RT Journal
A1 Wang, Xiangxiu
A1 Wang, Wen
A1 Wang, Yiman
A1 Chen, Jia
A1 Liu, Guifen
A1 Zhang, Yong
T1 Antibody-free profiling of transcription factor occupancy during early embryogenesis by FitCUT&RUN
JF Genome Research 
JO Genome Research 
YR 2022 
FD February 01 
VO 32 
IS 2 
SP 378 
OP 388 
DO 10.1101/gr.275837.121 
UL http://genome.cshlp.org/content/32/2/378.abstract 
AB Key transcription factors (TFs) play critical roles in zygotic genome activation (ZGA) during early embryogenesis, whereas genome-wide occupancies of only a few factors have been profiled during ZGA due to the limitation of cell numbers or the lack of high-quality antibodies. Here, we present FitCUT&RUN, a modified CUT&RUN method, in which an Fc fragment of immunoglobulin G is used for tagging, to profile TF occupancy in an antibody-free manner and demonstrate its reliability and robustness using as few as 5000 K562 cells. We applied FitCUT&RUN to zebrafish undergoing embryogenesis to generate reliable occupancy profiles of three known activators of zebrafish ZGA: Nanog, Pou5f3, and Sox19b. By profiling the time-series occupancy of Nanog during zebrafish ZGA, we observed a clear trend toward a gradual increase in Nanog occupancy and found that Nanog occupancy prior to the major phase of ZGA is important for the activation of some early transcribed genes.