Wenjia Shi, Yao Ma, Peilin Hu, Mi Pang, Xiaona Huang, Yiting Dang, Yuxin Xie, Danni Wu
{"title":"基于希尔功能的转录反应模型:非特异性结合和 RNAP 相互作用的影响","authors":"Wenjia Shi, Yao Ma, Peilin Hu, Mi Pang, Xiaona Huang, Yiting Dang, Yuxin Xie, Danni Wu","doi":"arxiv-2403.01702","DOIUrl":null,"url":null,"abstract":"Hill function is one of the widely used gene transcription regulation models.\nIts attribute of fitting may result in a lack of an underlying physical\npicture, yet the fitting parameters can provide information about biochemical\nreactions, such as the number of transcription factors (TFs) and the binding\nenergy between regulatory elements. However, it remains unclear when and how\nmuch biochemical information can Hill function provide in addition to fitting.\nHere, started from the interactions between TFs and RNA polymerase during\ntranscription regulation and both of their association-dissociation reactions\nat specific/nonspecific sites on DNA, the regulatory effect of TFs was deduced\nas fold change. We found that, for weak promoter, fold change can degrade into\nthe regulatory factor (Freg) which is closely correlated with Hill function. By\ndirectly comparing and fitting with Hill function, the fitting parameters and\ncorresponding biochemical reaction parameters in Freg were analyzed and\ndiscussed, where the single TF and multiple TFs that with cooperativity and\nbasic logic effects were considered. We concluded the strength of promoter and\ninteractions between TFs determine whether Hill function can reflect the\ncorresponding biochemical information. Our findings highlight the role of Hill\nfunction in modeling/fitting for transcriptional regulation, which also\nbenefits the preparation of synthetic regulatory elements.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"24 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Hill Function-based Model of Transcriptional Response: Impact of Nonspecific Binding and RNAP Interactions\",\"authors\":\"Wenjia Shi, Yao Ma, Peilin Hu, Mi Pang, Xiaona Huang, Yiting Dang, Yuxin Xie, Danni Wu\",\"doi\":\"arxiv-2403.01702\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Hill function is one of the widely used gene transcription regulation models.\\nIts attribute of fitting may result in a lack of an underlying physical\\npicture, yet the fitting parameters can provide information about biochemical\\nreactions, such as the number of transcription factors (TFs) and the binding\\nenergy between regulatory elements. However, it remains unclear when and how\\nmuch biochemical information can Hill function provide in addition to fitting.\\nHere, started from the interactions between TFs and RNA polymerase during\\ntranscription regulation and both of their association-dissociation reactions\\nat specific/nonspecific sites on DNA, the regulatory effect of TFs was deduced\\nas fold change. We found that, for weak promoter, fold change can degrade into\\nthe regulatory factor (Freg) which is closely correlated with Hill function. By\\ndirectly comparing and fitting with Hill function, the fitting parameters and\\ncorresponding biochemical reaction parameters in Freg were analyzed and\\ndiscussed, where the single TF and multiple TFs that with cooperativity and\\nbasic logic effects were considered. We concluded the strength of promoter and\\ninteractions between TFs determine whether Hill function can reflect the\\ncorresponding biochemical information. Our findings highlight the role of Hill\\nfunction in modeling/fitting for transcriptional regulation, which also\\nbenefits the preparation of synthetic regulatory elements.\",\"PeriodicalId\":501325,\"journal\":{\"name\":\"arXiv - QuanBio - Molecular Networks\",\"volume\":\"24 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-03-04\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"arXiv - QuanBio - Molecular Networks\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/arxiv-2403.01702\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Molecular Networks","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2403.01702","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
Hill Function-based Model of Transcriptional Response: Impact of Nonspecific Binding and RNAP Interactions
Hill function is one of the widely used gene transcription regulation models.
Its attribute of fitting may result in a lack of an underlying physical
picture, yet the fitting parameters can provide information about biochemical
reactions, such as the number of transcription factors (TFs) and the binding
energy between regulatory elements. However, it remains unclear when and how
much biochemical information can Hill function provide in addition to fitting.
Here, started from the interactions between TFs and RNA polymerase during
transcription regulation and both of their association-dissociation reactions
at specific/nonspecific sites on DNA, the regulatory effect of TFs was deduced
as fold change. We found that, for weak promoter, fold change can degrade into
the regulatory factor (Freg) which is closely correlated with Hill function. By
directly comparing and fitting with Hill function, the fitting parameters and
corresponding biochemical reaction parameters in Freg were analyzed and
discussed, where the single TF and multiple TFs that with cooperativity and
basic logic effects were considered. We concluded the strength of promoter and
interactions between TFs determine whether Hill function can reflect the
corresponding biochemical information. Our findings highlight the role of Hill
function in modeling/fitting for transcriptional regulation, which also
benefits the preparation of synthetic regulatory elements.