Hypoxic environment promotes angiogenesis and bone bridge formation by activating Notch/RBPJ signaling pathway in HUVECs
Genomics. 2024 Mar 25:110838. doi: 10.1016/j.ygeno.2024.110838. Online ahead of print.ABSTRACTAfter epiphyseal fracture, the epiphyseal plate is prone to ischemia and hypoxia, leading to the formation of bone bridge and deformity. However, the exact mechanism controlling the bone bridge formation remains unclear. Notch/RBPJ signaling axis has been indicated to regulate angiogenesis and osteogenic differentiation. Our study aims to investigate the mechanism of bone bridge formation after epiphyseal plate injury, and to provide a theoretical basis for new therapeutic approaches to prevent the bone bridge formation. The expre...
Source: Genomics - March 27, 2024 Category: Genetics & Stem Cells Authors: Wendong Liu Mincheng Zou Mimi Chen Zheng Zhang Yunpeng Mao Yuhao Yang Ya Liu Qin Shi Xiaodong Wang Fuyong Zhang Source Type: research

Study on the interaction protein of transcription factor Smad3 based on TurboID proximity labeling technology
Genomics. 2024 Mar 25:110839. doi: 10.1016/j.ygeno.2024.110839. Online ahead of print.ABSTRACTTurboID is a highly efficient biotin-labelling enzyme, which can be used to explore a number of new intercalating proteins due to the very transient binding and catalytic functions of many proteins. TGF-β/Smad3 signaling pathway is involved in many diseases, especially in diabetic nephropathy and inflammation. In this paper, a stably cell line transfected with Smad3 were constructed by using lentiviral infection. To further investigate the function of TGF-β/Smad3, the protein labeling experiment was conducted to find the interac...
Source: Genomics - March 27, 2024 Category: Genetics & Stem Cells Authors: Biao Yan Ting Zeng Xiaoshan Liu Yuanyuan Guo Hongguang Chen Shuang Guo Wu Liu Source Type: research

Discovery and characterization of sgRNA-sequence-independent DNA cleavage from CRISPR/Cas9 in mouse embryos
Genomics. 2024 Mar 25:110836. doi: 10.1016/j.ygeno.2024.110836. Online ahead of print.ABSTRACTThe CRISPR/Cas9 system can induce off-target effects in programmed gene editing, but there have been few reports on cleavage detection and their affection in embryo development. To study these events, sgRNAs with different off-target rates were designed and compared after micro-injected into mouse zygotes, and γH2AX was used for DNA cleavage sites analysis by immunostaining and CUT&Tag. Although the low off-target sgRNA were usually selected for production gene editing animals, γH2AX immunofluorescence indicated that there w...
Source: Genomics - March 27, 2024 Category: Genetics & Stem Cells Authors: Liyun Yang Lijiao Chen Yang Zheng Li Deng Raoxian Bai Ting Zhang Zhengbo Wang Shangang Li Source Type: research

Boosting edgeR (robust) by dealing with missing observations and gene-specific outliers in RNA-Seq profiles and its application to explore biomarker genes for diagnosis and therapies of ovarian cancer
Genomics. 2024 Mar 23:110834. doi: 10.1016/j.ygeno.2024.110834. Online ahead of print.ABSTRACTThe edgeR (Robust) is a popular approach for identifying differentially expressed genes (DEGs) from RNA-Seq profiles. However, it shows weak performance against gene-specific outliers and is unable to handle missing observations. To address these issues, we proposed a pre-processing approach of RNA-Seq count data by combining the iLOO-based outlier detection and random forest-based missing imputation approach for boosting the performance of edgeR (Robust). Both simulation and real RNA-Seq count data analysis results showed that th...
Source: Genomics - March 25, 2024 Category: Genetics & Stem Cells Authors: Bandhan Sarker Md Matiur Rahaman Muhammad Habibulla Alamin Md Ariful Islam Md Nurul Haque Mollah Source Type: research

Boosting edgeR (robust) by dealing with missing observations and gene-specific outliers in RNA-Seq profiles and its application to explore biomarker genes for diagnosis and therapies of ovarian cancer
Genomics. 2024 Mar 23:110834. doi: 10.1016/j.ygeno.2024.110834. Online ahead of print.ABSTRACTThe edgeR (Robust) is a popular approach for identifying differentially expressed genes (DEGs) from RNA-Seq profiles. However, it shows weak performance against gene-specific outliers and is unable to handle missing observations. To address these issues, we proposed a pre-processing approach of RNA-Seq count data by combining the iLOO-based outlier detection and random forest-based missing imputation approach for boosting the performance of edgeR (Robust). Both simulation and real RNA-Seq count data analysis results showed that th...
Source: Genomics - March 25, 2024 Category: Genetics & Stem Cells Authors: Bandhan Sarker Md Matiur Rahaman Muhammad Habibulla Alamin Md Ariful Islam Md Nurul Haque Mollah Source Type: research

Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq
In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of...
Source: Genomics - March 23, 2024 Category: Genetics & Stem Cells Authors: Zhenghao Lv Guohu Lan Baiyi Bai Penghao Yu Chuantang Wang He Zhang Chao Zhong Xinhua Zhao Haiqiu Yu Source Type: research

Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq
In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of...
Source: Genomics - March 23, 2024 Category: Genetics & Stem Cells Authors: Zhenghao Lv Guohu Lan Baiyi Bai Penghao Yu Chuantang Wang He Zhang Chao Zhong Xinhua Zhao Haiqiu Yu Source Type: research

Identification of candidate genes associated with peanut pod length by combined analysis of QTL-seq and RNA-seq
In this study, quantitative trait loci sequencing (QTL-seq) was performed using the F2 population constructed by a short-pod variety Tifrunner (Tif) and a long-pod line Lps, and a 0.77 Mb genomic region on chromosome 07 was identified as the candidate region for PL. Then, the candidate region was narrowed to a 265.93 kb region by traditional QTL approach. RNA-seq analysis showed that there were four differentially expressed genes (DEGs) in the candidate region, among which Arahy.PF2L6F (AhCDC48) and Arahy.P4LK2T (AhTAA1) were speculated to be PL-related candidate genes. These results were informative for the elucidation of...
Source: Genomics - March 23, 2024 Category: Genetics & Stem Cells Authors: Zhenghao Lv Guohu Lan Baiyi Bai Penghao Yu Chuantang Wang He Zhang Chao Zhong Xinhua Zhao Haiqiu Yu Source Type: research

GCN2-eIF2 α signaling pathway negatively regulates the growth of triploid crucian carp
In this study, genes associated with the GCN2-eIF2α pathway (pkr, pek, gcn2, eif2α) are founded lower expression levels in the triploid crucian carp (3nCC) muscle compared to that of the red crucian carp (RCC). In muscle effect stage embryos of the 3nCC, the mRNA levels of this pathway genes are generally lower than those of RCC, excluding hri and fgf21. Inhibiting gcn2 in 3nCC embryos downregulates downstream gene expression (eif2α, atf4, fgf21), accelerating embryonic development. In contrast, overexpressing of eif2α can alter the expression levels of downstream genes (atf4 and fgf21), and decelerates the embryonic d...
Source: Genomics - March 22, 2024 Category: Genetics & Stem Cells Authors: Xuejing Wang Fangyuan Peng Shuli Yuan Zhen Huang Lingwei Tang Song Chen Jinhui Liu Wen Fu Liangyue Peng Wenbin Liu Yamei Xiao Source Type: research

Effects of CRISPR/Cas9 targeting of the myo-inositol biosynthesis pathway on hyper-osmotic tolerance of tilapia cells
Genomics. 2024 Mar 20:110833. doi: 10.1016/j.ygeno.2024.110833. Online ahead of print.ABSTRACTMyo-inositol is an important compatible osmolyte in vertebrates. This osmolyte is produced by the myo-inositol biosynthesis (MIB) pathway composed of myo-inositol phosphate synthase and inositol monophosphatase . These enzymes are among the highest upregulated proteins in tissues and cell cultures from teleost fish exposed to hyperosmotic conditions indicating high importance of this pathway for tolerating this type of stress. CRISPR/Cas9 gene editing of tilapia cells produced knockout lines of MIB enzymes and control genes. Metab...
Source: Genomics - March 22, 2024 Category: Genetics & Stem Cells Authors: Jens Hamar Avner Cnaani Dietmar K ültz Source Type: research

A comprehensive comparison of molecular and phenotypic profiles between hepatitis B virus (HBV)-infected and non-HBV-infected hepatocellular carcinoma by multi-omics analysis
This study may provide insights into the profiles of HBV+ and HBV- HCCs, and guide rational therapeutic interventions for HCC patients.PMID:38513875 | DOI:10.1016/j.ygeno.2024.110831 (Source: Genomics)
Source: Genomics - March 21, 2024 Category: Genetics & Stem Cells Authors: Zijie Wu Zehua Dong Jiangti Luo Weiwei Hu Yue Tong Xiangdong Gao Wenbing Yao Hong Tian Xiaosheng Wang Source Type: research

A comprehensive comparison of molecular and phenotypic profiles between hepatitis B virus (HBV)-infected and non-HBV-infected hepatocellular carcinoma by multi-omics analysis
This study may provide insights into the profiles of HBV+ and HBV- HCCs, and guide rational therapeutic interventions for HCC patients.PMID:38513875 | DOI:10.1016/j.ygeno.2024.110831 (Source: Genomics)
Source: Genomics - March 21, 2024 Category: Genetics & Stem Cells Authors: Zijie Wu Zehua Dong Jiangti Luo Weiwei Hu Yue Tong Xiangdong Gao Wenbing Yao Hong Tian Xiaosheng Wang Source Type: research

Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection
In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions. The TIFY gene family exhibited expansion and possessed gene redundancy resulting from tobacco ploidy change. In addition, most NtTIFYs equivalently expressed in roots, stems and leaves, while NtTIFY1, N...
Source: Genomics - March 16, 2024 Category: Genetics & Stem Cells Authors: Huifen Zhang Zhengwen Liu Ruimei Geng Min Ren Lirui Cheng Dan Liu Caihong Jiang Liuying Wen Zhiliang Xiao Aiguo Yang Source Type: research

Mutational profile evaluates metastatic capacity of Chinese colorectal cancer patients, revealed by whole-exome sequencing
In conclusion, this study identified the unique characteristics of gene mutations in Chinese patients with colorectal cancer, and is a valuable reference for personalized treatment in Chinese CRC patients.PMID:38492821 | DOI:10.1016/j.ygeno.2024.110809 (Source: Genomics)
Source: Genomics - March 16, 2024 Category: Genetics & Stem Cells Authors: Yian Yang Jiawei Chen Honghua Peng Zhigang Xiao Wei Xu Mingchuan Zheng Zheng Li Peiguo Cao Source Type: research

Genome-wide identification of the TIFY gene family in tobacco and expression analysis in response to Ralstonia solanacearum infection
In this study, genome-wide identification of TIFY members in tobacco and their expression pattern analysis in response to Ralstonia solanacearum infection were performed. A total of 33 TIFY genes were identified, including the TIFY, PPD, ZIM&ZML and JAZ subfamilies. Promoter analysis results indicated that a quantity of light-response, drought-response, SA-response and JA-response cis-elements exist in promoter regions. The TIFY gene family exhibited expansion and possessed gene redundancy resulting from tobacco ploidy change. In addition, most NtTIFYs equivalently expressed in roots, stems and leaves, while NtTIFY1, N...
Source: Genomics - March 16, 2024 Category: Genetics & Stem Cells Authors: Huifen Zhang Zhengwen Liu Ruimei Geng Min Ren Lirui Cheng Dan Liu Caihong Jiang Liuying Wen Zhiliang Xiao Aiguo Yang Source Type: research