Drosophila Dosage Compensation Loci Associate with a Boundary-Forming Insulator Complex

ABSTRACT

Chromatin entry sites (CES) are 100- to 1,500-bp elements that recruit male-specific lethal (MSL) complexes to the X chromosome to upregulate expression of X-linked genes in male flies. CES contain one or more ∼20-bp GA-rich sequences called MSL recognition elements (MREs) that are critical for dosage compensation. Recent studies indicate that CES also correspond to boundaries of X-chromosomal topologically associated domains (TADs). Here, we show that an ∼1,000-kDa complex called the late boundary complex (LBC), which is required for the functioning of the Bithorax complex boundary Fab-7, interacts specifically with a special class of CES that contain multiple MREs. Mutations in the MRE sequences of three of these CES that disrupt function in vivo abrogate interactions with the LBC. Moreover, reducing the levels of two LBC components compromises MSL recruitment. Finally, we show that several of the CES that are physically linked to each other in vivo are LBC interactors.

KEYWORDS:

• insulators
• boundaries
• TADs
• dosage compensation
• Drosophila
• male-specific lethal complexes
• chromatin entry sites
• MSL recognition elements
• CLAMP
• GAGA factor

SUPPLEMENTAL MATERIAL

Supplemental material for this article may be found at https://doi.org/10.1128/MCB.00253-17.

ACKNOWLEDGMENTS

We thank Anton Golovnin, Pavel Georgiev, Elissa Lei, Victor Corces, Carl Wu, Mitzi Kuroda, John Lis, and David Gilmour for the gift of antibodies.

This work was supported by a grant from the NIH (R01GM098461-1), an American Cancer Society Research Scholar grant (123682-RSG-13-040-01-DMC), and a Pew Biomedical Scholars program grant awarded to E.L. and to P.S. (GM043432). A.K. and P.S. also acknowledge support from grants to the Gene Biology Institute by the Russian Federation Ministry of Education and Science (RF 14.B25.31.0022) and the Russian Scientific Foundation (16-14-10346).

We have no conflicts of interest to disclose.

Author contributions were as follows: conceptualization, E.G.K., A.K., D.W., P.S., and E.L.; investigations, E.G.K., A.K., D.W., and T.A.; writing of the original draft, P.S. and E.L.; writing, review, and editing, E.G.K., A.K., P.S., and E.L.; funding acquisition, P.S. and E.L.; supervision, P.S. and E.L.