1.Expert Consensus on the Ethical Requirements for Generative AI-Assisted Academic Writing
You-Quan BU ; Yong-Fu CAO ; Zeng-Yi CHANG ; Hong-Yu CHEN ; Xiao-Wei CHEN ; Yuan-Yuan CHEN ; Zhu-Cheng CHEN ; Rui DENG ; Jie DING ; Zhong-Kai FAN ; Guo-Quan GAO ; Xu GAO ; Lan HU ; Xiao-Qing HU ; Hong-Ti JIA ; Ying KONG ; En-Min LI ; Ling LI ; Yu-Hua LI ; Jun-Rong LIU ; Zhi-Qiang LIU ; Ya-Ping LUO ; Xue-Mei LV ; Yan-Xi PEI ; Xiao-Zhong PENG ; Qi-Qun TANG ; You WAN ; Yong WANG ; Ming-Xu WANG ; Xian WANG ; Guang-Kuan XIE ; Jun XIE ; Xiao-Hua YAN ; Mei YIN ; Zhong-Shan YU ; Chun-Yan ZHOU ; Rui-Fang ZHU
Chinese Journal of Biochemistry and Molecular Biology 2025;41(6):826-832
With the rapid development of generative artificial intelligence(GAI)technologies,their widespread application in academic research and writing is continuously expanding the boundaries of sci-entific inquiry.However,this trend has also raised a series of ethical and regulatory challenges,inclu-ding issues related to authorship,content authenticity,citation accuracy,and accountability.In light of the growing involvement of AI in generating academic content,establishing an open,controllable,and trustworthy ethical governance framework has become a key task for safeguarding research integrity and maintaining trust within the academic community.This expert consensus outlines ethical requirements across key stages of AI-assisted academic writing-including topic selection,data management,citation practices,and authorship attribution.It aims to clarify the boundaries and ethical obligations surrounding AI use in academic writing,ensuring that technological tools enhance efficiency without compromising in-tegrity.The goal is to provide guidance and institutional support for building a responsible and sustainable research ecosystem.
2.Study on the Correlation between Palm Temperature,Disease Activity,and Traditional Chinese Medicine Syndrome Types in Patients with Rheumatoid Arthritis
Xiao-shuang HOU ; Li-min PAN ; Chen-jing GAO ; Ya-ping LUO
Progress in Modern Biomedicine 2025;25(9):1517-1524,1548
Objective:To explore the correlation between palm temperature,disease activity,and traditional chinese medicine syndrome types in patients with rheumatoid arthritis(RA).Methods:80 RA patients(RA group)who were admitted to our hospital from April 2022 to June 2024 were selected,they were divided into high group(DAS28 score>5.1 score)and low to moderate group(2.6 score ≤ DAS28 score≤5.1 score)according to the 28 joint disease activity scores(DAS28).70 healthy volunteers who underwent physical examinations during the same period(control group)were selected.The palm temperature,erythrocyte sedimentation rate(ESR),C-reactive protein(CRP),and DAS28 scores between the control group and RA group were compared.The palm temperature,ESR,and CRP levels between low to moderate group and high group were compared.The correlation between palm temperature and disease activity,ESR,and CRP levels in RA patients was analyzed by Pearson correlation.The distribution of traditional chinese medicine syndrome types in RA patients was observed,the palm temperature,ESR,and CRP levels of RA patients with different traditional chinese medicine syndrome types were compared.Results:The palm temperature,ESR,CRP levels,and DAS28 score in the RA group were higher than those in the control group(P<0.05).The palm temperature,ESR,and CRP levels in the high group were higher than those in the low to moderate group(P<0.05).Pearson correlation analysis results showed that,the palm temperature of RA patients was positively correlated with DAS28 score,ESR,and CRP levels(P<0.05).Among 80 RA patients,there were 17 cases(21.25%)of liver and kidney deficiency syndrome,23 cases(29.02%)of cold and dampness obstruction syndrome,14 cases(17.86%)of qi and blood deficiency syndrome,17 cases(21.47%)of damp heat obstruction syndrome,and 9 cases(11.52%)of phlegm and blood stasis obstruction syndrome.The palm temperature,ESR,and CRP levels of patients with Qi and blood deficiency syndrome,liver and kidney deficiency syndrome,and phlegm and blood stasis obstruction syndrome increased in sequence and were higher than those of patients with damp heat obstruction syndrome and cold and dampness obstruction syndrome(P<0.05).There was no statistical difference in palm temperature,ESR,and CRP levels between the groups of damp heat obstruction syndrome and cold and dampness obstruction syndrome(P>0.05).Conclusion:There is a certain correlation between the palm temperature and disease activity and traditional chinese medicine syndrome types of RA patients.Regular observation of palm temperature,ESR,CRP levels,and DAS28 score is helpful for assessing the condition of RA patients.
3.Dual-modal Magnetic Resonance Imaging Contrast Agents Based on Polymetallic Nanoclusters for Targeted Diagnosis of Prostate Cancer
Qing-Dong LI ; Peng WANG ; Jian-Min XIAO ; Wen-Juan GAO ; Zhen-Hong XIA ; Gui-Long ZHANG ; Zheng-Yan WU
Chinese Journal of Analytical Chemistry 2025;53(4):602-611
Fe/Mn/Gd polymetallic nanooxide(FMGN)were prepared by one-step solvent thermal reaction by using Fe(acac)3,Mn(acac)2 and Gd(acac)3 as reaction precursors.Next,hyaluronic acid(HA)was used to modify FMGN to fabricate tumor-targeting T 1-T 2 dual-mode magnetic resonance imaging(MRI)contrast agent(HA-FMGN)for accurate diagnosis of prostate cancer.The structure and morphology of FMGN were observed by transmission electron microscope(TEM).It was found that FMGN exhibited a uniform nanocluster spherical structure when the feeding ratio of iron acetylacetonate,manganese acetylacetonate,and gadolinium acetylacetonate was 3:2:1.X-ray diffraction(XRD)analysis showed that FMGN had a typical inverse spinel structure of Mn doped Fe 3O 4,with Gd existing in the form of amorphous gadolinium oxide.The longitudinal relaxivity(r 1)and transverse relaxivity(r 2)of FMGN were 13.395 and 428.535 L/(mmol·s),respectively,measured by 0.5 T MRI analyzer,which proved that FMGN had excellent T 1-T 2 dual-mode MRI contrast capability.The cytotoxicity and hemolysis test found that HA-FMGN didn't damage red cells and induce toxicity for normal cells,indicating that HA-FMGN had excellent cell biocompatibility.The internalization efficacy of HA-FMGN was observed by CLSM,and the results showed that HA-FMGN possessed excellent prostate tumor-targeting ability.In vivo MRI experiment showed that HA-FMGN significantly enhanced T 1 and T 2 weighted MRI signal to noise ratio(SNR)of prostate tumor,which promoted the accurate diagnosis of orthotopic prostate cancer.
4.Predictive value and related mechanism of serum sialic acid on microvascular invasion in patients with intrahepatic cholangiocarcinoma
Jiao WEI ; Jun JI ; Yueping ZHAN ; Linlin WU ; Xuewen XU ; Chenjun HUANG ; Peicheng FANG ; Xiao XIAO ; Min XU ; Chunfang GAO
Chinese Journal of Laboratory Medicine 2025;48(1):56-64
Objective:To explore the value and related mechanism of preoperative serum sialic acid (SA) on evaluating microvascular invasion (MVI) in patients with intrahepatic cholangiocarcinoma (ICC).Methods:A total of 91 patients who underwent surgical resection and were pathologically diagnosed with ICC from December 2020 to September 2024 at the Oriental Hepatobiliary Surgery Hospital affiliated to the Naval Medical University were included in this retrospective analysis. The patients were divided into non-MVI (41 cases) and MVI groups (50 cases). The general data and laboratory examination indexes were collected and analyzed. Univariate and multivariate logistic regression analyses were performed to identify independent risk factors for predicting MVI. The predictive value of serum indicators for MVI was evaluated by receiver operating characteristic curves. The correlation between MVI and SA was analyzed by point-biserial correlation. ICC cells stably overexpressing β-galactoside α2, 6-sialyltransferase 1 (ST6GAL1) were generated through lentiviral transfection. ST6GAL1 protein expression and mRNA expression were detected by Western blot and quantitative real-time polymerase chain reaction, respectively. Sambucus nigra (SNA) lectin fluorescence staining was used to detect α2, 6-sialylation levels on cells. Cell migration ability was assessed by wound healing and Transwell assays, and cell proliferation was evaluated by colony formation assays.Results:Compared with the non-MVI group, patients in the MVI group exhibited significantly higher levels of fibrinogen, aspartate aminotransferase, gamma-glutamyl transferase, alkaline phosphatase, SA and 5′-nucleotidase (5′-NT) (all P<0.05). Multivariate logistic regression analysis revealed that SA ( OR=1.01,95% CI 1.01-1.02, P=0.023) was the only independent predictor for MVI. The area under curve of SA in predicting MVI was 0.757 (95% CI 0.640-0.870), sensitivity 67.65%, specificity 77.78%. SA was positively correlated with MVI ( r=0.443, P<0.001). ICC cells overexpressing ST6GAL1 were featured with increased mean fluorescence intensity of SNA lectin, and increased level of α2, 6-sialylation on the cell surface (both P<0.05). The number of colonies formed by hypersialylated ICC cells was also increased ( P<0.05), and both the migration rate and the number of migrating cells were significantly higher ( P<0.05). Conclusions:Serum SA is an independent predictor for MVI in ICC patients. Hypersialylation in ICC cells is associated with higher malignancy.
5.Changes in hepatic phase Ⅱ detoxification enzymes and their mechanism in metabolic associated steatohepatitis (MASH) induced by MCD diet in mice
Jiaqin GAO ; Bin ZUO ; Chaoqun PI ; Min XIAO ; Jiaxin WANG ; Wenjing TAO ; Yang HE
Chinese Journal of Hepatology 2025;33(11):1080-1089
Objective:To investigate the changes in hepatic phase II detoxification enzymes and their mechanism in metabolic associated steatohepatitis (MASH) induced by a methionine-choline-deficient (MCD) diet in mice.Methods:Ten C57BL/6J mice were randomly divided into two groups, with five mice in each group, and fed with a control diet (NCD group) and a methionine-choline-deficient diet (MCD group) for four consecutive weeks to establish the MASH model in mice. Mice body weight was recorded weekly. Mice peripheral blood and liver tissue samples were collected after four weeks. The liver histopathological changes were observed by hematoxylin-eosin staining and Sirius red staining in liver tissue. The levels of plasma alanine aminotransferase (ALT), aspartate aminotransferase (AST) and triglycerides were measured by an automatic biochemical analyzer. Triglyceride and total cholesterol were used to evaluate the lipid accumulation condition in the liver of mice with Oil red O staining. Real-time fluorescence quantitative PCR was used to detect the expression of liver inflammatory factors interleukin (IL)-1β and monocyte chemoattractant protein-1 (MCP-1) condition. Transcriptome sequencing and bioinformatics were used to analyze the changes in gene expression profiles in the liver of mice and screen differentially expressed genes. The expression conditions of phase Ⅱ detoxification enzymes glutathione S-transferase mu 4 (GSTM4), dihydronicotinamide riboside:quinone oxidoreductases (NQO-2), sulfotransferase 1β1 (SULT1β1), and uridine diphosphate glucuronosyltransferase 2 family, polypeptide A3(UGT2A3) were verified by real-time fluorescent quantitative PCR. Plasma malondialdehyde content, total antioxidant capacity (T-AOC), plasma and liver glutathione content were determined using commercial kits. The expression of nuclear factor E2-related factor 2 (Nrf2), GSTM4, and UGT1A6 was examined by Western blotting. The independent sample t-test was used for comparison between the groups. Results:The body weight of mice in the MCD group showed a gradual downward trend, while the body weight of mice in the NCD group did not change significantly following four weeks of different dietary feeding. The MCD group mice liver had yellow-white appearance with round edges. The liver/body mass index was significantly lower in the NCD group ( t=3.216, P<0.01). Hematoxylin-eosin staining showed that hepatocytes in the MCD group had an occurrence of fatty degeneration accompanied by inflammatory cell infiltration, with a higher NAFLD activity score (NAS) compared to the NCD group ( t=7.155, P<0.001). Sirius red staining showed that the the liver of the MCD group had mildly increased periportal fibers. Plasma biochemical tests indicated that plasma ALT, AST, and triglyceride levels were significantly higher in the MCD group than those in the NCD group ( t=8.920, P<0.001; t=6.696, P<0.001; t=3.904, P<0.01). Oil red O staining showed that a large number of lipid droplets accumulated in the liver tissue of the MCD group and were more severe than those in the NCD group ( t=7.405, P<0.001). The triglyceride content was significantly higher in the liver of the mice in the MCD group than that in the NCD group ( t=3.559, P<0.01), and the expression of inflammatory factors IL-1β and MCP-1 was significantly increased ( t=2.562 and 2.391, respectively, P<0.05). Transcriptome sequencing analysis showed that the expression profile of genes related to lipid metabolism was changed in the liver tissue of the mice in the MCD group. The expression of multiple phase Ⅱ detoxification enzymes was significantly downregulated. Real-time fluorescence quantitative PCR verification demonstrated that the expression of four phase Ⅱ detoxification enzymes GSTM4, NQO2, SUIL1β1, and UGT2A3 were significantly lower in the liver of the mice in the MCD group than those in the NCD group ( t=2.498, 3.570, 3.768, and 4.166, respectively, P<0.05). The detection kit showed that compared with the NCD group, the malondialdehyde content in the liver of mice in the MCD group increased ( t=3.601, P<0.01), while the plasma total glutathione ( t=11.93, P<0.001) and reduced glutathione levels were significantly reduced ( t=3.635, P<0.01). The total antioxidant capacity of the liver decreased ( t=2.872, P<0.05), and the total glutathione and reduced glutathione levels in the liver were significantly increased ( t=3.175 and 3.064, P<0.05). Western blotting showed that the expression of Nrf2, GSTM4, and UGT1A6 proteins was significantly lower in the MCD group than that in the NCD group ( t=3.385, 2.990, 2.168, P<0.05). Conclusions:The expressions of multiple phase Ⅱ detoxification enzymes and antioxidant capacity are reduced in the liver of MASH mice induced by the MCD diet, and its mechanism is related to the down-regulation of the expression of the upstream regulatory factor Nrf2 protein.
6.Efficacy and Safety of Yangxue Qingnao Pills Combined with Amlodipine in Treatment of Hypertensive Patients with Blood Deficiency and Gan-Yang Hyperactivity: A Multicenter, Randomized Controlled Trial.
Fan WANG ; Hai-Qing GAO ; Zhe LYU ; Xiao-Ming WANG ; Hui HAN ; Yong-Xia WANG ; Feng LU ; Bo DONG ; Jun PU ; Feng LIU ; Xiu-Guang ZU ; Hong-Bin LIU ; Li YANG ; Shao-Ying ZHANG ; Yong-Mei YAN ; Xiao-Li WANG ; Jin-Han CHEN ; Min LIU ; Yun-Mei YANG ; Xiao-Ying LI
Chinese journal of integrative medicine 2025;31(3):195-205
OBJECTIVE:
To evaluate the clinical efficacy and safety of Yangxue Qingnao Pills (YXQNP) combined with amlodipine in treating patients with grade 1 hypertension.
METHODS:
This is a multicenter, randomized, double-blind, and placebo-controlled study. Adult patients with grade 1 hypertension of blood deficiency and Gan (Liver)-yang hyperactivity syndrome were randomly divided into the treatment or the control groups at a 1:1 ratio. The treatment group received YXQNP and amlodipine besylate, while the control group received YXQNP's placebo and amlodipine besylate. The treatment duration lasted for 180 days. Outcomes assessed included changes in blood pressure, Chinese medicine (CM) syndrome scores, symptoms and target organ functions before and after treatment in both groups. Additionally, adverse events, such as nausea, vomiting, rash, itching, and diarrhea, were recorded in both groups.
RESULTS:
A total of 662 subjects were enrolled, of whom 608 (91.8%) completed the trial (306 in the treatment and 302 in the control groups). After 180 days of treatment, the standard deviations and coefficients of variation of systolic and diastolic blood pressure levels were lower in the treatment group compared with the control group. The improvement rates of dizziness, headache, insomnia, and waist soreness were significantly higher in the treatment group compared with the control group (P<0.05). After 30 days of treatment, the overall therapeutic effects on CM clinical syndromes were significantly increased in the treatment group as compared with the control group (P<0.05). After 180 days of treatment, brachial-ankle pulse wave velocity, ankle brachial index and albumin-to-creatinine ratio were improved in both groups, with no statistically significant differences (P>0.05). No serious treatment-related adverse events occurred during the study period.
CONCLUSIONS
Combination therapy of YXQNP with amlodipine significantly improved symptoms such as dizziness and headache, reduced blood pressure variability, and showed a trend toward lowering urinary microalbumin in hypertensive patients. These findings suggest that this regimen has good clinical efficacy and safety. (Registration No. ChiCTR1900022470).
Humans
;
Amlodipine/adverse effects*
;
Drugs, Chinese Herbal/adverse effects*
;
Male
;
Female
;
Hypertension/complications*
;
Middle Aged
;
Treatment Outcome
;
Drug Therapy, Combination
;
Adult
;
Blood Pressure/drug effects*
;
Double-Blind Method
;
Aged
;
Antihypertensive Agents/adverse effects*
7.Shexiang Tongxin Dropping Pill Improves Stable Angina Patients with Phlegm-Heat and Blood-Stasis Syndrome: A Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.
Ying-Qiang ZHAO ; Yong-Fa XING ; Ke-Yong ZOU ; Wei-Dong JIANG ; Ting-Hai DU ; Bo CHEN ; Bao-Ping YANG ; Bai-Ming QU ; Li-Yue WANG ; Gui-Hong GONG ; Yan-Ling SUN ; Li-Qi WANG ; Gao-Feng ZHOU ; Yu-Gang DONG ; Min CHEN ; Xue-Juan ZHANG ; Tian-Lun YANG ; Min-Zhou ZHANG ; Ming-Jun ZHAO ; Yue DENG ; Chang-Jiang XIAO ; Lin WANG ; Bao-He WANG
Chinese journal of integrative medicine 2025;31(8):685-693
OBJECTIVE:
To evaluate the efficacy and safety of Shexiang Tongxin Dropping Pill (STDP) in treating stable angina patients with phlegm-heat and blood-stasis syndrome by exercise duration and metabolic equivalents.
METHODS:
This multicenter, randomized, double-blind, placebo-controlled clinical trial enrolled stable angina patients with phlegm-heat and blood-stasis syndrome from 22 hospitals. They were randomized 1:1 to STDP (35 mg/pill, 6 pills per day) or placebo for 56 days. The primary outcome was the exercise duration and metabolic equivalents (METs) assessed by the standard Bruce exercise treadmill test after 56 days of treatment. The secondary outcomes included the total angina symptom score, Chinese medicine (CM) symptom scores, Seattle Angina Questionnaire (SAQ) scores, changes in ST-T on electrocardiogram and adverse events (AEs).
RESULTS:
This trial enrolled 309 patients, including 155 and 154 in the STDP and placebo groups, respectively. STDP significantly prolonged exercise duration with an increase of 51.0 s, compared to a decrease of 12.0 s with placebo (change rate: -11.1% vs. 3.2%, P<0.01). The increase in METs was significantly greater in the STDP group than in the placebo group (change: -0.4 vs. 0.0, change rate: -5.0% vs. 0.0%, P<0.01). The improvement of total angina symptom scores (25.0% vs. 0.0%), CM symptom scores (38.7% vs. 11.8%), reduction of nitroglycerin consumption (100.0% vs. 11.3%), and all domains of SAQ, were significantly greater with STDP than placebo (all P<0.01). The changes in Q-T intervals at 28 and 56 days from baseline were similar between the two groups (both P>0.05). Twenty-five participants (16.3%) with STDP and 16 (10.5%) with placebo experienced AEs (P=0.131), with no serious AEs observed.
CONCLUSION
STDP could improve exercise tolerance in patients with stable angina and phlegm-heat and blood stasis syndrome, with a favorable safety profile. (Registration No. ChiCTR-IPR-15006020).
Humans
;
Double-Blind Method
;
Drugs, Chinese Herbal/adverse effects*
;
Male
;
Female
;
Middle Aged
;
Angina, Stable/physiopathology*
;
Aged
;
Syndrome
;
Treatment Outcome
;
Placebos
;
Tablets
8.Glucocorticoid Discontinuation in Patients with Rheumatoid Arthritis under Background of Chinese Medicine: Challenges and Potentials Coexist.
Chuan-Hui YAO ; Chi ZHANG ; Meng-Ge SONG ; Cong-Min XIA ; Tian CHANG ; Xie-Li MA ; Wei-Xiang LIU ; Zi-Xia LIU ; Jia-Meng LIU ; Xiao-Po TANG ; Ying LIU ; Jian LIU ; Jiang-Yun PENG ; Dong-Yi HE ; Qing-Chun HUANG ; Ming-Li GAO ; Jian-Ping YU ; Wei LIU ; Jian-Yong ZHANG ; Yue-Lan ZHU ; Xiu-Juan HOU ; Hai-Dong WANG ; Yong-Fei FANG ; Yue WANG ; Yin SU ; Xin-Ping TIAN ; Ai-Ping LYU ; Xun GONG ; Quan JIANG
Chinese journal of integrative medicine 2025;31(7):581-589
OBJECTIVE:
To evaluate the dynamic changes of glucocorticoid (GC) dose and the feasibility of GC discontinuation in rheumatoid arthritis (RA) patients under the background of Chinese medicine (CM).
METHODS:
This multicenter retrospective cohort study included 1,196 RA patients enrolled in the China Rheumatoid Arthritis Registry of Patients with Chinese Medicine (CERTAIN) from September 1, 2019 to December 4, 2023, who initiated GC therapy. Participants were divided into the Western medicine (WM) and integrative medicine (IM, combination of CM and WM) groups based on medication regimen. Follow-up was performed at least every 3 months to assess dynamic changes in GC dose. Changes in GC dose were analyzed by generalized estimator equation, the probability of GC discontinuation was assessed using Kaplan-Meier curve, and predictors of GC discontinuation were analyzed by Cox regression. Patients with <12 months of follow-up were excluded for the sensitivity analysis.
RESULTS:
Among 1,196 patients (85.4% female; median age 56.4 years), 880 (73.6%) received IM. Over a median 12-month follow-up, 34.3% (410 cases) discontinued GC, with significantly higher rates in the IM group (40.8% vs. 16.1% in WM; P<0.05). GC dose declined progressively, with IM patients demonstrating faster reductions (median 3.75 mg vs. 5.00 mg in WM at 12 months; P<0.05). Multivariate Cox analysis identified age <60 years [P<0.001, hazard ratios (HR)=2.142, 95% confidence interval (CI): 1.523-3.012], IM therapy (P=0.001, HR=2.175, 95% CI: 1.369-3.456), baseline GC dose ⩽7.5 mg (P=0.003, HR=1.637, 95% CI: 1.177-2.275), and absence of non-steroidal anti-inflammatory drugs use (P=0.001, HR=2.546, 95% CI: 1.432-4.527) as significant predictors of GC discontinuation. Sensitivity analysis (545 cases) confirmed these findings.
CONCLUSIONS
RA patients receiving CM face difficulties in following guideline-recommended GC discontinuation protocols. IM can promote GC discontinuation and is a promising strategy to reduce GC dependency in RA management. (Trial registration: ClinicalTrials.gov, No. NCT05219214).
Adult
;
Aged
;
Female
;
Humans
;
Male
;
Middle Aged
;
Arthritis, Rheumatoid/drug therapy*
;
Glucocorticoids/therapeutic use*
;
Medicine, Chinese Traditional
;
Retrospective Studies
9.Erratum: Publisher erratum to "Fenofibrate-promoted hepatomegaly and liver regeneration are PPARα-dependent and partially related to the YAP pathway" Acta Pharmaceutica Sinica B 14 (2024) 2992-3008.
Shicheng FAN ; Yue GAO ; Pengfei ZHAO ; Guomin XIE ; Yanying ZHOU ; Xiao YANG ; Xuan LI ; Shuaishuai ZHANG ; Frank J GONZALEZ ; Aijuan QU ; Min HUANG ; Huichang BI
Acta Pharmaceutica Sinica B 2025;15(6):3354-3354
[This corrects the article DOI: 10.1016/j.apsb.2024.03.030.].
10.Genome-wide investigation of transcription factor footprints and dynamics using cFOOT-seq.
Heng WANG ; Ang WU ; Meng-Chen YANG ; Di ZHOU ; Xiyang CHEN ; Zhifei SHI ; Yiqun ZHANG ; Yu-Xin LIU ; Kai CHEN ; Xiaosong WANG ; Xiao-Fang CHENG ; Baodan HE ; Yutao FU ; Lan KANG ; Yujun HOU ; Kun CHEN ; Shan BIAN ; Juan TANG ; Jianhuang XUE ; Chenfei WANG ; Xiaoyu LIU ; Jiejun SHI ; Shaorong GAO ; Jia-Min ZHANG
Protein & Cell 2025;16(11):932-952
Gene regulation relies on the precise binding of transcription factors (TFs) at regulatory elements, but simultaneously detecting hundreds of TFs on chromatin is challenging. We developed cFOOT-seq, a cytosine deaminase-based TF footprinting assay, for high-resolution, quantitative genome-wide assessment of TF binding in both open and closed chromatin regions, even with small cell numbers. By utilizing the dsDNA deaminase SsdAtox, cFOOT-seq converts accessible cytosines to uracil while preserving genomic integrity, making it compatible with techniques like ATAC-seq for sensitive and cost-effective detection of TF occupancy at the single-molecule and single-cell level. Our approach enables the delineation of TF footprints, quantification of occupancy, and examination of chromatin influences on TF binding. Notably, cFOOT-seq, combined with FootTrack analysis, enables de novo prediction of TF binding sites and tracking of TF occupancy dynamics. We demonstrate its application in capturing cell type-specific TFs, analyzing TF dynamics during reprogramming, and revealing TF dependencies on chromatin remodelers. Overall, cFOOT-seq represents a robust approach for investigating the genome-wide dynamics of TF occupancy and elucidating the cis-regulatory architecture underlying gene regulation.
Transcription Factors/genetics*
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Humans
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Chromatin/genetics*
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Animals
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Binding Sites
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Mice
;
DNA Footprinting/methods*

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