Journal of Genetics and Genomics

Journal of Genetics and Genomics in 2023: progresses and beyond

Xiu-Fen Song, Xiaoxuan Guo, Jing Zhao, Yutian Zhang, Yuan Qin, Jianru Zuo

2024, 51(1): 1-2. doi: 10.1016/j.jgg.2023.12.008

Abstract (2) PDF (1)

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The evolving views of hematopoiesis: from embryo to adulthood and from in vivo to in vitro

Yifan Zhang, Feng Liu

2024, 51(1): 3-15. doi: 10.1016/j.jgg.2023.09.005

Abstract (75) PDF (8)

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The hematopoietic system composed of hematopoietic stem and progenitor cells (HSPCs) and their differentiated lineages serves as an ideal model to uncover generic principles of cell fate transitions. From gastrulation onwards, there successively emerge primitive hematopoiesis (that produces specialized hematopoietic cells), pro-definitive hematopoiesis (that produces lineage-restricted progenitor cells), and definitive hematopoiesis (that produces multipotent HSPCs). These nascent lineages develop in several transient hematopoietic sites and finally colonize into lifelong hematopoietic sites. The development and maintenance of hematopoietic lineages are orchestrated by cell-intrinsic gene regulatory networks and cell-extrinsic microenvironmental cues. Owing to the progressive methodology (e.g., high-throughput lineage tracing and single-cell functional and omics analyses), our understanding of the developmental origin of hematopoietic lineages and functional properties of certain hematopoietic organs has been updated; meanwhile, new paradigms to characterize rare cell types, cell heterogeneity and its causes, and comprehensive regulatory landscapes have been provided. Here, we review the evolving views of HSPC biology during developmental and postnatal hematopoiesis. Moreover, we discuss recent advances in the in vitro induction and expansion of HSPCs, with a focus on the implications for clinical applications.

Insights into plant salt stress signaling and tolerance

Huapeng Zhou, Haifan Shi, Yongqing Yang, Xixian Feng, Xi Chen, Fei Xiao, Honghui Lin, Yan Guo

2024, 51(1): 16-34. doi: 10.1016/j.jgg.2023.08.007

Abstract (401) PDF (88)

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Soil salinization is an essential environmental stressor, threatening agricultural yield and ecological security worldwide. Saline soils accumulate excessive soluble salts which are detrimental to most plants by limiting plant growth and productivity. It is of great necessity for plants to efficiently deal with the adverse effects caused by salt stress for survival and successful reproduction. Multiple determinants of salt tolerance have been identified in plants, and the cellular and physiological mechanisms of plant salt response and adaption have been intensely characterized. Plants respond to salt stress signals and rapidly initiate signaling pathways to re-establish cellular homeostasis with adjusted growth and cellular metabolism. This review summarizes the advances in salt stress perception, signaling, and response in plants. A better understanding of plant salt resistance will contribute to improving crop performance under saline conditions using multiple engineering approaches. The rhizosphere microbiome-mediated plant salt tolerance as well as chemical priming for enhanced plant salt resistance are also discussed in this review.

Reconstructing cell lineage trees with genomic barcoding: approaches and applications

Zizhang Li, Wenjing Yang, Peng Wu, Yuyan Shan, Xiaoyu Zhang, Feng Chen, Junnan Yang, Jian-Rong Yang

2024, 51(1): 35-47. doi: 10.1016/j.jgg.2023.05.011

Abstract (133) PDF (5)

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In multicellular organisms, developmental history of cell divisions and functional annotation of terminal cells can be organized into a cell lineage tree (CLT). The reconstruction of the CLT has long been a major goal in developmental biology and other related fields. Recent technological advancements, especially those in editable genomic barcodes and single-cell high-throughput sequencing, have sparked a new wave of experimental methods for reconstructing CLTs. Here we review the existing experimental approaches to the reconstruction of CLT, which are broadly categorized as either image-based or DNA barcode-based methods. In addition, we present a summary of the related literature based on the biological insight provided by the obtained CLTs. Moreover, we discuss the challenges that will arise as more and better CLT data become available in the near future. Genomic barcoding-based CLT reconstructions and analyses, due to their wide applicability and high scalability, offer the potential for novel biological discoveries, especially those related to general and systemic properties of the developmental process.

LSM14B coordinates protein component expression in the P-body and controls oocyte maturation

Huiru Zhang, Tao Zhang, Xiang Wan, Chang Chen, Shu Wang, Dongdong Qin, Lufan Li, Luping Yu, Xin Wu

2024, 51(1): 48-60. doi: 10.1016/j.jgg.2023.07.006

Abstract (171) PDF (9)

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The generation of mature and healthy oocytes is the most critical event in the entire female reproductive process, and the mechanisms regulating this process remain to be studied. Here, we demonstrate that Smith-like (LSM) family member 14B (LSM14B) regulates oocyte maturation, and the loss of LSM14B in mouse ovaries leads to abnormal oocyte MII arrest and female infertility. Next, we find the aberrant transcriptional activation, indicated by abnormal non-surrounded nucleolus and surrounded nucleolus oocyte proportions, and abnormal chromosome assembly and segregation in Lsm14b-deficient mouse oocytes. The global transcriptome analysis suggests that many transcripts involved in cytoplasmic processing body (P-body) function are altered in Lsm14b-deficient mouse oocytes. Deletion of Lsm14b results in the expression and/or localization changes of P-body components (such as LSM14A, DCP1A, and 4E-T). Notably, DDX6, a key component of the P-body, is downregulated and accumulates in the nuclei in Lsm14b-deficient mouse oocytes. Taken together, our data suggest that LSM14B links mouse oocyte maturation to female fertility through the regulation of the P-body.

Thyroid-stimulating hormone-thyroid hormone signaling contributes to circadian regulation through repressing clock2/npas2 in zebrafish

Cheng Ji, Yue Ou, Wangjianfei Yu, Jiaxin Lv, Fanmiao Zhang, Huashan Li, Zeyun Gu, Jiayuan Li, Zhaomin Zhong, Han Wang

2024, 51(1): 61-74. doi: 10.1016/j.jgg.2023.05.015

Abstract (296) PDF (30)

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Thyroid-stimulating hormone (TSH) is important for the thyroid gland, development, growth, and metabolism. Defects in TSH production or the thyrotrope cells within the pituitary gland cause congenital hypothyroidism (CH), resulting in growth retardation and neurocognitive impairment. While human TSH is known to display rhythmicity, the molecular mechanisms underlying the circadian regulation of TSH and the effects of TSH-thyroid hormone (TH) signaling on the circadian clock remain elusive. Here we show that TSH, thyroxine (T₄), triiodothyronine (T₃), and tshba display rhythmicity in both larval and adult zebrafish and tshba is regulated directly by the circadian clock via both E'-box and D-box. Zebrafish tshba^-/- mutants manifest congenital hypothyroidism, with the characteristics of low levels of T₄ and T₃ and growth retardation. Loss or overexpression of tshba alters the rhythmicity of locomotor activities and expression of core circadian clock genes and hypothalamic-pituitary-thyroid (HPT) axis-related genes. Furthermore, TSH-TH signaling regulates clock2/npas2 via the thyroid response element (TRE) in its promoter, and transcriptome analysis reveals extensive functions of Tshba in zebrafish. Together, our results demonstrate that zebrafish tshba is a direct target of the circadian clock and in turn plays critical roles in circadian regulation along with other functions.

Microbiome and metabolome dysbiosis analysis in impaired glucose tolerance for the prediction of progression to diabetes mellitus

Boxun Zhang, Xuan Zhang, Zhen Luo, Jixiang Ren, Xiaotong Yu, Haiyan Zhao, Yitian Wang, Wenhui Zhang, Weiwei Tian, Xiuxiu Wei, Qiyou Ding, Haoyu Yang, Zishan Jin, Xiaolin Tong, Jun Wang, Linhua Zhao

2024, 51(1): 75-86. doi: 10.1016/j.jgg.2023.08.005

Abstract (132) PDF (6)

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Gut microbiota and circulating metabolite dysbiosis predate important pathological changes in glucose metabolic disorders; however, comprehensive studies on impaired glucose tolerance (IGT), a diabetes mellitus (DM) precursor, are lacking. Here, we perform metagenomic sequencing and metabolomics on 47 pairs of individuals with IGT and newly diagnosed DM and 46 controls with normal glucose tolerance (NGT); patients with IGT are followed up after 4 years for progression to DM. Analysis of baseline data reveals significant differences in gut microbiota and serum metabolites among the IGT, DM, and NGT groups. In addition, 13 types of gut microbiota and 17 types of circulating metabolites showed significant differences at baseline before IGT progressed to DM, including higher levels of Eggerthella unclassified, Coprobacillus unclassified, Clostridium ramosum, L-valine, L-norleucine, and L-isoleucine, and lower levels of Eubacterium eligens, Bacteroides faecis, Lachnospiraceae bacterium 3_1_46FAA, Alistipes senegalensis, Megaspaera elsdenii, Clostridium perfringens, α-linolenic acid, 10E,12Z-octadecadienoic acid, and dodecanoic acid. A random forest model based on differential intestinal microbiota and circulating metabolites can predict the progression from IGT to DM (AUC = 0.87). These results suggest that microbiome and metabolome dysbiosis occur in individuals with IGT and have important predictive values and potential for intervention in preventing IGT from progressing to DM.

Ancient mitochondrial genome depicts sheep maternal dispersal and migration in Eastern Asia

Liu Yang, Xing Zhang, Yaning Hu, Piao Zhu, Hua Li, Zhenyu Peng, Hai Xiang, Xinying Zhou, Xingbo Zhao

2024, 51(1): 87-95. doi: 10.1016/j.jgg.2023.06.002

Abstract (227) PDF (16)

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Sheep have been one of the most important groups of animals since ancient times. However, the knowledge of their migration routes and genetic relationships is still poorly understood. To investigate sheep maternal migration histories alongside Eurasian communications routes, in this study, we obtain mitochondrial genomes (mitogenomes) from 17 sheep remains in 6 Chinese sites and 1 Uzbekistan site dated 4429–3100 years before present (BP). By obtaining the mitogenomes from the sheep (4429–3556 BP) found in the Tongtian Cave site in Xinjiang, Altai region of northwest China, our results support the emergence of haplogroup C sheep in Xinjiang as early as 4429–3556 BP. The combined phylogenetic analyses with extant ancient and modern sheep mitogenomes suggest that the Uzbekistan-Altai region may have been a migration hub for early sheep in eastern Asia. At least two migration events have taken place for sheep crossing Eurasia to China, one passing by Uzbekistan and Northwest China to the middle and lower reaches of the Yellow River at approximately 4000 BP and another following the Altai region to middle Inner Mongolia from 4429 BP to 2500 BP. Overall, this study provides further evidence for early sheep utilization and migration patterns in Eastern Asia.

The nodule-specific transcriptional repressor Top Hub 4 regulates nodule structure and nitrogen fixation capacity in soybean

Kui Ge, Qi Lv, Shengcai Chen, Zhenhao Guo, Yaqi Peng, Yimian Chen, Shiyong Sun, Xuelu Wang

2024, 51(1): 96-99. doi: 10.1016/j.jgg.2023.07.005

Abstract (235) PDF (25)

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Multi-omics analyses of G6PD deficiency variants in Chinese population

He Ji, Jiahuan Chen, Peide Huang, Zhimin Feng, Weining Hu, Mengyao Dai, Xiaohui Sun, Xiao Jin, Guangquan Chen, Guang Ning, Lin Li, Weiqing Wang, Yanan Cao

2024, 51(1): 100-104. doi: 10.1016/j.jgg.2023.08.008

Abstract (133) PDF (8)

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A systematic evaluation of computational methods for predicting translated non-canonical ORFs from ribosome profiling data

Tianyu Lei, Yue Chang, Chao Yao, Hong Zhang

2024, 51(1): 105-108. doi: 10.1016/j.jgg.2023.08.010

Abstract (161) PDF (15)

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Corrigendum to ‘The power of “controllers”: Transposon-mediated duplicated genes evolve towards neofunctionalization’ [Journal of Genetics and Genomics (2023) 50, 462–472]

Huijing Ma, Mengxia Wang, Yong E. Zhang, Shengjun Tan

2024, 51(1): 109-109. doi: 10.1016/j.jgg.2023.12.002

Abstract (0) PDF (0)

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2024 Vol. 51, No. 1