Journal of Genetics and Genomics

Molecular epigenetic mechanisms for the memory of temperature stresses in plants

Zhaoxu Gao, Yue Zhou, Yuehui He

2022, 49(11): 991-1001. doi: 10.1016/j.jgg.2022.07.004

Abstract (596) PDF (87)

Abstract:
The sessile plants encounter various stresses; some are prolonged, whereas some others are recurrent. Temperature is crucial for plant growth and development, and plants often encounter adverse high temperature fluctuations (heat stresses) as well as prolonged cold exposure such as seasonal temperature drops in winter when grown in temperate regions. Many plants can remember past temperature stresses to get adapted to adverse local temperature changes to ensure survival and/or reproductive success. Here, we summarize chromatin-based mechanisms underlying acquired thermotolerance or thermomemory in plants and review recent progresses on molecular epigenetic understanding of ‘remembering of prolonged cold in winter’ or vernalization, a process critical for various over-wintering plants to acquire competence to flower in the coming spring. In addition, perspectives on future study in temperature stress memories of economically-important crops are discussed.

Single-cell transcriptomics reveals cell type diversity of human prostate

Yang Chen, Peng Zhang, Jinling Liao, Jiwen Cheng, Qin Zhang, Tianyu Li, Haiying Zhang, Yonghua Jiang, Fangxing Zhang, Yanyu Zeng, Linjian Mo, Haibiao Yan, Deyun Liu, Qinyun Zhang, Chunlin Zou, Gong-Hong Wei, Zengnan Mo

2022, 49(11): 1002-1015. doi: 10.1016/j.jgg.2022.03.009

Abstract (506) PDF (57)

Abstract:
Extensive studies have been performed to describe the phenotypic changes occurring during malignant transformation of the prostate. However, the cell types and associated changes that contribute to the development of prostate diseases and cancer remain elusive, largely due to the heterogeneous composition of prostatic tissues. Here, we conduct a comprehensive evaluation of four human prostate tissues by single-cell RNA sequencing (scRNA-seq) to analyze their cellular compositions. We identify 18 clusters of cell types, each with distinct gene expression profiles and unique features; of these, one cluster of epithelial cells (Ep) is found to be associated with immune function. In addition, we characterize a special cluster of fibroblasts and aberrant signaling changes associated with prostate cancer (PCa). Moreover, we provide insights into the epithelial changes that occur during the cellular senescence and aging. These results expand our understanding of the unique functional associations between the diverse prostatic cell types and the contributions of specific cell clusters to the malignant transformation of prostate tissues and PCa development.

Single-cell RNA-seq analysis of testicular somatic cell development in pigs

Lingkai Zhang, Ming Guo, Zidong Liu, Ruifang Liu, Yi Zheng, Taiyong Yu, Yinghua Lv, Hongzhao Lu, Wenxian Zeng, Tao Zhang, Chuanying Pan

2022, 49(11): 1016-1028. doi: 10.1016/j.jgg.2022.03.014

Abstract (302) PDF (40)

Abstract:
Spermatogenesis is the process by which diploid male germ cells propagate and differentiate into haploid flagellated spermatozoa. This highly complicated process is dependent on testicular somatic cells maturation. While the role of these somatic cells in spermatogenesis is relatively well established, knowledge about their development and maturation, particularly at the molecular level, is limited. In this study, we profiled the testicular single-cell transcriptomes of Guanzhong black pigs at the age of 7, 30, 60, 90, and 150 days. Five types of Sertoli cells, five types of Leydig cells, and four types of peritubular myoid cells were identified. Histological analysis revealed the changes in proliferation levels and marker gene expressions, and the prion-like protein gene (PRND) was identified as a novel marker for Sertoli cells. Additionally, integrated analyses of porcine and human datasets revealed similarities between human and pig testicular somatic cells. Overall, the data obtained in this study contribute to the understanding of testicular development in pigs as a model species.

The ZFP541-KCTD19 complex is essential for pachytene progression by activating meiotic genes during mouse spermatogenesis

Yushan Li, Ranran Meng, Shanze Li, Bowen Gu, Xiaotong Xu, Haihang Zhang, Xinshui Tan, Tianyu Shao, Jiawen Wang, Dan Xu, Fengchao Wang

2022, 49(11): 1029-1041. doi: 10.1016/j.jgg.2022.03.005

Abstract (355) PDF (29)

Abstract:
Meiosis is essential for fertility in sexually reproducing species and this sophisticated process has been extensively studied. Notwithstanding these efforts, key factors involved in meiosis have not been fully characterized. In this study, we investigate the regulatory roles of zinc finger protein 541 (ZFP541) and its interacting protein potassium channel tetramerization domain containing 19 (KCTD19) in spermatogenesis. ZFP541 is expressed from leptotene to the round spermatid stage, while the expression of KCTD19 is initiated in pachytene. Depletion of Zfp541 or Kctd19 leads to infertility in male mice and delays progression from early to mid/late pachynema. In addition, Zfp541^-/- spermatocytes show abnormal programmed DNA double-strand break repair, impaired crossover formation and resolution, and asynapsis of the XY chromosomes. ZFP541 interacts with KCTD19, histone deacetylase 1/2 (HDAC1/2), and deoxynucleotidyl transferase terminal-interacting protein 1 (DNTTIP1). Moreover, ZFP541 binds to and activates the expression of genes involved in meiosis and post-meiosis including Kctd19; in turn, KCTD19 promotes the transcriptional activation activity of ZFP541. Taken together, our studies reveal that the ZFP541/KCTD19 signaling complex, acting as a key transcription regulator, plays an indispensable role in male fertility by regulating pachytene progression.

Fecal microbiota transplantation from young donor mice improves ovarian function in aged mice

Li Xu, Qiankun Zhang, Xiaowei Dou, Yipeng Wang, Jianwei Wang, Yong Zhou, Xingyin Liu, Jing Li

2022, 49(11): 1042-1052. doi: 10.1016/j.jgg.2022.05.006

Abstract (407) PDF (23)

Abstract:
Advanced maternal age is characterized by declines in the quantity and quality of oocytes in the ovaries, and the aging process is accompanied by changes in gut microbiota composition. However, little is known about the relationship between gut microbiota and ovarian aging. By using fecal microbiota transplantation (FMT) to transplant material from young (5-week-old) into aged (42-week-old) mice, we find that the composition of gut microbiota in FMT-treated mice presents a “younger-like phenotype” and an increase of commensal bacteria, such as Bifidobacterium and Ruminococcaceae. Moreover, the FMT-treated mice show increased anti-inflammatory cytokine IL-4 and decreased pro-inflammatory cytokine IFN-γ. Fertility tests for assessing ovarian function reveal that the first litter size of female FMT-treated mice is significantly higher than that of the non-FMT group. Morphology analysis demonstrates a dramatic decrease in follicle atresia and apoptosis as well as an increase in cellular proliferation in the ovaries of the FMT-treated mice. Our results also show that FMT improves the immune microenvironment in aged ovaries, with decreased macrophages and macrophage-derived multinucleated giant cells (MNGCs). These results suggest that FMT from young donors could be a good choice for delaying ovarian aging.

Genetic structure and domestication footprints of the tusk, coat color, and ear morphology in East Chinese pigs

Sumei Zheng, Pan Xu, Zhongping Wu, Hui Zhang, Desen Li, Shaojuan Liu, Bingbing Liu, Jun Ren, Hao Chen, Min Huang

2022, 49(11): 1053-1063. doi: 10.1016/j.jgg.2022.03.011

Abstract (229) PDF (32)

Abstract:
The domestication and artificial selection of wild boars have led to dramatic morphological and behavioral changes, especially in East Chinese (ECN) pigs. Here, we provide insights into the population structure and current genetic diversity of representative ECN pig breeds. We identify a 500-kb region containing six tooth development-relevant genes with almost completely different haplotypes between ECN pigs and Chinese wild boars or European domestic pigs. Notably, the c.195A>G missense mutation in exon 2 of AMBN may cause alterations in its protein structure associated with tusk degradation in ECN pigs. In addition, ESR1 may play an important role in the reproductive performance of ECN pigs. A major haplotype of the large lop ear-related MSRB3 gene and eight alleles in the deafness-related GRM7 gene may affect ear morphology and hearing in ECN pigs. Interestingly, we find that the two-end black (TEB) coat color in Jinhua pigs is most likely caused by EDNRB with genetic mechanisms different from other Chinese TEB pigs. This study identifies key loci that may be artificially selected in Chinese native pigs related to the tusk, coat color, and ear morphology, thus providing new insights into the genetic mechanisms of domesticated pigs.

Deciphering the regulatory code of histone modifications in plants

Zhaohong Li, Dongwei Li, Ye Li, Xiaoping Guo, Ruolin Yang

2022, 49(11): 1064-1067. doi: 10.1016/j.jgg.2022.07.003

Abstract (480) PDF (62)

Abstract:

Whole-genome sequence-based association study for immune cells in an eight-breed pig heterogeneous population

Qing Zhang, Jing Li, Yifeng Zhang, Huanfa Gong, Zhimin Zhou, Wenwu Xu, Zhongzi Wu, Yingchun Sun, Tao Jiang, Ziqi Ling, Shijun Xiao, Lusheng Huang, Bin Yang

2022, 49(11): 1068-1071. doi: 10.1016/j.jgg.2021.09.003

Abstract (416) PDF (55)

Abstract:

Viral receptor profiles of masked palm civet revealed by single-cell transcriptomics

Peiwen Ding, Haoyu Wang, Jiacheng Zhu, Fuyu An, Jinqian Xu, Xiangning Ding, Lihua Luo, Weiying Wu, Qiuyu Qin, Yanan Wei, Wandong Zhao, Zhiyuan Lv, Haimeng Li, Yixin Zhu, Meiling Li, Wensheng Zhang, Yanan Zhang, Zhihua Ou, Huan Liu, Yan Hua

2022, 49(11): 1072-1075. doi: 10.1016/j.jgg.2022.04.009

Abstract (274) PDF (23)

Abstract:

Ancient DNA traces a Chinese 5400-year-old cat specimen as leopard cat (Prionailurus bengalensis)

Shilun Zhu, Zehui Chen, Songmei Hu, Weilin Wang, Peng Cao, Feng Liu, Qingyan Dai, Xiaotian Feng, Ruowei Yang, Wanjing Ping, Qiaomei Fu

2022, 49(11): 1076-1079. doi: 10.1016/j.jgg.2022.07.005

Abstract (609) PDF (55)

Abstract:

2022 Vol. 49, No. 11