{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T17:06:45Z","timestamp":1784308005983,"version":"3.55.0"},"posted":{"date-parts":[[2026,5,31]]},"group-title":"Genetics","reference-count":73,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,5,31]],"date-time":"2026-05-31T00:00:00Z","timestamp":1780185600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["5R35GM126975"],"award-info":[{"award-number":["5R35GM126975"]}]},{"name":"NIH","award":["1R01GM137062"],"award-info":[{"award-number":["1R01GM137062"]}]},{"name":"NIH","award":["DP2AI171161"],"award-info":[{"award-number":["DP2AI171161"]}]},{"DOI":"10.13039\/100031445","name":"New Jersey Commission on Cancer Research","doi-asserted-by":"crossref","award":["COCR23PDF011"],"award-info":[{"award-number":["COCR23PDF011"]}],"id":[{"id":"10.13039\/100031445","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Princeton Bioengineering Biocondensates Program"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>\n                  The head-to-tail pairing of the\n                  <jats:italic>nhomie<\/jats:italic>\n                  and\n                  <jats:italic>homie<\/jats:italic>\n                  boundaries is responsible for the formation of a stem-loop TAD (topologically associated domain) that encompasses the\n                  <jats:italic>even-skipped<\/jats:italic>\n                  (\n                  <jats:italic>eve<\/jats:italic>\n                  ) gene and its regulatory elements. TAD boundaries like\n                  <jats:italic>homie<\/jats:italic>\n                  and\n                  <jats:italic>nhomie<\/jats:italic>\n                  have partner preferences and one mechanism thought to be important in linking compatible boundaries is shared binding sites for the same architectural protein. Both\n                  <jats:italic>eve<\/jats:italic>\n                  boundaries have a single binding site for the polydactyl zinc finger protein Su(Hw). Here we have investigated the role of the shared Su(Hw) sites in the long-distance regulation of a dual reporter by the\n                  <jats:italic>eve<\/jats:italic>\n                  enhancers. Consistent with this mechanism, we find that when the transgene\n                  <jats:italic>nhomie<\/jats:italic>\n                  or\n                  <jats:italic>homie<\/jats:italic>\n                  boundary has a mutation in the Su(Hw) binding site, reporter activation by the\n                  <jats:italic>eve<\/jats:italic>\n                  enhancers is severely compromised. Using MicroC we show the mutating the single Su(Hw) substantially weakens the ability of the\n                  <jats:italic>nhomie<\/jats:italic>\n                  and\n                  <jats:italic>homie<\/jats:italic>\n                  boundaries in the transgene to physically pair with the two endogenous\n                  <jats:italic>eve<\/jats:italic>\n                  boundaries. Su(Hw) binding sites are not, however, sufficient as the\n                  <jats:italic>gypsy<\/jats:italic>\n                  su(Hw) insulator is unable to support long-distance regulation. In a less demanding transvection assay mutations in the\n                  <jats:italic>nhomie<\/jats:italic>\n                  and\n                  <jats:italic>homie<\/jats:italic>\n                  Su(hw) site have only a modest effect on regulatory interactions. The\n                  <jats:italic>eve<\/jats:italic>\n                  boundaries can mediate transvection with the\n                  <jats:italic>gypsy<\/jats:italic>\n                  insulator; however. they are not compatible with the dCTCF\n                  <jats:italic>Fab-8<\/jats:italic>\n                  boundary even in the transvection assay. Finally, we show that the regulatory and physical interactions of the\n                  <jats:italic>nhomie<\/jats:italic>\n                  boundary in the transgene and the two endogenous\n                  <jats:italic>eve<\/jats:italic>\n                  boundaries are incompatible with the popular cohesin-loop extrusion model.\n                <\/jats:p>","DOI":"10.64898\/2026.05.28.727987","type":"posted-content","created":{"date-parts":[[2026,5,31]],"date-time":"2026-05-31T21:05:12Z","timestamp":1780261512000},"source":"Crossref","is-referenced-by-count":0,"title":["Shared binding sites for the chromosomal architectural protein Su(Hw) mediate physical interactions between\n                  <i>Drosophila<\/i>\n                  TAD boundaries"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7047-5445","authenticated-orcid":false,"given":"Wenfan","family":"Ke","sequence":"first","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 08540"},{"name":"Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miki","family":"Fujioka","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brendan","family":"Wang","sequence":"additional","affiliation":[{"name":"Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany","family":"Park","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amina","family":"Kurbidaeva","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6589-981X","authenticated-orcid":false,"given":"Yuri","family":"Pritykin","sequence":"additional","affiliation":[{"name":"Lewis Sigler Institute of Integrative Genomics, Princeton University, Princeton, NJ 08540"},{"name":"Department of Computer Science, Princeton University, Princeton, NJ 08540"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James B","family":"Jaynes","sequence":"additional","affiliation":[{"name":"Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, PA, 19107"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Schedl","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Princeton University, Princeton, NJ 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