2021 Vol. 12, No. 1

Gene expression labeling and conditional manipulation of gene function are important for elaborate dissection of gene functions. Han et al. developed a high-efficient bidirectional knockin strategy called Bi-FoRe to simultaneously generate paired positive and negative conditional alleles, both tagged with two different fluorescent reporters, through NHEJmediated bacterial backbone-free targeted insertion facilitated by CRISPR/Cas system in zebrafish. Conditional knockout and conditional gene restoration could be achieved through Cre-induced inversion of positive and negative alleles, respectively, coupled with switch of fluorescent reporters, allowing generation of genetic mosaics for lineage tracing. Furthermore, differential fluorescent labeling of positive and negative alleles enables early, simple and efficient discrimination of individual live embryos bearing different genotypes, prior to emergence of morphological phenotypes and in large quantities.

Tsen-Hwang Shaw: Founder of Vertebrate Zoology in China
Fuwen Wei, Dehua Wang
2021, 12(1): 1-3. doi: 10.1007/s13238-020-00780-0
Genetic tracing of HCoV-19 for the re-emerging outbreak of COVID-19 in Beijing, China
Jing Yang, Peihua Niu, Lijuan Chen, Liang Wang, Li Zhao, Baoying Huang, Juncai Ma, Songnian Hu, Linhuan Wu, Guizhen Wu, Chun Huang, Yuhai Bi, Wenjie Tan
2021, 12(1): 4-6. doi: 10.1007/s13238-020-00772-0
Insights into epigenetic patterns in mammalian early embryos
Ruimin Xu, Chong Li, Xiaoyu Liu, Shaorong Gao
2021, 12(1): 7-28. doi: 10.1007/s13238-020-00757-z
Mammalian fertilization begins with the fusion of two specialized gametes, followedby majorepigenetic remodeling leading to the formation of a totipotent embryo. During the development of the pre-implantation embryo, precise reprogramming progress is a prerequisite for avoiding developmental defects or embryonic lethality, but the underlying molecular mechanisms remain elusive. For the past few years, unprecedented breakthroughs have been made in mapping the regulatory network of dynamic epigenomes during mammalian early embryo development, taking advantage of multiple advances and innovations in low-input genome-wide chromatin analysis technologies. The aim of this review is to highlight the most recent progress in understanding the mechanisms of epigenetic remodeling during early embryogenesis in mammals, including DNA methylation, histone modifications, chromatin accessibility and 3D chromatin organization.
Pioneer of prostate cancer: past, present and the future of FOXA1
Mona Teng, Stanley Zhou, Changmeng Cai, Mathieu Lupien, Housheng Hansen He
2021, 12(1): 29-38. doi: 10.1007/s13238-020-00786-8
Prostate cancer is the most commonly diagnosed noncutaneous cancers in North American men. While androgen deprivation has remained as the cornerstone of prostate cancer treatment, resistance ensues leading to lethal disease. Forkhead box A1 (FOXA1) encodes a pioneer factor that induces open chromatin conformation to allow the binding of other transcription factors. Through direct interactions with the Androgen Receptor (AR), FOXA1 helps to shape AR signaling that drives the growth and survival of normal prostate and prostate cancer cells. FOXA1 also possesses an AR-independent role of regulating epithelial-to-mesenchymal transition (EMT). In prostate cancer, mutations converge onto the coding sequence and cis-regulatory elements (CREs) of FOXA1, leading to functional alterations. In addition, FOXA1 activity in prostate cancer can be modulated post-translationally through various mechanisms such as LSD1-mediated protein demethylation. In this review, we describe the latest discoveries related to the function and regulation of FOXA1 in prostate cancer, pointing to their relevance to guide future clinical interventions.
Research article
Bi-FoRe: an efficient bidirectional knockin strategy to generate pairwise conditional alleles with fluorescent indicators
Bingzhou Han, Yage Zhang, Xuetong Bi, Yang Zhou, Christopher J. Krueger, Xinli Hu, Zuoyan Zhu, Xiangjun Tong, Bo Zhang
2021, 12(1): 39-56. doi: 10.1007/s13238-020-00747-1
Gene expression labeling and conditional manipulation of gene function are important for elaborate dissection of gene function. However, contemporary generation of pairwise dual-function knockin alleles to achieve both conditional and geno-tagging effects with a single donor has not been reported. Here we first developed a strategy based on a flipping donor named FoRe to generate conditional knockout alleles coupled with fluorescent allele-labeling through NHEJ-mediated unidirectional targeted insertion in zebrafish facilitated by the CRISPR/ Cas system. We demonstrated the feasibility of this strategy at sox10 and isl1 loci, and successfully achieved Cre-induced conditional knockout of target gene function and simultaneous switch of the fluorescent reporter, allowing generation of genetic mosaics for lineage tracing. We then improved the donor design enabling efficient one-step bidirectional knockin to generate paired positive and negative conditional alleles, both tagged with two different fluorescent reporters. By introducing Cre recombinase, these alleles could be used to achieve both conditional knockout and conditional gene restoration in parallel; furthermore, differential fluorescent labeling of the positive and negative alleles enables simple, early and efficient realtime discrimination of individual live embryos bearing different genotypes prior to the emergence of morphologically visible phenotypes. We named our improved donor as Bi-FoRe and demonstrated its feasibility at the sox10 locus. Furthermore, we eliminated the undesirable bacterial backbone in the donor using minicircle DNA technology. Our system could easily be expanded for other applications or to other organisms, and coupling fluorescent labeling of gene expression and conditional manipulation of gene function will provide unique opportunities to fully reveal the power of emerging single-cell sequencing technologies.
Dynamic cell transition and immune response landscapes of axolotl limb regeneration revealed by single-cell analysis
Hanbo Li, Xiaoyu Wei, Li Zhou, Weiqi Zhang, Chen Wang, Yang Guo, Denghui Li, Jianyang Chen, Tianbin Liu, Yingying Zhang, Shuai Ma, Congyan Wang, Fujian Tan, Jiangshan Xu, Yang Liu, Yue Yuan, Liang Chen, Qiaoran Wang, Jing Qu, Yue Shen, Shanshan Liu, Guangyi Fan, Longqi Liu, Xin Liu, Yong Hou, Guang-Hui Liu, Ying Gu, Xun Xu
2021, 12(1): 57-66. doi: 10.1007/s13238-020-00763-1
Sirt1 regulates testosterone biosynthesis in Leydig cells via modulating autophagy
Muhammad Babar Khawar, Chao Liu, Fengyi Gao, Hui Gao, Wenwen Liu, Tingting Han, Lina Wang, Guoping Li, Hui Jiang, Wei Li
2021, 12(1): 67-75. doi: 10.1007/s13238-020-00771-1
Correction to: Novel and potent inhibitors targeting DHODH are broad-spectrum antivirals against RNA viruses including newly-emerged coronavirus SARS-CoV-2
Rui Xiong, Leike Zhang, Shiliang Li, Yuan Sun, Minyi Ding, Yong Wang, Yongliang Zhao, Yan Wu, Weijuan Shang, Xiaming Jiang, Jiwei Shan, Zihao Shen, Yi Tong, Liuxin Xu, Yu Chen, Yingle Liu, Gang Zou, Dimitri Lavillete, Zhenjiang Zhao, Rui Wang, Lili Zhu, Gengfu Xiao, Ke Lan, Honglin Li, Ke Xu
2021, 12(1): 76-80. doi: 10.1007/s13238-020-00792-w