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The intricacies of isomiRs: from classification to clinical relevance. 等位基因的复杂性：从分类到临床意义。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-06-10 DOI: 10.1016/j.tig.2024.05.007
Viktoria Wagner, Eckart Meese, Andreas Keller
{"title":"The intricacies of isomiRs: from classification to clinical relevance.","authors":"Viktoria Wagner, Eckart Meese, Andreas Keller","doi":"10.1016/j.tig.2024.05.007","DOIUrl":"10.1016/j.tig.2024.05.007","url":null,"abstract":"<p><p>MicroRNAs (miRNAs) and isoforms of their archetype, called isomiRs, regulate gene expression via complementary base-pair binding to messenger RNAs (mRNAs). The partially evolutionarily conserved isomiR sequence variations are differentially expressed among tissues, populations, and genders, and between healthy and diseased states. Aiming towards the clinical use of isomiRs as diagnostic biomarkers and for therapeutic purposes, several challenges need to be addressed, including (i) clarification of isomiR definition, (ii) improved annotation in databases with new standardization (such as the mirGFF3 format), and (iii) improved methods of isomiR detection, functional verification, and in silico analysis. In this review we discuss the respective challenges, and highlight the opportunities for clinical use of isomiRs, especially in the light of increasing amounts of next-generation sequencing (NGS) data.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"784-796"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141307435","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
Gene for eye placement comes into focus. 眼位基因成为焦点。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-06-27 DOI: 10.1016/j.tig.2024.06.004
Justin P Kumar
{"title":"Gene for eye placement comes into focus.","authors":"Justin P Kumar","doi":"10.1016/j.tig.2024.06.004","DOIUrl":"10.1016/j.tig.2024.06.004","url":null,"abstract":"<p><p>The Drosophila compound eye is an attractive system for unraveling how tissues are specified and patterned. Puli et al. recently demonstrated that eye size and spacing are controlled by the defective proventriculus (dve) gene. This impacts our understanding of hypertelorism, a disorder associated with mutations in special AT-rich binding protein 1 (SATB1), the human ortholog of Dve.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"734-735"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141472638","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
Butterflies in your stomach? Not an issue for nearly 8000 species of fishes. 胃里有蝴蝶？对于近 8000 种鱼类来说，这不是问题。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-07-29 DOI: 10.1016/j.tig.2024.07.002
Donovan P German
{"title":"Butterflies in your stomach? Not an issue for nearly 8000 species of fishes.","authors":"Donovan P German","doi":"10.1016/j.tig.2024.07.002","DOIUrl":"10.1016/j.tig.2024.07.002","url":null,"abstract":"<p><p>The gastric stomach is a hallmark of vertebrate evolution, yet is missing in nearly 25% of living fish species and some mammals. New work by Kato et al. shows how a cassette of genes relating to acid production, pepsins, cell adhesion, and developmental control are repeatedly lost in animals that have also lost their stomachs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"731-733"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857159","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
(Single-stranded DNA) gaps in understanding BRCAness. (单链 DNA）在理解 BRCAness 方面存在差距。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-05-23 DOI: 10.1016/j.tig.2024.04.013
Anne Schreuder, Tiemen J Wendel, Carlo G V Dorresteijn, Sylvie M Noordermeer
{"title":"(Single-stranded DNA) gaps in understanding BRCAness.","authors":"Anne Schreuder, Tiemen J Wendel, Carlo G V Dorresteijn, Sylvie M Noordermeer","doi":"10.1016/j.tig.2024.04.013","DOIUrl":"10.1016/j.tig.2024.04.013","url":null,"abstract":"<p><p>The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"757-771"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094338","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
Building the brain mosaic: an expanded view. 构建大脑马赛克：扩展视角。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-06-08 DOI: 10.1016/j.tig.2024.05.008
Sahibjot Sran, Amanda Ringland, Tracy A Bedrosian
{"title":"Building the brain mosaic: an expanded view.","authors":"Sahibjot Sran, Amanda Ringland, Tracy A Bedrosian","doi":"10.1016/j.tig.2024.05.008","DOIUrl":"10.1016/j.tig.2024.05.008","url":null,"abstract":"<p><p>The complexity of the brain is closely tied to its nature as a genetic mosaic, wherein each cell is distinguished by a unique constellation of somatic variants that contribute to functional and phenotypic diversity. Postzygotic variation arising during neurogenesis is recognized as a key contributor to brain mosaicism; however, recent advances have broadened our understanding to include sources of neural genomic diversity that develop throughout the entire lifespan, from embryogenesis through aging. Moving beyond the traditional confines of neurodevelopment, in this review, we delve into the complex mechanisms that enable various origins of brain mosaicism.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"747-756"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11387136/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141297293","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
A multi-epigenomic map of endurance exercise training. 耐力运动训练的多表观基因组图谱
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-07-12 DOI: 10.1016/j.tig.2024.06.005
Adam P Sharples
{"title":"A multi-epigenomic map of endurance exercise training.","authors":"Adam P Sharples","doi":"10.1016/j.tig.2024.06.005","DOIUrl":"10.1016/j.tig.2024.06.005","url":null,"abstract":"<p><p>The Molecular Transducers of Physical Activity Consortium (MoTrPAC) aims to comprehensively map molecular alterations in response to acute exercise and chronic training. In one of a recent series of papers from MoTrPAC, Nair et al. provide the first multi-epigenomic and transcriptomic integration across eight tissues in both sexes following adaptation to endurance exercise training (EET).</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"736-738"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141604508","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
Viral cis-regulatory elements as sensors of cellular states and environmental cues. 作为细胞状态和环境线索传感器的病毒顺式调节元件
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-05-30 DOI: 10.1016/j.tig.2024.05.004
Jaice T Rottenberg, Tommy H Taslim, Luis F Soto-Ugaldi, Lucia Martinez-Cuesta, Camila Martinez-Calejman, Juan I Fuxman Bass
{"title":"Viral cis-regulatory elements as sensors of cellular states and environmental cues.","authors":"Jaice T Rottenberg, Tommy H Taslim, Luis F Soto-Ugaldi, Lucia Martinez-Cuesta, Camila Martinez-Calejman, Juan I Fuxman Bass","doi":"10.1016/j.tig.2024.05.004","DOIUrl":"10.1016/j.tig.2024.05.004","url":null,"abstract":"<p><p>To withstand a hostile cellular environment and replicate, viruses must sense, interpret, and respond to many internal and external cues. Retroviruses and DNA viruses can intercept these cues impinging on host transcription factors via cis-regulatory elements (CREs) in viral genomes, allowing them to sense and coordinate context-specific responses to varied signals. Here, we explore the characteristics of viral CREs, the classes of signals and host transcription factors that regulate them, and how this informs outcomes of viral replication, immune evasion, and latency. We propose that viral CREs constitute central hubs for signal integration from multiple pathways and that sequence variation between viral isolates can rapidly rewire sensing mechanisms, contributing to the variability observed in patient outcomes.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"772-783"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11387143/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141184959","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
Histone oxidation as a new mechanism of metabolic control over gene expression. 组蛋白氧化是基因表达的一种新的代谢控制机制。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-09-01 Epub Date: 2024-06-23 DOI: 10.1016/j.tig.2024.05.012
Benjamin N Gantner, Flavio R Palma, Cezar Kayzuka, Riccardo Lacchini, Daniel R Foltz, Vadim Backman, Neil Kelleher, Ali Shilatifard, Marcelo G Bonini
{"title":"Histone oxidation as a new mechanism of metabolic control over gene expression.","authors":"Benjamin N Gantner, Flavio R Palma, Cezar Kayzuka, Riccardo Lacchini, Daniel R Foltz, Vadim Backman, Neil Kelleher, Ali Shilatifard, Marcelo G Bonini","doi":"10.1016/j.tig.2024.05.012","DOIUrl":"10.1016/j.tig.2024.05.012","url":null,"abstract":"<p><p>The emergence of aerobic respiration created unprecedented bioenergetic advantages, while imposing the need to protect critical genetic information from reactive byproducts of oxidative metabolism (i.e., reactive oxygen species, ROS). The evolution of histone proteins fulfilled the need to shield DNA from these potentially damaging toxins, while providing the means to compact and structure massive eukaryotic genomes. To date, several metabolism-linked histone post-translational modifications (PTMs) have been shown to regulate chromatin structure and gene expression. However, whether and how PTMs enacted by metabolically produced ROS regulate adaptive chromatin remodeling remain relatively unexplored. Here, we review novel mechanistic insights into the interactions of ROS with histones and their consequences for the control of gene expression regulation, cellular plasticity, and behavior.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"739-746"},"PeriodicalIF":13.6,"publicationDate":"2024-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11387142/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141443765","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
Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade. 曙光基因组学的进展：揭开一个复杂支系迷人的生物学面纱。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2024-08-14 DOI: 10.1016/j.tig.2024.07.007
Oskar Fields, Michael J Hammond, Xiao Xu, Ellis C O'Neill
{"title":"Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade.","authors":"Oskar Fields, Michael J Hammond, Xiao Xu, Ellis C O'Neill","doi":"10.1016/j.tig.2024.07.007","DOIUrl":"https://doi.org/10.1016/j.tig.2024.07.007","url":null,"abstract":"<p><p>Euglenids have long been studied due to their unique physiology and versatile metabolism, providing underpinnings for much of our understanding of photosynthesis and biochemistry, and a growing opportunity in biotechnology. Until recently there has been a lack of genetic studies due to their large and complex genomes, but recently new technologies have begun to unveil their genetic capabilities. Whilst much research has focused on the model organism Euglena gracilis, other members of the euglenids have now started to receive due attention. Currently only poor nuclear genome assemblies of E. gracilis and Rhabdomonas costata are available, but there are many more plastid genome sequences and an increasing number of transcriptomes. As more assemblies become available, there are great opportunities to understand the fundamental biology of these organisms and to exploit them for biotechnology.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":""},"PeriodicalIF":13.6,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141989529","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
Advisory Board and Contents 咨询委员会和内容
IF 11.4 2区 生物学
Trends in Genetics Pub Date : 2024-08-05 DOI: 10.1016/s0168-9525(24)00156-2
{"title":"Advisory Board and Contents","authors":"","doi":"10.1016/s0168-9525(24)00156-2","DOIUrl":"https://doi.org/10.1016/s0168-9525(24)00156-2","url":null,"abstract":"No Abstract","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":"27 1","pages":""},"PeriodicalIF":11.4,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141942640","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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