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Advances in lasso peptide discovery, biosynthesis, and function. 套索肽的发现、生物合成和功能方面的进展。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-31 DOI: 10.1016/j.tig.2024.08.002
Susanna E Barrett, Douglas A Mitchell
{"title":"Advances in lasso peptide discovery, biosynthesis, and function.","authors":"Susanna E Barrett, Douglas A Mitchell","doi":"10.1016/j.tig.2024.08.002","DOIUrl":"10.1016/j.tig.2024.08.002","url":null,"abstract":"<p><p>Lasso peptides are a large and sequence-diverse class of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products characterized by their slip knot-like shape. These unique, highly stable peptides are produced by bacteria for various purposes. Their stability and sequence diversity make them a potentially useful scaffold for biomedically relevant folded peptides. However, many questions remain about lasso peptide biosynthesis, ecological function, and diversification potential for biomedical and agricultural applications. This review discusses new insights and open questions about lasso peptide biosynthesis and biological function. The role that genome mining has played in the development of new methodologies for discovering and diversifying lasso peptides is also discussed.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"950-968"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537843/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142114735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Rewards and dangers of regulatory innovation. 监管创新的回报与危险。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-20 DOI: 10.1016/j.tig.2024.07.010
Luca Comai
{"title":"Rewards and dangers of regulatory innovation.","authors":"Luca Comai","doi":"10.1016/j.tig.2024.07.010","DOIUrl":"10.1016/j.tig.2024.07.010","url":null,"abstract":"<p><p>Adaptive evolution often involves structural variation affecting genes or cis-regulatory changes that engender novel and favorable gain-of-function gene regulation. Such mutation could result in a favorable dominant trait. At the same time, the gene product could be dosage sensitive if its change in concentration disrupts another trait. As a result, the mutant allele would display dosage-sensitive pleiotropy (DSP). By minimizing imbalance while conserving the favorable dominant effect, heterozygosity can increase fitness and result in heterosis. The properties of these alleles are consistent with evidence from multiple studies that indicate increased fitness of heterozygous regulatory mutations. DSP can help explain mysterious properties of heterosis as well as other effects of hybridization.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"917-926"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142019599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Wheat genomics: genomes, pangenomes, and beyond. 小麦基因组学：基因组、泛基因组及其他。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-26 DOI: 10.1016/j.tig.2024.07.004
Vijay K Tiwari, Gautam Saripalli, Parva K Sharma, Jesse Poland
{"title":"Wheat genomics: genomes, pangenomes, and beyond.","authors":"Vijay K Tiwari, Gautam Saripalli, Parva K Sharma, Jesse Poland","doi":"10.1016/j.tig.2024.07.004","DOIUrl":"10.1016/j.tig.2024.07.004","url":null,"abstract":"<p><p>There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"982-992"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142082542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder. ReNU综合症--一种新发现的神经发育障碍。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-10-01 DOI: 10.1016/j.tig.2024.09.005
Vanessa F Burns, Elizabeth J Radford
{"title":"ReNU syndrome - a newly discovered prevalent neurodevelopmental disorder.","authors":"Vanessa F Burns, Elizabeth J Radford","doi":"10.1016/j.tig.2024.09.005","DOIUrl":"10.1016/j.tig.2024.09.005","url":null,"abstract":"<p><p>Two recent papers have identified genetic variants in the noncoding gene RNU4-2 to cause a frequent neurodevelopmental disorder. This work will have a substantial impact on the rare disease community, leading to thousands of diagnoses worldwide. These studies also highlight the untapped diagnostic potential of noncoding regions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"914-916"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367344","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The very early evolution of biological complexity. 生物复杂性的早期进化
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-09-25 DOI: 10.1016/j.tig.2024.09.001
Aaron D Goldman, Gregory P Fournier
{"title":"The very early evolution of biological complexity.","authors":"Aaron D Goldman, Gregory P Fournier","doi":"10.1016/j.tig.2024.09.001","DOIUrl":"10.1016/j.tig.2024.09.001","url":null,"abstract":"<p><p>All extant life is descended from a common ancestor, which, despite being very ancient, appears to have been a complex cellular organism. A new study by Moody et al. shows that this ancestor was not only a complex cell, but also lived within a microbial ecology likely inhabited by other complex cells.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"912-913"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142332465","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Computational methods for allele-specific expression in single cells. 单细胞中等位基因特异性表达的计算方法。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-08-10 DOI: 10.1016/j.tig.2024.07.003
Guanghao Qi, Alexis Battle
{"title":"Computational methods for allele-specific expression in single cells.","authors":"Guanghao Qi, Alexis Battle","doi":"10.1016/j.tig.2024.07.003","DOIUrl":"10.1016/j.tig.2024.07.003","url":null,"abstract":"<p><p>Allele-specific expression (ASE) is a powerful signal that can be used to investigate multiple molecular mechanisms, such as cis-regulatory effects and imprinting. Single-cell RNA-sequencing (scRNA-seq) enables ASE characterization at the resolution of individual cells. In this review, we highlight the computational methods for processing and analyzing single-cell ASE data. We first describe a bioinformatics pipeline to obtain ASE counts from raw reads synthesized from previous literature. We then discuss statistical methods for detecting allelic imbalance and its variability across conditions using scRNA-seq data. In addition, we describe other methods that use single-cell ASE to address specific biological questions. Finally, we discuss future directions and emphasize the need for an integrated, optimized bioinformatics pipeline, and further development of statistical methods for different technologies.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"939-949"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11537817/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141914574","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Honeybees' novel complementary sex-determining system: function and origin. 蜜蜂的新型互补性决定系统：功能和起源。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-01 Epub Date: 2024-09-03 DOI: 10.1016/j.tig.2024.08.001
Jana Seiler, Martin Beye
{"title":"Honeybees' novel complementary sex-determining system: function and origin.","authors":"Jana Seiler, Martin Beye","doi":"10.1016/j.tig.2024.08.001","DOIUrl":"10.1016/j.tig.2024.08.001","url":null,"abstract":"<p><p>Complementary sex determination regulates female and male development in honeybees (Apis mellifera) via heterozygous versus homo-/hemizygous genotypes of the csd (complementary sex determiner) gene involving numerous naturally occurring alleles. This lineage-specific function offers a rare opportunity to understand an undescribed regulatory mechanism and the molecular evolutionary path leading to this mechanism. We reviewed recent advances in understanding how Csd recognizes different versus identical protein variants, how these variants regulate downstream pathways and sexual differentiation, and how this mechanism has evolved and been shaped by evolutionary forces. Finally, we highlighted the shared regulatory principles of sex determination despite the diversity of primary signals and demonstrated that lineage-specific mutations are very informative for characterizing newly evolved functions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"969-981"},"PeriodicalIF":13.6,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142134472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A molecular mechanism for environmental sex determination. 环境性别决定的分子机制
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-29 DOI: 10.1016/j.tig.2024.07.005
Xiaojing Li, John K Colbourne
{"title":"A molecular mechanism for environmental sex determination.","authors":"Xiaojing Li, John K Colbourne","doi":"10.1016/j.tig.2024.07.005","DOIUrl":"10.1016/j.tig.2024.07.005","url":null,"abstract":"<p><p>Daphnia produce genetically identical males and females; their sex is determined by environmental conditions. Recently, Kato et al. identified isoform switching events in Daphnia as a gene regulatory mechanism for sex-specific development. This finding uncovers the impact of alternative usage of gene isoforms on this extreme phenotypic plasticity trait.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"817-818"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857158","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
New insights into oocyte cytoplasmic lattice-associated proteins. 对卵母细胞胞质晶格相关蛋白的新认识。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-07-01 DOI: 10.1016/j.tig.2024.06.002
Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio
{"title":"New insights into oocyte cytoplasmic lattice-associated proteins.","authors":"Carlo Giaccari, Francesco Cecere, Lucia Argenziano, Angela Pagano, Andrea Riccio","doi":"10.1016/j.tig.2024.06.002","DOIUrl":"10.1016/j.tig.2024.06.002","url":null,"abstract":"<p><p>Oocyte maturation and preimplantation embryo development are critical to successful pregnancy outcomes and the correct establishment and maintenance of genomic imprinting. Thanks to novel technologies and omics studies in human patients and mouse models, the importance of the proteins associated with the cytoplasmic lattices (CPLs), highly abundant structures found in the cytoplasm of mammalian oocytes and preimplantation embryos, in the maternal to zygotic transition is becoming increasingly evident. This review highlights the recent discoveries on the role of these proteins in protein storage and other oocyte cytoplasmic processes, epigenetic reprogramming, and zygotic genome activation (ZGA). A better comprehension of these events may significantly improve clinical diagnosis and pave the way for targeted interventions aiming to correct or mitigate female fertility issues and genomic imprinting disorders.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"880-890"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141494289","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Artificial intelligence in plant breeding. 人工智能在植物育种中的应用。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-10-01 Epub Date: 2024-08-07 DOI: 10.1016/j.tig.2024.07.001
Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li
{"title":"Artificial intelligence in plant breeding.","authors":"Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan, Zhangping Huang, Awais Rasheed, Sarah Hearne, Boddupalli Prasanna, Xinhai Li, Huihui Li","doi":"10.1016/j.tig.2024.07.001","DOIUrl":"10.1016/j.tig.2024.07.001","url":null,"abstract":"<p><p>Harnessing cutting-edge technologies to enhance crop productivity is a pivotal goal in modern plant breeding. Artificial intelligence (AI) is renowned for its prowess in big data analysis and pattern recognition, and is revolutionizing numerous scientific domains including plant breeding. We explore the wider potential of AI tools in various facets of breeding, including data collection, unlocking genetic diversity within genebanks, and bridging the genotype-phenotype gap to facilitate crop breeding. This will enable the development of crop cultivars tailored to the projected future environments. Moreover, AI tools also hold promise for refining crop traits by improving the precision of gene-editing systems and predicting the potential effects of gene variants on plant phenotypes. Leveraging AI-enabled precision breeding can augment the efficiency of breeding programs and holds promise for optimizing cropping systems at the grassroots level. This entails identifying optimal inter-cropping and crop-rotation models to enhance agricultural sustainability and productivity in the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"891-908"},"PeriodicalIF":13.6,"publicationDate":"2024-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141908320","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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