Simultaneous Transcriptional and Epigenomic Profiling from Specific Cell Types within Heterogeneous Tissues In Vivo

Abstract

SUMMARY Epigenomic mechanisms direct distinct gene expression programs for different cell types. Various in vivo tissues have been subjected to epigenomic analysis; however, these studies have been limited by cellular heterogeneity resulting in composite gene expression and epigenomic profiles. Here, we introduce “NuTRAP”, a transgenic mouse that allows simultaneous isolation of cell type-specific translating mRNA and chromatin from complex tissues. Using NuTRAP, we successfully characterize gene expression and epigenomic states of various adipocyte populations in vivo, revealing significant differences compared to either whole adipose tissue or in vitro adipocyte cell lines. We find that ChIP-seq using NuTRAP is highly efficient, scalable, and robust with even limited cell input. We further demonstrate the general utility of NuTRAP by analyzing hepatocyte-specific epigenomic states. The NuTRAP mouse is a resource that provides a powerful system for cell type-specific gene expression and epigenomic profiling.

Genetic Depletion of Adipocyte Creatine Metabolism Inhibits Diet-Induced Thermogenesis and Drives Obesity

“…BAT was used for these measurements because it is the most homogeneous of the adipose tissue depots, in that the majority of cells from the tissue are bona fide adipocytes (Roh et al, 2017). This is particularly relevant, as measurement of creatine after purification of adipocytes is complicated by the fact that the creatine transporter promotes release of creatine from cells (Bera et al, 2008; Dodd et al, 1999).…”

Crosstalk between KCNK3-Mediated Ion Current and Adrenergic Signaling Regulates Adipose Thermogenesis and Obesity

“…The aP2-Prdm16 mice were maintained in the Spiegelman laboratory (Seale et al, 2011). The Ucp1 -cre mice and NuTRAP mice were obtained from Dr. Evan Rosen at Beth Israel Deaconess Medical Center (Kong et al, 2014 and Roh et al, 2017). All strains were on the C57BL6 background.…”

“…NuTRAP mice (Roh et al, 2017) was crossed to Adiponectin-cre mice (Jax 028020) to achieve adipocyte-specific expression of the tagged ribosomes. Small pieces (50–100 mg) of frozen brown, inguinal white and epididymal white adipose tissues were Dounce homogenized in 4 mL homogenization buffer (50 mM Tris [pH 7.5], 12 mM MgCl2, 100 mM KCl, 1% NP-40, 100 mg/mL cycloheximide, 1 mg/mL sodium heparin, 2mMDTT, 0.2 U/mL RNasin, and 1x Complete EDTA- free protease inhibitor; Roche).…”

Profound functional and molecular diversity of mitochondria revealed by cell type-specific profiling in vivo

“…This approach has been recently extended to organelles, e.g. to explore mitochondrial (22) and lysosomal (23) metabolomes in vitro, organellar DNA in invertebrates (24) or to correlate transcriptional and epigenetic signatures (25). To study mitochondrial diversity among cell types in situ, i.e.…”