Genomics

Dataset Information

164

Distinct Enhancer Classes in Drosophila Bind Different Architectural Proteins and Mediate Unique Chromatin Interactions and 3D Architecture [Hi-C]


ABSTRACT: In this study, we further characterized the hkCP and dCP enhancers, which were identified by STARR-seq, and shown to have an intrinsic capacity to interact with a specific type of core promoter depending on the presence of a DRE motif [9]. hkCP enhancers are marked by H3K4me3, associated with TAD borders, and mediate large TSS-clustered interactions to promote robust transcription. Furthermore, they contain the architectural proteins CAP-H2, Chromator, DREF and Z4. In contrast, dCP enhancers are marked by H3K4me1, associated with chromatin loop anchors and are more commonly associated with single TSS-contacts. dCP enhancers are depleted of the hkCP-specific architectural proteins and show an enrichment for Fs(1)h-L and Rad21 instead. Thus, our data supports the model that the unique occupancy of architectural proteins in the distinct enhancer classes are key contributors to the types of interactions that enhancers can mediate genome-wide, ultimately affecting enhancer-promoter specificity. Overall design: Analysis of the protein occupancy and chromatin interactions of the two distinct enhancer classes in Drosophila

INSTRUMENT(S): Illumina HiSeq 2000 (Drosophila melanogaster)

SUBMITTER: Victor G Corces  

PROVIDER: GSE80701 | GEO | 2016-11-16

SECONDARY ACCESSION(S): PRJNA319740

REPOSITORIES: GEO

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Publications

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture.

Cubeñas-Potts Caelin C   Rowley M Jordan MJ   Lyu Xiaowen X   Li Ge G   Lei Elissa P EP   Corces Victor G VG  

Nucleic acids research 20170201 4


Eukaryotic gene expression is regulated by enhancer-promoter interactions but the molecular mechanisms that govern specificity have remained elusive. Genome-wide studies utilizing STARR-seq identified two enhancer classes in Drosophila that interact with different core promoters: housekeeping enhancers (hkCP) and developmental enhancers (dCP). We hypothesized that the two enhancer classes are occupied by distinct architectural proteins, affecting their enhancer-promoter contacts. By evaluating C  ...[more]

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