Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development
Espinola SM, Götz M, Bellec M, Messina O, Fiche JB, Houbron C, Dejean M, Reim I, Cardozo Gizzi AM, Lagha M, Nollmann M (2021)
Publication Type: Journal article
Publication year: 2021
Journal
DOI: 10.1038/s41588-021-00816-z
Abstract
Acquisition of cell fate is thought to rely on the specific interaction of remote cis-regulatory modules (CRMs), for example, enhancers and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly within multicellular developing organisms. In the present study, we employ Hi-M, a single-cell spatial genomics approach, to detect CRM–promoter looping interactions within topologically associating domains (TADs) during early Drosophila development. By comparing cis-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses reveal that multiple CRMs spatially coalesce to form hubs. Loops and CRM hubs are established early during development, before the emergence of TADs. Moreover, CRM hubs are formed, in part, via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach provides insight into the role of CRM–promoter interactions in defining transcriptional states, as well as distinct cell types.
Authors with CRIS profile
Involved external institutions
Centre de Biochimie Structurale (CBS)
France (FR)
Institut de Génétique Moléculaire de Montpellier (IGMM)
France (FR)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) / National Scientific and Technical Research Council
Argentina (AR)
France (FR)
Institut de Génétique Moléculaire de Montpellier (IGMM)
France (FR)
Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) / National Scientific and Technical Research Council
Argentina (AR)
How to cite
APA:
Espinola, S.M., Götz, M., Bellec, M., Messina, O., Fiche, J.B., Houbron, C.,... Nollmann, M. (2021). Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development. Nature Genetics. https://doi.org/10.1038/s41588-021-00816-z
MLA:
Espinola, Sergio Martin, et al. "Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during early Drosophila development." Nature Genetics (2021).
BibTeX: Download