dbEMT 2.0: an updated database for epithelial-mesenchymal transition genes with experimentally verified information and pre-calculated regulation information for cancer metastasis
Publication date: Available online 21 December 2019Source: Journal of Genetics and GenomicsAuthor(s): Min Zhao, Yining Liu, Chong Zheng, Hong Qu (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - December 21, 2019 Category: Genetics & Stem Cells Source Type: research
Integration of lipidomics and metabolomics for in-depth understanding of cellular mechanism and disease progression
Publication date: Available online 18 December 2019Source: Journal of Genetics and GenomicsAuthor(s): Raoxu Wang, Bowen Li, Sin Man Lam, Guanghou ShuiAbstractMass spectrometry (MS)-based omics technologies are now widely used to profile small molecules in multiple matrices to confer comprehensive snapshots of cellular metabolic phenotypes. The metabolomes of cells, tissues and organisms comprise a variety of molecules including lipids, amino acids, sugars, organic acids, etc. Metabolomics mainly focus on the last three classes, while lipidomics has emerged as an independent omics owing to the complexities of the organismal...
Source: Journal of Genetics and Genomics - December 20, 2019 Category: Genetics & Stem Cells Source Type: research
DOT1L is involved in breast cancer metastasis via transcriptional regulation of MALAT1 and ZEB2
Publication date: Available online 17 December 2019Source: Journal of Genetics and GenomicsAuthor(s): Yang Duan, Xingyan Zhang, Lihong Yang, Xu Dong, Zhanye Zheng, Yiming Cheng, Hao Chen, Bei Lan, Dengwen Li, Jun Zhou, Chenghao Xuan (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - December 18, 2019 Category: Genetics & Stem Cells Source Type: research
Glycolysis regulates gene expression by promoting the crosstalk between H3K4me3 and H3K14ac in Saccharomyces cerevisiae
Publication date: Available online 11 December 2019Source: Journal of Genetics and GenomicsAuthor(s): Yinsheng Wu, Shihao Zhang, Xuanyunjing Gong, Qi Yu, Yuan Zhang, Mingdan Luo, Xianhua Zhang, Jerry L. Workman, Xilan Yu, Shanshan LiAbstractCells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. However, how cells transduce nutrient availability to appropriate gene expression response via histone modifications remains largely unknown. Here, we report that glucose specifically induces histone H3K4 trimethylation (H3K4me3), an evolutionarily conserved histone covalent mod...
Source: Journal of Genetics and Genomics - December 11, 2019 Category: Genetics & Stem Cells Source Type: research
Drosophila CTP synthase can form distinct substrate- and product-bound filaments
In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPs, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can co-exist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation. (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - November 30, 2019 Category: Genetics & Stem Cells Source Type: research
Site-directed RNA editing (SDRE): Off-target effects and their countermeasures
Publication date: Available online 27 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Shaoshuai Mao, Yajing Liu, Shisheng Huang, Xingxu Huang, Tian ChiAbstractSite-directed RNA editing (SDRE) is invaluable to basic research and medicine, and has emerged as a new frontier in genome editing. The past few years have witnessed a surge of interest in SDRE, with SDRE tools emerging at a breathtaking pace. However, off-target effects of SDRE remain a tough problem, which constitutes a major hurdle to their clinical applications. Here we discuss the diverse strategies for combating off-target editing, drawing lesso...
Source: Journal of Genetics and Genomics - November 28, 2019 Category: Genetics & Stem Cells Source Type: research
PDGF signaling from pharyngeal pouches promotes arch artery morphogenesis
Publication date: Available online 25 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Aihua Mao, Mingming Zhang, Jie Liu, Yu Cao, Qiang WangAbstractThe great vessels of the heart originate from the pharyngeal arch arteries (PAAs). Anomalies of the PAAs often occur together with pharyngeal pouch malformations, but the reasons for this phenomenon are not fully understood. In the current study, we show that PDGF signaling derived from the pharyngeal pouches plays an important function in PAA vasculogenesis. During PAA development in zebrafish embryos, pdgfαa and pdgfαb are expressed in the developing pharyng...
Source: Journal of Genetics and Genomics - November 25, 2019 Category: Genetics & Stem Cells Source Type: research
Engineering guide RNA to reduce the off-target effects of CRISPR
Publication date: Available online 23 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Jing Wu, Hao YinAbstractAs versatile and robust genome editing tools, clustered regularly interspaced short palindromic repeats (CRISPR) technologies have been broadly used in basic research, biotechnology and therapeutic development. Off-target mutagenesis by CRISPR systems has been demonstrated, and various methods have been developed to markedly increase their specificity. In this review, we highlight the efforts of producing and modifying guide RNA to minimize off-target activities, including sequence and structure des...
Source: Journal of Genetics and Genomics - November 23, 2019 Category: Genetics & Stem Cells Source Type: research
Advances in Detecting and Reducing Off-target Effects Generated by CRISPR-mediated Genome Editing
Publication date: Available online 22 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Jin-Jing Li, Shunyan Hong, Wan-Jin Chen, Erwei Zuo, Hui YangAbstractCRISPR-mediated genome editing is a revolutionary technology for genome manipulation that utilizes the CRISPR-Cas systems and base editors. Currently, poor efficiency and off-target problems have impeded the application of CRISPR systems. The on-target efficiency has been improved in several advanced versions of CRISPR systems, whereas the off-target detection still remains a key challenge. Here, we outline the different versions of CRISPR systems and off-...
Source: Journal of Genetics and Genomics - November 22, 2019 Category: Genetics & Stem Cells Source Type: research
A behavioral paradigm to study the persistence of reward memory extinction in Drosophila
Publication date: Available online 16 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Lingling Wang, Qi Yang, Binyan Lu, Lianzhang Wang, Yi Zhong, Qian Li (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - November 16, 2019 Category: Genetics & Stem Cells Source Type: research
Rapid breeding of pink-fruited tomato hybrids using the CRISPR/Cas9 system
Publication date: Available online 24 October 2019Source: Journal of Genetics and GenomicsAuthor(s): Tianxia Yang, Lei Deng, Wei Zhao, Ruoxi Zhang, Hongling Jiang, Zhibiao Ye, Chang-Bao Li, Chuanyou Li (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
RASSF6-TRIM16 axis promotes cell proliferation, migration and invasion in esophageal squamous cell carcinoma
In this study, we performed immunohistochemistry (IHC) assay. The results show that RASSF6 is upregulated in ESCC and that the elevated expression level of RASSF6 is associated with lymph node metastasis and poor survival of ESCC patients. Consistent with the clinical observations, the upregulation of RASSF6 greatly promotes ESCC cell proliferation, migration and invasion as well as the cell cycle transition to G1/S phase in vitro. According to models in vivo, the downregulation of RASSF6 considerably inhibits ESCC tumor growth and lung metastasis. Mechanistically, RASSF6 negatively regulates the tumor suppressor tripartit...
Source: Journal of Genetics and Genomics - November 14, 2019 Category: Genetics & Stem Cells Source Type: research
Evolutionary selection on MDA5 and LGP2 in the chicken preserves antiviral competence in the absence of RIG-I
Publication date: Available online 5 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Ling Xu, Dandan Yu, Yu Fan, Yi-Ping Liu, Yong-Gang Yao (Source: Journal of Genetics and Genomics)
Source: Journal of Genetics and Genomics - November 6, 2019 Category: Genetics & Stem Cells Source Type: research
Embryonic lineage tracing with Procr-CreER marks balanced hematopoietic stem cell fate during entire mouse lifespan
In this study, we revealed that Procr expression was detected principally in phenotypical vascular endothelium co-expressing Dll4 and CD44 in the mid-gestation mouse embryos, and could enrich all the HSCs of the embryonic day 11.5 (E11.5) aorta-gonad-mesonephros (AGM) region. We then used a temporally restricted genetic tracing strategy to irreversibly label the Procr-expressing cells at E9.5. Interestingly, most labeled mature HSCs in multiple sites (such as AGM) around E11.5 were functionally categorized as lymphomyeloid-balanced HSCs assessed by direct transplantation. Furthermore, the labeled cells contributed to an av...
Source: Journal of Genetics and Genomics - November 6, 2019 Category: Genetics & Stem Cells Source Type: research
Histone modifications and their regulatory roles in plant development and environmental memory
Publication date: Available online 2 November 2019Source: Journal of Genetics and GenomicsAuthor(s): Ting Zhao, Zhenping Zhan, Danhua JiangAbstractPlants grow in dynamic environments where they receive diverse environmental signals. Swift and precise control of gene expression is essential for plants to align their development and metabolism with fluctuating surroundings. Modifications on histones serve as “histone code” to specify chromatin and gene activities. Different modifications execute distinct functions on the chromatin, promoting either active transcription or gene silencing. Histone writers, erasers, and rea...
Source: Journal of Genetics and Genomics - November 4, 2019 Category: Genetics & Stem Cells Source Type: research
