Micro-C in Solanum Uncovers Conserved Genome Folding and Epigenetically Defined Loops with Bifunctional Enhancer-Silencer Activity

Long-range chromatin loops are key to genome organization, yet their landscape in plants remains poorly defined. Here, we generated a 1.45-billion-contact Micro-C map of cultivated tomato (Solanum lycopersicum) that resolves ~4,600 loops, seven times more than previous Hi-C data. Loop anchors segregate into two epigenetic classes: 1) promoter-centered loops with anchors enriched for RNA polymerase II, accessible chromatin, active histone modifications, and 2) loops with anchors enriched for Polycomb-linked or heterochromatic signatures. Both classes strongly repel young Gypsy retrotransposons, while retaining older copies directly at the anchor, revealing an age-selective filter. Unlike mammalian genome organization, loop anchors rarely overlap insulation boundaries, indicating that loop and domain formation are largely independent. Cross-species Micro-C in two wild tomatoes shows conserved anchor positions despite rapid sequence turnover. Integrating cross-species transcriptomics further reveals a dual regulatory role for promoter-anchored loops: they can enhance expression when paired with activating chromatin or poise/repress it via H3K27me3-rich, distal anchors. These data provide a high-resolution framework for interpreting plant gene regulation in 3D and a resource to probe how looping shapes trait variation and can be leveraged in breeding.