Genomics, proteomics & bioinformatics最新文献_第6页

DRED: A Comprehensive Database of Genes Related to Repeat Expansion Diseases. DRED：与重复扩增疾病相关的基因综合数据库。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae068

Qingqing Shi, Min Dai, Yingke Ma, Jun Liu, Xiuying Liu, Xiu-Jie Wang

{"title":"DRED: A Comprehensive Database of Genes Related to Repeat Expansion Diseases.","authors":"Qingqing Shi, Min Dai, Yingke Ma, Jun Liu, Xiuying Liu, Xiu-Jie Wang","doi":"10.1093/gpbjnl/qzae068","DOIUrl":"10.1093/gpbjnl/qzae068","url":null,"abstract":"Expansion of tandem repeats in genes often causes severe diseases, such as fragile X syndrome, Huntington's disease, and spinocerebellar ataxia. However, information on genes associated with repeat expansion diseases is scattered throughout the literature, systematic prediction of potential genes that may cause diseases via repeat expansion is also lacking. Here, we develop DRED, a Database of genes related to Repeat Expansion Diseases, as a manually-curated database that covers all known 61 genes related to repeat expansion diseases reported in PubMed and OMIM, along with the detailed repeat information for each gene. DRED also includes 516 genes with the potential to cause diseases via repeat expansion, which were predicted based on their repeat composition, genetic variations, genomic features, and disease associations. Various types of information on repeat expansion diseases and their corresponding genes/repeats are presented in DRED, together with links to external resources, such as NCBI and ClinVar. DRED provides user-friendly interfaces with comprehensive functions, and can serve as a central data resource for basic research and repeat expansion disease-related medical diagnosis. DRED is freely accessible at http://omicslab.genetics.ac.cn/dred, and will be frequently updated to include newly reported genes related to repeat expansion diseases.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696699/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes. 利用人群匹配参考基因组增强全基因组测序数据中的变异调用。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae070

Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu

{"title":"Enhancing Variant Calling in Whole-exome Sequencing Data Using Population-matched Reference Genomes.","authors":"Shuming Guo, Zhuo Huang, Yanming Zhang, Yukun He, Xiangju Chen, Wenjuan Wang, Lansheng Li, Yu Kang, Zhancheng Gao, Jun Yu, Zhenglin Du, Yanan Chu","doi":"10.1093/gpbjnl/qzae070","DOIUrl":"10.1093/gpbjnl/qzae070","url":null,"abstract":"Whole-exome sequencing (WES) data are frequently used for cancer diagnosis and genome-wide association studies (GWAS), based on high-coverage read mapping, informative variant calling, and high-quality reference genomes. The center position of the currently used genome assembly, GRCh38, is now challenged by two newly published telomere-to-telomere (T2T) genomes, T2T-CHM13 and T2T-YAO, and it becomes urgent to have a comparative study to test population specificity using the three reference genomes based on real case WES data. Here, we report our analysis along this line for 19 tumor samples collected from Chinese patients. The primary comparison of the exon regions among the three references reveals that the sequences in up to ∼ 1% of target regions in T2T-YAO are widely diversified from GRCh38 and may lead to off-target in sequence capture. However, T2T-YAO still outperforms GRCh38 by obtaining 7.41% of more mapped reads. Due to more reliable read-mapping and closer phylogenetic relationship with the samples than GRCh38, T2T-YAO reduces half of variant calls of clinical significance which are mostly benign, while maintaining sensitivity in identifying pathogenic variants. T2T-YAO also outperforms T2T-CHM13 in reducing calls of Chinese-specific variants. Our findings highlight the critical need for employing population-specific reference genomes in genomic analysis to ensure accurate variant analysis and the significant benefits of tailoring these approaches to the unique genetic background of each ethnic group.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11687947/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142396282","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells. RAG-seq：NSR引物和转座酶标记介导的单细胞链特异性总RNA测序。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae072

Ping Xu, Zhiheng Yuan, Xiaohua Lu, Peng Zhou, Ding Qiu, Zhenghao Qiao, Zhongcheng Zhou, Li Guan, Yongkang Jia, Xuan He, Ling Sun, Youzhong Wan, Ming Wang, Yang Yu

{"title":"RAG-seq: NSR-primed and Transposase Tagmentation-mediated Strand-specific Total RNA Sequencing in Single Cells.","authors":"Ping Xu, Zhiheng Yuan, Xiaohua Lu, Peng Zhou, Ding Qiu, Zhenghao Qiao, Zhongcheng Zhou, Li Guan, Yongkang Jia, Xuan He, Ling Sun, Youzhong Wan, Ming Wang, Yang Yu","doi":"10.1093/gpbjnl/qzae072","DOIUrl":"10.1093/gpbjnl/qzae072","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of cellular diversity with unprecedented resolution. However, many current methods are limited in capturing full-length transcripts and discerning strand orientation. Here, we present RAG-seq, an innovative strand-specific total RNA sequencing technique that combines not-so-random (NSR) primers with Tn5 transposase-mediated tagmentation. RAG-seq overcomes previous limitations by delivering comprehensive transcript coverage and maintaining strand orientation, which are essential for accurate quantification of overlapping genes and detection of antisense transcripts. Through optimized reverse transcription with oligo-dT primers, rRNA depletion via Depletion of Abundant Sequences by Hybridization (DASH), and linear amplification, RAG-seq enhances sensitivity and reproducibility, especially for low-input samples and single cells. Application to mouse oocytes and early embryos highlights RAG-seq's superior performance in identifying stage-specific antisense transcripts, shedding light on their regulatory roles during early development. This advancement represents a significant leap in transcriptome analysis within complex biological contexts.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11658833/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142484016","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases. RNA 5-甲基胞嘧啶修饰：调节分子、生物功能和人类疾病。

Genomics, proteomics & bioinformatics Pub Date : 2024-12-03 DOI: 10.1093/gpbjnl/qzae063

Yanfang Lu, Liu Yang, Qi Feng, Yong Liu, Xiaohui Sun, Dongwei Liu, Long Qiao, Zhangsuo Liu

{"title":"RNA 5-Methylcytosine Modification: Regulatory Molecules, Biological Functions, and Human Diseases.","authors":"Yanfang Lu, Liu Yang, Qi Feng, Yong Liu, Xiaohui Sun, Dongwei Liu, Long Qiao, Zhangsuo Liu","doi":"10.1093/gpbjnl/qzae063","DOIUrl":"10.1093/gpbjnl/qzae063","url":null,"abstract":"RNA methylation modifications influence gene expression, and disruptions of these processes are often associated with various human diseases. The common RNA methylation modification 5-methylcytosine (m5C), which is dynamically regulated by writers, erasers, and readers, widely occurs in transfer RNAs (tRNAs), messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), enhancer RNAs (eRNAs), and other non-coding RNAs (ncRNAs). RNA m5C modification regulates metabolism, stability, nuclear export, and translation of RNA molecules. An increasing number of studies have revealed the critical roles of the m5C RNA modification and its regulators in the development, diagnosis, prognosis, and treatment of various human diseases. In this review, we summarized the recent studies on RNA m5C modification and discussed the advances in its detection methodologies, distribution, and regulators. Furthermore, we addressed the significance of RNAs modified with m5C marks in essential biological processes as well as in the development of various human disorders, from neurological diseases to cancers. This review provides a new perspective on the diagnosis, treatment, and monitoring of human diseases by elucidating the complex regulatory network of the epigenetic m5C modification.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11634542/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142335110","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

iMFP-LG: Identification of Novel Multi-Functional Peptides by Using Protein Language Models and Graph-Based Deep Learning. iMFP-LG：利用蛋白质语言模型和基于图的深度学习识别新型多功能肽。

Genomics, proteomics & bioinformatics Pub Date : 2024-11-25 DOI: 10.1093/gpbjnl/qzae084

Jiawei Luo, Kejuan Zhao, Junjie Chen, Caihua Yang, Fuchuan Qu, Yumeng Liu, Xiaopeng Jin, Ke Yan, Yang Zhang, Bin Liu

{"title":"iMFP-LG: Identification of Novel Multi-Functional Peptides by Using Protein Language Models and Graph-Based Deep Learning.","authors":"Jiawei Luo, Kejuan Zhao, Junjie Chen, Caihua Yang, Fuchuan Qu, Yumeng Liu, Xiaopeng Jin, Ke Yan, Yang Zhang, Bin Liu","doi":"10.1093/gpbjnl/qzae084","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae084","url":null,"abstract":"Functional peptides are short amino acid fragments that have a wide range of beneficial functions for living organisms. The majority of previous research focused on mono-functional peptides, but a growing number of multi-functional peptides have been discovered. Although there have been enormous experimental efforts to assay multi-functional peptides, only a small fraction of millions of known peptides have been explored. Effective and precise techniques for identifying multi-functional peptides can facilitate their discovery and mechanistic understanding. In this article, we presented a method iMFP-LG for identifying multi-functional peptides based on protein language models (pLMs) and graph attention networks (GATs). Comparison results showed that iMFP-LG outperforms state-of-the-art methods on both multi-functional bioactive peptides and multi-functional therapeutic peptides datasets. The interpretability of iMFP-LG was also illustrated by visualizing attention patterns in pLMs and GATs. Regarding the outstanding performance of iMFP-LG on the identification of multi-functional peptides, we employed iMFP-LG to screen novel candidate peptides with both ACP and AMP functions from millions of known peptides in the UniRef90. As a result, 8 candidate peptides were identified, and 1 candidate that exhibits both antibacterial and anticancer effects was confirmed through molecular structure alignment and biological experiments. We anticipate that iMFP-LG can assist in the discovery of multi-functional peptides and contribute to the advancement of peptide drug design.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142712263","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences. VISTA：病毒基因组序列快速分类分配工具。

Genomics, proteomics & bioinformatics Pub Date : 2024-11-14 DOI: 10.1093/gpbjnl/qzae082

Tao Zhang, Yiyun Liu, Xutong Guo, Xinran Zhang, Xinchang Zheng, Mochen Zhang, Yiming Bao

{"title":"VISTA: A Tool for Fast Taxonomic Assignment of Viral Genome Sequences.","authors":"Tao Zhang, Yiyun Liu, Xutong Guo, Xinran Zhang, Xinchang Zheng, Mochen Zhang, Yiming Bao","doi":"10.1093/gpbjnl/qzae082","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae082","url":null,"abstract":"The rapid expansion of the number of viral genome sequences in public databases necessitates a scalable, universal, and automated preliminary taxonomic framework for comprehensive virus studies. Here, we introduce VISTA (Virus Sequence-based Taxonomy Assignment), a computational tool that employs a novel pairwise sequence comparison system and an automatic demarcation threshold identification framework for virus taxonomy. Leveraging physio-chemical property sequences, k-mer profiles, and machine learning techniques, VISTA constructs a robust distance-based framework for taxonomic assignment. Functionally similar to PASC (Pairwise Sequence Comparison), a widely used virus assignment tool based on pairwise sequence comparison, VISTA demonstrates superior performance by providing significantly improved separation for taxonomic groups, more objective taxonomic demarcation thresholds, greatly enhanced speed, and a wider application scope. We successfully applied VISTA to 38 virus families, as well as to the class Caudoviricetes. This demonstrates VISTA's scalability, robustness, and ability to automatically and accurately assign taxonomy to both prokaryotic and eukaryotic viruses. Furthermore, the application of VISTA to 679 unclassified prokaryotic virus genomes recovered from metagenomic data identified 46 novel virus families. VISTA is available as both a command line tool and a user-friendly web portal at https://ngdc.cncb.ac.cn/vista.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635082","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics. 猪基因组揭示了导致猪特征的基因内容变异和结构变异。

Genomics, proteomics & bioinformatics Pub Date : 2024-11-13 DOI: 10.1093/gpbjnl/qzae081

Heng Du, Yue Zhuo, Shiyu Lu, Wanying Li, Lei Zhou, Feizhou Sun, Gang Liu, Jian-Feng Liu

{"title":"Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.","authors":"Heng Du, Yue Zhuo, Shiyu Lu, Wanying Li, Lei Zhou, Feizhou Sun, Gang Liu, Jian-Feng Liu","doi":"10.1093/gpbjnl/qzae081","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae081","url":null,"abstract":"Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142635075","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Enzymes Repertoires and Genomic Insights into Lycium Barbarum Pectin Polysaccharides Biosynthesis. 枸杞果胶多糖生物合成的酵素再现和基因组洞察。

Genomics, proteomics & bioinformatics Pub Date : 2024-11-04 DOI: 10.1093/gpbjnl/qzae079

Haiyan Yue, Yiheng Tang, Aixuan Li, Lili Zhang, Yiwei Niu, Yiming Zhang, Hao Wang, Jianjun Luo, Yi Zhao, Shunmin He, Chang Chen, Runsheng Chen

{"title":"Enzymes Repertoires and Genomic Insights into Lycium Barbarum Pectin Polysaccharides Biosynthesis.","authors":"Haiyan Yue, Yiheng Tang, Aixuan Li, Lili Zhang, Yiwei Niu, Yiming Zhang, Hao Wang, Jianjun Luo, Yi Zhao, Shunmin He, Chang Chen, Runsheng Chen","doi":"10.1093/gpbjnl/qzae079","DOIUrl":"https://doi.org/10.1093/gpbjnl/qzae079","url":null,"abstract":"Lycium barbarum, a member of the Solanaceae family, represents an important eudicot lineage with homology of food and medicine. Lycium barbarum pectin polysaccharides (LBPPs) are key bioactive ingredients of Lycium barbarum, and are among the few polysaccharides with both biocompatibility and biomedical activity. While previous studies have primarily focused on the functional properties of LBPPs, the mechanisms of biosynthesis and transport by key enzymes remain poorly understood. Here, we reported the completion of a 2.18-gigabase reference genome of Lycium barbarum, reconstructed the first entire biosynthesis of pectin polysaccharides and sugar transport, and characterized the important genes responsible for backbone extending, sidechain synthesis, and modification of pectin polysaccharides. Additionally, we characterized long non-coding RNAs (lncRNAs) associated with polysaccharide metabolism and identified a specific rhamnogalacturonan I (RG-I) rhamnosyltransferase, RRT3020, which enhances RG-I biosynthesis in LBPPs. These newly identified enzymes and pivotal genes endow L. barbarum with specific pectin biosynthesis capabilities, distinguishing it from other Solanaceae species. Our findings provide a foundation for evolutionary studies and molecular breeding to enhance the diverse applications of L. barbarum.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142570796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility. N6-甲基腺苷修饰在配子发生和胚胎发生中的作用：对生育能力的影响

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae050

Yujie Wang, Chen Yang, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang, Chengqi Yi

{"title":"The Role of N6-methyladenosine Modification in Gametogenesis and Embryogenesis: Impact on Fertility.","authors":"Yujie Wang, Chen Yang, Hanxiao Sun, Hui Jiang, Pin Zhang, Yue Huang, Zhenran Liu, Yaru Yu, Zuying Xu, Huifen Xiang, Chengqi Yi","doi":"10.1093/gpbjnl/qzae050","DOIUrl":"10.1093/gpbjnl/qzae050","url":null,"abstract":"The most common epigenetic modification of messenger RNAs (mRNAs) is N6-methyladenosine (m6A), which is mainly located near the 3' untranslated region of mRNAs, near the stop codons, and within internal exons. The biological effect of m6A is dynamically modulated by methyltransferases (writers), demethylases (erasers), and m6A-binding proteins (readers). By controlling post-transcriptional gene expression, m6A has a significant impact on numerous biological functions, including RNA transcription, translation, splicing, transport, and degradation. Hence, m6A influences various physiological and pathological processes, such as spermatogenesis, oogenesis, embryogenesis, placental function, and human reproductive system diseases. During gametogenesis and embryogenesis, genetic material undergoes significant changes, including epigenomic modifications such as m6A. From spermatogenesis and oogenesis to the formation of an oosperm and early embryogenesis, m6A changes occur at every step. m6A abnormalities can lead to gamete abnormalities, developmental delays, impaired fertilization, and maternal-to-zygotic transition blockage. Both mice and humans with abnormal m6A modifications exhibit impaired fertility. In this review, we discuss the dynamic biological effects of m6A and its regulators on gamete and embryonic development and review the possible mechanisms of infertility caused by m6A changes. We also discuss the drugs currently used to manipulate m6A and provide prospects for the prevention and treatment of infertility at the epigenetic level.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514847/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141473856","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer. 整合分子生物学发现肿瘤镁含量低是结直肠癌的一个驱动因素

Genomics, proteomics & bioinformatics Pub Date : 2024-10-15 DOI: 10.1093/gpbjnl/qzae053

Rou Zhang, Meng Hu, Yu Liu, Wanmeng Li, Zhiqiang Xu, Siyu He, Ying Lu, Yanqiu Gong, Xiuxuan Wang, Shan Hai, Shuangqing Li, Shiqian Qi, Yuan Li, Yang Shu, Dan Du, Huiyuan Zhang, Heng Xu, Zongguang Zhou, Peng Lei, Hai-Ning Chen, Lunzhi Dai

{"title":"Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer.","authors":"Rou Zhang, Meng Hu, Yu Liu, Wanmeng Li, Zhiqiang Xu, Siyu He, Ying Lu, Yanqiu Gong, Xiuxuan Wang, Shan Hai, Shuangqing Li, Shiqian Qi, Yuan Li, Yang Shu, Dan Du, Huiyuan Zhang, Heng Xu, Zongguang Zhou, Peng Lei, Hai-Ning Chen, Lunzhi Dai","doi":"10.1093/gpbjnl/qzae053","DOIUrl":"10.1093/gpbjnl/qzae053","url":null,"abstract":"Magnesium (Mg) deficiency is associated with increased risk and malignancy in colorectal cancer (CRC), yet the underlying mechanisms remain elusive. Here, we used genomic, proteomic, and phosphoproteomic data to elucidate the impact of Mg deficiency on CRC. Genomic analysis identified 160 genes with higher mutation frequencies in Low-Mg tumors, including key driver genes such as KMT2C and ERBB3. Unexpectedly, initiation driver genes of CRC, such as TP53 and APC, displayed higher mutation frequencies in High-Mg tumors. Additionally, proteomic and phosphoproteomic data indicated that low Mg content in tumors may activate epithelial-mesenchymal transition (EMT) by modulating inflammation or remodeling the phosphoproteome of cancer cells. Notably, we observed a negative correlation between the phosphorylation of DBN1 at S142 (DBN1S142p) and Mg content. A mutation in S142 to D (DBN1S142D) mimicking DBN1S142p up-regulated MMP2 and enhanced cell migration, while treatment with MgCl2 reduced DBN1S142p, thereby reversing this phenotype. Mechanistically, Mg2+ attenuated the DBN1-ACTN4 interaction by decreasing DBN1S142p, which in turn enhanced the binding of ACTN4 to F-actin and promoted F-actin polymerization, ultimately reducing MMP2 expression. These findings shed new light on the crucial role of Mg deficiency in CRC progression and suggest that Mg supplementation may be a promising preventive and therapeutic strategy for CRC.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11514849/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141763491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0