Chromatin profiling of Drosophila CNS subpopulations identifies active transcriptional enhancers

Abstract

One of the key issues in studying transcriptional regulation during development is how to employ genome-wide assays that reveals sites of open chromatin and transcription factor binding to efficiently identify biologically relevant genes and enhancers. Analysis of Drosophila CNS midline cell development provides a useful system for studying transcriptional regulation at the genomic level due to a large, well-characterized set of midline-expressed genes and in vivo validated enhancers. In this study, FAIRE-seq on FACS-purified midline cells was performed and the midline FAIRE data were compared with whole-embryo FAIRE data. We find that regions of the genome with a strong midline FAIRE peak and weak whole-embryo FAIRE peak overlap with known midline enhancers and provide a useful predictive tool for enhancer identification. In a complementary analysis, we compared a large dataset of fragments that drive midline expression in vivo with the FAIRE data. Midline enhancer fragments with a midline FAIRE peak tend to be near midline-expressed genes, whereas midline enhancers without a midline FAIRE peak were often distant from midline-expressed genes and unlikely to drive midline transcription in vivo.

Perspectives on Gene Regulatory Network Evolution

“…On the other hand, chromatin profiling alone has limited ability to predict spatio-temporal specificity of a given CRM, even when performed in a tissue-specific manner [e.g. 51], and moreover, cannot be focused to a particular GRN. Given that genes, and developmental genes in particular, frequently have multiple CRMs, determining the right set of CRMs necessary to study a GRN of interest—especially in several species—can be a challenge.…”

Enhancer identification and activity evaluation in the red flour beetle,Tribolium castaneum

“…One such method is Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in combination with next generation sequencing (FAIRE-seq), which identifies open chromatin regions genome-wide (Simon et al, 2012). FAIRE-seq has been used in Drosophila , showing that open chromatin regions often correspond to enhancers and other CREs (McKay and Lieb, 2013; Pearson et al, 2016; Uyehara et al, 2017). In addition, FAIRE-seq requires less input material and does not rely on antibodies, thus making it less technically demanding compared to techniques like Chromatin Immunoprecipitation sequencing (ChIP-seq).…”

CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

“…Recent studies have provided insights into chromatin accessibility of individual cell-types using accessibility assays coupled with cell sorting [33]. Whilst these strategies have been proven to produce meaningful biological data, they suffer from being technically challenging, particularly with regards to cell isolation.…”