Journal of Genetics and Genomics

Molecular mechanisms underlying cTAGE5/MEA6-mediated cargo transport and biological functions

Tiantian Ma, Feng Zhang, Yaqing Wang, Zhiheng Xu

2022, 49(6): 519-522. doi: 10.1016/j.jgg.2022.04.001

Abstract (167) PDF (140)

Abstract:
Coat protein complex II (COPII)-coated vesicles are responsible for transporting the cargoes from the endoplasmic reticulum (ER) to different destinations. cTAGE5/MEA6 is essential for the development and function of different organs. It regulates the assembly of COPII carrier and cargo trafficking through direct or indirect interaction with COPII components. cTAGE5/MEA6 mainly coordinates with another scaffold protein, TANGO1, to play essential roles in the trafficking and secretion of both large and small cargoes in multiple organs. In this viewpoint, we would like to discuss the molecular mechanisms underlying cTAGE5/MEA6-mediated cargo transport and biological functions.

Single-cell transcriptomic profiling of the hypothalamic median eminence during aging

Zhen-Hua Chen, Si Li, Mingrui Xu, Candace C. Liu, Hongying Ye, Ben Wang, Qing-Feng Wu

2022, 49(6): 523-536. doi: 10.1016/j.jgg.2022.01.001

Abstract (518) PDF (202)

Abstract:
Aging is a slow and progressive natural process that compromises the normal functions of cells, tissues, organs, and systems. The aging of the hypothalamic median eminence (ME), a structural gate linking neural and endocrine systems, may impair hormone release, energy homeostasis, and central sensing of circulating molecules, leading to systemic and reproductive aging. However, the molecular and cellular features of ME aging remain largely unknown. Here, we describe the transcriptional landscape of young and middle-aged mouse ME at single-cell resolution, revealing the common and cell type-specific transcriptional changes with age. The transcriptional changes in cell-intrinsic programs, cell-cell crosstalk, and cell-extrinsic factors highlight five molecular features of ME aging and also implicate several potentially druggable targets at cellular, signaling, and molecular levels. Importantly, our results suggest that vascular and leptomeningeal cells may lead the asynchronized aging process among diverse cell types and drive local inflammation and cellular senescence via a unique secretome. Together, our study uncovers how intrinsic and extrinsic features of each cell type in the hypothalamic ME are changed by the aging process, which will facilitate our understanding of brain aging and provide clues for efficient anti-aging intervention at the middle-aged stage.

Ancient DNA reveals the maternal genetic history of East Asian domestic pigs

Ming Zhang, Yichen Liu, Zhipeng Li, Peng Lü, Jacob D. Gardner, Maolin Ye, Jihuai Wang, Miaomiao Yang, Jing Shao, Weilin Wang, Qingyan Dai, Peng Cao, Ruowei Yang, Feng Liu, Xiaotian Feng, Lizhao Zhang, Enwei Li, Yunzheng Shi, Zehui Chen, Shilun Zhu, Weiwei Zhai, Tao Deng, Ziyuan Duan, E. Andrew Bennett, Songmei Hu, Qiaomei Fu

2022, 49(6): 537-546. doi: 10.1016/j.jgg.2021.11.014

Abstract (375) PDF (172)

Abstract:
Zoo-archaeological and genetic evidence suggest that pigs were domesticated independently in Central China and Eastern Anatolia along with the development of agricultural communities and civilizations. However, the genetic history of domestic pigs, especially in China, has not been fully explored. In this study, we generate 42 complete mitochondrial DNA sequences from ~7500- to 2750-year-old individuals from the Yellow River basin. Our results show that the maternal genetic continuity of East Asian domestic pigs dates back to at least the Early to Middle Neolithic. In contrast, the Near Eastern ancestry in European domestic pigs saw a near-complete genomic replacement by the European wild boar. The majority of East Asian domestic pigs share close haplotypes, and the most recent common ancestor of most branches dates back to less than 20,000 years before present, inferred using new substitution rates of whole mitogenomes or combined protein-coding regions. Two major population expansion events of East Asian domestic pigs coincided with changes in climate, widespread adoption of introduced crops, and the development of agrarian societies. These findings add to our understanding of the maternal genetic composition and help to complete the picture of domestic pig evolutionary history in East Asia.

Genome sequence and transcriptome of Sorbus pohuashanensis provide insights into population evolution and leaf sunburn response

Dongxue Zhao, Yan Zhang, Yizeng Lu, Liqiang Fan, Zhibin Zhang, Jian Zheng, Mao Chai

2022, 49(6): 547-558. doi: 10.1016/j.jgg.2021.12.009

Abstract (373) PDF (155)

Abstract:
Sorbus pohuashanensis (Hance) Hedl. is a potential horticulture and medicinal plant, but its genomic and genetic backgrounds remain unknown. Here, we sequence and assemble the S.pohuashanensis reference genome using PacBio long reads. Based on the new reference genome, we resequence a core collection of 22 Sorbus spp. samples, which are divided into 2 groups (G1 and G2) based on phylogenetic and PCA analyses. These phylogenetic clusters are highly consistent with their classification based on leaf shape. Natural hybridization between the G1 and G2 groups is evidenced by a sample (R21) with a highly heterozygous genotype. Nucleotide diversity (π) analysis shows that G1 has a higher diversity than G2 and that G2 originated from G1. During the evolution process, the gene families involved in photosynthesis pathways expanded and the gene families involved in energy consumption contracted. RNA-seq data suggests that flavonoid biosynthesis and heat-shock protein (HSP)-heat-shock factor (HSF) pathways play important roles in protection against sunburn. This study provides new insights into the evolution of Sorbus spp. genomes. In addition, the genomic resources, and the identified genetic variations, especially those related to stress resistance, will help future efforts to produce and breed Sorbus spp.

Zebrafish Foxc1a controls ventricular chamber maturation by directly regulating wwtr1 and nkx2.5 expression

Luqingqing He, Qinxin Zhang, Dongya Jiang, Yunfeng Zhang, Yuxuan Wei, Yuxi Yang, Nan Li, Shuang Wang, Yunyun Yue, Qingshun Zhao

2022, 49(6): 559-568. doi: 10.1016/j.jgg.2021.12.002

Abstract (403) PDF (141)

Abstract:
Chamber maturation is a significant process in cardiac development. Disorders of this crucial process lead to a range of congenital heart defects. Foxc1a is a critical transcription factor reported to regulate the specification of cardiac progenitor cells. However, little is known about the role of Foxc1a in modulating chamber maturation. Previously, we reported that foxc1a-null zebrafish embryos exhibit disrupted heart structures and functions. In this study, we observe that ventricle structure and cardiomyocyte proliferation are abolished during chamber maturation in foxc1a-null zebrafish embryos. To observe the endogenous localization of Foxc1a in the hearts of living embryos, we insert eyfp at the foxc1a genomic locus using TALEN. Analysis of the knockin zebrafish show that foxc1a is widely expressed in ventricular cardiomyocytes during chamber development. Cardiac RNA sequencing analysis reveals the downregulated expression of the Hippo signaling effector wwtr1. Dual-luciferase and chromatin immunoprecipitation assays reveal that Foxc1a can bind directly to three sites in the wwtr1 promoter region. Furthermore, wwtr1 mRNA overexpression is sufficient to reverse the ventricle defects during chamber maturation. Conditional overexpression of nkx2.5 also partially rescues the ventricular defects during chamber development. These findings demonstrate that wwtr1 and nkx2.5 are direct targets of Foxc1a during ventricular chamber maturation.

The gut microbiome and microbial metabolites in acute myocardial infarction

Chenglin Liu, Zhonghan Sun, Shalaimaiti Shali, Zhendong Mei, Shufu Chang, Hanjun Mo, Lili Xu, Yanni Pu, Huihui Guan, Guo-Chong Chen, Qibin Qi, Zhexue Quan, Ji Qi, Kang Yao, Yuxiang Dai, Yan Zheng, Junbo Ge

2022, 49(6): 569-578. doi: 10.1016/j.jgg.2021.12.007

Abstract (234) PDF (105)

Abstract:
Emerging evidence has highlighted the role of gut microbiome in human health. However, the integrative role of gut microbiome and microbial metabolites in acute myocardial infarction (AMI) remains unclear. The current study profiles the microbial community through 16S rRNA gene sequencing and shotgun metagenomic sequencing and measures fecal short-chain fatty acids and circulating choline pathway metabolites among 117 new-onset AMI cases and 78 controls. Significant microbial alternations are observed in AMI patients compared with controls (P=0.001). The abundances of nine species (e.g., Streptococcus salivarius and Klebsiella pneumoniae) are positively associated, and one species (Roseburia hominis) is inversely associated with AMI status and severity. A gut microbial score at disease onset is associated with the risk of major adverse cardiovascular events in 3.2 years (hazard ratio[95% CI]:2.01[1.04-4.24]) in AMI patients. The molar proportions of fecal acetate and butyrate are higher, and the circulating levels of choline and carnitine are lower in AMI patients than in controls. In addition, disease classifiers show that AMI cases and controls have a more distinct pattern in taxonomical composition than in pathways or metabolites. Our findings suggest that microbial composition and functional potentials are associated with AMI status and severity.

Interruption of Klf5 acetylation in basal progenitor cells promotes luminal commitment by activating Notch signaling

Baotong Zhang, Siyuan Xia, Mingcheng Liu, Xiawei Li, Shimin Shuai, Wei Tao, Yixiang Li, Jianping Jenny Ni, Wei Zhou, Lan Liao, Jianming Xu, Jin-Tang Dong

2022, 49(6): 579-582. doi: 10.1016/j.jgg.2021.11.013

Abstract (303) PDF (131)

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Allele-specific expression and splicing provide insight into the phenotypic differences between thin- and fat-tailed sheep breeds

Fei Wang, Junjie Shao, Sangang He, Yingwei Guo, Xiangyu Pan, Yu Wang, Hojjat Asadollahpour Nanaei, Lei Chen, Ran Li, Han Xu, Zhirui Yang, Mingjun Liu, Yu Jiang

2022, 49(6): 583-586. doi: 10.1016/j.jgg.2021.12.008

Abstract (385) PDF (163)

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Effects of interaction between single nucleotide polymorphisms and psychosocial factors on the response to antidepressant treatment in patients with major depressive disorder

Di Luan, Dongfang You, Yaqian Wu, Fangfang Wu, Zhi Xu, Ling Li, Jiao Jiao, Aini Zhang, Haixia Feng, Yan Kong, Yang Zhao, Zhijun Zhang

2022, 49(6): 587-589. doi: 10.1016/j.jgg.2021.11.012

Abstract (266) PDF (16)

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Variants in the Wnt co-receptor LRP6 are associated with familial exudative vitreoretinopathy

Shujin Li, Mu Yang, Yunqi He, Xiaoyan Jiang, Rulian Zhao, Wenjing Liu, Lulin Huang, Yi Shi, Xiao Li, Kuanxiang Sun, Yeming Yang, Periasamy Sundaresan, Peiquan Zhao, Zhenglin Yang, Xianjun Zhu

2022, 49(6): 590-594. doi: 10.1016/j.jgg.2021.11.010

Abstract (292) PDF (160)

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A simple and precise method (Y2H-in-frame-seq) improves yeast two-hybrid screening with cDNA libraries

Yinghui Gu, Guannan Li, Ping Wang, Yan Guo, Jingrui Li

2022, 49(6): 595-598. doi: 10.1016/j.jgg.2021.11.008

Abstract (7578) PDF (142)

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2022 Vol. 49, No. 6