{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,13]],"date-time":"2026-05-13T01:57:12Z","timestamp":1778637432526,"version":"3.51.4"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2017,5,4]],"date-time":"2017-05-04T00:00:00Z","timestamp":1493856000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U1435222"],"award-info":[{"award-number":["U1435222"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"Natural Science Foundation of China","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Transcription factor binding sites (TFBSs) are clustered in the human genome, forming the TFBS-clustered regions that regulate gene transcription, which requires dynamic chromatin configurations between promoters and distal regulatory elements. Here, we propose a regulatory model called spatially adjacent TFBS-clustered regions (SATs), in which TFBS-clustered regions are connected by spatial proximity as identified by high-resolution Hi-C data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>TFBS-clustered regions forming SATs appeared less frequently in gene promoters than did isolated TFBS-clustered regions, whereas SATs as a whole appeared more frequently. These observations indicate that multiple distal TFBS-clustered regions combined to form SATs to regulate genes. Further examination confirmed that a substantial portion of genes regulated by SATs were located between the paired TFBS-clustered regions instead of the downstream. We reconstructed the chromosomal conformation of the H1 human embryonic stem cell line using the ShRec3D algorithm and proposed the SAT regulatory model.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx282","type":"journal-article","created":{"date-parts":[[2017,5,3]],"date-time":"2017-05-03T19:11:11Z","timestamp":1493838671000},"page":"2611-2614","source":"Crossref","is-referenced-by-count":2,"title":["Exploring spatially adjacent TFBS-clustered regions with Hi-C data"],"prefix":"10.1093","volume":"33","author":[{"given":"Hebing","family":"Chen","sequence":"first","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuai","family":"Jiang","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhuo","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hao","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yiming","family":"Lu","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaochen","family":"Bo","sequence":"additional","affiliation":[{"name":"Beijing Institute of Radiation Medicine, Beijing, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2017,5,4]]},"reference":[{"key":"2023020206262583500_btx282-B1","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.cell.2005.08.020","article-title":"Core transcriptional regulatory circuitry in human embryonic stem cells","volume":"122","author":"Boyer","year":"2005","journal-title":"Cell"},{"key":"2023020206262583500_btx282-B2","doi-asserted-by":"crossref","first-page":"8465.","DOI":"10.1038\/srep08465","article-title":"An integrative analysis of TFBS-clustered regions reveals new transcriptional regulation models on the accessible chromatin landscape","volume":"5","author":"Chen","year":"2015","journal-title":"Sci. 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