DNA–Protein Binding is Dominated by Short Anchoring Elements
Abstract Unveiling the complexities of gene expression regulation, the study explores the intricate DNA‐binding mechanisms of transcription factors (TFs). By employing the KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, “anchoring eleme...
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| Format: | Article |
| Language: | English |
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Wiley
2025-05-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202414823 |
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| author | Hong Chen Yongping Xu Hao Ge Xiao‐Dong Su |
| author_facet | Hong Chen Yongping Xu Hao Ge Xiao‐Dong Su |
| author_sort | Hong Chen |
| collection | DOAJ |
| description | Abstract Unveiling the complexities of gene expression regulation, the study explores the intricate DNA‐binding mechanisms of transcription factors (TFs). By employing the KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, “anchoring elements” (AEs), 3–4 base pair sequences, are identified in Arabidopsis WRKY and human PU.1 TFs crucial for binding affinity. Building on the BEESEM method, the study introduces the AEEscape algorithm, which advances the AE concept by creating a precise model of the position‐specific k‐mer binding energy landscape. This method allows for the direct identification of the dominant role of AEs from experimental data. Moreover, when integrated with genomic data, it reveals an energetic funnel around transcription factor binding sites (TFBSs), which is directly correlated with the density of AEs (AED). The findings not only offer a fresh perspective on TF‐TFBS interactions but also highlight the critical role of AED in gene regulation. These insights can pave the way for innovative strategies to manipulate gene expression. |
| format | Article |
| id | doaj-art-a256d19b72fa4a7e8b646d1d7c6b6a90 |
| institution | OA Journals |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-a256d19b72fa4a7e8b646d1d7c6b6a902025-08-20T01:52:42ZengWileyAdvanced Science2198-38442025-05-011219n/an/a10.1002/advs.202414823DNA–Protein Binding is Dominated by Short Anchoring ElementsHong Chen0Yongping Xu1Hao Ge2Xiao‐Dong Su3State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC) Peking University Beijing 100871 ChinaState Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC) Peking University Beijing 100871 ChinaBeijing International Center for Mathematical Research (BICMR) and Biomedical Pioneering Innovation Center (BIOPIC) Peking University Beijing 100871 ChinaState Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, and Biomedical Pioneering Innovation Center (BIOPIC) Peking University Beijing 100871 ChinaAbstract Unveiling the complexities of gene expression regulation, the study explores the intricate DNA‐binding mechanisms of transcription factors (TFs). By employing the KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, “anchoring elements” (AEs), 3–4 base pair sequences, are identified in Arabidopsis WRKY and human PU.1 TFs crucial for binding affinity. Building on the BEESEM method, the study introduces the AEEscape algorithm, which advances the AE concept by creating a precise model of the position‐specific k‐mer binding energy landscape. This method allows for the direct identification of the dominant role of AEs from experimental data. Moreover, when integrated with genomic data, it reveals an energetic funnel around transcription factor binding sites (TFBSs), which is directly correlated with the density of AEs (AED). The findings not only offer a fresh perspective on TF‐TFBS interactions but also highlight the critical role of AED in gene regulation. These insights can pave the way for innovative strategies to manipulate gene expression.https://doi.org/10.1002/advs.202414823anchoring element (AE)anchoring element density (AED)transcription factor and DNA interactiontranscription factor binding site (TFBS) |
| spellingShingle | Hong Chen Yongping Xu Hao Ge Xiao‐Dong Su DNA–Protein Binding is Dominated by Short Anchoring Elements Advanced Science anchoring element (AE) anchoring element density (AED) transcription factor and DNA interaction transcription factor binding site (TFBS) |
| title | DNA–Protein Binding is Dominated by Short Anchoring Elements |
| title_full | DNA–Protein Binding is Dominated by Short Anchoring Elements |
| title_fullStr | DNA–Protein Binding is Dominated by Short Anchoring Elements |
| title_full_unstemmed | DNA–Protein Binding is Dominated by Short Anchoring Elements |
| title_short | DNA–Protein Binding is Dominated by Short Anchoring Elements |
| title_sort | dna protein binding is dominated by short anchoring elements |
| topic | anchoring element (AE) anchoring element density (AED) transcription factor and DNA interaction transcription factor binding site (TFBS) |
| url | https://doi.org/10.1002/advs.202414823 |
| work_keys_str_mv | AT hongchen dnaproteinbindingisdominatedbyshortanchoringelements AT yongpingxu dnaproteinbindingisdominatedbyshortanchoringelements AT haoge dnaproteinbindingisdominatedbyshortanchoringelements AT xiaodongsu dnaproteinbindingisdominatedbyshortanchoringelements |