Analysis of chromatin boundary activity in Drosophila cells

Mo Li, Vladimir E. Belozerov, Haini N. Cai*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

9 Scopus citations


Background: Chromatin boundaries, also known as insulators, regulate gene activity by organizing active and repressive chromatin domains and modulate enhancer-promoter interactions. However, the mechanisms of boundary action are poorly understood, in part due to our limited knowledge about insulator proteins, and a shortage of standard assays by which diverse boundaries could be compared. Results: We report here the development of an enhancer-blocking assay for studying insulator activity in Drosophila cultured cells. We show that the activities of diverse Drosophila insulators including suHw, SF1, SF1b, Fab7 and Fab8 are supported in these cells. We further show that double stranded RNA (dsRNA)-mediated knockdown of SuHw and dCTCF factors disrupts the enhancer-blocking function of suHw and Fab8, respectively, thereby establishing the effectiveness of using RNA interference in our cell-based assay for probing insulator function. Conclusion: The novel boundary assay provides a quantitative and efficient method for analyzing insulator mechanism and can be further exploited in genome-wide RNAi screens for insulator components. It provides a useful tool that complements the transgenic and genetic approaches for studying this important class of regulatory elements.

Original languageEnglish (US)
Article number109
JournalBMC Molecular Biology
StatePublished - Dec 11 2008
Externally publishedYes

Bibliographical note

Funding Information:
We thank Sharmila Roy, Kevin Liu and Ping Shen for useful discussion; Jim Kadonaga, Sally Elgin, Scott Barolo for plasmids. This work is supported in part by a grant from the NIH.

ASJC Scopus subject areas

  • Molecular Biology


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