Stem-loops and circle-loops.
“Once in a while you get shown the light in the strangest of places if you look at it right.” MicroC contact profile for Drosophila wild-type (yw) stage 14 embryos. A) eve and neighboring TADs (TI, TJ, TK TL, TM and TN). The eve TAD is a volcano with a plume that is anchored by nhomie (nh) and homie (h). The plume is generated by crosslinking of sequences in neighboring TADs. At the bottom of the plume, TL sequences are linked to sequences in TM close to eve including ter94. At the next level, sequences in TK are linked to TM. In addition, sequences in LM are linked to sequences in TM located beyond the TER94 gene. At the next level, sequences in TJ are linked to sequences in TM. Note that interactions between sequences in TL and TJ and sequences in TM close to the eve TAD are somewhat less frequent than those farther away from the eve TAD. Sequences in the neighboring TAD also interact with each other as indicated. For example, sequences in TK and TJ interact with each other (J-K) and also with interact with sequences in TI (I-K and I-J). B) The Bithorax Abd-B gene and the parasegment (PS) specific regulatory domains, iab-3, iab-4, iab-5, iab-6, iab-7, iab-8. iab-4 regulates the abd-A gene in PS9. iab-5 regulates Abd-B in PS10, iab-6 regulates Abd-B in PS11, iab-7 regulates Abd-B in PS12 and iab-8 regulates Abd-B in PS13. The domains are separated from each other by the boundary elements Fab-4, Mcp, Fab-6, Fab-7, and Fab-8 as indicated. The AB-I boundary is located upstream of the Abd-B promoter. Each regulatory domain corresponds to a TAD. Though insulated from each other, each TAD interacts with its immediate neighbor. For example, iab-5 interacts with its immediate neighbor iab-4 and iab-6 to give 4-5 and 5-6 respectively. It also interacts with the next-next door neighbor iab-7 (5-7) and even its next-next-next door neighbor iab-8 (5-8). (x: Scarlet Begonias GD: 1974).