Genomics, proteomics & bioinformatics最新文献_第5页

RNA Modifications and Epitranscriptomics. RNA修饰和上皮转录组学。

Genomics, proteomics & bioinformatics Pub Date : 2023-08-01 Epub Date: 2023-10-19 DOI: 10.1016/j.gpb.2023.10.002

Chengqi Yi, Jianhua Yang

引用次数: 0

Characteristics of N⁶-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii. 莱茵衣藻有性生殖过程中n6 -甲基腺苷修饰的特征。

Genomics, proteomics & bioinformatics Pub Date : 2023-08-01 Epub Date: 2022-05-10 DOI: 10.1016/j.gpb.2022.04.004

Ying Lv, Fei Han, Mengxia Liu, Ting Zhang, Guanshen Cui, Jiaojiao Wang, Ying Yang, Yun-Gui Yang, Wenqiang Yang

{"title":"Characteristics of N6-methyladenosine Modification During Sexual Reproduction of Chlamydomonas reinhardtii.","authors":"Ying Lv, Fei Han, Mengxia Liu, Ting Zhang, Guanshen Cui, Jiaojiao Wang, Ying Yang, Yun-Gui Yang, Wenqiang Yang","doi":"10.1016/j.gpb.2022.04.004","DOIUrl":"10.1016/j.gpb.2022.04.004","url":null,"abstract":"The unicellular green alga Chlamydomonas reinhardtii (hereafter Chlamydomonas) possesses both plant and animal attributes, and it is an ideal model organism for studying fundamental processes such as photosynthesis, sexual reproduction, and life cycle. N6-methyladenosine (m6A) is the most prevalent mRNA modification, and it plays important roles during sexual reproduction in animals and plants. However, the pattern and function of m6A modification during the sexual reproduction of Chlamydomonas remain unknown. Here, we performed transcriptome and methylated RNA immunoprecipitation sequencing (MeRIP-seq) analyses on six samples from different stages during sexual reproduction of the Chlamydomonas life cycle. The results show that m6A modification frequently occurs at the main motif of DRAC (D = G/A/U, R = A/G) in Chlamydomonas mRNAs. Moreover, m6A peaks in Chlamydomonas mRNAs are mainly enriched in the 3' untranslated regions (3'UTRs) and negatively correlated with the abundance of transcripts at each stage. In particular, there is a significant negative correlation between the expression levels and the m6A levels of genes involved in the microtubule-associated pathway, indicating that m6A modification influences the sexual reproduction and the life cycle of Chlamydomonas by regulating microtubule-based movement. In summary, our findings are the first to demonstrate the distribution and the functions of m6A modification in Chlamydomonas mRNAs and provide new evolutionary insights into m6A modification in the process of sexual reproduction in other plant organisms.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10787120/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138453356","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

mvPPT: A Highly Efficient and Sensitive Pathogenicity Prediction Tool for Missense Variants mvPPT:一种高效灵敏的错义变异致病性预测工具

Genomics, proteomics & bioinformatics Pub Date : 2022-01-06 DOI: 10.1101/2022.01.05.475156

S. Tong, Ke Fan, Zai-wei Zhou, Lin-Yun Liu, Shu-Qing Zhang, Yinghui Fu, Guangchao Wang, Ying Zhu, Yong-Chun Yu

引用次数: 1

deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues deCS:人体组织中单细胞RNA测序数据的系统细胞类型注释工具

Genomics, proteomics & bioinformatics Pub Date : 2021-09-22 DOI: 10.1101/2021.09.19.460993

Guangsheng Pei, F. Yan, L. Simon, Yulin Dai, P. Jia, Zhongming Zhao

{"title":"deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues","authors":"Guangsheng Pei, F. Yan, L. Simon, Yulin Dai, P. Jia, Zhongming Zhao","doi":"10.1101/2021.09.19.460993","DOIUrl":"https://doi.org/10.1101/2021.09.19.460993","url":null,"abstract":"Single-cell RNA sequencing (scRNA-seq) is revolutionizing the study of complex and dynamic cellular mechanisms. However, cell-type annotation remains a main challenge as it largely relies on a priori knowledge and manual curation, which is cumbersome and less accurate. The increasing number of scRNA-seq data sets, as well as numerous published genetic studies, motivated us to build a comprehensive human cell type reference atlas. Here, we present deCS (decoding Cell type-Specificity), an automatic cell type annotation method augmented by a comprehensive collection of human cell type expression profiles and marker genes. We used deCS to annotate scRNA-seq data from various tissue types and systematically evaluated the annotation accuracy under different conditions, including reference panels, sequencing depth and feature selection strategies. Our results demonstrated that expanding the references is critical for improving annotation accuracy. Compared to many existing state-of-the-art annotation tools, deCS significantly reduced computation time and increased accuracy. deCS can be integrated into the standard scRNA-seq analytical pipeline to enhance cell type annotation. Finally, we demonstrated the broad utility of deCS to identify trait-cell type associations in 51 human complex traits, providing deeper insights into the cellular mechanisms of disease pathogenesis. All documents, including source code, user manual, demo data, and tutorials, are freely available at https://github.com/bsml320/deCS.","PeriodicalId":94020,"journal":{"name":"Genomics, proteomics & bioinformatics","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86778324","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: 12

RegVar: Tissue-specific Prioritization of Non-coding Regulatory Variants RegVar:非编码调控变异的组织特异性优先级

Genomics, proteomics & bioinformatics Pub Date : 2021-04-19 DOI: 10.1101/2021.04.17.440295

Hao Lu, Luyu Ma, Cheng Quan, Lei Li, Yiming Lu, Gangqiao Zhou, Chenggang Zhang

引用次数: 1