Tissue- and Expression Level–Specific Chromatin Looping at Maize b1 Epialleles

This work examines the involvement of chromatin looping in the transcriptional regulation of two epialleles of the maize ( Zea mays ) b1 gene, B-I and B9 . These two epialleles are tissue-specifically regulated and are involved in paramutation. B-I and B9 are expressed at high and low levels, respectively. A hepta-repeat ∼100 kb upstream of the transcription start site (TSS) is required for both paramutation and high b1 expression. Using chromosome conformation capture, we show that the hepta-repeat physically interacts with the TSS region in a tissue- and expression level–specific manner. Multiple repeats are required to stabilize this interaction. High b1 expression is mediated by a multiloop structure; besides the hepta-repeat, other sequence regions physically interact with the TSS as well, and these interactions are epiallele- and expression level–specific. Formaldehyde-assisted isolation of regulatory elements uncovered multiple interacting regions as potentially regulatory.