{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T09:01:56Z","timestamp":1785402116203,"version":"3.56.0"},"reference-count":43,"publisher":"MDPI AG","issue":"13","license":[{"start":{"date-parts":[[2026,6,23]],"date-time":"2026-06-23T00:00:00Z","timestamp":1782172800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62361047"],"award-info":[{"award-number":["62361047"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32160216"],"award-info":[{"award-number":["32160216"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["62361047"],"award-info":[{"award-number":["62361047"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"award":["32160216"],"award-info":[{"award-number":["32160216"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>In hepatocellular carcinoma (HepG2), aberrant histone modifications are closely linked to long non-coding RNA (lncRNA) expression. However, existing computational models lack physical interpretability at specific promoter coordinates. To address this, we developed a position-specific statistical scoring model based on adjacent and next-adjacent nucleotide frequencies. We trained two independent, position-specific matrices representing increased and decreased modification states across 600 bp promoter windows centered on the true signal summits. Finally, ten-fold cross-validation revealed that significant energy differences between sequences with increased and decreased histone signals enable excellent classification performance. These results indicted a strong correlation between the total energy of local DNA structures and histone modification signal.<\/jats:p>","DOI":"10.3390\/ijms27135653","type":"journal-article","created":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T03:09:17Z","timestamp":1782270557000},"page":"5653","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["An Energy Model Based on Molecular Structure for Predicting Histone Modification Levels at lncRNA Promoter Regions in HepG2 Cells"],"prefix":"10.3390","volume":"27","author":[{"given":"Menglan","family":"Li","sequence":"first","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1142-1209","authenticated-orcid":false,"given":"Yingli","family":"Chen","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"},{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qianzhong","family":"Li","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"},{"name":"State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengyu","family":"Du","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanyuan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Inner Mongolia Autonomous Region Key Laboratory of Biophysics and Bioinformatics, School of Physical Science and Technology, Inner Mongolia University, Hohhot 010021, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,23]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Wolinska, E., and Skrzypczak, M. 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