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* ; Humans ; Chromatin/genetics* ; Animals ; Binding Sites ; Mice ; DNA Footprinting/methods*

Objective: To compare the immunomodulatory capability to allergic asthma between orally taken Lactococcus lactis and Lactobacillus Lactobacillus plantarum in dust mite-sensitized mice. Methods: C57BL/6 mice were divided into four groups;Group N,M,L and P.Mice in M,Land P groups were sensitized with 2 % mite extract on day 0,7and 14 and challenged with 4% mite extract on day 21,22,23 and 24.Meanwhile we fed Lactococcus lactis and Lactobacillus plantarum to mice in L and P group respectively from each day of sensitization on as well as from the first day of challenge on,continuing for five days.Mice in N and M group were treated with saline as control.Histopathologic examination in the lung tissues of the mice was performed at day 3 after the last challenge.Cell count and classification,and Th1/Th2 cytokine levels in BALF were measured simultaneously.Isolated splenocytes from the mice were subjected to the detection of cell proliferation by BrdU incorporation in response to the mite extract.Using ELISA,the levels of Th1/Th2 cytokines in the supernatant of mite-stimulated splenocytes were measured. Results: Pulmonary allergic inflammation with eosinophilic infiltration as well as increased levels of IL-4 and IL-5 in BALF were observed in mice sensitized/challenged with mite extract(Group M).Pulmonary inflammation was decreased significantly in group L concomitant with down regulated levels of IL-4 and IL-5,total cell count and the percentage of eosinophils in BALF(P

Objective:To investigate the effect of lactic acid bacteria on P38 signaling in immune response to dust time in mite-sensitized mice.Methods:40 C57BL/6 mice in Group M,P and C,except for N(saline control),were sensitized and challenged with mite extract.Mice in C and P were simultaneously fed to Lactococcus lactis and Lactobacillus respectively.Total cell count and classification in BALF were done and IL-4 level detected by ELISA.Western blot were performed for detection of P38 signaling from mice's spleen cells stimulated with mite extract.Results:IL-4 level,total cell count and the percentage of eosinophils in BALF were significantly lower in Group C(P