Journal of Genetics and Genomics

Brassinosteroid signaling and molecular crosstalk with nutrients in plants

Chao Han, Lingyan Wang, Jinyang Lyu, Wen Shi, Lianmei Yao, Min Fan, Ming-Yi Bai

2023, 50(8): 541-553. doi: 10.1016/j.jgg.2023.03.004

Abstract (474) PDF (36)

Abstract:

As sessile organisms, plants have evolved sophisticated mechanisms to optimize their growth and development in response to fluctuating nutrient levels. Brassinosteroids (BRs) are a group of plant steroid hormones that play critical roles in plant growth and developmental processes as well as plant responses to environmental stimuli. Recently, multiple molecular mechanisms have been proposed to explain the integration of BRs with different nutrient signaling processes to coordinate gene expression, metabolism, growth, and survival. Here, we review recent advances in understanding the molecular regulatory mechanisms of the BR signaling pathway and the multifaceted roles of BR in the intertwined sensing, signaling, and metabolic processes of sugar, nitrogen, phosphorus, and iron. Further understanding and exploring these BR-related processes and mechanisms will facilitate advances in crop breeding for higher resource efficiency.

Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto)

Haopeng He, Hechuan Yang, Randy Foo, Wharton Chan, Feng Zhu, Yunsong Liu, Xuming Zhou, Liang Ma, Lin-Fa Wang, Weiwei Zhai

2023, 50(8): 554-562. doi: 10.1016/j.jgg.2023.05.002

Abstract (251) PDF (226)

Abstract:
As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the microevolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.

CRISPR-detector: fast and accurate detection, visualization, and annotation of genome-wide mutations induced by genome editing events

Lei Huang, Dan Wang, Haodong Chen, Jinnan Hu, Xuechen Dai, Chuan Liu, Anduo Li, Xuechun Shen, Chen Qi, Haixi Sun, Dengwei Zhang, Tong Chen, Yuan Jiang

2023, 50(8): 563-572. doi: 10.1016/j.jgg.2023.03.010

Abstract (256) PDF (21)

Abstract:
The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing. To track on/off-target events with emerging new editing techniques, improved bioinformatic tools are indispensable. Existing tools suffer from limitations in speed and scalability, especially with whole-genome sequencing (WGS) data analysis. To address these limitations, we have developed a comprehensive tool called CRISPR-detector, a web-based and locally deployable pipeline for genome editing sequence analysis. The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline, with additional novel annotation and visualization modules designed to fit CRISPR applications. Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing. CRISPR-detector offers optimized scalability, enabling WGS data analysis beyond Browser Extensible Data file-defined regions, with improved accuracy due to haplotype-based variant calling to handle sequencing errors. In addition, the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users. These advantages facilitate rapid and efficient detection of mutations induced by genome editing events, especially for datasets generated from WGS. The web-based version of CRISPR-detector is available at https://db.cngb.org/crispr-detector, and the locally deployable version is available at https://github.com/hlcas/CRISPR-detector.

Identification of FUT7 hypomethylation as the blood biomarker in the prediction of early-stage lung cancer

Rong Qiao, Feifei Di, Jun Wang, Yujie Wei, Tian Xu, Liping Dai, Wanjian Gu, Baohui Han, Rongxi Yang

2023, 50(8): 573-581. doi: 10.1016/j.jgg.2023.02.014

Abstract (251) PDF (23)

Abstract:
Early detection of lung cancer (LC) is vital for reducing LC-related mortality. However, noninvasive diagnostic tools remain a great challenge. We aim to identify blood-based biomarkers for the early detection of LC. Here, LC-associated hypomethylation in alpha-1,3-fucosyltransferase VII (FUT7) is identified via the Illumina 850K array in a discovery study and validated by mass spectrometry in two independent casecontrol studies with blood samples from 1720 LC patients (86.8% LC at stage I, blood is collected before surgery and treatment) and 3143 healthy controls. Compared to the controls, blood-based FUT7 hypomethylation is identified in LC patients at stage I, and even in LC patients with malignant nodules ≤1 cm and in patients with adenocarcinoma in situ. Gender plays a role in the LC-associated FUT7 hypomethylation in blood, which is more significant in males than in females. We also reveal that FUT7 hypomethylation in LC could be enhanced by the advanced stage of cancer, involvement of lymph nodes, and larger tumor size. Based on a large sample size and semi-quantitative methods, our study reveals a strong association between blood-based FUT7 hypomethylation and LC, suggesting that methylation signatures in blood may be a group of potential biomarkers for detection of early-stage LC.

Addition of the T5 exonuclease increases the prime editing efficiency in plants

Zhen Liang, Yuqing Wu, Yingjie Guo, Sha Wei

2023, 50(8): 582-588. doi: 10.1016/j.jgg.2023.03.008

Abstract (247) PDF (34)

Abstract:
Prime editing (PE) is a versatile genome editing tool without the need for double-stranded DNA breaks or donor DNA templates, but is limited by low editing efficiency. We previously fused the M-MLV reverse transcriptase to the Cas9 nickase, generating the PE2 (v1) system, but the editing efficiency of this system is still low. Here we develop different versions of PE2 by adding the 50-to-30 exonuclease at different positions of the nCas9-M-MLV RT fusion protein. PE2 (v2), in which the T5 exonuclease fused to the N-terminus of the nCas9-MMLV fusion protein enhances prime editing efficiency of base substitutions, deletions, and insertions at several genomic sites by 1.7- to 2.9-fold in plant cells compared to PE2 (v1). The improved editing efficiency of PE2 (v2) is further confirmed by generating increased heritable prime edits in stable transgenic plants compared to the previously established PE-P1, PE-P2, and PPE systems. Using PE2 (v2), we generate herbicide-resistant rice by simultaneously introducing mutations causing amino acid substitutions at two target sites. The PE efficiency is further improved by combining PE2 (v2) and dualpegRNAs. Taken together, the increased genome editing efficiency of PE2 (v2) developed in this study may enhance the applications of PE in plants.

Histone methylation readers MRG1/MRG2 interact with the transcription factor TCP14 to positively modulate cytokinin sensitivity in Arabidopsis

Fan Wang, Xixi Cai, Huizhe Wei, Linghao Zhang, Aiwu Dong, Wei Su

2023, 50(8): 589-599. doi: 10.1016/j.jgg.2023.02.011

Abstract (262) PDF (26)

Abstract:
Cytokinins influence many aspects of plant growth and development. Although cytokinin biosynthesis and signaling have been well studied in planta, little is known about the regulatory effects of epigenetic modifications on the cytokinin response. Here, we reveal that mutations to Morf Related Gene (MRG) proteins MRG1/MRG2, which are readers of trimethylated histone H3 lysine 4 and lysine 36 (H3K4me3 and H3K36me3), result in cytokinin hyposensitivity during various developmental processes, including callus induction and root and seedling growth inhibition. Similar to the mrg1 mrg2 mutant, plants with a defective AtTCP14, which belongs to the TEOSINTE BRANCHED, CYCLOIDEA, AND PROLIFERATING CELL FACTOR (TCP) transcription factor family, are insensitive to cytokinin. Furthermore, the transcription of several genes related to cytokinin signaling pathway is altered. Specifically, the expression of Arabidopsis thaliana HISTIDINE-CONTAINING PHOSPHOTRANSMITTER PROTEIN 2 (AHP2) decreases significantly in the mrg1 mrg2 and tcp14-2 mutants. We also confirm the interaction between MRG2 and TCP14 in vitro and in vivo. Thus, MRG2 and TCP14 can be recruited to AHP2 after recognizing H3K4me3/H3K36me3 markers and promote the histone-4 lysine-5 acetylation to further enhance AHP2 expression. In summary, our research elucidate a previously unknown mechanism mediating the effects of MRG proteins on the magnitude of the cytokinin response.

Parallel evolution of fish bi-modal breathing and expansion of olfactory receptor (OR) genes: toward a universal ORs nomenclature

Liliana Silva, Tito Mendes, Luana Ramos, Guojie Zhang, Agostinho Antunes

2023, 50(8): 600-610. doi: 10.1016/j.jgg.2023.03.006

Abstract (187) PDF (9)

Abstract:
Olfactory receptors (ORs) play a key role in the prime sensorial perception, being highly relevant for intra/ interspecific interactions. ORs are a subgroup of G-protein coupled receptors that exhibit highly complex subgenomes in vertebrates. However, OR repertoires remain poorly studied in fish lineages, precluding finely retracing their origin, evolution, and diversification, especially in the most basal groups. Here, we conduct an exhaustive gene screening upon 43 high-quality fish genomes exhibiting varied gene repertoires (2e583 genes). While the early vertebrates performed gas exchange through gills, we hypothesize that the emergence of new breathing structures (swim bladder and paired lungs) in early osteichthyans may be associated with expansions in the ORs gene families sensitive to airborne molecules. Additionally, we verify that the OR repertoire of moderns actinopterygians has not increased as expected following a whole genome duplication, likely due to regulatory mechanisms compensating the gene load excess. Finally, we identify 25 distinct OR families, allowing us to propose an updated universal nomenclature for the fish ORs.

High-throughput base editing KO screening of cellular factors for enhanced GBE

Jie Yang, Dongdong Zhao, Xiagu Zhu, Yuanzhao Yang, Bo Li, Siwei Li, Chang-Hao Bi, Xue-Li Zhang

2023, 50(8): 611-614. doi: 10.1016/j.jgg.2023.05.007

Abstract (256) PDF (25)

Abstract:

Homozygous nonsense variants of KCTD19 cause male infertility in humans and mice

Yan Zhang, Xuzhao Huang, Qiaoqiao Xu, Mei Yu, Mingxue Shu, Shiling Shan, Yun Fan, Shiqi Li, Chengzhe Tao, Ying Zhao, Juan Ji, Yufeng Qin, Chuncheng Lu, Yankai Xia, Feng Zhang

2023, 50(8): 615-619. doi: 10.1016/j.jgg.2023.05.008

Abstract (194) PDF (26)

Abstract:

VdMKK1-mediated cell wall integrity is essential for virulence in vascular wilt pathogen Verticillium dahliae

Jiaqi Li, Juan Tian, Huan Cao, Mengli Pu, Xiaxia Zhang, Yanjun Yu, Zhi Wang, Zhaosheng Kong

2023, 50(8): 620-623. doi: 10.1016/j.jgg.2023.03.001

Abstract (280) PDF (27)

Abstract:

Corrigendum to “lncRNA NEAT1 is required for splenic erythroid differentiation” [Journal of Genetics and Genomics (2023) 50, 454e457]

Xiaoru Zhang, Yingnan Zhang, Guangfeng Geng, Jie Gao, Jingyuan Tong, Lihong Shi, Jinhua Liu

2023, 50(8): 624-624. doi: 10.1016/j.jgg.2023.07.001

Abstract (68) PDF (0)

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2023 Vol. 50, No. 8