Epigenomics-Based Identification of Major Cell Identity Regulators within Heterogeneous Cell Populations

Abstract

Cellular heterogeneity within embryonic and adult tissues is involved in multiple biological and pathological processes. Here, we present a simple epigenomic strategy that allows the functional dissection of cellular heterogeneity. By integrating H3K27me3 chromatin immunoprecipitation sequencing (ChIP-seq) and RNA sequencing (RNA-seq) data, we demonstrate that the presence of broad H3K27me3 domains at transcriptionally active genes reflects the heterogeneous expression of major cell identity regulators. Using dorsoventral patterning of the spinal neural tube as a model, the proposed approach successfully identifies the majority of previously known dorsoventral patterning transcription factors with high sensitivity and precision. Moreover, poorly characterized patterning regulators can be similarly predicted, as shown for ZNF488, which confers p1/p2 neural progenitor identity. Finally, we show that, as our strategy is based on universal chromatin features, it can be used to functionally dissect cellular heterogeneity within various organisms and tissues, thus illustrating its potential applicability to a broad range of biological and pathological contexts.

GPR17 is an Essential Component of the Negative Feedback Loop of the Sonic Hedgehog Signalling Pathway in Neural Tube Development

“…By contrast, FoxA2, which is expressed in the floor plate, downregulated GPR17 (Fig 1E, lanes 1 and 3), which was consistent with the observation that the GPR17 expression was lower in the floor plate region. Znf488 (also known as Zfp488), which is expressed in the same regions as Olig2 [29,30], did not have a significant effect on GPR17 expression (Fig 1E, lanes 1 and 4). These data supported the idea that GPR17 expression is targeted by Olig2 [28], and becomes exclusive to the floor plate as development progresses.…”

Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs

“…ChIPs were performed in p2hNCC and chicken FNP as previously described (Rada-Iglesias et al, 2012;Rehimi et al, 2016). Briefly, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and formaldehyde was quenched by 0.125 M glycine.…”

GPR17 is an essential regulator for the temporal adaptation of Sonic hedgehog signalling in neural tube development

“…2E, lanes 1 and 3), which was consistent with the observation that the Gpr17 expression was lower in the floor-plate region. Znf488 (also known as Zfp488), which is expressed in the same regions as Olig2 (Rehimi et al, 2016;, did not have a significant effect on GPR17 expression ( Fig. 2H, lanes 1 and 4).…”