Fig. 4: Transcription factor dynamics driving expression during the cell cycle.
From: Cell cycle gene regulation dynamics revealed by RNA velocity and deep-learning
A Motif activities for families of transcription factors across the cell cycle in mESCs, ductal cells, and human fibroblasts. The red boxes identify two waves of transcription in the G1 phases for more differentiated cell lines. B The comparison of motif activities with the respective mRNA levels around the cell cycle for Yy1 and E2f1 in mESCs, Ybx1 for ductal cells, and FOXM1 for human fibroblasts. These comparisons allow clarifying whether the regulation is happening more at the transcriptional level or the protein level. The Pearson’s correlation coefficients between spliced reads and motif activities are reported (r values) as well as the exact tests of no-correlation (p values). C Dunn et al.58 identified two sets of TFs at the core of the pluripotency maintenance network in mESCs, the first responsible for the integration of the signals (input) and the latter for taking a fate decision (computation). The heatmap shows their activities around the cell cycle of mESCs for the pluripotency factors for which the binding motifs are known. The ‘input’ motifs are active in late G2/M while the ‘computation’ factors in the early G1.
