z-logo
open-access-imgOpen Access
Enhancer identification and activity evaluation in the red flour beetle, Tribolium castaneum
Author(s) -
Yi-Ting Lai,
Kevin D. Deem,
Ferran Borràs-Castells,
Nagraj Sambrani,
Heike Rudolf,
Kushal Suryamohan,
Ezzat El-Sherif,
Marc S. Halfon,
Daniel J. McKay,
Yoshinori Tomoyasu
Publication year - 2018
Publication title -
development
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.754
H-Index - 325
eISSN - 1477-9129
pISSN - 0950-1991
DOI - 10.1242/dev.160663
Subject(s) - biology , red flour beetle , enhancer , context (archaeology) , chromatin , computational biology , genetics , evolutionary biology , insect , gene , gene expression , botany , paleontology
Evolution of cis-regulatory elements (such as enhancers) plays an important role in the production of diverse morphology. However, a mechanistic understanding is often limited by the absence of methods to study enhancers in species outside of established model systems. Here, we sought to establish methods to identify and test enhancer activity in the red flour beetle, Tribolium castaneum. To identify possible enhancer regions, we first obtained genome-wide chromatin profiles from various tissues and stages of Tribolium via FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)-sequencing. Comparison of these profiles revealed a distinct set of open chromatin regions in each tissue and stage. In addition, comparison of the FAIRE data to sets of computationally predicted (SCRMshaw) enhancers revealed a very high overlap between the two datasets. Second, using nubbin in the wing and hunchback in the embryo as case studies, we established the first universal reporter assay system that works in various contexts in Tribolium, and in a cross-species context. Together, these advances will facilitate investigation of cis-evolution and morphological diversity in Tribolium and other insects.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.
Having issues? You can contact us here