Abstract
Chromatin organization and gene activity are responsive to developmental and environmental cues. Although many genes are transcribed throughout development and across cell types, much of gene regulation is highly cell-type specific. To readily track chromatin features at the resolution of cell types within complex tissues, we developed and validated chromatin affinity purification from specific cell types by chromatin immunoprecipitation (CAST-ChIP), a broadly applicable biochemical procedure. RNA polymerase II (Pol II) CAST-ChIP identifies ~1,500 neuronal and glia-specific genes in differentiated cells within the adult Drosophila brain. In contrast, the histone H2A.Z is distributed similarly across cell types and throughout development, marking cell-type-invariant Pol II-bound regions. Our study identifies H2A.Z as an active chromatin signature that is refractory to changes across cell fates. Thus, CAST-ChIP powerfully identifies cell-type-specific as well as cell-type-invariant chromatin states, enabling the systematic dissection of chromatin structure and gene regulation within complex tissues such as the brain.
Highlights
Developmental programs and environmental responses depend on the cell-type-specific expression of genes, mediated by the temporal and spatial regulation of transcription and chromatin structure (Bonn et al, 2012; Heintzman et al, 2009; modENCODE Consortium et al, 2010)
We identified regions of high chromatin immunoprecipitation (ChIP) enrichment in the head, glia, and neurons, and merged them into regions of interest (ROIs; see Experimental Procedures; Figure 1C; Table S1)
Since we observed that H2A.Z ROIs often overlapped two neighboring chromatin domains, such as constitutive and silent or constitutive and dynamically active chromatin (Figures 7B, S7C, and S7D), we investigated the relationship between H2A.Z and insulator-binding proteins, both of which have previously been shown to localize at promoters with a broad transcription start sites (TSSs) (Nègre et al, 2010; Rach et al, 2011)
Summary
Developmental programs and environmental responses depend on the cell-type-specific expression of genes, mediated by the temporal and spatial regulation of transcription and chromatin structure (Bonn et al, 2012; Heintzman et al, 2009; modENCODE Consortium et al, 2010). Much of our understanding of development and physiology hinges on our ability to dissect cell-type-invariant transcriptional responses from highly cell-type-specific ones, but existing tools to obtain such information are limited. Chromatin contributes to both cell-type-specific and cell-type-invariant gene expression (Dixon et al, 2012; Filion et al, 2010), determining cell fate, yet exhibiting plasticity. Specific chromatin marks correlate with different activation states of RNA Polymerase II (Pol II), such as binding, poising/pausing, and elongation, promoting correct levels of gene expression in distinct cell types throughout development (Dixon et al, 2012; Filion et al, 2010; Gaertner et al, 2012)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
