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The impact of IDR phosphorylation on the RNA binding profiles of proteins IDR 磷酸化对蛋白质 RNA 结合情况的影响
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-05-04 DOI: 10.1016/j.tig.2024.04.004
Miha Modic, Maksimiljan Adamek, Jernej Ule
{"title":"The impact of IDR phosphorylation on the RNA binding profiles of proteins","authors":"Miha Modic, Maksimiljan Adamek, Jernej Ule","doi":"10.1016/j.tig.2024.04.004","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.004","url":null,"abstract":"<p>Due to their capacity to mediate repetitive protein interactions, intrinsically disordered regions (IDRs) are crucial for the formation of various types of protein–RNA complexes. The functions of IDRs are strongly modulated by post-translational modifications (PTMs). Phosphorylation is the most common and well-studied modification of IDRs, which can alter homomeric or heteromeric interactions of proteins and impact their ability to phase separate. Moreover, phosphorylation can influence the RNA-binding properties of proteins, and recent studies demonstrated its selective impact on the global profiles of protein–RNA binding and regulation. These findings highlight the need for further integrative approaches to understand how signalling remodels protein–RNA networks in cells.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"49 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140834143","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 molecular basis of phenotypic evolution: beyond the usual suspects 表型进化的分子基础：超越常见的疑点
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-05-03 DOI: 10.1016/j.tig.2024.04.010
Rong-Chien Lin, Bianca T. Ferreira, Yao-Wu Yuan
{"title":"The molecular basis of phenotypic evolution: beyond the usual suspects","authors":"Rong-Chien Lin, Bianca T. Ferreira, Yao-Wu Yuan","doi":"10.1016/j.tig.2024.04.010","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.010","url":null,"abstract":"<p>It has been well documented that mutations in coding DNA or <em>cis</em>-regulatory elements underlie natural phenotypic variation in many organisms. However, the development of sophisticated functional tools in recent years in a wide range of traditionally non-model systems have revealed many ‘unusual suspects’ in the molecular bases of phenotypic evolution, including upstream open reading frames (uORFs), cryptic splice sites, and small RNAs. Furthermore, large-scale genome sequencing, especially long-read sequencing, has identified a cornucopia of structural variation underlying phenotypic divergence and elucidated the composition of supergenes that control complex multi-trait polymorphisms. In this review article we highlight recent studies that demonstrate this great diversity of molecular mechanisms producing adaptive genetic variation and the panoply of evolutionary paths leading to the ‘grandeur of life’.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"89 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140834148","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
Genetic architecture of brain morphology and overlap with neuropsychiatric traits 大脑形态的遗传结构及其与神经精神特征的重叠
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-05-02 DOI: 10.1016/j.tig.2024.04.005
Yi-Jun Ge, Yan Fu, Weikang Gong, Wei Cheng, Jin-Tai Yu
{"title":"Genetic architecture of brain morphology and overlap with neuropsychiatric traits","authors":"Yi-Jun Ge, Yan Fu, Weikang Gong, Wei Cheng, Jin-Tai Yu","doi":"10.1016/j.tig.2024.04.005","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.005","url":null,"abstract":"<p>Uncovering the genetic architectures of brain morphology offers valuable insights into brain development and disease. Genetic association studies of brain morphological phenotypes have discovered thousands of loci. However, interpretation of these loci presents a significant challenge. One potential solution is exploring the genetic overlap between brain morphology and disorders, which can improve our understanding of their complex relationships, ultimately aiding in clinical applications. In this review, we examine current evidence on the genetic associations between brain morphology and neuropsychiatric traits. We discuss the impact of these associations on the diagnosis, prediction, and treatment of neuropsychiatric diseases, along with suggestions for future research directions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"58 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140834023","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
Formaldehyde regulates one-carbon metabolism and epigenetics. 甲醛调节一碳代谢和表观遗传学。
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-03-18 DOI: 10.1016/j.tig.2024.03.002
Marcus J C Long, Yimon Aye
{"title":"Formaldehyde regulates one-carbon metabolism and epigenetics.","authors":"Marcus J C Long, Yimon Aye","doi":"10.1016/j.tig.2024.03.002","DOIUrl":"10.1016/j.tig.2024.03.002","url":null,"abstract":"<p><p>Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT)-1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against it. This provides a new lens for understanding the effects of formaldehyde on gene regulation.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"381-382"},"PeriodicalIF":11.4,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140177735","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
Clocks at sea: the genome-editing tide is rising. 海上时钟：基因组编辑浪潮正在兴起。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-02-08 DOI: 10.1016/j.tig.2024.01.006
Erica R Kwiatkowski, Joshua J C Rosenthal, Patrick Emery
{"title":"Clocks at sea: the genome-editing tide is rising.","authors":"Erica R Kwiatkowski, Joshua J C Rosenthal, Patrick Emery","doi":"10.1016/j.tig.2024.01.006","DOIUrl":"10.1016/j.tig.2024.01.006","url":null,"abstract":"<p><p>The coastline is a particularly challenging environment for its inhabitants. Not only do they have to cope with the solar day and the passing of seasons, but they must also deal with tides. In addition, many marine species track the phase of the moon, especially to coordinate reproduction. Marine animals show remarkable behavioral and physiological adaptability, using biological clocks to anticipate specific environmental cycles. Presently, we lack a basic understanding of the molecular mechanisms underlying circatidal and circalunar clocks. Recent advances in genome engineering and the development of genetically tractable marine model organisms are transforming how we study these timekeeping mechanisms and opening a novel era in marine chronobiology.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"387-397"},"PeriodicalIF":13.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139713425","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
Unraveling the diversity and cultural heritage of fruit crops through paleogenomics. 通过古基因组学揭示水果作物的多样性和文化遗产。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-02-28 DOI: 10.1016/j.tig.2024.02.003
Meirav Meiri, Guy Bar-Oz
{"title":"Unraveling the diversity and cultural heritage of fruit crops through paleogenomics.","authors":"Meirav Meiri, Guy Bar-Oz","doi":"10.1016/j.tig.2024.02.003","DOIUrl":"10.1016/j.tig.2024.02.003","url":null,"abstract":"<p><p>Abundant and plentiful fruit crops are threatened by the loss of diverse legacy cultivars which are being replaced by a limited set of high-yielding ones. This article delves into the potential of paleogenomics that utilizes ancient DNA analysis to revive lost diversity. By focusing on grapevines, date palms, and tomatoes, recent studies showcase the effectiveness of paleogenomic techniques in identifying and understanding genetic traits crucial for crop resilience, disease resistance, and nutritional value. The approach not only tracks landrace dispersal and introgression but also sheds light on domestication events. In the face of major future environmental challenges, integrating paleogenomics with modern breeding strategies emerges as a promising avenue to significantly bolster fruit crop sustainability.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"398-409"},"PeriodicalIF":13.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11079635/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139998312","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
Helitrons: genomic parasites that generate developmental novelties. 螺旋体：产生发育新特性的基因组寄生虫。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-02-29 DOI: 10.1016/j.tig.2024.02.002
Daniela Barro-Trastoy, Claudia Köhler
{"title":"Helitrons: genomic parasites that generate developmental novelties.","authors":"Daniela Barro-Trastoy, Claudia Köhler","doi":"10.1016/j.tig.2024.02.002","DOIUrl":"10.1016/j.tig.2024.02.002","url":null,"abstract":"<p><p>Helitrons, classified as DNA transposons, employ rolling-circle intermediates for transposition. Distinguishing themselves from other DNA transposons, they leave the original template element unaltered during transposition, which has led to their characterization as 'peel-and-paste elements'. Helitrons possess the ability to capture and mobilize host genome fragments, with enormous consequences for host genomes. This review discusses the current understanding of Helitrons, exploring their origins, transposition mechanism, and the extensive repercussions of their activity on genome structure and function. We also explore the evolutionary conflicts stemming from Helitron-transposed gene fragments and elucidate their domestication for regulating responses to environmental challenges. Looking ahead, further research in this evolving field promises to bring interesting discoveries on the role of Helitrons in shaping genomic landscapes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"437-448"},"PeriodicalIF":13.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140013758","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
Recombination in bdelloid rotifer genomes: asexuality, transfer and stress. 双壳轮虫基因组的重组：无性、转移和压力。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-03-08 DOI: 10.1016/j.tig.2024.02.001
Christopher G Wilson, Tymoteusz Pieszko, Reuben W Nowell, Timothy G Barraclough
{"title":"Recombination in bdelloid rotifer genomes: asexuality, transfer and stress.","authors":"Christopher G Wilson, Tymoteusz Pieszko, Reuben W Nowell, Timothy G Barraclough","doi":"10.1016/j.tig.2024.02.001","DOIUrl":"10.1016/j.tig.2024.02.001","url":null,"abstract":"<p><p>Bdelloid rotifers constitute a class of microscopic animals living in freshwater habitats worldwide. Several strange features of bdelloids have drawn attention: their ability to tolerate desiccation and other stresses, a lack of reported males across the clade despite centuries of study, and unusually high numbers of horizontally acquired, non-metazoan genes. Genome sequencing is transforming our understanding of their lifestyle and its consequences, while in turn providing wider insights about recombination and genome organisation in animals. Many questions remain, not least how to reconcile apparent genomic signatures of sex with the continued absence of reported males, why bdelloids have so many horizontally acquired genes, and how their remarkable ability to survive stress interacts with recombination and other genomic processes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"422-436"},"PeriodicalIF":13.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140066261","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 heterogeneous genetic architectures of orofacial clefts. 口面裂的异质遗传结构。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-05-01 Epub Date: 2024-03-13 DOI: 10.1016/j.tig.2024.02.004
Kelsey Robinson, Sarah W Curtis, Elizabeth J Leslie
{"title":"The heterogeneous genetic architectures of orofacial clefts.","authors":"Kelsey Robinson, Sarah W Curtis, Elizabeth J Leslie","doi":"10.1016/j.tig.2024.02.004","DOIUrl":"10.1016/j.tig.2024.02.004","url":null,"abstract":"<p><p>Orofacial clefts (OFCs) are common, affecting 1:1000 live births. OFCs occur across a phenotypic spectrum - including cleft lip (CL), cleft lip and palate (CLP), or cleft palate (CP) - and can be further subdivided based on laterality, severity, or specific structures affected. Herein we review what is known about the genetic architecture underlying each of these subtypes, considering both shared and subtype-specific risks. While there are more known genetic similarities between CL and CLP than CP, recent research supports both shared and subtype-specific genetic risk factors within and between phenotypic classifications of OFCs. Larger sample sizes and deeper phenotyping data will be of increasing importance for the discovery of novel genetic risk factors for OFCs and various subtypes going forward.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"410-421"},"PeriodicalIF":13.6,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140121342","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
Exploring the role of phage plasmids in gene transfers 探索噬菌体质粒在基因转移中的作用
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-04-29 DOI: 10.1016/j.tig.2024.04.011
Agnieszka K. Szczepankowska, Małgorzata Łobocka
{"title":"Exploring the role of phage plasmids in gene transfers","authors":"Agnieszka K. Szczepankowska, Małgorzata Łobocka","doi":"10.1016/j.tig.2024.04.011","DOIUrl":"https://doi.org/10.1016/j.tig.2024.04.011","url":null,"abstract":"<p>Bacteriophages and plasmids drive horizontal gene transfer (HGT) in bacteria. Phage-plasmids (P-Ps) are hybrids of plasmid and phages. Pfeifer and Rocha recently demonstrated that P-Ps can serve as intermediates in gene exchanges between these two types of elements, identified categories of preferentially transferred genes, and reconstructed gene flows involving phage P1-like P-Ps.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"21 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140811290","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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