Cis-regulatory chromatin loops arise before TADs and gene activation, and are independent of cell fate during development

Abstract

<jats:title>Abstract</jats:title><jats:p>During development, naïve cells gradually acquire distinct cell fates, through sophisticated mechanisms of precise spatio-temporal gene regulation. Acquisition of cell fate is thought to rely on the specific interaction of remote <jats:italic>cis</jats:italic>-regulatory modules (e.g. enhancers, silencers) (CRM) and target promoters. However, the precise interplay between chromatin structure and gene expression is still unclear, particularly in single cells within multicellular developing organisms. Here we employ Hi-M, a single-cell spatial genomics approach, to systematically detect CRM-promoter looping interactions within topological associating domains (TADs) during <jats:italic>Drosophila</jats:italic> development. By comparing <jats:italic>cis</jats:italic>-regulatory loops in alternate cell types, we show that physical proximity does not necessarily instruct transcriptional states. Moreover, multi-way analyses revealed the existence of local interactions between multiple remote CRMs to form hubs. We found that loops and CRM hubs are established early during development, prior to the emergence of TADs. Moreover, CRM hubs are formed via the action of the pioneer transcription factor Zelda and precede transcriptional activation. Our approach offers a new perspective on the role of CRM-promoter interactions in defining transcriptional activation and repression states, as well as distinct cell types.</jats:p>

An explainable artificial intelligence approach for decoding the enhancer histone modifications code and identification of novel enhancers in Drosophila

“…One possibility is that these putative enhancers are not as strong as the common ones and they might be missed by experimental methods. Alternatively, they might be primed enhancers [74], enhancers displaying most of the active marks, but not activating transcription yet. Based on our analysis, we cannot exclude that some of the putative enhancers are primed enhancers.…”

The role of insulators and transcription in 3D chromatin organisation of flies

“…Furthermore, even in the case when a promoter has a 3D contact with a regulatory sequence, less than 10% of genes display differential expression when the contact is lost, but the same is true at maintained loops. This suggests that the presence of chromatin loops would not be essential for controlling gene transcription in the majority of cases 58,[63][64][65] .…”

Navigating the crowd: visualizing coordination between genome dynamics, structure, and transcription

“…However, the dependency between chromatin architecture and transcription regulation in vivo is a matter of debate. For instance, contacts between cis-regulatory elements precede gene activation during Drosophila development and remain regardless of the transcriptional state [169]. A few studies also found that enhancer-promoter proximity is not always indicative of the transcriptional state [94,170].…”