RT Journal
A1 Li, Zihe
A1 Xu, Ziyu
A1 Zhu, Lei
A1 Qin, Tao
A1 Ma, Jinrui
A1 Feng, Zhanying
A1 Yue, Huishan
A1 Guan, Qing
A1 Zhou, Botong
A1 Han, Ge
A1 Zhang, Guokun
A1 Li, Chunyi
A1 Jia, Shuaijun
A1 Qiu, Qiang
A1 Hao, Dingjun
A1 Wang, Yong
A1 Wang, Wen
T1 High-quality sika deer omics data and integrative analysis reveal genic and cellular regulation of antler regeneration
JF Genome Research 
JO Genome Research 
YR 2025 
FD January 01 
VO 35 
IS 1 
SP 188 
OP 201 
DO 10.1101/gr.279448.124 
UL http://genome.cshlp.org/content/35/1/188.abstract 
AB The antler is the only organ that can fully regenerate annually in mammals. However, the regulatory pattern and mechanism of gene expression and cell differentiation during this process remain largely unknown. Here, we obtain comprehensive assembly and gene annotation of the sika deer (Cervus nippon) genome. We construct, together with large-scale chromatin accessibility and gene expression data, gene regulatory networks involved in antler regeneration, identifying four transcription factors, MYC, KLF4, NFE2L2, and JDP2, with high regulatory activity across the whole regeneration process. Comparative studies and luciferase reporter assay suggest the MYC expression driven by a cervid-specific regulatory element might be important for antler regenerative ability. We further develop a model called combinatorial TF Oriented Program (cTOP), which integrates single-cell data with bulk regulatory networks and find PRDM1, FOSL1, BACH1, and NFATC1 as potential pivotal factors in antler stem cell activation and osteogenic differentiation. Additionally, we uncover interactions within and between cell programs and pathways during the regeneration process. These findings provide insights into the gene and cell regulatory mechanisms of antler regeneration, particularly in stem cell activation and differentiation.