Journal of Genetics and Genomics

Pei Zhang, Mingqiu Dai

2022, 49(12): 1081-1092. doi: 10.1016/j.jgg.2022.05.004

Abstract (488) PDF (61)

Abstract:
Circular RNAs (circRNAs) are covalently closed single-stranded RNA molecules, which are widespread in eukaryotic cells. As regulatory molecules, circRNAs have various functions, such as regulating gene expression, binding miRNAs or proteins, and being translated into proteins, which are important for cell proliferation and cell differentiation, individual growth and development, as well as many other biological processes. However, compared with that in animal models, studies of circRNAs in plants lags behind and, particularly, the regulatory mechanisms of biogenesis and molecular functions of plant circRNAs remain elusive. Recent studies have shown that circRNAs are wide spread in plants with tissue- or development-specific expression patterns and are responsive to a variety of environmental stresses. In this review, we summarize these advances, focusing on the regulatory mechanisms of biogenesis, molecular and biological functions of circRNAs, and the methods for investigating circRNAs. We also discuss the challenges and the prospects of plant circRNA studies.

Generation of Plvap-CreER and Car4-CreER for genetic targeting of distinct lung capillary populations

Zhenqian Zhang, Bin Zhou

2022, 49(12): 1093-1100. doi: 10.1016/j.jgg.2022.08.001

Abstract (287) PDF (36)

Abstract:
It has been reported recently that there are two distinct subpopulations of capillary endothelial cells in the mammalian lungs: gCap (general capillary) and aCap (aerocyte). They are identified by two unique markers, respectively: plasmalemmal vesicle-associated protein (PLVAP) and carbonic anhydrase IV (CAR4). Here, we report two novel knock-in mouse lines Plvap-CreER and Car4-CreER, which genetically target gCap and aCap, respectively. Induced by tamoxifen, the Plvap-CreER and Car4-CreER alleles mediate specific and efficient Cre-loxP recombinations in PLVAP⁺ gCap and CAR4⁺ aCap, respectively, in the lungs. These two mouse lines are useful genetic tools to investigate cell fates and functions of PLVAP⁺ and CAR4⁺ cells in lung homeostasis, injury and repair.

Cdx1b protects intestinal cell fate by repressing signaling networks for liver specification

Qingxia Jin, Yuqi Gao, Shimin Shuai, Yayue Chen, Kaiyuan Wang, Jun Chen, Jinrong Peng, Ce Gao

2022, 49(12): 1101-1113. doi: 10.1016/j.jgg.2022.11.006

Abstract (284) PDF (30)

Abstract:
In mammals, the expression of the homeobox family member Cdx2/CDX2 is restricted within the intestine. Conditional ablation of the mouse Cdx2 in the endodermal cells causes a homeotic transformation of the intestine towards the esophagus or gastric fate. In this report, we show that null mutants of zebrafish cdx1b, encoding the counterpart of mammalian CDX2, could survive more than 10 days post fertilization, a stage when the zebrafish digestive system has been well developed. Through RNA sequencing (RNA-seq) and single-cell sequencing (scRNA-seq) of the dissected intestine from the mutant embryos, we demonstrate that the loss-of-function of the zebrafish cdx1b yields hepatocyte-like intestinal cells, a phenotype never observed in the mouse model. Further RNA-seq data analysis, and genetic double mutants and signaling inhibitor studies reveal that Cdx1b functions to guard the intestinal fate by repressing, directly or indirectly, a range of transcriptional factors and signaling pathways for liver specification. Finally, we demonstrate that heat shock-induced overexpression of cdx1b in a transgenic fish abolishes the liver formation. Therefore, we demonstrate that Cdx1b is a key repressor of hepatic fate during the intestine specification in zebrafish.

Long-term correction of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration

Xi Chen, Xuran Niu, Yang Liu, Rui Zheng, Lei Yang, Jian Lu, Shuming Yin, Yu Wei, Jiahao Pan, Ahmed Sayed, Xueyun Ma, Meizhen Liu, Fengxiang Jing, Mingyao Liu, Jiazhi Hu, Liren Wang, Dali Li

2022, 49(12): 1114-1126. doi: 10.1016/j.jgg.2022.06.001

Abstract (554) PDF (48)

Abstract:
CRISPR/Cas9-mediated site-specific insertion of exogenous genes holds potential for clinical applications. However, it is still infeasible because homologous recombination (HR) is inefficient, especially for non-dividing cells. To overcome the challenge, we report that a homology-independent targeted integration (HITI) strategy is used for permanent integration of high-specificity-activity Factor IX variant (F9 Padua, R338L) at the albumin (Alb) locus in a novel hemophilia B (HB) rat model. The knock-in efficiency reaches 3.66%, as determined by droplet digital PCR (ddPCR). The clotting time is reduced to a normal level four weeks after treatment, and the circulating factor IX (FIX) level is gradually increased up to 52% of the normal level over nine months even after partial hepatectomy, demonstrating the amelioration of hemophilia. Through primer-extension-mediated sequencing (PEM-seq), no significant off-target effect is detected. This study not only provides a novel model for HB but also identifies a promising therapeutic approach for rare inherited diseases.

Systematic annotation of conservation states provides insights into regulatory regions in rice

Xinkai Zhou, Tao Zhu, Wen Fang, Ranran Yu, Zhaohui He, Dijun Chen

2022, 49(12): 1127-1137. doi: 10.1016/j.jgg.2022.04.003

Abstract (290) PDF (19)

Abstract:
Plant genomes contain a large fraction of noncoding sequences. The discovery and annotation of conserved noncoding sequences (CNSs) in plants is an ongoing challenge. Here we report the application of comparative genomics to systematically identify CNSs in 50 well-annotated Gramineae genomes using rice (Oryza sativa) as the reference. We conduct multiple-way whole-genome alignments to the rice genome. The rice genome is annotated as 20 conservation states (CSs) at single-nucleotide resolution using a multivariate hidden Markov model (ConsHMM) based on the multiple-genome alignments. Different states show distinct enrichments for various genomic features, and the conservation scores of CSs are highly correlated with the level of associated chromatin accessibility. We find that at least 33.5% of the rice genome is highly under selection, with more than 70% of the sequence lying outside of coding regions. A catalog of 855,366 regulatory CNSs is generated, and they significantly overlapped with putative active regulatory elements such as promoters, enhancers, and transcription factor binding sites. Collectively, our study provides a resource for elucidating functional noncoding regions of the rice genome and an evolutionary aspect of regulatory sequences in higher plants.

The CXCR4-CXCL12 axis promotes T cell reconstitution via efficient hematopoietic immigration

Fangying Zhao, Yafang Lu, Zhifan Li, Jiangyong He, Nianfei Cui, Lingfei Luo, Li Li

2022, 49(12): 1138-1150. doi: 10.1016/j.jgg.2022.04.005

Abstract (225) PDF (18)

Abstract:
T cells play a critical role in immunity to protect against pathogens and malignant cells. T cell immunodeficiency is detrimental, especially when T cell perturbation occurs during severe infection, irradiation, chemotherapy, and age-related thymic atrophy. Therefore, strategies that enhance T cell reconstitution provide considerable benefit and warrant intensive investigation. Here, we report the construction of a T cell ablation model in Tg(coro1a:DenNTR) zebrafish via metronidazole administration. The nascent T cells are mainly derived from the hematopoietic cells migrated from the kidney, the functional homolog of bone marrow and the complete recovery time is 6.5 days post-treatment. The cxcr4b gene is upregulated in the responsive hematopoietic cells. Functional interference of CXCR4 via both genetic and chemical manipulations does not greatly affect T lymphopoiesis, but delays T cell regeneration by disrupting hematopoietic migration. In contrast, cxcr4b accelerates the replenishment of hematopoietic cells in the thymus. Consistently, Cxcl12b, a ligand of Cxcr4, is increased in the thymic epithelial cells of the injured animals. Decreased or increased expression of Cxcl12b results in compromised or accelerated T cell recovery, respectively, similar to those observed with Cxcr4b. Taken together, our study reveals a role of CXCR4-CXCL12 signaling in promoting T cell recovery and provides a promising target for the treatment of immunodeficiency due to T cell injury.

Recombination and mutation shape variations in the major histocompatibility complex

Yuying Sun, Fang Yuan, Ling Wang, Dongfa Dai, Zhijian Zhang, Fei Liang, Nan Liu, Juan Long, Xiao Zhao, Yongzhi Xi

2022, 49(12): 1151-1161. doi: 10.1016/j.jgg.2022.03.006

Abstract (269) PDF (50)

Abstract:
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.

Molecular spectrum of thalassemia in tropical Hainan Island of southern China: high allele frequency with low health burden

Yanquan Lai, Fangchao Tao, Yu Zou, Min Huang, Kaiting Lin, Yang Li, Weilun Huang, Wanjun Zhou

2022, 49(12): 1162-1164. doi: 10.1016/j.jgg.2022.03.010

Abstract (306) PDF (15)

Abstract:

Nuclear EPL-HAM complex is essential for the development of chloroplasts

Bo Ding, Hongli Xie, Kangning Zhang, He Li, Yushi Gao, Jing Zhang, Bin Xu, Lianwei Peng, Guofeng Yang, Guo-Liang Wang, Upinder Gill, Zeng-Yu Wang, Maofeng Chai

2022, 49(12): 1165-1168. doi: 10.1016/j.jgg.2022.04.006

Abstract (320) PDF (53)

Abstract:

AtPQT11, a P450 enzyme, detoxifies paraquat via N-demethylation

Yi-Jie Huang, Yue-Ping Huang, Jin-Qiu Xia, Zhou-Ping Fu, Yi-Fan Chen, Yi-Peng Huang, Aimin Ma, Wen-Tao Hou, Yu-Xing Chen, Xiaoquan Qi, Li-Ping Gao, Cheng-Bin Xiang

2022, 49(12): 1169-1173. doi: 10.1016/j.jgg.2022.04.007

Abstract (318) PDF (25)

Abstract:

GenomeSyn: a bioinformatics tool for visualizing genome synteny and structural variations

Zu-Wen Zhou, Zhi-Guang Yu, Xiao-Ming Huang, Jin-Shen Liu, Yi-Xiong Guo, Ling-Ling Chen, Jia-Ming Song

2022, 49(12): 1174-1176. doi: 10.1016/j.jgg.2022.03.013

Abstract (978) PDF (101)

Abstract:

2022 Vol. 49, No. 12