PgmNr D192: Developmental Regulomes – Resolving Enhancer-Protein Interactions with Temporal and Tissue-Specificity.

Authors:
Robert P. Zinzen 1 ; Sabrina Krueger 1 ; Djordje Vasiljevic 2 ; Matthias Selbach 2 ; Robert P. Zinzen 1


Institutes
1) Berlin Institute of Medical Systems Biology (BIMSB-MDC), Berlin, Germany; 2) Max Delbruck Centre for Molecular Medicine (MDC), Berlin, Germany.


Keyword: cis-regulatory logic

Abstract:

Tightly coordinated control of gene expression is essential, especially in development. Cis-regulatory elements (CRMs) like enhancers act as information integration hubs to drive and regulate spatio-temporal gene expression by interpreting the specific cellular environment (transcription factor (TF) availability, chromatin state, etc.) to translate the available regulatory information into transcriptional responses.

While it is possible to identify CRMs globally, we are largely unable to explain the exact spatio-temporal activities that individual identified enhancers actually drive when tested in vivo over the course of development. Our knowledge of the suit of regulatory interactions that converge on individual enhancers is all too often incomplete. In order to accurately predict and model enhancer activity in vivo, identification of these inputs remains a crucial challenge.

We have developed a method that allows for the biochemical isolation of defined regulatory elements from whole animals to high purities. We show that protein:DNA interactions remain stable during purification and that mass spectrometry can identify specific CRM:protein interactions, including TFs, as well as chromatin modulators and local nucleosome components. The major advantage of our approach is that using the genetic accessibility of Drosophila, we are not limited to querying such interactions at developmental stages, but we can do so in a tissue- and cell type-specific manner. For the first time, we are able to extract specific DNA elements from embryos and identify their tissue-specific regulatory interactions (i.e. their ‘regulomes’) to ask what renders an enhancer active in one tissue, but inactive in another, how these interactions change over the course of development, and how they depend on activity state?

Deploying this method to query enhancer:protein interactions of neurectodermal enhancers has revealed dozens of potential regulators, known and novel, which we are now being tested for their global roles in early nervous system patterning.

The method presented here is broadly applicable to the identification of specific DNA:protein interactions in vivo with temporal and tissue-specificity and should be expandable for the identification of other potential regulators including lncRNAs and local genome architecture.



Flybase Genetic Index:
1. FlyBase gene symbol: vnd; FBgn: FBgn0261930
2. FlyBase gene symbol: ind; FBgn: FBgn0025776
3. FlyBase gene symbol: Dr; FBgn: FBgn0000492
4. FlyBase gene symbol: Su(H); FBgn: FBgn0004837