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Fig. 3 | Genome Biology

Fig. 3

From: CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos

Fig. 3

Non-synchronized de novo transcription in developing zebrafish embryos. a A schematic of time-lapse imaging of eppk1 and 100537515 gene expressions in different cell cycles of developing embryos. About 70 image stacks were recorded every 2 min during cell cycle 12–13 from 3.3 to 6 hpf, or every 5 min during cell cycle 14 from 4 to 10 hpf, and cell cycle 15 from 9.5 to 13 hpf. The image stacks were 0.4 μm z-step distance and then were analyzed by maximum intensity projection. b Representative images of dPspCas13b-EGFP tracking de novo transcription of eppk1 with Cy3-geppk1s, recorded every 2 min from 4 to 6 hpf during EVL of cell cycle 13, see also Additional file 7: Movie 3. Green arrowheads indicate puncta 1, referred to as the first detected initial transcription site in each cell throughout the study, and magenta arrowheads indicate puncta 2, the later initial transcription site in each cell throughout the study. c Non-synchronized de novo transcription of inter-alleles at eppk1 in developing zebrafish embryos. Normalized intensity at the transcription sites recorded over time in b. Puncta 1 and 2 are indicative of the two transcription sites. Initial expression of puncta 1 and puncta 2 are asynchrony. Transcriptional burst shows switching a promoter from activated state to inactivated state. d Non-synchronized de novo transcription of EVL cells. Statistics of de novo transcription events of two genes eppk1 (left) and 100537515 (right) in individual cell cycles (cell cycles 13 and 14, respectively), in which their de novo transcription is first detected. Three types of de novo transcription events are recorded throughout one cell cycle: (1) only one allele is transcribed (blue); (2) two alleles are transcribed at the same time (black); (3) two alleles are transcribed sequentially (orange). See also Additional file 1: Fig. S8f, g for original data. See also Fig. 3e for detail. e Time difference in initial transcription between individual inter-alleles of eppk1 and 100537515 during de novo expression in cell cycles 13 and 14, respectively. See also Additional file 1: Fig. S8f, g for original data. Data are represented as mean ± SD

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