilitates the discovery of condition-dependent enhancers within their native biological context.
- HDI-STARR-seq is adaptable for studying enhancers across various species and tissues by utilizing appropriate promoter sequences.
