Meta-loops are large chromosomal loops that connect specific neuronal genes with non-coding DNA elements, enabling megabase-range regulation of gene transcription in fly neurons. To reveal how highly specific meta-loop interactions form, we developed an unbiased approach to identify proteins from Drosophila adult head extracts that associate with four meta-loop anchors and a control. This approach revealed both known and new factors involved in meta-loop formation, including Lola-I which we functionally validate as a meta-loop anchor binding protein required a small subset of meta-loops.