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Unraveling aging from transcriptomics. 从转录组学揭示衰老。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2024-10-17 DOI: 10.1016/j.tig.2024.09.006
Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han
{"title":"Unraveling aging from transcriptomics.","authors":"Yuanfang Huang, Shouxuan Zhu, Shuai Yao, Haotian Zhai, Chenyang Liu, Jing-Dong J Han","doi":"10.1016/j.tig.2024.09.006","DOIUrl":"10.1016/j.tig.2024.09.006","url":null,"abstract":"<p><p>Research into aging constitutes a pivotal endeavor aimed at elucidating the underlying biological mechanisms governing aging and age-associated diseases, as well as promoting healthy longevity. Recent advances in transcriptomic technologies, such as bulk RNA sequencing (RNA-seq), single-cell transcriptomics, and spatial transcriptomics, have revolutionized our ability to study aging at unprecedented resolution and scale. These technologies present novel opportunities for the discovery of biomarkers, elucidation of molecular pathways, and development of targeted therapeutic strategies for age-related disorders. This review surveys recent breakthroughs in different types of transcripts on aging, such as mRNA, long noncoding (lnc)RNA, tRNA, and miRNA, highlighting key findings and discussing their potential implications for future studies in this field.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"218-235"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142480921","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 new hypothesis to explain disease dominance. 一个解释疾病优势的新假说。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-03-01 Epub Date: 2025-01-08 DOI: 10.1016/j.tig.2024.11.009
Brian Juvik, Lara Falcucci, Pia R Lundegaard, Didier Y R Stainier
{"title":"A new hypothesis to explain disease dominance.","authors":"Brian Juvik, Lara Falcucci, Pia R Lundegaard, Didier Y R Stainier","doi":"10.1016/j.tig.2024.11.009","DOIUrl":"10.1016/j.tig.2024.11.009","url":null,"abstract":"<p><p>The onset and progression of dominant diseases are thought to result from haploinsufficiency or dominant negative effects. Here, we propose transcriptional adaptation (TA), a newly identified response to mRNA decay, as an additional cause of some dominant diseases. TA modulates the expression of so-called adapting genes, likely via mRNA decay products, resulting in genetic compensation or a worsening of the phenotype. Recent studies have challenged the current concepts of haploinsufficiency or poison proteins as the mechanisms underlying certain dominant diseases, including Brugada syndrome, hypertrophic cardiomyopathy, and frontotemporal lobar degeneration. We hypothesize that for these and other dominant diseases, when the underlying mutation leads to mRNA decay, the phenotype is due at least partly to the dysregulation of gene expression via TA.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"187-193"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958929","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 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 : 2025-03-01 Epub 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":"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":"251-260"},"PeriodicalIF":13.6,"publicationDate":"2025-03-01","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
Mitochondrial-derived microproteins: from discovery to function. 线粒体来源的微蛋白：从发现到功能。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2024-12-16 DOI: 10.1016/j.tig.2024.11.010
Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen
{"title":"Mitochondrial-derived microproteins: from discovery to function.","authors":"Kelvin Yen, Brendan Miller, Hiroshi Kumagai, Ana Silverstein, Pinchas Cohen","doi":"10.1016/j.tig.2024.11.010","DOIUrl":"10.1016/j.tig.2024.11.010","url":null,"abstract":"<p><p>Given the uniqueness of the mitochondria, and the fact that they have their own genome, mitochondrial-derived microproteins (MDPs) are similar to, but different from, nuclear-encoded microproteins. The discovery of an increasing number of microproteins from this organelle and the importance of mitochondria to cellular and organismal health make it a priority to study this novel class of proteins in search of possible therapeutic targets and cures. In this review, we discuss the history of MDP discovery, describe the function of each MDP, and conclude with future goals and techniques to help discover more MDPs.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"132-145"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142848403","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
Exploring the world of small proteins in plant biology and bioengineering. 探索植物生物学和生物工程中的小蛋白质世界。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2024-10-14 DOI: 10.1016/j.tig.2024.09.004
Louise Petri, Anne Van Humbeeck, Huanying Niu, Casper Ter Waarbeek, Ashleigh Edwards, Maurizio Junior Chiurazzi, Ylenia Vittozzi, Stephan Wenkel
{"title":"Exploring the world of small proteins in plant biology and bioengineering.","authors":"Louise Petri, Anne Van Humbeeck, Huanying Niu, Casper Ter Waarbeek, Ashleigh Edwards, Maurizio Junior Chiurazzi, Ylenia Vittozzi, Stephan Wenkel","doi":"10.1016/j.tig.2024.09.004","DOIUrl":"10.1016/j.tig.2024.09.004","url":null,"abstract":"<p><p>Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the function of these proteins. The study of these small proteins has contributed to a greater comprehension of protein regulation. In addition to sequence homology, sequence-divergent small proteins have the potential to function as microProtein mimics, binding to structurally related proteins. Moreover, a multitude of other small proteins encoded by short open reading frames (sORFs) and peptides, derived from diverse sources such as long noncoding RNAs (lncRNAs) and miRNAs, contribute to a variety of biological processes. The potential of small proteins is evident, offering promising avenues for bioengineering that could revolutionize crop performance and reduce reliance on agrochemicals in future agriculture.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"170-180"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481007","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
Finding functional microproteins. 寻找功能性微蛋白。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2025-01-02 DOI: 10.1016/j.tig.2024.12.001
Sikandar Azam, Feiyue Yang, Xuebing Wu
{"title":"Finding functional microproteins.","authors":"Sikandar Azam, Feiyue Yang, Xuebing Wu","doi":"10.1016/j.tig.2024.12.001","DOIUrl":"10.1016/j.tig.2024.12.001","url":null,"abstract":"<p><p>Genome-wide translational profiling has uncovered the synthesis in human cells of thousands of microproteins, a class of proteins traditionally overlooked in functional studies. Although an increasing number of these microproteins have been found to play critical roles in cellular processes, the functional relevance of the majority remains poorly understood. Studying these low-abundance, often unstable proteins is further complicated by the challenge of disentangling their functions from the noncoding roles of the associated DNA, RNA, and the act of translation. This review highlights recent advances in functional genomics that have led to the discovery of >1000 human microproteins required for optimal cell proliferation. Ongoing technological innovations will continue to clarify the roles and mechanisms of microproteins in both normal physiology and disease, potentially opening new avenues for therapeutic exploration.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"107-118"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11794006/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142928770","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
Cis to trans: small ORF functions emerging through evolution. 从顺式到反式：进化过程中出现的小型 ORF 功能。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2024-11-27 DOI: 10.1016/j.tig.2024.10.012
Casimiro Baena-Angulo, Ana Isabel Platero, Juan Pablo Couso
{"title":"Cis to trans: small ORF functions emerging through evolution.","authors":"Casimiro Baena-Angulo, Ana Isabel Platero, Juan Pablo Couso","doi":"10.1016/j.tig.2024.10.012","DOIUrl":"10.1016/j.tig.2024.10.012","url":null,"abstract":"<p><p>Hundreds of thousands of small open reading frames (smORFs) of less than 100 codons exist in every genome, especially in long noncoding RNAs (lncRNAs) and in the 5' leaders of mRNAs. smORFs are often discarded as nonfunctional, but ribosomal profiling (RiboSeq) reveals that thousands are translated, while characterised smORF functions have risen from anecdotal to identifiable trends: smORFs can either have a cis-noncoding regulatory function (involving low translation of nonfunctional peptides) or full coding function mediated by robustly translated peptides, often having cellular and physiological roles as membrane-associated regulators of canonical proteins. The evolutionary context reveals that many smORFs represent new genes emerging de novo from noncoding sequences. We suggest a mechanism for this process, where cis-noncoding smORF functions provide niches for the subsequent evolution of full peptide functions.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"119-131"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741061","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
Microproteins: emerging roles as antibiotics. 微蛋白：作为抗生素的新角色。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2025-01-13 DOI: 10.1016/j.tig.2024.12.004
Benjamin Galeota-Sprung, Ami S Bhatt, Cesar de la Fuente-Nunez
{"title":"Microproteins: emerging roles as antibiotics.","authors":"Benjamin Galeota-Sprung, Ami S Bhatt, Cesar de la Fuente-Nunez","doi":"10.1016/j.tig.2024.12.004","DOIUrl":"10.1016/j.tig.2024.12.004","url":null,"abstract":"<p><p>Recent advances in computational prediction and experimental techniques have detected previously unknown microproteins, particularly in the human microbiome. These small proteins, produced by diverse microbial species, are emerging as promising candidates for new antibiotics.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"104-106"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142985302","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 cryptic immunopeptidome in health and disease. 健康和疾病中的隐性免疫肽组。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2024-10-09 DOI: 10.1016/j.tig.2024.09.003
Eralda Kina, Jean-David Larouche, Pierre Thibault, Claude Perreault
{"title":"The cryptic immunopeptidome in health and disease.","authors":"Eralda Kina, Jean-David Larouche, Pierre Thibault, Claude Perreault","doi":"10.1016/j.tig.2024.09.003","DOIUrl":"10.1016/j.tig.2024.09.003","url":null,"abstract":"<p><p>Peptides presented by MHC proteins regulate all aspects of T cell biology. These MHC-associated peptides (MAPs) form what is known as the immunopeptidome and their comprehensive analysis has catalyzed the burgeoning field of immunopeptidomics. Advances in mass spectrometry (MS) and next-generation sequencing have facilitated significant breakthroughs in this area, some of which are highlighted in this article on the cryptic immunopeptidome. Here, 'cryptic' refers to peptides and proteins encoded by noncanonical open reading frames (ORFs). Cryptic MAPs derive mainly from short unstable proteins found in normal, infected, and neoplastic cells. Cryptic MAPs show minimal overlap with cryptic proteins found in whole-cell extracts. In many cancer types, most cancer-specific MAPs are cryptic.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"162-169"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401991","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
Ribosome profiling reveals hidden world of small proteins. 核糖体分析揭示了小蛋白质的隐藏世界。
IF 13.6 2区 生物学
Trends in Genetics Pub Date : 2025-02-01 Epub Date: 2025-01-14 DOI: 10.1016/j.tig.2024.12.010
Gregory Tong, Thomas F Martinez
{"title":"Ribosome profiling reveals hidden world of small proteins.","authors":"Gregory Tong, Thomas F Martinez","doi":"10.1016/j.tig.2024.12.010","DOIUrl":"10.1016/j.tig.2024.12.010","url":null,"abstract":"<p><p>The development of ribosome profiling (Ribo-seq) by Ingolia et al. introduced a powerful new method for monitoring translation genome-wide. Application of Ribo-seq across multiple organisms has since revealed thousands of unannotated translated small open reading frames (ORFs) and enhanced efforts to study their encoded proteins, called microproteins.</p>","PeriodicalId":54413,"journal":{"name":"Trends in Genetics","volume":" ","pages":"101-103"},"PeriodicalIF":13.6,"publicationDate":"2025-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016597","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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