Perspectives on the use of super-enhancers as a defining feature of cell/tissue-identity genes

Abstract

Super-enhancers (SE) have become a popular concept and are widely used as a feature defining key identity genes. Here, we provide perspectives on the use of SE to define and identify cell/tissue-identity genes. By mining SE and their associated genes using murine functional genomics data, we highlight and discuss current limitations and open questions regarding both the sensitivity and specificity of identity genes/transcription factors predicted by SE. In this context, we point to cell/tissue-specific promoters as an important additional level of information, which we propose to combine with SE when aiming to define potential identity genes.

Keywords::

• cell identity
• epigenome
• promoters
• super-enhancers
• transcription factors
• transcriptome

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/suppl/10.2217/epi-2019-0290

Financial & competing interests disclosure

Work in our laboratory is supported by grants from the Fondation pour la Recherche Médicale (Equipe labellisée, DEQ20150331724), ‘European Genomic Institute for Diabetes’ (E.G.I.D., ANR-10-LABX-46) and European Commission. B Staels is supported by the European Research Council (ERC Grant Immunobile, contract 694717). The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.