Target Specificities of Estrogen Receptor-Related Receptors: Analysis of Binding Sequences and Identification of Rb1-Inducible Coiled-Coil 1 (Rb1cc1) as a Target Gene

Abstract

Estrogen receptor-related receptors (ERRs) are orphan members of the nuclear receptor superfamily. A single AGGTCA sequence element preceded by three conserved nucleotides has been identified as a specific recognition motif of ERRs. Here we performed systematic analyses of target sequences on all three ERR subtypes, alpha, beta and gamma. In electrophoretic gel-mobility shift assay and transcriptional reporter assays, they exhibited similar patterns of recognition specificities, showing extremely broad ranges of target sequences. We searched a mouse promoter database for a gene carrying possible ERR-binding sequences. The Rb-1 inducible coiled-coil 1 (Rb1cc1) gene was found to contain two putative ERR binding elements, named response element (RE)-1 and RE-2, in the promoter region. In gene reporter assays, RE-2, but not RE-1, functioned as an effective cis-regulatory element for transactivation by ERRalpha in the presence of a coactivator, peroxisome proliferator-activated receptor gamma coactivator-1alpha. Mutational analyses suggested that RE-2 is recognized by ERRalpha partly as a monovalent element, but also as a direct repeat motif separated by four spacer nucleotides. In vivo binding of ERRalpha to the Rb1cc1 promoter region was confirmed by the chromatin immunoprecipitation assay. Thus, Rb1cc1 is a target gene of ERRalpha, driven by a novel type of recognition sequence.

Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

“…However, when the first monomer had negative orientation (k and l), then motifs were spaced by either 2 or 6 bp. Akter et al 41 tested 12 paired motifs (direct and inverted) with the competitive EMSA and found the increased binding of estrogen-related receptors to direct repeats with 0, 2, and 4 bp spacing and to inverted repeats with 0 and 3 bp spacing. Thus, the in vivo ChIP-seq data confirmed in vitro EMSA data by Akter et al , although the motifs (h), (k), and (l) found in the ChIP-seq data (Fig.…”

Importance of the Sequence-Directed DNA Shape for Specific Binding Site Recognition by the Estrogen-Related Receptor

“…To gain insight into the unexpected behavior of ERRα DBD on the embERRE/IR3sequence, we explored more sequences belonging to either the IR3-type of REs or to the natural extended ERREs. We found diversity in the migration pattern inside each of the two different types, as shown for tff1 ERE-IR3 (16, 42) and the rb1cc1 IR3 (43) as examples of IR3-binding sites, or tra ERRE and tff1 ERRE as examples of ERRE natural DNA REs (Figures 1C,E). While the tff1 ERE-IR3 and the tra ERRE result into a single low migration band, the rb1cc1 IR3 and the tff1 ERRE give a more complex migration pattern with mainly two bands, a lower migration band and a delayed migration band similar to what is observed in the case of ERRα DBD-embERRE/IR3.…”