Systematische Analyse von Enhancer Wechselwirkungen

Projekt: Forschungsförderung

Projektdetails

Abstract

Wider research context: Genome-wide association studies have identified numerous risk loci for diseases
and traits. Most of these sites are not located within the coding part of a gene but in intronic and intergenic
regions, suggesting that many of them affect regulatory elements such as enhancers. Enhancers can be
identified either through epigenomic mapping of enhancer marks or based on their intrinsic ability to enhance
reporter gene expression. But the overlap between these two methods is not complete and many elements
present a clear epigenomic signature but are not able to activate a reporter gene outside their endogenous
context. These “enhancer-like elements” have sometimes been ignored since it was assumed that they
might not have a function at the endogenous locus. Our previous data show that a lack of intrinsic enhancer
activity does not equal functional irrelevance at the endogenous locus. Deletion experiments of individual
epigenomically identified enhancer elements without intrinsic enhancer activity led to lower target gene
expression.
Objectives: The study of enhancer-like elements is only possible through laborious and time-consuming
manipulation of the endogenous locus, therefore many open questions remain: which elements can activate
transcription at the endogenous locus but not in reporter constructs? Do these elements regulate
transcription with a different mechanism compared to canonical elements?
Approach: The work centers around a novel clearly defined synthetic locus that allows enhancer integration
at varying distances to a promoter locus, alone and in combinations with other elements. We will test the
intrinsic potential for gene regulation of enhancer-like elements using massively parallel reporter assays
within our synthetic locus. We will analyze the interplay of individual elements with each other, and we will
determine whether different classes of elements can be distinguished. We will mechanistically dissect the
role of enhancer-like elements in 3D genome organization and use deep learning-based approaches to
identify differences between canonical enhancers and enhancer-like elements. Together, we will elucidate
whether enhancer-like elements activate transcription through a fundamentally different mechanism
compared to canonical enhancers.
Innovation: The work laid out in this proposal will build the foundation to illuminate the role of different classes
of enhancers in gene regulation and how mutations in these often-ignored regions could lead to misregulation
of transcription.
Primary Researchers involved: The research project will be carried out by Christa Buecker and her lab. The
work will be supported through tight collaborations with Alex Stark (DeepSTARR to computationally dissect
differences among distinct enhancer classes) and Anton Goloborodko (3D analysis and modelling of
interaction frequencies of promoters and enhancers).
KurztitelSystem. Analyse - Enhancer Wechselwirk.
StatusLaufend
Tatsächlicher Beginn/ -es Ende1/05/2430/04/28