TY  - JOUR
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
Y1  - 2025/01/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 188 
EP  - 201 
DO  - 10.1101/gr.279448.124 
VL  - 35 
IS  - 1 
UR  - http://genome.cshlp.org/content/35/1/188.abstract 
N2  - 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. 
ER  -