RT Journal
A1 Chen, Yujie
A1 Hou, Yiran
A1 Zeng, Qinglin
A1 Wang, Irene
A1 Shang, Meiru
A1 Shin, Kwangdeok
A1 Hemauer, Christopher
A1 Xing, Xiaoyun
A1 Kang, Junsu
A1 Zhao, Guoyan
A1 Wang, Ting
T1 Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
JF Genome Research 
JO Genome Research 
YR 2025 
FD January 01 
VO 35 
IS 1 
SP 202 
OP 218 
DO 10.1101/gr.279372.124 
UL http://genome.cshlp.org/content/35/1/202.abstract 
AB Following amputation, zebrafish regenerate their injured caudal fin through lineage-restricted reprogramming. Although previous studies have charted various genetic and epigenetic dimensions of this process, the intricate gene regulatory programs shared by, or unique to, different regenerating cell types remain underinvestigated. Here, we mapped the regulatory landscape of fin regeneration by applying paired snRNA-seq and snATAC-seq on uninjured and regenerating fins. This map delineates the regulatory dynamics of predominant cell populations at multiple stages of regeneration. We observe a marked increase in the accessibility of chromatin regions associated with regenerative and developmental processes at 1 dpa, followed by a gradual closure across major cell types at later stages. This pattern is distinct from that of transcriptomic dynamics, which is characterized by several waves of gene upregulation and downregulation. We identified and in vivo validated cell-type-specific and position-specific regeneration-responsive enhancers and constructed regulatory networks by cell type and stage. Our single-cell resolution transcriptomic and chromatin accessibility map across regenerative stages provides new insights into regeneration regulatory mechanisms and serves as a valuable resource for the community.