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Role of ATP-dependent chromatin remodelers in meiosis. 依赖 ATP 的染色质重塑器在减数分裂中的作用
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-16 DOI: 10.1016/j.tig.2024.10.004
Sheetal Paliwal, Partha Dey, Swarangi Tambat, Akira Shinohara, Gunjan Mehta
{"title":"Role of ATP-dependent chromatin remodelers in meiosis.","authors":"Sheetal Paliwal, Partha Dey, Swarangi Tambat, Akira Shinohara, Gunjan Mehta","doi":"10.1016/j.tig.2024.10.004","DOIUrl":"https://doi.org/10.1016/j.tig.2024.10.004","url":null,"abstract":"<p><p>In eukaryotic cells, DNA is wrapped around histone octamers to compact the genome. Although such compaction is required for the precise segregation of the genome during cell division, it restricts the DNA-protein interactions essential for several cellular processes. During meiosis, a specialized cell division process that produces gametes, several DNA-protein interactions are crucial for assembling meiosis-specific chromosome structures, meiotic recombination, chromosome segregation, and transcriptional regulation. The role of chromatin remodelers (CRs) in facilitating DNA-protein transactions during mitosis is well appreciated, whereas how they facilitate meiosis-specific processes is poorly understood. In this review, we summarize experimental evidence supporting the role of CRs in meiosis in various model systems and suggest future perspectives to advance the field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142645208","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 good, the bad, and Neanderthalic immunity. 好的、坏的和尼安德特人的免疫力。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-14 DOI: 10.1016/j.tig.2024.10.010
Susannah Selber-Hnatiw, Sirui Zhou
{"title":"The good, the bad, and Neanderthalic immunity.","authors":"Susannah Selber-Hnatiw, Sirui Zhou","doi":"10.1016/j.tig.2024.10.010","DOIUrl":"https://doi.org/10.1016/j.tig.2024.10.010","url":null,"abstract":"<p><p>Introgression with archaic hominins and subsequent natural selection has shaped the immune system of modern humans. Recently, Sun et al. investigated the immunity advantages of a Neanderthalic variant in the membrane-bound immunoglobulin G1 (IGHG1) gene, activating pathogen-specific antibody production toward modern threats yet conversely increasing the risk of autoimmune diseases.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640456","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
Can developmental signals shatter or mend our genomes? 发育信号能粉碎或修补我们的基因组吗？
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-07 DOI: 10.1016/j.tig.2024.10.006
Yimiao Qu, Kyle M Loh
{"title":"Can developmental signals shatter or mend our genomes?","authors":"Yimiao Qu, Kyle M Loh","doi":"10.1016/j.tig.2024.10.006","DOIUrl":"https://doi.org/10.1016/j.tig.2024.10.006","url":null,"abstract":"<p><p>Consensus holds that most cells in the embryo are genetically identical and have healthy genomes. However, embryonic cells with abnormal chromosomes are surprisingly frequent. In a recent publication, de Jaime-Soguero et al. report that extracellular developmental signaling pathways, including BMP, FGF, and WNT, can promote or prevent chromosome instability in certain cell types.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142607437","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
Yes, polygenic sex determination is a thing! 是的，多基因性别决定是个东西！
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-11-05 DOI: 10.1016/j.tig.2024.10.003
Thomas D Kocher, Richard P Meisel, Tony Gamble, Kristen A Behrens, William J Gammerdinger
{"title":"Yes, polygenic sex determination is a thing!","authors":"Thomas D Kocher, Richard P Meisel, Tony Gamble, Kristen A Behrens, William J Gammerdinger","doi":"10.1016/j.tig.2024.10.003","DOIUrl":"https://doi.org/10.1016/j.tig.2024.10.003","url":null,"abstract":"<p><p>The process of sexual development in animals is modulated by a variety of mechanisms. Some species respond to environmental cues, while, in others, sex determination is thought to be controlled by a single 'master regulator' gene. However, many animals respond to a combination of environmental cues (e.g., temperature) and genetic factors (e.g., sex chromosomes). Even among species in which genetic factors predominate, there is a continuum between monofactorial and polygenic systems. The perception that polygenic systems are rare may result from experiments that lack the statistical power to detect multiple loci. Intellectual biases against the existence of polygenic sex determination (PSD) may further arise from misconceptions about the regulation of developmental processes and a misreading of theoretical results on the stability of polygenic systems of sex determination.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142592117","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
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
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